PgrR , Peptide glycan recycling Regulator .
The transcriptional repressor FliZ controls the transcription of genes involved in the regulation of curli expression and the motility system .
It consist of two domains , an amino-terminal domain that contains a potential helix-turn-helix DNA-binding motif and a carboxy-terminal domain involved in co-inducer-recognition .
Expression of ttdR ( dan gene ) is positively autoregulated in response to L-tartrate and activated by the two-component system DcuSR in the presence of L-tartrate , meso-tartrate , D-malate or fumarate .
Based on biochemical experiments and electron micrographs using a norR mutant carrying a deletion of the N-terminal domain , it has been proposed that NorR binds as a hexameric ring to DNA .
The products of the catabolism of short-chain fatty acids appear to be the substrates in the biosynthesis of this polymer .
A ycjZ mutant shows a defect in swarming motility , but no defect in swimming motility .
RclR : reactive chlorine resistance R .
PdhR , pyruvate dehydrogenase complex regulator , regulates genes involved in the pyruvate dehydrogenase complex .
On the other hand , in vivo protein-protein interaction assays suggested that both systems together form a single large signaling unit .
The repressor gene of this operon is positioned at the 3 ?
The chromosomal ArsR shows 75 % identity to ArsR of Escherichia coli plasmid R773 and 26 % identity to staphylococcal plasmid pI258 and pSX267 ArsR proteins .
The crystal structure of the LsrR protein complexed with the native signal ( phosphor-Al-2 , D5P ) was determined .
OxyR consists of 305 amino acid residues and is a member of the LysR-family of bacterial transcription factors .
In prerecruitment , the protein first binds to RNA polymerase in solution , and the binary complex then scans the DNA to find its binding sites .
RelB production relieves established RelE-mediated translation inhibition and inhibition-of-cell-growth , indicating that growth inhibition is not irreversible .
MtlA takes up exogenous mannitol , releasing the phosphate ester , mannitol-1-P , into the cell cytoplasm , but it is not clear which of the two metabolites is the inducer of MtlR .
It is still disputed whether these sites actually resemble the low-affinity binding sites for nickel ions or whether these sites function as potassium-binding sites .
Upon removal of the inducer , SoxS is degraded by the Lon-protease .
Regulation has been described .
Moreover , DNA-binding of NikR is abolished in the absence of K + .
The transcriptional activator FUR , for Ferric Uptake Regulation , is capable of controlling its own synthesis and controls the transcription of genes involved in iron-homeostasis and a minor sigma factor that initiates transcription of ferric citrate-transport genes in response to the presence of periplasmic iron ( III ) dicitrate .
Dan is a DNA-binding protein with recognition preference for the GTTNATT sequence .
Under N deficiency , GlnB and GlnK are uridylylated ( GlnB-UMP ) , and in this conformation these proteins can not bind to NtrB .
It was proposed that Hha enhances the oligomerization of Hns/StpA which is necessary to form DNA-protein filaments to repress transcription .
On the other hand , ExuR is similar to UxuR ARRAY ( 0x1602fd8 ) , and apparently both act together and are capable of cross-talk to regulate expression of the uxu operon .
The cross-regulation of OmpR by CpxA , ArcB , or acetyl phosphate results in phosphorylation of OmpR in response to different conditions .
IHF is a heterodimer consisting of the two subunits , IhfA ( HimA ) and IhfB ( HimD , Hip ) , that share about 25 % amino acid identity .
BluF is an antagonist of BluR .
UhpA is the response regulator in the unusual two-component regulatory system comprised of three proteins , UhpA/UhpB/UhpC , and is a member of the NarL subfamily of response regulators .
ArgR has two domains : the N-terminal domain , which contains a winged-helix-turn-helix DNA-binding motif and the C-terminal domain , which contains a motif that binds L-arginine and a motif for oligomerization .
This transcriptional regulator is negatively autoregulated and is expressed under nitrogen-limiting conditions .
In FliZ , this ?-helix contains a positively charged amino acid ( R108 ) that is involved in recognition-of-the-extended -- 10-promoter .
GadE activates transcription of two additional AraC-like transcriptional activators , GadX and GadW .
It is also involved in the bacterial stringent-response .
PspA appears to bind to the W56 loop of PspF , which is a region that contains residues 50-62 .
BaeR suppresses envZ and phoR/creC mutations .
MraZ is similar in both structure and sequence to the DNA-binding transition-state regulator AbrB from Bacillus subtilis .
Leonhartsberger et al suggested that this protein binds to degenerate regions 16 bp in length ( CATTTCGTACGAAATG ) .
This interaction is attenuated under Cad-inducing conditions ( low pH , increased lysine levels ) .
Repression of the bglG operon by StpA occurs as a molecular adapter and only in the presence of the N-terminal H-NS protein domain , which comprises the core for dimerization .
The central AAA + domain does not contain the two conserved submotives in this family ( ESELF and GAFTGA ) responsible for interaction-with-?54 .
YefM is a transcriptional DNA-binding autorepressor for the yefM-yoeB operon .
GadE is encoded by the gadE-mdtEF operon , inducible by low pH which is located in the region called the acid fitness island .
Allostery arises as a natural consequence of changes in global low-frequency protein fluctuations on ligand binding , and there are conserved residues crucial for allosteric control .
This regulator removes methyl groups ( as well as larger groups ) from the guanine and thymine substrates and transfers them to its own cysteine residue ( Cys-321 ) in the C-terminal domain .
The mazEF system causes a programmed-cell-death response-to-stresses including starvation and antibiotics .
Expression of emrR is not osmoregulated .
The inducer-binding sites for the members of this family appear to have arisen by convergent evolution .
RclR relies on the reversible oxidation of conserved redox-sensitive cysteine residues to specifically sense RCS and control the expression of genes essential for survival under reactive chlorine ( HOCl ) stress .
YiaJ is negatively autoregulated , and coordinately represses transcription of the divergent yiaK-S operon , related to degradation of l-lyxose .
Although AllS binding does not depend on the presence of allantoin , this compound appears to be necessary for activation , perhaps by interacting with AllS .
The physiological inducer is unknown .
The ?-d-glucuronides repressor , UidR , is a transcriptional repressor .
CynR binds cooperatively to a 60-bp region that contains two 9-bp repeats separated by 34 bp .
The C-terminal domain of FliZ contains an ?-helix that is similar to helix 3.0 of ?S , and this structure promotes DNA-binding .
Dan is highly expressed in cells grown under hypoxic or anaerobic conditions , and it plays a role in local folding of DNA .
The binding region overlaps the -35 region of the promoter for the cyn operon and both the -10 and -35 region of its own promoter .
The cooperative binding of H-NS to DNA is related to protein-protein interactions .
al. ( 2013 ) have suggested that the term sialoregulon be given to genes that are directly regulated by NanR and the term sialostimulon be used for genes affected by the by-products of sialic-acid-metabolism .
BetI is an unusual repressor because it remains bound to DNA during induction .
The C-terminal domain of Rob is similar to a portion of the enzyme GalT .
Ma et al. added to this regulatory interaction the GadW protein , showing that it inhibits GadX and that in some cases it activates in the absence of GadX .
CytR belongs to the GalR/LacI-family of transcriptional regulators .
For this reason these regulators bind the same operators , in the cis regulatory regions , with different affinities .
AtoC-dependent atoDAEB transcription requires the presence and binding of IHF .
In systematic studies of oligomerization , it was shown that some members of the LysR-family , like Cbl , interact with other members of the family to form heterodimers , but the physiological significance of this is unknown .
The crystal structure of AcrR shows that this protein is folded into nine ?-helices distributed in two domains : the DNA-binding domain , which forms the typical helix-turn-helix in the N-terminal domain , and the ligand-binding domain , which forms a large internal cavity for multidrug-binding in the C-terminal domain .
NemR contains five Cys residues , at positions 70 , 78 , 88 , 121 , and 125 , in a total of 199 residues .
The YqhC transcriptional activator directly binds to the promoter region of the yqhD gene , which contains the SoxS-like binding sequence as well as a 24-bp palindrome .
MelR binds to the less-conserved site ( -42.5 ) with less strength ; this binding occurs only in the presence of melibiose , and it is absolutely required for expression of melAp .
These genes are involved in amino acid biosynthesis and catabolism , nutrient transport , pili synthesis , and other cellular functions , including 1-carbon metabolism .
Transcriptome expression analysis showed a global antagonistic effect between FliZ and ?S that resulted in physiological traits , including flagellum-mediated motility and curli fimbria-mediated adhesion .
Synthesis of these operons is induced when Escherichia coli is grown on d-xylose in the absence of glucose .
GadX is one of the regulators of the acid resistance system and is encoded by the unusual gadXW operon , which is located in the region called the acid fitness island .
HdfR is a transcriptional regulator that belongs to the LysR-family .
In a subset of the class I promoters the sox-mar-rob box is separated by ~ 30 bp from the -10 hexamer but can be functional in either orientation .
The high-resolution structure based on solid-state NMR spectra from full-length H-NS has been determined .
Reviews : .
The binding of SoxS with DNA or RNA polymerase protects it from degradation .
Golding et al. showed that GalR is the major repressor of the gal operon .
Ma et al. proposed that the binding targets for GadE consist of 20-nucleotide sequences that possess nonconserved motifs , called the GAD box , and suggested that it is a regulator that may form a complex with GadX .
MarA , multiple antibiotic resistance participates in controlling several genes involved in resistance to antibiotics , oxidative stress organic solvents and heavy metals .
Some phenotypes caused by RstA have been identified by mutational analysis .
The transcription factor RbsR , for Ribose Repressor , is negatively autoregulated and controls the transcription of the operon involved in ribose catabolism and transport .
The LacI protein belongs to the GalR/LacI-family and as a member of this family of transcriptional regulators , LacI contains three domains : a helix-turn-helix motif located in the N-terminus , the central-domain that binds to LacI sugar ligands , and the C-terminal , which comprises the tetramerization domain .
The N-terminal domain is expected to bind two manganese ions per monomer , in analogy to BsMntR from B. subtilis , which has been crystallized with and without bound manganese .
In addition , YefM also functions as an antitoxin to form a complex with YoeB , which is a toxin that is counteracted by YefM antitoxin .
The metJ gene , which is autoregulated , is transcribed divergently from the metBL operon , which is repressed by MetJ .
AllS , allantoin , transcriptional activator participates in controlling genes involved in the utilization of allantoin as a nitrogen source .
CRP belongs to the CRP-FNR superfamily of transcription factors .
LldR , formerly named lactate regulator , is a transcription factor that controls expression of genes involved in transport and catabolism of L-lactate .
In addition GadX also activates the transcription of the central activator involved in the acid response .
The transcriptional activator MtlR , for Mannitol Rrgulator , is capable of controlling its own synthesis and it controls the transcription of the operon involved in mannitol utilization .
The third inducer , phenylpropionate ( PP ) , acts synergistically with DHPP and 3HPP .
Saturated acyl-ACP or acyl-CoA competes with the unsaturated fatty acids for binding to FabR but does not trigger DNA-binding .
The two cluster formations are induced by the N-terminal domain-driven oligomerization of the protein .
The cognate sensor kinase ArcB is membrane associated and has three cytoplasmic domains ; a transmitter , a receiver , and a phosphotransfer ( HPt ) domain .
The lrhA gene is transcribed alone , and it is under positive autoregulation by LrhA .
In one regulatory region , the protein binds to a single site , whereas it binds to two sites arranged as inverted repeats in another region .
HU belongs to a family of DNA architectural proteins and acts mostly as a regulatory or accessory factor , stabilizing a correct nucleoprotein complex .
Dan contains two sets of Cys-Cys pairs : one consisting of Cys170 and Cys193 , and other of Cys288 and Cys296 .
Binding of tryptophan stabilizes the HTH and alters the orientation of the HTH such that the repressor fits into the major grooves .
Expression of this operon requires growth on l-fucose or l-rhamnose under anaerobic conditions .
The HipAB toxin-antitoxin system appears to be regulated at the level of HipB stability .
A microarray analysis showed that the master regulator , FlhD2C2 , regulates several nonflagellar genes , but the direct effect has not been determined .
NikR , Nickel-responsive repressor , is a tetramer and consists of two domains .
This transcriptional activator belongs to the LuxR family of activators .
In the presence of l-rhamnose , RhaS binds in tandem to repeat sequences upstream of the rhaAp and rhaTp intergenic regions .
The ARG box generally overlaps the promoter sequence and the transcriptional start site therefore , it was suggested that it represses the transcription by steric exclusion of RNA polymerase binding .
ArcA represses operons involved in respiratory metabolism , including those that encode products such as the tricarboxylic-acid-cycle enzymes , enzymes of the glyoxylate shunt , and enzymes of the pathway for fatty-acid-degradation .
These characteristics point toward identical modes of action for MalY and Aes .
Expression of alpA increases 6.5-fold upon deletion of tqsA ; alpA expression may thus be involved in biofilm-formation .
Although DNA-binding by GutM does not depend on the presence of glucitol , this compound appears to be necessary for derepressing gutM , perhaps by interacting with GutR .
However , they show only one different residue in their helix-turn-helix motifs , suggesting that they recognize similar DNA-binding sites .
The phenylacetic acid regulator PaaX , is a transcriptional repressor that participates in controlling transcriptional regulation of genes involved in the catabolism of an aromatic compound , phenylacetic acid ( PA ) .
It was therefore predicted to play a role in the heat shock response .
The lengths of the degenerate binding sites of NhaR were defined according to the matrix shown for this regulator in the database RegPrecise , which contains matrices generated from alignments of orthologous regions .
IscR binds cooperatively to DNA , and four protomers bind to one palindromic site .
In the presence of citrate and under anaerobic conditions it activates genes for citrate fermentation , the citCDEFXGT operon , the citAB operon , and mdh , as well as the exuTR operon for dissimilation of hexuronate .
Reviews : .
It is probable that YqhC regulates its own expression , since it is inducible by furfural .
The importance of the N125 and D149 residues of the N-terminal in the recognition of the sugar effector-binding site has been determined .
NikR mediates two levels of repression .
Crystal structures of this domain have been solved .
Mutants .
Therefore , these two regulators bind cooperatively to fully activate the operons related with transport and degradation of l-rhamnose .
At the posttranscriptional level , it is subject to regulation by the sRNAs Hfq and DsrA .
YdeO activates genes involved in the cellular response to acid resistance .
The NikR tetramer contains four high-affinity nickel-binding sites located at the subunit interfaces of the C-terminal domain and additional low-affinity metal-binding sites .
It has an approximately fivefold-lower affinity for DNA than StpA and has a major preference for curved DNA .
Like the other members of this family , it has an N-terminal domain that contains a helix-turn-helix ( HTH ) motif for DNA-binding and a C-terminal domain for dimerization , inducer-binding and protein contact with CRP .
The sox-mar-rob box contains an invariant A at position 1 , two recognition elements , the RE1 at postion 4-7 and RE2 at position 15-18 , and a 7-bp A/T-rich spacer separating these elements .
While glyoxylate favors the inactive dimeric state of IclR , pyruvate increases the binding of IclR to the aceBp promoter by stabilizing the active tetrameric form of the protein .
It is considered a global regulator of carbohydrate-metabolism .
The effects of HU protein enhancements on DNA flexibility and the cyclization rate have been determined , based on a Monte Carlo approach , by Czapla et al. .
YefM has similarity to the Axe protein of the Txe-Axe toxin-antitoxin pair , which is encoded by a multidrug-resistance episome isolated from Enterococcus faecium .
On other hand , the genes of the aceBAK operon are expressed to varied degrees due to two facts : first , they are differentially regulated at the translational level , and second , there is a putative premature transcriptional termination in the region preceding the aceK gene .
MelR binds to five target sites in the melAp region .
Synthesis of these genes is induced when Escherichia coli is grown in the absence of glucose , and under anaerobic conditions it can ferment L-ascorbate ; under aerobic conditions it is functional in the presence of casein acid hydrolysate .
tdc : threonine dehydratase .
FeaR controls expression of a pathway for the degradation of potentially toxic aromatic compounds .
Thus , this regulator maintains the iron-homeostasis during high levels of nickel .
Thus , FabR senses the ratio , rather than the absolute amount , of unsaturated and saturated fatty acids and adjusts expression of fabA and fabB to balance the composition of saturated and unsaturated acyl-ACP .
It is negatively autoregulated , sensitive to catabolite control , and coordinately activates transcription of a divergent operon related to propionate-catabolism .
Here , the presence of L-ascorbate-6-P breaks this configuration down into DNA-free UlaR homodimers and allows transcription to proceed .
These regulators bind cooperatively to activate transcription of the unusual operon rhaSR , which encodes two transcriptional regulators , RhaS and RhaR ( 30 % identical ) , both members of the AraC/XylS-family of transcriptional regulators and involved in l-rhamnose-transport and degradation .
Its gene products are involved in the production of colanic acid , a component of the biofilm matrix , via the Rcs phosphorelay system .
As a member of the group of ?54-dependent transcriptional regulators , FhlA contains three domains : a possible sensory-domain located in the N-terminus that probably modulates the activity of the C-terminal domain the central-domain , which is probably involved in open complex formation , ATP-hydrolysis , and interaction-with-?54 and formate and the C-terminal domain , which contains a helix-turn-helix motif for DNA-binding .
Generally , this protein activates genes involved in anaerobic metabolism and represses genes involved in aerobic metabolism .
The tetrameric state is not perturbed by Ni ( II ) or Co ( II ) binding .
Gavigan et al. ( 1999 ) and Perini et al. ( 1996 ) showed that CytR binds in tandem in the regulated intergenic region .
The AppY , acid phosphatase , transcriptional regulator induces the expression of energy metabolism genes under anaerobiosis , stationary phase , and phosphate starvation .
The protein CsgD , for Curlin subunit gene D , is a transcriptional regulator that regulates a number of genes involved in the Curli assembly , transport , and structural components which are important for biofilm-formation .
IHF and H-NS might modulate the bending and necessary access of the adiAp promoter for activation .
The acriflavine resistance regulator , AcrR , regulates the expression of genes involved in multidrug-transport and is classified in the nodulation-resistance division family .
PhoB binds to the Pho box , which has been described as two direct 11-bp repeats consisting of successive 7-bp direct repeats followed by an A/T-rich region of 4 bp , situated 10 bp upstream of the -10 region .
CRP has been adapted to respond to different external and internal stimuli according to the particular ecological niches occupied by the bacterium .
Iron homeostasis influences the evolution of ciprofloxacin resistance .
This regulator is part of the glpEGR operon , yet it can also be constitutively expressed as an independent ARRAY ( 0x1577a08 ) transcription unit .
Based on genomic SELEX and gene-expression analyses , NemR could be affecting other genes , such as ydhF-ydhL , gloA , sapABCDF , yeaU , pck yeaT , and yhgE however , the regulation of the genes under control of NemR requires more detailed studies before it can be solved .
The Galactose isorepressor , GalS , is a DNA-binding transcription factor that represses transcription of the operons involved in transport and catabolism of D-galactose .
On the other hand , GalR is highly homologous in its amino acid sequence to GalS ( 55 % identical and 88 % similar ) ; apparently both act together and are capable of cross-talk to regulate expression of the gal regulon .
Deletion of any single toxin-antitoxin system encoding an RNase has no effect on persister formation , but deleting ten such systems dramatically reduces persister formation .
SoxR is the transcriptional activator for soxS and a sensor for superoxide and nitric oxide through its -LSB- 2Fe-2S -RSB- center .
An sdiA ydiV double mutant reduces cAMP levels , which inhibits quorum-sensing system 2 .
YehU/YehT has a negative effect on expression of the yhjX gene of the YpdA/YpdB system , which suggests an interconnectivity between the two systems .
These genes are coupled to the nitrogen regulatory ( Ntr ) system , which is ?54 dependent , through Nac , whose transcription is activated by NtrC .
On the other hand , SdiA is highly homologous to quorum-sensing transcription factors that belong to the LuxR family .
Initially thought to only function as a transcriptional regulator that represses genes involved in transport and de novo synthesis of NAD , NadR was later shown to have nicotinamide mononucleotide ( NMN ) adenylyltransferase-activity and predicted to have ribosylnicotinamide kinase activity .
NtrB functions as a membrane-associated protein kinase that in response to limitation of N and carbon-limited growth is autophosphorylated .
Cbl does not require a ligand to binds to its DNA-binding site , but the activity of this protein is negatively regulated by the 5 ' - phophosulfate cofactor .
These proteins activate a common set of about 50 target genes the marA/soxS/rob regulon , involved in antibiotic resistance superoxide resistance and tolerance to organic solvents and heavy metals .
The crystal structure of the C-terminal domain of IclR ( 2.3 Å ) has been solved .
This modification enables IscR to bind to type 1 DNA-binding sites .
For this reason , in the absence of H-NS the StpA protein is rapidly degraded in a Lon-protease-dependent manner protection from proteolytic degradation appears to be mediated by a direct interaction between StpA and H-NS .
The RelE-RelB system is involved in regulation-of-cell-growth under conditions with limited nutrients .
The response regulator NarL belongs to the LuxR/UhpA-family and is part of the two-component system NarX-NarL .
Shiga toxin-encoding prophages have been observed to integrate at the mlrA gene of enterohemorrhagic E. coli .
DNA-replication is also regulated directly by ArgP when it binds to three 13-mers located in the origin of replication ( OriC ) , blocking the DNA opening by DnaA and inhibiting this cellular-process .
The binding to low-affinity sites and introduction of sharp bends in chromosomal DNA promote the formation of rod-like condensed structures in chromosomal DNA .
The NtrC-P binds to an inverted repeat sequence that can be located at a considerable distance from the start site of transcription .
CsiR is expressed upon carbon starvation and has a repressor effect during the stationary phase .
For this , IHF stabilizes the bending of the DNA to facilitate binding of the bivalent integrase molecules .
The ydh operon is activated by FNR and suppressed by NarP and NarL .
AraC binds to five target sites in the araBp region .
FadR , Fatty acid degradation Regulon is a multifunctional dual regulator that exerts negative control over the fatty acid degradative regulon and acetate-metabolism whereas it is responsible for maximal expression of unsaturated-fatty-acid-biosynthesis .
The membrane-bound part of EIICBGlc is essential for Mlc inactivation .
In addition , Tramonti et al. provided evidence that the transcription of the gadXW operon is regulated to a posttranscriptional level by a gadY small RNA .
UidR negatively regulates its own synthesis and represses transcription of the uid operon , which is involved in transport and degradation of ?-glucosides .
Additionally , its operon is activated by insertion of IS1 into the yiaJ gene .
PspF is composed of two domains : the N-terminal catalytic domain , common to members of the AAA + protein family ( ATPase associated with various cellular activities ) , and a C-terminal helix-turn-helix DNA-binding domain .
Currently , no inducer for this regulator has been reported in the literature .
When assembled into a ring , the AAA + domain uses the energy from ATP-binding , hydrolysis , and product release to remodel the ?54-RNA polymerase holoenzyme so that it can transition from the closed to the open complex .
FruR is inactivated upon the interaction of the inducers .
NhaR is composed of two domains : the amino-terminal domain , which contains the DNA-binding region , and the carboxy-terminal domain , which is possibly responsible for inducer-binding .
NagC is present at low levels within the bacterial cell .
The crystal structures of cAMP-CRP , cAMP-CRP bound to DNA , the cAMP-CRP-?-CTD-DNA complex , and the solution structure , as well as the crystal structure of apo-CRP , have been solved .
The contact regions through which both proteins interact are represented by two amino acid residues in the C-terminal domains of RhaS ( D241 and D250 ) and ?70 ( R599 and K593 ) .
ATPase activity may result in transient presentation of the site that interacts with ?54 .
They typically form tetramers in solution that can be regarded as dimers of dimers .
In the presence of nitrite , NarX phosphorylates NarP but acts primarily as a phosphatase for NarL-P .
Mutations in the N-terminal region of MazE affect its ability to suppress parD mutations in the episomal killer system .
It shows two domains , the N-terminal domain involved in DNA-binding via a helix-turn-helix and the C-terminal domain involved in dimerization and in cleavage activity .
At concentrations of > 2 nM , L-ascorbate-6-P displaces UlaR from its operator site .
RclR contains two conserved cysteine residues ( Cys-21 and Cys-89 ) and two conserved histidine residues ( His-42 and His-75 ) .
In class I promoters , the activators bind upstream of the -35 box and are generally oriented in the backward direction , while in class II promoters the proteins overlap the -35 promoter hexamer and generally are oriented in the forward direction .
Gene induction occurs when the physiological inducer , d-xylose , binds to XylR and when cellular cyclic AMP levels are high .
Contrary to the suggestion made by , has suggested that argP is not autoregulated .
RutR : pyrimidine utilization , rut repressor .
Expression of putA is reduced by prolonged exposure to osmotic stress .
RcdA , also known as YbjK , belongs to the TetR family and is involved in the regulation of a number of stress response genes , biofilm-formation , and transcription regulator genes .
BaeR exhibits high degrees of sequence similarity with the transcriptional regulators OmpR and PhoB and belongs to the OmpR subfamily whose members contain a DNA-binding motif in the C-terminal domain .
For example , expression of nrf is activated by FNR and repressed by IHF and Fis .
The N-terminal domain is the DNA-binding domain and is homologous to MarA and SoxS and the C-terminal domain of AraC .
RbsR belongs to the GalR/LacI-family , which forms a bundle of four helices characteristic of proteins of an HTH DNA contact motif .
At neutral cytoplasmic pH , a disulfide bond is formed in the periplasmic domain of CadC to inactivate it .
The L1 loop is known to interact with ?54 , presumably with region I of ?54 .
It has been experimentally verified that methylglyoxal ( MG ) and not NEM is the real inducer for the nemRA operon .
AsnC is a transcriptional regulator that activates the expression of asnA , a gene involved in the synthesis of asparagine .
UlaR is a DNA-binding transcription factor of 251 amino acids that is expressed constitutively and that coordinately represses transcription of a divergent operon ( ula ) involved in transport and utilization of L-ascorbate-catabolism .
PhoP is a dual transcriptional regulator that is activated in response to low extracellular levels of divalent cations , e.g. , magnesium or calcium .
This motif is composed of a two-stranded antiparallel ?-ribbon that lies along the DNA major groove , two outer ?-helices that interact with adjacent proteins along the DNA , and two inner ?-helices that form the subunit interface .
Allose utilization regulator , AlsR , negatively controls the expression of genes involved in transport and catabolism of D-allose and low-affinity transport of D-ribose .
The GcvA binding sites do not show a clear conservation in their sequences except for a short 5 ' - CTAAT-3 ' region .
Transcription of the mazEF addiction module is repressed by high concentrations of guanosine 3 ' ,5 ' - bispyrophosphate ( ppGpp ) , suggesting that amino acid starvation induces lethality via RelA and the MazE-MazF system .
Under high-osmolarity conditions , ompF is repressed by DNA looping while the ompC gene is expressed , but under low-osmolarity conditions the effects on these genes are the reverse , i.e. , ompC expression is repressed while ompF expression is increased .
Regulation has been described .
LeuO belongs to the LysR transcriptional regulator family and contains a helix-turn-helix DNA-binding domain .
LrhA is a protein that belongs to the LysR-family and , like the members of this family , LrhA contains three different domains : an N-terminal helix-turn-helix domain for DNA-binding , a coinducer-recognition domain in-the-center-of-the-protein , and a C-terminal domain that contains a cluster of four cysteine and two histidine residues .
ComR is a member of the TetR family of transcriptional repressors and has been implicated in the the response of E. coli K-12 to copper .
In accordance with other helix-turn-helix DNA-binding repressors , AgaR may bind to DNA as a tetramer .
This regulator belongs to the histone-like-family of transcriptional regulators and the structure of the protein consists of two structured domains which are separated by a flexible linker .
The bend angle induced by IHF is approximately 160 ° .
Each monomer of GadW binds to one of these conserved sequences .
Genes identified by microarray analysis include several for repression by SutR , sutR , ydcO , pfkB , fliZ , and cysE , while activation of SutR was identified only for ypfN .
The crystal structure of the LacI binding site for allosteric effectors has been resolved .
OxyR consists of two domains , the N-terminal domain , carrying a helix-turn-helix motif , and the C-terminal regulatory domain .
LrhA appears to recognize and bind to a partial palindromic DNA sequence of 13 bp that shows low similarity to the general consensus for LysR-family members .
They are divergently orientated and expressed from nonoverlapping face-to-face ( convergent ) promoters , and their transcripts are complementary at their 5 ' ends .
It inhibits posttranslationally ornithine decarboxylase ( ODC ) which is a key enzyme for biosynthesis of the polyamines which are essential components for cellular-growth and proliferation .
The transcription expression analysis of some genes with BolA mutants and the presence of a putative helix-turn-helix motif for DNA-binding suggest that BolA is a transcriptional regulator , although its regulatory mechanism and specific DNA-binding site remain to be determined .
In Escherichia coli K-12 , PhoP activates transcription of a large collection of genes involved in Mg2 + homeostasis , resistance to antimicrobial peptides , acid resistance , and LPS modification .
StpA has RNA chaperone-activity in vitro and in vivo , and the RNA chaperone-activity of StpA is influenced by the structural stability of the RNA target molecule .
Expression of gutM is increased in the presence of glucitol and in the absence of glucose .
The dimer is composed of two identical six-helical subunits , where four of the helices intertwine with the corresponding helices from the other subunit .
The typical motif of members of this family , the ribbon-helix-helix motif for DNA-binding , has been observed in the crystalline structure of MetJ .
A model of the mechanism of action of Ada has been proposed .
ydeO is transcribed in an operon together with the gene safA .
A model of binding and reaction progression is presented elsewhere .
Lrp might also play a topological role in dynamic DNA packaging .
Ma et al. added to this regulatory interaction with the GadW protein , showing that it inhibits GadX and that in some cases it activates in the absence of GadX .
RcnR is not similar to any other known transcriptional regulator ; instead , it is homologous to other proteins whose genes are encoded next to genes encoding putative metal efflux proteins , metalloenzymes , or copper chaperones -LSB- and just a few ( 13 % ) of the homologs to cardiolipin synthases or membrane proteins -RSB- .
In the crystal structures , the receiver-domain forms a symmetric dimer .
PgrR negatively controls ycjY-ymjD-ymjC-mpaA operon expression and binds to the palindromic sequence ATCATTT-AAATGAT .
NtrC has three domains : an N-terminal receiver-domain that contains the conserved Asp-54 residue that is phosphorylated a central ATP-binding AAA + that cleaves ATP to produce energy used in the process of open complex formation , mediates a phosphorylation-dependent oligomerization , and interacts-with-RNA-polymerase through the highly conserved GAFTGA motif and a C-terminal domain , which contains a helix-turn-helix motif for DNA-binding and is involved in dimerization and in phosphorylation-independent oligomerization .
A BLAST analysis showed AtoC is homologous in proteobacteria , enterobacteria , eubacteria , and spirochetes .
On the other hand , its C-terminal domain , probably used by a yet-to-be-identified effector , showed no similarity to any of the hitherto-characterized MerR-family members .
BluR functions as a repressor for genes involved in the modulation of biofilm-formation and for acid resistance genes .
It consists of three domains , an amino-terminal domain involved in effector-recognition , a catalytic domain , and a carboxy-terminal DNA-binding domain .
Review : .
Comparative analysis of intergenic DNA sequences showed the consistent occurrence of KdgR possible binding sites upstream of the genes not related to the transport and catabolism of KDG .
McbR is negatively autoregulated and , in addition , repressed by YgiV .
Galactitol regulator , GatR , negatively controls the expression of an operon involved in transport and catabolism of hexitol galactitol .
A crystal structure of ModE has been solved at 2.1 Å resolution .
We have modified the reported length of the binding site of this protein to 13 bp , according to the proposal by Teo et al. .
NarP consists of the N-terminal receiver-domain and a C-terminal DNA-binding domain .
In the absence of nitrate and nitrite , NarX and NarQ stimulate the dephosphorylation of NarL-P and NarP-P .
NarL consists of the N-terminal receiver-domain and a C-terminal DNA-binding domain .
This sugar is sensed by UhpC , which interacts with UhpB to stimulate its autophosphorylation .
Expression of the periplasmic-binding-proteins for peptide-transport , OppA and DppA , is repressed by PhoB .
This heterotetrameric regulator activates class II genes involved in the flagellar basal body proteins of the export machinery , the flagellar ? subunit ( FliA ) , and its anti-? factor , FlgM .
EnvZ is an osmosensor histidine kinase and is known to be a transmembrane protein composed of three domains : an external sensory-domain ( amino-terminal ) , a cytoplasmic transmitter domain ( carboxyl terminal ) , and a transmembrane hydrophobic central-domain .
The binding targets for FlhD2C2 consist of two repeat sequences that possess conserved motifs ; each heterodimer ( FlhDC ) binds to one of these conserved sequences , which are separated by a 10 - to 11-bp spacer .
The L2 loop is thought to coordinate movement of the L1 loop .
In unphosphorylated NarL , the DNA-binding site of the output domain is blocked by the receiver-domain .
This protein binds to DNA as a tetramer to regulate transcription ; however , in the presence of phosphorylated autoinducer 2 ( AI-2 ) or ADP-P , the tetramer dissociates into dimers , and the interaction of LsrR with DNA is greatly reduced .
In addition , EIIAGlc blocks the uptake of inducer by blocking the transport systems ( inducer exclusion ) .
It is believed that the switch between the octameric and hexadecameric states modulated by leucine affects the binding and the activity of Lrp at its target genes .
Four peaks were located in type A spacers of divergent transcription units ( TUs ) , and eight peaks were identified within type B spacers upstream of one TU but downstream of the preceding TUs .
Synthesis of these operons is induced when E. coli is grown in the presence of inducer ( D-galactose ) and the absence glucose .
Additionally , the N-terminal region has a helix-turn-helix DNA-binding domain .
To repress transcription , MtlR recognizes DNA-binding sites that overlap the initiation site for transcription of the mtlADR operon , preventing RNA polymerase binding but no consensus sequence has been identified .
Based on cross-linking analysis of wild-type and mutant ArgR proteins , it has been shown that the C-terminus is more important in cer/Xer site-specific recombination than in DNA-binding .
The binding of DPD to LsrR inactivates LsrR , but phosphorylated DPD appears to specifically inactivate the action of LsrR on the expression of genes for autoinducer 2 uptake and processing ( lsrACDBFG-tam operon ) and lsrR itself .
Lysine Regulator , LysR , is negatively autoregulated and coordinately activates transcription of the divergent gene which encodes the enzyme that catalyzes the last step in lysine-biosynthesis .
This binding is inhibited when uracil and thymine bind to RutR , although the effect is greater for uracil than for thymine .
Three dimeric forms exist in Escherichia coli : two homodimers , EcHU?2 and EcHU?2 , and a heterodimer , HU?? .
Based on a crystal structure of ZraR from Salmonella enterica serovar Typhimurium , it has been suggested that this protein may function as a dodecamer .
In systematic studies of oligomerization , it was shown that some members of the LysR-family , like HdfR , interact with other members of the family to form heterodimers , but the physiological significance of this is unknown .
Little is known about the regulatory role of HdfR , and the binding sites for this transcription factor have not yet been determined .
A conformational change in PspF is observed in the presence of ATP .
The dual function of NagC requires it to bind simultaneously to two operators in order to form a DNA loop .
The YefM antitoxin forms a heterotrimeric complex with the YoeB toxin ( YefM2-YoeB ) .
The system discriminates between nitrate and nitrite .
The solution structure of the methylated N-terminal domain of Ada has been determined by NMR and mass spectrometry .
The C-terminal domain blocks in addition proteolytic degradation by Lon-protease .
Although bluR and bluF are transcribed in the same direction and located next to each other on the chromosome , they do not constitute an operon .
Moreover , OxyR activates the synthesis of the small , noncoding oxyS RNA .
The sensory-domain of FNR contains five cysteine residues , four of which are essential for linking the -LSB- 4Fe-4S -RSB- cluster .
In contrast , NarQ phosphorylates NarL and NarP in response to both nitrate and nitrite .
Based on the structure of Mlc-DNA-binding-transcriptional-repressor , models for the three-dimensional structure of NagC and for the binding of GlcNAc-6-P were developed .
ArcA is a response regulator and is activated as a DNA-binding protein by phosphorylation .
An autoinhibitory effect on transcription has been observed and an inversion mechanism also contributes to transcriptional regulation .
The transcription of asnC sometimes traverses the origin of replication and continues into gidA , possibly explaining the effect on gidA expression .
rob expression is enhanced at the stationary phase and under glucose and phosphate starvation , and it was suggested that expression of rob is ?S dependent .
The crystal structures of MtlR from Vibrio parahaemolyticus and its homolog , the YggD protein from Shigella flexneri , have been determined .
This protein consist of two domains , an amino-terminal domain involved in dimerization and a carboxy-terminal domain indispensable for DNA-recognition .
The binding targets for GadW consist of 21-nucleotide-long directed repeat sequences that possess conserved motifs , called the GAD box , which is proposed to be the binding site for GadW and GadX .
AtoC is the response regulator in the two-component regulatory system AtoC/AtoS .
DnaA plays an important role in initiating chromosomal replication to bind sequences in the chromosomal origin .
RcnR binds to two sites in the rcnA-rcnR intergenic region with the sequence TACT-G ( 6 ) - N-AGTA .
This filament interacts with the LexA dimer to activate its self-cleavage activity by an allosteric mechanism , causing the dissociation of LexA from its DNA targets and the induction of the SOS regulon for the repair of broken DNA .
The activities of GadW and GadX are indispensable upon entry into the stationary phase in response to acid pH .
The glucitol regulator , GutM , is a DNA-binding transcription factor that regulates an operon ( gut ) involved in transport and utilization of glucitol .
However , in vitro studies have shown that YqjI can be affected by other divalent metals .
This DNA sequence consists of a palindromic sequence of 18 bp , called the ARG box .
Indirectly , this protein also regulates the transcription of several genes involved in motility , chemotaxis , and flagellum synthesis by directly controlling the expression of the master regulator FlhDC .
MtlR belongs to the Pfam 05068 family , a new class of transcription factors in bacteria that may regulate gene-expression indirectly as part of a larger transcriptional complex .
Distinct functional roles for both regulators have been proposed , and it has been shown that there is little direct coregulation of the two .
IHF plays a role in DNA supercoilingand DNA duplex destabilization and affects processes such as DNA-replication , recombination , and the expression of many genes .
It also acts as a global repressor for the mar-sox-rob regulon .
Catabolite repression in E. coli is mediated by the interplay of CRP , adenylate cyclase , cAMP , and the glucose-specific enzyme IIA ( EIIAGlc ) of the phosphoenolpyruvate : sugar phosphotransferase system .
SoxS , MarA , and Rob belong to the AraC/XylS-family of transcriptional regulators and , like other members of this family , they have two helix-turn-helix ( HTH ) motifs for DNA-binding : one of them , located in the N-terminal region , interacts with the element RE1 of the Mar-Sox-Rob box , and the HTH located in the C-terminal region interacts with the element RE2 .
Autoregulation of SgrR is not affected by phosphosugar stress .
This protein , which belongs to the IclR-family of transcriptional regulators , has a helix-turn-helix motif to bind DNA in its N-terminal domain and a 22-residue motif , specific to an IclR subfamily , in its C-terminal domain .
This dimeric protein recognizes and binds an imperfect inverted repeat DNA sequence .
The crystal structure of the repressor-operator complex reveals that specific binding is mostly mediated by contacts to the phosphate backbone and water-mediated hydrogen bonds , suggesting that the intrinsic DNA structure rather than the specific base pairs are recognized , a mechanism which has been termed indirect readout .
The activities of GadX and GadW are indispensable upon entry into the stationary phase in response to acid pH .
GcvR is an accessory protein that binds directly to GcvA , bending DNA to form a repression complex ( GcvA/GcvR ) in the regulatory region of the gcvT operon .
Here , IHF acts to facilitate the formation of the loop between the upstream bound activator and the ?54 holoenzyme .
EbgR ( for evolved ?-galactosidase repressor ) negatively regulates genes involved in the evolved ?-galactosidase system , which constitutes an alternative for lactose utilization in cells with mutations on the lacZ gene .
The output domain belongs to the winged-helix-turn-helix family of transcription factors .
For this reason , in the absence of H-NS the StpA protein is rapidly degraded in a Lon-protease-dependent manner protection from proteolytic degradation appears to be mediated by direct interaction between StpA and H-NS .
In addition , this regulator represses transcription of genes related to gluconate metabolism .
Phosphorylation changes the relative orientation of the subunits to each other , such that orientational constraints between the output domains are lost , allowing the tandem head-to-tail orientation for the active conformation .
The crystal structures of the regulatory domain of OxyR in both its reduced and oxidized forms have been solved .
The mhpR gene , which is located downstream of the genes it regulates and in the opposite direction , appears to be expressed constitutively .
mqsR is cotranscribed with the downstream gene mqsA , and their respective open reading frames are separated by 1 bp .
Mutations in ebgR and ebgA , however , enhance its catalytic-activity and enable rapid growth on lactose as a sole carbon source .
Transcriptomic and statistical modeling analyses with Zn concentration shifts showed a transient change in the activity of the iron regulator Fur and of the oxidative stress regulator SoxS ; these findings suggest a competitive binding mechanism for the physiology of Zn and Fe uptake .
Mlc forms tetramers in solution .
In addition , it also regulates genes related to cell surface-associated structures .
Cells carrying a MarA mutation in a glutamic acid residue ( E89A ) were able to express higher resistance to superoxides than those harboring wild-type MarA .
In the presence of l-rhamnose , RhaR binds in tandem to two repeat sequences upstream of the rhaS intergenic region to activate transcription by overlapping the -35 box of rhaSp .
On the other hand , AsnC is negatively autoregulated , but the presence of asparagine does not affect this regulation .
Synthesis of this operon is induced when Escherichia coli is grown on l-idonate/5KG in the absence of glucose and gluconate .
In addition to AdoMet , the metabolites 5 ' - deoxy-5 ' - ( methylthio ) adenosine ( MTA ) and adenine ( Ade ) also bind with high affinity to MetJ , but the biological effects of this binding are not known .
The antitoxin , MazE , is subject to degradation by ClpP-ClpA protease complex and exhibits a short ( 30 minute ) half life , whereas the toxin , MazF , is much more stable .
In addition , the OmpR regulon evolved with different responses and roles in the two species during acid stress .
An exhaustive analysis of the ArcA-response-regulator was carried out , based on different experimental methodologies , High-throughputs ( ChIP-chip and ChIP-seq ) , bioinformatic analysis , DNase I footprinting , and gene-expression profiling , and the results showed that ArcA is a global repressor of carbon oxidation pathways .
Mlc repressor function is disabled by binding of Mlc to an actively-transported and dephosphorylated form of PtsG ( EIICBGlc ) .
It represses transcription from the murQ promoter and also interferes with its own transcription .
The binding targets for ModE consist of inverted repeat sequences that possess conserved motifs ; each monomer binds to one of these conserved sequences .
For this reason the length of the CytR DNA-binding site is variable .
CreB and CreC are part of the creABCD operon .
CspA acts as a positive transcription factor of at least two cold shock genes : hns and gyrA cspA has been shown to negatively regulate its own expression as the result of attenuation of transcription .
The Lys9 residue is essential for recognition-of-put-promoter-DNA .
The role of ArgR in this latter reaction may be structural .
In class I promoters , the ?70 R4 region binds to the -35 box and SoxS binds upstream of the hexamer , but in class II promoters SoxS binds to the -35 box , occluding the binding of ?70 R4 .
H-NS forms two compact clusters associated with each copy of the chromosome .
The location and spacing of the binding sites vary considerably in different promoters , and most promoters are also codependent on additional regulators , e.g. , the oxygen sensor FNR , IHF , or Fis .
Sometimes the transcription of asnC ends at a terminator located downstream of this gene or by the DnaA protein that binds to a DnaA box blocking the transcribing RNA polymerase .
Based on microarray analyses of Escherichia coli , 2,3-butanedione ( 2,3-BD ) and glyoxylic acid ( GA ) , volatile organic compounds ( VOCs ) emitted from Bacillus subtilis , mediated global changes in gene-expression related to motility and antibiotic resistance phenotypes that affected the expression of more than 100 genes .
Richard et al. proposed that GadX can sense intracellular Na + concentrations , but the mechanism is not known .
In class I promoters , the activators bind upstream of the -35 box and are generally oriented in a backwards direction , while in class II promoters the proteins overlap the -35 promoter hexamer and generally are oriented in the forward direction .
In addition to the four high-affinity nickel-binding sites , the crystal structure reveals two binding sites for potassium ions , bridging the metal - and DNA-binding domains .
After prolonged O2 exposure , the -LSB- 2Fe-2S -RSB- cluster is destroyed , and apo-FNR , which lacks an Fe-S cluster , is the primary form of FNR under aerobiosis .
Rob consists of two domains and belongs to the AraC/XylS-family .
This repressor responds to N-acetylgalactosamine and d-galactosamine in the medium .
Nevertheless , the signal to which DicA responds is still unknown .
In addition , expression of the kdpFABC operon is regulated by the phosphoryl group transfer chain Ntr-PTS : dephosphorylated enzyme IIANtr binds to KdpD , and this interaction strongly stimulates KdpD kinase activity .
As a member of the LysR-family , this transcription factor is composed of two domains : the N-terminal domain , which has a potential helix-turn-helix DNA-binding motif in the DNA-binding region , and the C-terminal inducer-binding domain .
Therefore , specificity is believed to be due to the sequence-dependent structural parameters of the DNA , where A/T-rich regions play an important role .
The binding targets of MalT consist of 10-nucleotide-long direct repeat sequences that possess conserved motifs ; each monomer binds to one of these conserved sequences .
The binding targets for MelR consist of 18-nucleotide-long repeat sequences that possess conserved motifs ; each monomer binds to one of these conserved sequences .
Mlc forms stable dimers and binds to palindromic operator sites .
It is induced by tyramine , and in the absence of glucose , it activates the expression of amine oxidase and phenylacetaldehyde-dehydrogenase , proteins involved in 2-phenylethylamine-catabolism .
DNA-binding protein under anaerobic conditions , Dan , formerly TtdR or YgiP , is an LysR-type transcriptional regulator for L-tartrate fermentation .
The crystal structures of the C-terminal domain , apo-NikR , nickel-activated NikR , and NikR in complex with its operator DNA have been solved .
Its expression is strongly induced at low temperatures .
The identified 15-bp sequence motif is structured with flanking CAG/CTG triplets and a central AT-rich signal .
DhaR regulates transcription by coiled-coil-helix rotation , and this provides the mechanism for transmitting the binding signal from the GAF/PAS domains to the C-terminal DNA-binding domain .
IclR represses aceBAK transcription through two mechanisms ( 1 ) binding to the proximal site , overlapping the -35 promoter box , and preventing RNA polymerase binding and ( 2 ) binding to the distal site after the RNA polymerase has bound to the promoter and formed the open complex , avoiding the polymerase escape of the promoter through its interaction with the ?-subunits .
Reviews : .
In 1986 , Blanco et al. proposed that total repression of UidR is achieved in the presence of UxuR , suggesting the possibility that UidR and UxuR form a complex .
Under poor growth conditions , BolA is essential for normal cell morphology during both the exponential and stationary growth phases and in response to sudden carbon starvation .
This palindromic property of the PaaX site as well as the presence of a helix-turn helix motif in the protein have been the basis for suggestions that PaaX binds DNA as a dimer .
In contrast , NarQ phosphorylates NarL and NarP in response to both nitrate and nitrite .
SoxS is a dual transcriptional activator and participates in the removal of superoxide and nitric oxide and protection from organic solvents and antibiotics .
Binding to these sites is enhanced when MqsA is bound to MqsR .
His48 and His110 are the residues that participate in the low-affinity Ni ( II ) - binding response .
SdaR responds to d-galactarate and d-glucarate , and even better to d-glycerate to activate the genes it regulates .
FUR is a transcriptional repressor but also can be an activator ; the positive regulation of this regulator is mediated by the indirect effect of RhyB , which is an antisense small RNA .
Members of this group contain three domains : the sensory-domain located in the N-terminus , the central-domain involved in ATP-hydrolysis and interaction-with-?54 , and the C-terminal domain , which contains a helix-turn-helix motif .
Based on high-temperature molecular dynamics simulation and NMR experiments , information has been obtained about the structural and dynamic features at the atomic level for the N2 < -- > I2 thermal transition of the EcHU?2 homodimer .
Many of these genes are involved in the catabolism of secondary carbon sources ( for reviews , see .
Through atoDAEB operon regulation , AtoC modules positively the biosynthesis and the intracellular distribution of poly - ( R ) -3 - hydroxybutyrate ( cPHB ) , a biopolymer with many physiological roles .
MalT is a STAND transcription factor , Signal Transduction ATP bases with numerous domains .
On the other hand , in vivo protein-protein interaction assays suggest that both systems together form a single large signaling unit .
In the case of Rob , it appears that only one of the two HTH motifs makes base-specific contacts with DNA .
RclR homologs are found in a variety of proteobacteria as well as in a few actinobacteria .
Due to the ability of CitB/DpiA to bind to A/T-rich sequences , multiple other roles have been assigned to CitB .
Review : .
AtoC : acetoacetate br > Review : .
comR knockout mutants have lower cytoplasmic copper levels compared to the wild type when exposed to copper .
The E. coli multidrug-resistance regulator EmrR , negatively regulates the transcription of genes that code for multidrug-resistance pumps that extrude structurally unrelated antimicrobial agents from the cell and possibly it also represses a gene that codes for a porin .
YpdA/YpdB is activated during growth in an amino acid-rich milieu , such as LB medium .
NagC has a helix-turn-helix motif in its N-terminal part .
Two zinc ions are bound to each monomer .
Studies based on the dynamic oligomers showed that oxidized small HypT oligomers ( tetramers ) are the activation-competent species , whereas the docameric ring-like structures are the storage form .
The crystal structure of the C-terminal regulatory domain of Cbl ( 2.8 Å ) has been solved .
FadR binds DNA as an apo-protein , and it is released when it binds long-chain acyl-CoA .
It directly activates at least six operons , among which the b1500-ydeO operon encodes two additional activator proteins .
In the absence of inductor , this repressor binds in tandem to inverted repeat sequences that consist of 20-nucleotide-long DNA target sites .
Both mechanisms of regulation require the presence of the sRNA chaperone Hfq ; therefore , it was suggested that another small RNA , in addition to RprA , that regulates rpoS translation is regulated by LrhA .
lexA is the first gene in the lexA-dinF operon dinF encodes a member of the MATE family of multidrug efflux transporters .
This regulator is positively autoregulated and co-regulates with CRP , a global transcriptional regulator ; these regulators bind cooperatively to activate transcription of an operon related to transport and catabolism of l-idonate .
The response regulator OmpR , for Outer-membrane-protein Regulator , belongs to the two-component system EnvZ/OmpR .
In 1986 , Blanco et al. proposed that total repression of UxuR is achieved in the presence of UidR , suggesting the possibility that UxuR and UidR form a complex .
CitB/DpiA binds to sequences with a very high A + T content .
During anaerobiosis , TdcR participates in controlling several genes involved in transport and metabolism of threonine and serine .
This assumes a primary role for HypT in downregulating iron acquisition genes in order to prevent further synthesis of iron uptake proteins .
NemR binds to a region 16 bp in length , and its consensus is a palindromic sequence , TAGACCnnnnGGTCTA , which is referred as the NemR box .
Published reports disagree about whether MazF causes cell lysis in the absence of MazE or whether the toxin causes reversible inhibition-of-cell-growth , inhibiting translation and replication without causing cell inviability .
The SoxR protein , for Superoxide Response protein , is negatively autoregulated and controls the transcription of the regulon involved in defense against redox-cycling drugs and in responses to nitric oxide .
KdpE activates expression of the kdpFABC operon encoding the P-type-ATPase KdpFABC , a high-affinity potassium-transport system .
Dan belongs to the same family of growth phase-specific nucleoid proteins as Fis , Dps , HU , IHF , and H-NS .
In an electrophoretic mobility shift assay it was shown that Dan binds to the ttdA-ttdR intergenic region .
This interaction prevents-access-to-the-?54-RNA-polymerase-complex .
The crystal structure of FlhDC has been solved to 3 Å resolution .
The expression of lrhA is repressed by the RcsCDB phosphorelay system and by the DNA motor protein FtsK .
Each monomer of GadX binds to one of these conserved sequences .
YdeO expression is induced by UV irradiation via the EvgS/EvgA system and thus controls the expression of 21 genes .
The Cu efflux regulator , CueR , regulates genes related to the primary copper-homeostasis system in response to the presence of copper , silver , or gold ions .
PspF does not contain a regulatory domain typical for other bEBP proteins ; instead , its activity is negatively controlled by PspA acting in trans .
MetJ finds its target sites rapidly by facilitated diffusion .
At the R1 PY promoter , ArcA acts in conjunction with TraJ .
A microarray analysis suggests that NarP activates 14 operons and represses 37 operons .
The Carbohydrate diacid regulator , CdaR , or sugar diacid regulator , SdaR , regulates genes involved in the uptake and metabolism of galactarate and glucarate , and it is also autoregulated .
It has been suggested that ZraS functions as a zinc receptor .
In the atoDAEB regulatory region there are two of these sites arranged as inverted repeats separated by 1 bp .
YehT protects three repeats of the motif upstream of the yjiY gene , which have been designated M1 to M3 and were identified using the MEME tool .
Lee et al. showed that the transcription which SdiA mediates is controlled by indole , but whether this effect is indirect or direct is not known .
While Cad1 contains an inverted repeat sequence , Cad2 lacks either an inverted repeat or a palindromic sequence .
The binding targets for XylR consist of 18-nucleotide-long directed repeat sequences that possess conserved motifs ; each monomer binds to one of these conserved sequences XylR belongs to the AraC/XylS-family .
The DNA-binding and dimerization domains are characteristic of the MerR-family of proteins .
It dimerizes in apo-CRP , with the DNA-recognition helix F buried within its core .
In this system the full repression of the ula regulon requires IHF and binding of UlaR to four operator sites , possibly involving UlaR-mediated DNA loop formation .
A probable conformational change upon oxidation allows the protein to bind DNA to regulate transcription .
This cofactor is required for DNA-binding .
Currently , no inducer for this regulator has been reported in the literature .
This protein binds to the CusR box , which is a palindromic sequence also conserved in other organisms ; the sequence is located in the regulatory regions of genes involved in copper-responsive systems and is regulated by proteins homologous to CusR .
Review : .
The molecule inducer is represented by different N-acyl-L-homoserine lactones ( AHLs ) , which are signaling molecules involved in communication between bacteria ( quorum-sensing systems ) .
The YehT-binding site consists of two direct repeats of the sequence motif ACC -LSB- G/A -RSB- CT -LSB- C/T -RSB- A , and these are linked by a 13-bp spacer .
Thus , the DNA-binding affinity of MurR is affected specifically by MurNAc-6-P .
For expression of cydAB , it has been shown that ArcA-P antagonizes H-NS .
In the presence of glucose it increases the intracellular concentration of the metabolites d-fructose 1-phosphate and d-fructose 1,6-phosphate , which interact with FruR to prevent its binding or displacement of the target operons .
In vitro transcription assays indicate that the ?-CTD of the RNA polymerase is partially dispensable for RhaR activation and is required for CRP activation of the rhaSR operon .
AlpA is a transcriptional regulator of intA expression .
Cyanate decreases the amount of bending , suggesting that the change in bending acts as a transcriptional switch .
The transcriptional dual regulator CynR , cyanate regulator , activates the expression of the cyn operon , which is involved in use of cyanate as a sole nitrogen source , in the presence of the inducer cyanate .
Both genes , rstA , encoding the response regulator , and rstB , encoding the sensor kinase , are transcribed together in an operon that is induced under low-Mg2 + growth conditions through the PhoP/PhoQ two-component system .
Richard et al. proposed that GadW can sense intracellular Na + concentrations , but the mechanism is not known .
The binding targets for AraC consist of 17-nucleotide-long direct repeat sequences that possess conserved motifs ; each monomer binds to one of these conserved sequences .
PhoB is a dual transcription regulator that activates expression of the Pho regulon in response to environmental Pi .
To repress transcription , GutR recognizes DNA-binding sites , but no consensus sequence has been identified .
The ascG gene is transcribed divergently from the operon it regulates ascG is paralogous to galR .
It has also been proposed that AdiY is not the only regulator of the adi system , but the conditions under which AdiY functions remain unknown .
Cross talk between the mar and rob systems plays an important role in the response to salicylate .
The Propionate Regulator , PrpR , is a transcription factor that controls expression of genes involved in catabolism of propionate .
This dithiolate coordination confers the metal ion selectivity for +1 ions .
The crystal structure of Mlc has been determined to 2.85 and 2.7 Å resolution and Mlc in complex with four molecules of enzyme IIBGlc ( EIIB ) to 2.85 Å resolution .
The antitoxin MqsA belongs to the toxin-antitoxin system MqsR-MqsA , which controls biofilm-formation and triggers programmed-cell-death in E. coli .
Thus , MarA E89A acts more like SoxS than MarA in exhibiting greater activation and binding at the class I promoter .
Although GutM binding does not depend on the presence of glucitol , this compound appears to be necessary for derepressing gutM , perhaps by interacting with GutR .
KdpD exhibits both kinase and phosphatase activities towards KdpE .
RstA appears to control genes involved in different biological-processes , such as acid tolerance , curli fimbria formation , and anaerobic-respiration , among others .
Review : .
Expression of the mlrA gene is RpoS-regulated in an avian pathogenic E. coli strain .
The latter , like EnvY , also has a putative transmembrane region .
However , when it was found that this protein only regulates two genes , the suggestion was rejected and it was proposed that probably high concentrations of fatty acids could degrade the protein instead of it binding to the regulator .
This regulator removes methyl groups ( as well as larger groups ) from the guanine and thymine substrates and transfers them to its own cysteine residue ( Cys-321 ) in the C-terminal domain .
RbsR represses not only the rbs operon for transport and utilization of D-ribose but also the de novo synthesis of purine nucleotides from D-ribose 5-phosphate .
For example , IHF was originally found to be required for the site-specific recombination of phage & lambda ; with the chromosome .
This site contains inverted repeats with the consensus CCTGA/GA/G separated by 6 bp .
Synthesis of these operons is induced when E. coli is grown in the presence of the inducer ( D-galactose ) and the absence glucose .
Spectroscopy studies and structural modeling of the GAF-domain identified five candidate ligands for the nonheme iron and suggested a model in which it is coordinated in a pseudo-octahedral environment by three aspartate residues , an arginine , and a cysteine .
The receiver-domain of NarL and NarP could function as a stabilizer of the carboxyl-terminal domain ( CTD ) ; it enhances DNA-binding and/or enables repression per se in vivo .
The data reveal that the active and inactive receiver-domains dimerize in two different orientations relative to each other .
MlrA is found at a higher level in the hierarchy of the transcription factor network .
This regulator is part of the gntRKU operon , yet it can also be constitutively expressed as an independent ARRAY ( 0x156d848 ) transcription unit .
This protein belongs to the large LysR-family of transcriptional regulators and it is positively regulated by CysB , which is similar to Cbl ( 40 % identity ) .
GalS and GalR have only two substitutions in the first helix of the N-terminal domain .
In class I promoters the second N and in class II promoters the third N of the consensus FNR site tend to be an A-T .
When one of these ligands is bound to the C-terminal domain of AcrR , a conformational change in the N-terminal domain releases the regulator from its DNA-binding site .
MetJ belongs to the ribbon-helix-helix family of regulatory proteins .
Reviews : .
In systematic studies of oligomerization , it was shown that some members of the LysR-family , like OxyR , interact with other members of the family to form heterodimers , but the physiological significance of this is unknown .
Although interaction between TdcA and the regulatory region of the tdc operon has not been demonstrated , it has been suggested that TdcA recognizes and binds to an inverted repeat located upstream of the operon .
SoxR and SoxS are two transcription factors that govern a set of genes in which the two regulators act sequentially .
NanR is a member of the FadR/GntR-family .
Mlc is a member of the ROK ( repressor , ORFs , kinases ) ( NagC/XylR ) family of proteins , which contains at least two distinct classes of proteins : xylose repressor ( XylR ) and a series of glucose/fructose kinases .
Each of the sensors , NarX and NarQ , is able to phosphorylate NarL and NarP , leading to the activation of both proteins .
Deletion of basR prevents the FeSO4 - , ZnSO4 - , and NH4VO3-mediated induction of eptA , arnB , and yibD and results in sensitivity to the cationic agent polymyxin B .
They activate a common set of genes , but the expression and activity of each one of these proteins are induced by different signals : the activity of Rob is increased with dipyridyl , bile salts , or decanoate , and the transcription of MarA and SoxS is increased by the aromatic weak acid salicylate and oxidative stress respectively .
Diverse aldehydes induce the yqhC-dependent expression of yqhD and dkgA genes .
The monomer in the FNR dimer that makes contact with the RNA polymerase and the activating region in FNR that makes the contact depends on the class of promoter , class I or class II .
Based on genomic SELEX screen analysis , it was identified as a highly probable regulator for 12-16 operons involved in various steps of sulfur-utilization , playing an important role in the coordination of expression of the genes involved in this metabolic pathway .
MatA is a LuxR-type transcription factor that is directly involved , as a positive regulator acting at transcriptional and posttranscriptional levels , in the expression of the mat operon in meningitis isolate strain IHE 3034 .
Reviews : .
Moreover , inactivation of penicillin-binding protein 3 , FtsI , either chemically or genetically , induces SOS in E. coli .
Reviews : .
The yqhD and dkgA genes encode NADPH-dependent oxidoreductases , and both are involved in furfural reduction .
These regulators form homodimers and heterodimers in vivo .
Fucose regulator , FucR , acts as an activator of operons involved in fucose-transport and degradation .
It responds to extracellular pyruvate .
Phenylethylamine regulator , FeaR , is considered an activator of phenylacetate-synthesis from 2-phenylethylamine ( PEA ) .
PutA is a flavoprotein with mutually exclusive functions as a transcriptional repressor and membrane-associated enzyme .
Therefore , it has been suggested that the main role of DpiA/CitB is regulation of citrate fermentation .
A solution structure of the entire protein using small-angle X-ray scattering ( SAXS ) show that PutA is a symmetric V-shaped dimer .
BaeR has been shown to regulate directly genes involved in drug-resistance and indirectly appears to regulate genes involved in several cellular-processes , such as flagellum biosynthesis , chemotaxis , and maltose-transport .
It has been demonstrated , in E. coli as in other bacteria , that RutR binds to several coding regions located hundreds of base pairs downstream of the start codon .
This induction was determined by ChIP-chip analysis with DNA-RNAP occupancy when cells were exposed to growth-inhibitory concentrations of MG .
ArsR has a helix-turn-helix motif for DNA-binding , a metal-binding site and a dimerization domain .
Expression of mcbR is induced by overexpression of the lsr operon regulators LsrR and LsrK , the quorum-sensing regulator MqsR , and the AI-2 exporter TqsA .
Under anaerobic and microaerobic conditions it activates transcription of the norVW operon , encoding a nitric oxide ( NO ) - reducing flavorubredoxin that detoxifies NO .
MarR is inactivated by salicylate , and then the operon is induced .
The intergenic region of norR and norVW carries three binding sites for NorR with a symmetrical 11-bp consensus sequence .
These changes were mediated by YpdB through the regulation of the transcription factors SoxS , YjhU , and the RpoS sigma factor , which were increased by treatment with ( 2,3-BD ) .
The crystal structure of the DNA-HU?? complex has been resolved .
In addition , expression of oxyR is positively regulated by cAMP-activated Crp protein during exponential growth and negatively regulated by RpoS when cells enter stationary phase .
Although little is known about the regulating mechanism of UidR , it has been shown to act as a repressor , binding to a putative inverted repeat sequence in a cooperative process with UxuR .
The FUR-binding sites were previously represented as regions of 19 bp , which were determined by footprinting of several promoter sequences .
Gueun % e ' ; et al. suggested that StpA may regulate the expression of a tributyltin-inducible operon .
ArcA represses transcription by directly binding to the promoter or by binding to sites overlapping an activator-binding site .
This suggests the possibility that BglJ controls , directly or indirectly , the expression of the bgl operon .
Different aligments and computational analysis of these sequences showed different overlapping 15-bp sequences : TGATAATnATTATCA , consisting of two inverted repeats of 7 bp separated by 1 bp .
It has also subsequently been described as a nucleoid-associated protein that shows apparently sequence-nonspecific DNA-binding activity .
The Rhamnose regulator , RhaR , is a transcription factor that regulates genes involved in l-rhamnose-degradation and coregulates with the global transcriptional regulator CRP .
StpA protein , for Suppressor of td phenotype A , is a nucleoid-associated multifunctional protein that acts as a transcriptional repressor in chromosomal DNA packaging and as a chaperone .
Five different small RNAs are known to regulate expression of CsgD at the post-transcriptional level ; reviewed in ; a sixth has recently been discovered .
The binding of the -LSB- 2Fe-2S -RSB- 1 + cluster allows IscR to induce a conformational change , mainly around the residue Glu43 , that modifies its DNA-binding affinity .
In response to increasing concentrations of nickel or cobalt , RcnR releases the repression of rcnA and rcnR to allow its expression .
In the absence of NO , the activity of the central catalytic AAA + domain of NorR is repressed by direct interaction between the GAF-domain and the ?54-interacting region of the AAA + domain .
In the presence of an inductor , GalS undergoes a conformational change that reduces its affinity for the operator .
No research has been done to determine the DNA-binding sites for EnvY .
Thus , transcription of catabolic genes is switched off .
Review : .
ArgP was first identified as an inhibitor of oriC-initiated DNA-replication in vitro .
Expression of comR is not affected by copper .
EnvR recognizes and binds a 24-bp palindromic DNA sequence .
On the other hand StpA may form heteromeric complexes with Hha and YdgT .
Transcription is induced upon biofilm-formation .
For example , HU introduces negative supercoiling in covalently closed circular DNA in the presence of topoisomerase I .
The binding targets for RhaS consist of 17-nucleotide-long sequences that possess conserved motifs ; each monomer binds to one of these conserved sequences .
DeoR is an octamer in solution and it forms multiple complexes ( oligomers ) in its target promoters ; the cooperative binding of this regulator to different tandem inverted repeat sequences generates a repression DNA loop .
nagC encodes the repressor of this regulon .
lsrR shows differential codon adaptation , resulting in differential translation efficiency signatures , in thermophilic microbes .
Genes identified by SELEX analysis include the following : paoC , xseB , thiI , ydcO , sutR , ynfG , ydiY , pfkB , fliZ , ypfN , yfgM , yfiC , tdcF , cysE , and yjcS .
However , the identification of an amino acid substitution in MalT that suppresses Aes inhibition without interfering with MalY inhibition suggests that the binding sites of the two inhibitory proteins are not the same .
Dpi : destabilizes plasmid inheritance .
soxS is divergently transcribed from soxR .
In vivo studies detected crosswise stimulus-dependent alterations in the expression of their respective target genes , and mutational analyses revealed that deletion of any of the components of the signal-transduction cascade affects the function of the other .
The sensitivity of CueR for copper ( I ) ions is extremely high ( in the zeptomolar range ) , which corresponds to less than one atom per cell .
CueR activates transcription by overlapping the -35 box of promoters and represses it by binding downstream of the transcription start site .
PspA inhibits PspF activity by direct interaction of the AAA + transcription-activation domain of PspF .
Other authors have proposed different lengths and consensus sequences for Ada , but Nakamura et al showed that deletions in this consensus sequence ( AAANNAAAGCGCA ) decrease the activity of ?-galactosidase .
The N-terminal dimerization domain mainly consists of ?-sheets and carries a hydrophobic pocket for binding of cAMP .
An lctR mutant is impaired in biofilm-formation .
FruR forms a complex with DNA in the absence of fructose 1-phosphate or fructose 1,6-phosphate , binding to an 18-bp-long sequence with an imperfect palindromic sequence .
The long 5 ' untranslated region of cspA mRNA contains a feature within the first 25 bases that is responsible for derepression of cspA expression and inhibition of synthesis of cellular proteins other than cold shock proteins following cold shock .
At low pH , formation of the disulfide bond is prevented , which in turn converts CadC into an active state , but only if lysine is present to inactivate to LysP , the negative regulator of CadC .
This protein consists of two functional domains , the N-terminal receiver-domain , which is phosphorylated , and the C-terminal output domain , which binds to DNA and interacts-with-the-?70 subunit of RNA polymerase to activate transcription .
BglJ-RcsB is active independently of RcsB phosphorylation .
It is a tetramer in solution .
When this protein activates genes involved in replication , it appears to bind to their regulatory regions without a coeffector .
This repressor binds in tandem to inverted repeat sequences that are 21 nucleotides long and possess conserved motifs .
NarL represses 41 operons involved in alternative respiratory pathways , such as fumarate reduction or fermentation of simple sugars .
A model of how CspA might affect the transcription of hns has been proposed .
RelB also represses transcription of relBEF .
The homeostasis of different metals in the cell is constantly monitored , and adequate pathways are activated or repressed to keep the metals within normal levels .
MlrA is part of a signaling-cascade that controls curli biosynthesis , in which c-di-GMP regulates through the diguanylate cyclase/phosphodiesterase ( DGC/PDE ) pair YegH/YhjH ( module I ) and the activity of the YdaM/YciR pair ( module II ) , which forms a signaling complex with MlrA .
It has been suggested that the most significant role of ArcA is under microaerobic conditions , while that of FNR is under more strictly anaerobic conditions .
MetJ represses the expression of genes involved in biosynthesis and transport of methionine .
The transcription of the gene atoC is induced by polyamines and histamine microarray analysis shows that OmpR may regulate the transcription of this gene .
It also regulates the expression of small riboregulators .
Two UhpA dimers bind to two sites with different affinities upstream of uhpT .
ArgR belongs to the ArgR/AhrC family , whose members are widely distributed in bacteria .
An inverted repeat sequence of 24 bp that overlaps the acrAB promoter has been identified as the AcrR-binding site .
In addition , the induction of sgrS expression by the nonmetabolizable glucose PTS substrate ( + / - ) - methyl glucoside is abolished in a sgrR mutant .
The octamer is composed of four dimers , each of which appears to recognize and bind an inverted repeat DNA sequence of 5 bp separated by 3 bp that are usually T or A base pairs .
NarP binds to two inverted heptamers separated by 2 bp , termed 7-2-7 sites .
The structure of the MazE-MazF complex is presented at 1.7 A resolution .
NarL and NarP act as antirepressors .
The complex is tetrameric and is comprised of a HipB homodimer that interacts with DNA , sandwiched by a monomer of HipA on each side .
As a member of the group of ?54-dependent transcriptional regulators , HyfR contains three domains : the sensory-domain , located in the N-terminus ; the central-domain , involved in open complex formation , ATP-hydrolysis , and interaction-with-?54 , and the C-terminal domain , which contains a helix-turn-helix motif for DNA-binding .
A strain from which all five toxin-antitoxin systems have been deleted shows no deficiency in its stress response or competitiveness under nutrient-limited conditions .
The Maltose regulator , MalT , is a transcription factor that activates transcription of several genes and operons involved in maltose catabolism and transport .
mngR shows differential codon adaptation , resulting in differential translation efficiency signatures , in thermophilic microbes .
SoxR contains two essential -LSB- 2Fe-2S -RSB- clusters for its transcriptional-activity .
NorR is a ?54-dependent transcriptional activator .
On the other hand , NtrC is sometimes autophosphorylated with small-molecule phospho donors .
In the HipB-HipA complex , each monomer of HipA interacts with two monomers of HipB .
Review : .
It is negatively autoregulated and coordinately represses transcription of a divergent operon that encodes a maltose-glucose PTS permease and a bifunctional protein that interacts directly with the MalT-transcriptional-activator .
The YehU/YehT and YpdA/YpdB two-component systems are activated and expression of the corresponding target genes was found to occur at the same time as the onset of the stationary phase .
Maltose inhibitor , MalI , is a repressor that controls genes related to the maltose system .
AdiY has a putative transmembrane region , suggesting that it may be a membrane-associated protein .
GalR and GalS have only two substitutions in the first helix of the N-terminal domain .
This sequence organization is common in yefM-yoeB regulatory regions in diverse genomes , suggesting that interaction of YefM-YoeB with these motifs is a conserved mechanism of operon autoregulation .
Reviews : .
The Exuronate repressor , ExuR , is a DNA-binding transcription factor that negatively regulates its own synthesis and represses transcription of the operons involved in transport and catabolism of galacturonate and glucuronate .
Independently , each repressor binds to DNA separately .
Expression of this regulator is also stimulated in presence of L-lactate , and this inductor promotes a conformational change that probably destabilizes the DNA loop , promoting the transcription open complex .
CitB/DpiA belongs to the two-component system DpiB/DpiA , or CitBA .
YoeB and YefM are a toxin-antitoxin pair .
On the other hand , 1,094 predicted sites for LeuO were identified using the position-specific scoring matrix method .
Both binding sites are necessary for cadBA activation .
Based on analysis with the Genomic SELEX screening system , PgrR was identified as a repressor of the expression of genes of the initial enzymes for peptidoglycan ( PG ) peptide-degradation as well as genes of the switch control between recycling and degradation of PG peptides , which are induced upon exposure to heat shock or membrane distortion .
In general the environmental conditions , such as low osmolarity , low growth temperature ( < 32 ° C ) , and low growth , affect the expression of csgD and the production of the biofilm and cellulose .
The ratio of dissociation of TreR -LSB- koff ( trehalose ) -RSB- / -LSB- koff ( trehalose/6-phosphate ) -RSB- is > / -2,800 , and its rate of association ( kon ) is > / -102 .
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The RNA polymerase RpoA and RpoD subunits are necessary for the transcriptional activation by UhpA which induces open complex formation , but the stabilization of this complex is CRP dependent .
This operon is divergently transcribed with the tdcR gene , whose product also activates the transcription of the operon .
ArsR : homologous to arsenate inducibility regulator .
Deletion of basR resulted in susceptibility to cell-killing by elevated levels of Fe ( III ) .
CreC can act as the the phosphate donor for PhoB in PhoR mutants ( and references therein ) but this activity is masked in PhoR + strains and the CreC/PhoB pathway is not responsive to phosphate levels .
Currently , the GadW/GadX-dependent circuit , involved in the GAD system , is under discussion and study .
The 3D structures of the receiver-domain in the absence and presence of the phosphoryl analog beryllium fluoride and of two constitutively active mutants of this domain have been solved .
LysP and CadC interact most strongly at pH7 .6 and at lysine concentrations of 1 µM or less , that is , under non-Cad-inducing conditions .
TrpR represses transcription by interfering with the ability of RNA polymerase to interact with the promoter .
The EvgA-YdeO-GadE circuit is very complex and involves feedback loops and autoactivation .
The C-terminal sugar-phosphate-binding domain belongs to the DeoR-C family of the ISOCOT superfamily and is structurally related to E. coli D-ribose-5-P isomerase .
On the other hand , orthologs of yqhC are also present in more distantly related Gram-negative bacteria .
The activity of tmRNA , SsrA , counteracts RelE-mediated translation inhibition .
Overproduction of AppY also causes an elevated spontaneous mutation rate .
In the presence of trehalose-6-phosphate and at low osmolarity levels , TreR derepresses an operon related to trehalose-transport and catabolism while trehalose is inactive .
Experimental support for this consensus sequence was obtained from footprinting , site-directed mutagenesis experiments , analysis of the affinity and stoichiometry of DNA-binding , gel retardation assays , etc. .
The lack of an evident transcription-termination structure in the intergenic region between adiY and adiC , separated by 137 bp , suggests the possibility of both genes being part of the same operon but further studies have failed to confirm this .
ArgP is a noncanonical regulator , as it binds to a number of additional sites in the genome without an apparent direct regulatory effect , exhibiting low-affinity binding to these sites .
NtrB is also able to dephosphorylate to NtrC .
Transcription of this operon is induced when E. coli is grown under anaerobic growth conditions and when the physiological inducer , formate , binds to the FhlA protein .
The genes that the YeiL transcriptional activator regulates have not been identified yet , but it has been proposed that this protein might regulate genes involved in post-exponential-phase nitrogen starvation .
The effector bio-5 ' - AMP is also a substrate in the BirA-mediated biotinylation of the biotin carboxyl carrier protein monomer ( apoBCCP ) , and this relationship results in repression of the biotin operon when the abundance of apoBCCP ( and therefore the cellular demand for biotin ) is reduced .
Most NarL-dependent promoters are also codependent on the oxygen sensor FNR , IHF , or Fis , implying that multiprotein complexes are involved in the transcriptional regulation of NarL target promoters .
On the other hand , Lee et al. ( 2013 ) reported that NemR contains six cysteines located at residue positions 21 , 98 , 106 , 116 , 149 , and 153 .
These data reveal that the output domains bind in a novel tandem arrangement , in which several monomers bind head to tail to successive 11-bp direct repeat sequences , coating one face of the double helix .
Dan may have a functional dichotomy , controlling both the structure and function of the nucleoid .
Reviews : .
The hexamer is the active form of ArgR , and L-arginine binds to ArgR and stabilizes the hexamer and increases its DNA affinity by allosteric activation .
The autophosphorylation of RstB appears to be stimulated by low pH. Subsequently , the phosphate group is transferred from RstB to RstA to activate it .
Phosphorylation induces the separation of both domains , resulting in the exposure of previously inaccessible DNA-binding residues and the formation of a new dimerization interface in the C-terminal domain .
XapR is homologous to AlsR ; they show 68 % of identity in an amino-terminal region of 60 amino acids .
Steps leading to open complex formation at the promoter have been examined using PspF and various nucleoside analogs .
Under aerobiosis , the apo-FNR monomer is exposed and can be degraded by the ClpXP protease .
HU-1 ( HupB ) and HU-2 ( HupA ) are closely related but differ by 28 residues , and they have a high content of hydrophobic residues represented mostly by alanine .
Based on biochemical analysis , a positive cooperative binding mechanism of PhoBDBD ( DNA-binding domain ) to its cognate DNA sequence and a decisive contribution of dimerization to the complex stability were demonstrated .
NadR is composed of three different domains : an N-terminal helix-turn-helix domain for DNA-binding , a central NMN adenylyltransferase domain that contains an ATP-binding site , and a C-terminal ribosylnicotinamide kinase domain .
Perhaps the IclR binding at both sites forms an intermolecular bridge that leads to a DNA loop structure and thus enhances the aceBAK repression .
This regulator belongs to the AraC/XylS-family of activators and occurs as both a monomer and a homodimer .
The binding sites for NarP overlap with the binding sites for NarL .
It seems the binding sites of RhaS are on a different face of the DNA relative to the rhaBAD operon .
Both sites resemble 25-bp imperfect palindromes but differ in their sequence .
HypT has five cysteine residues which contribute to control the DNA-binding activity of HypT in vitro .
In this repression system , GalR binds to two operators in the presence of HU , resulting in the formation of a repressor loop .
This gene codes for a protein that directly interacts with PhoQ to activate the PhoQ/PhoP system , which regulates genes , including Mg2 + transporters and lipopolysaccharide modification genes .
When StpA binds DNA , it is able to form a rigid filament , and thus the access to DNA is blocked .
tdcR is transcribed alone and is located divergently in the genome from the operon ( tdcABCD ) , whose transcription is activated by TdcR .
Synthesis of these genes is induced when E. coli is grown in the presence of KDG and under high-temperature conditions , between 32 and 35 ° C. Although little is known about the regulating mechanism of KdgR , it has been shown to act as a repressor that binds to a putative inverted repeat sequence .
The multifunctional protein NadR has enzymatic as well as regulatory activity .
HU is a transcriptional dual regulator .
It is composed of two domains .
This protein regulates the expression of the operons that encode components of a secondary pathway of iron-sulfur-cluster-assembly , iron-sulfur proteins , anaerobic-respiration enzymes , and biofilm-formation .
Nitric oxide ( NO ) is also able to inactivate FNR through the nitrosylation of the -LSB- 4Fe-4S -RSB- cluster , although NO is sensed by other transcription factors , and FNR appears only to function as a final safeguard against NO damage .
This protein negatively regulates its own synthesis , and in the absence of fructuronate it represses transcription of the cluster of operons involved in transport and degradation of the sugar acids ?-D-glucuronides , glucuronate , and gluconate .
GalS is negatively autoregulated , and its expression is increased in the presence of inducer and glucose .
CynR binds to DNA in the presence or absence of cyanate and induces bending of the DNA .
HypT belongs to the LysR-type transcriptional regulator family , which protects cells from HOCl damage .
AgaR binds in tandem to several repeat sequences in the intergenic regions of agaZp , agaRp , and agaSp to repress transcription by overlapping the -35 and -10 boxes .
However , the activity of ArgP depends on arginine and lysine to regulate genes involved in arginine-metabolism .
Leblanc et al. identified two flavonoids and also sodium tungstate as novel inducers to BaeSR .
Although the C-terminal domain and the N-terminal domain from DhaR are similar to those of other members of this group , its central-domain is not .
Reviews : .
There is intensive cross-regulation with the paralogous two-component system NarX-NarL .
This protein is autoregulated ; arsR is the first gene in the arsRBC operon that it regulates .
An RcnR structure study showed that it has a charged N-terminal region ( amino acids 1-34 ) , followed by a highly conserved region of primarily nonpolar amino acids ( 35-64 ) , that is , probably involved in binding metals .
AtoC , also known as antizyme protein ( Az ) , is a protein that regulates processes at the transcriptional and posttranslational levels .
The YafQ-DinJ toxin-antitoxin system was identified by its similarity to the RelE-RelB toxin-antitoxin system .
Expression of sdiAitself is regulated by a mechanism similar to quorum-sensing : exposure to conditioned medium results in a 50-80 % decrease in sdiA expression .
Nar class I promoters have a single Nar-binding site immediately adjacent to the promoter and Nar class II promoters have two Nar-binding sites upstream of the promoter and reference therein .
( FNRD154A ) 2 also recognizes an FNR-dependent promoter under aerobic conditions and maintains its promoter specificity and conformational stability .
CadC is a metal-sensitive transcriptional activator that regulates the expression of genes involved in cadaverine synthesis and excretion under low external pH and high concentrations of lysine .
LysR belongs to the family LysR , which contains three domains : an amino-terminal domain that contains a potential helix-turn-helix DNA-binding motif ; a central-domain , with response domains much less conserved , that possibly are important for coinducer-responsive transcription ; and a C-terminal domain that includes the key residues possibly involved in DNA interactions and coinducer response .
RcsB-BglJ is a pleiotropic transcriptional activator that coordinates regulation with global regulators , including CRP , LeuO , and HNS .
However , alignments made by the curators of this database showed that the sequence is less conserved in the upstream regions regulated .
In addition , GadW also activates the transcription of the central activator involved in the acid response .
This regulator acts as an activator by binding to cis-acting elements that overlap the upstream elements ( UP ) of the promoters regulated .
This regulator contains two functional domains : an N-terminal domain , which contains a motif for DNA-binding , and the C-terminal domain , which is involved in the interaction-with-the-RNA-polymerase .
The differential regulation of these genes might be caused by the degeneracy of their DNA-binding sites .
ArgP is a dimer with an estimated concentration of 100 to 400 molecules per cell ( that is , around 200 to 800 nM monomers ) .
The ModE dimer binds two molecules of molybdenum with a Kd of 0.8 mM .
In the absence of arabinose it interacts with the DNA-binding domain and constrains this domain , and it releases it in the presence of arabinose .
A high level of AscG is always present in wild-type Escherichia coli cells .
MhpR , hydroxyphenylpropionate regulator , participates in controlling the expression of several genes involved in degradation of phenylpropionate ( PP ) .
FabR , Fatty acid biosynthesis Regulator , represses expression of the fabA and fabB genes , which are essential for the synthesis of monounsaturated fatty acids .
Based on microarray assays , a new function as regulator of S-nitrosylation ( a nitrosative stress regulon ) under anaerobic conditions has been determined for OxyR and it is distinct from the OxyR regulon activated by oxidative stress .
Expression of yeiL increases during stationary phase under aerobic conditions and is positively autoregulated .
RcnR forms a stable tetramer and binds as a tetramer to one operator .
In addition , the genes regulated are induced when Escherichia coli is grown in the presence of the inductor , d-gloconate , and in the absence of glucose .
Nar class I promoters have a single Nar-binding site immediately adjacent to the promoter and Nar class II promoters have two Nar-binding sites upstream of the promoter and reference there in .
GlpR belongs to the DeoR family of transcriptional regulators .
Reviews : .
The expression of argP is induced by PhoB under phosphate starvation .
This HipAB system is involved in the high persistence , which is the capacity of the bacteria to survive prolonged exposure to antibiotics , and Kawano et al. also showed that this system is important for survival during the long-term stationary phase .
OxyR is also activated under nitrosative stress ; this reaction involves S-nitrosylation of OxyR .
RhaS is part of the unusual rhaSR operon that encodes two transcriptional regulators , RhaS and RhaR ( 30 % identical ) , both members of the AraC/XylS-family of transcriptional regulators .
In the presence of melibiose , MelR binds in tandem to repeat sequences in the melR/melAB intergenic region to activate transcription by overlapping the -35 box of the promoter melAp .
3 - ( 2,3-Dihydroxyphenyl ) propionate ( DHPP ) and 3-hydroxyphenylpropionate ( 3HPP ) , two intermediates of the metabolic pathways , are the principal inducers of MhpR .
Each of the sensors , NarQ and NarX , phosphorylates both NarP and NarL , leading to the activation of both proteins .
The complex is hexameric and is comprised of a MazE homodimer sandwiched between MazF homodimers .
The crystal structure of the HipB-HipA-DNA complex has been solved at 2.68 Å resolution .
When this protein represses genes involved in glucitol-transport and utilization , it appears to bind to their regulatory regions without a coeffector .
EmrR , which is also known as MprA , microcin production regulation , locus A has also been shown to be a repressor of plasmid-encoded genes involved in microcin biosynthesis .
FNR activates the transcription from class I and class II promoters , in which the FNR-binding sites are located around -61 , -71 , -82 , or -92 in class I and around -41.5 in class II .
Due to the autoregulation of crp , cAMP-CRP levels increase .
To activate transcription , GutM recognizes DNA-binding sites , but no consensus sequence has been identified .
At times CytR also repositions CRP to alternative DNA-binding sites that are not functional for activation .
The nickel ion is bound in a four-coordinate planar conformation to NikR in solution and in a six-coordinate conformation to NikR bound to DNA .
The lambda RexB protein has an inhibitory effect on ClpP-mediated proteolysis of MazE , increasing survival of lysogenized cells under conditions of amino acid deprivation .
This repressor binds in tandem to inverted repeat sequences that are 16 nucleotides long and possess conserved motifs ; each dimer binds to one of these conserved sequences .
Nac belongs to the LysR-family and features a helix-turn-helix motif located close to the N-terminus .
In the presence of d-xylose , XylR binds in tandem to four inverted repeat sequences in the xylAB/xylFGHR intergenic region to activate transcription by overlapping the ?
A norR mutant is completely defective with respect to anaerobic NO detoxification and is sensitive to reactive nitrogen intermediates generated from nitroprusside .
In particular , in the absence of D-galactose , GalR represses the galETKM operon .
McbR ( YncC ) regulates biofilm-formation and mucoidity by repressing expression of mcbA ( ybiM ) .
Upon addition of the inducer , Rob is released in its active form .
Crystallization has been described and the implications of the structure with respect to the binding of biotin and ATP have been discussed .
MlrA is a member of the MerR-family , containing the conserved N-terminal DNA-binding domain present in members of this family .
DeoR belongs to the DeoR family of transcriptional regulators .
However , the majority of these sites are not functional because they are not in the proper orientation or distance relative to the promoter .
It has been suggested that this N-terminal arm plays a key role in the regulation of the arabinose-dependent DNA-binding properties of the protein .
It binds to the N-terminal domain of BluR and inhibits the DNA-binding activity of BluR .
Specifically , when nickel and cobalt exceed the normal levels , cell-growth stops .
A flexible linker connects both domains .
Comparative analysis of intergenic DNA sequences showed the consistent occurrence of ExuR possible binding sites upstream of the genes related to the transport of gluconate ARRAY ( 0x1603a20 ) and with the transport and degradation of glucuronides ARRAY ( 0x1603b28 ) .
On the another hand , the transcription of lldR is also induced upon biofilm-formation compared to planktonic growth in both exponential and stationary phases .
Under salt stress , the universal stress protein UspC binds to KdpE and stabilizes the KdpD-KdpE-DNA complex ; therefore , this system can be activated even though K + accumulates under this environmental condition .
StpA may destabilize the small regulatory RNA MicF .
MlrA binds an AAAGTTGTACA ( 12N ) TGCACAATTTT palindromic sequence and probably induces DNA-underwinding , as in the case of MerR .
RelE and RelB exhibit a physical interaction , and RelE physically interacts with ribosomes .
Apparently it is the task of CueR and CopA to clear the toxic copper ions rapidly from the cytoplasm into the periplasmic space .
The genes regulated by Nac are transcribed by RNA polymerase ?70 .
IdaB is a member of the AAA chaperone-like family of ATPases that is required for the inhibition of the initiation of DNA-synthesis via antagonism of DnaA activity by the DNA-polymerase-III beta subunit ( sliding clamp ) .
The crystal structure of KdpE with and without bound beryllium fluoride has been solved .
The crystal structure of CspA has been determined by X-ray crystallography to a resolution of 2.0 Å also , the structure of CspA has been determined by NMR spectroscopy .
SoxS , MarA , and Rob bind as monomers to the same DNA site , a degenerate 20-bp sequence known as the Mar-Sox-Rob box , which has to be in a specific orientation and distance relative to the -35 and -10 boxes of the promoter .
The lability of cspA mRNA at high temperatures is mediated by cleavage toward its 3 ' end ; this cleavage is partially dependent on RNase E. Thus , cspA expression levels change in response to temperature fluctuations .
However , they show only one different residue in their helix-turn-helix motif , suggesting that they recognize similar DNA-binding sites .
MazE has similarity to episomal PemI .
Its secondary structure prediction shows three helices without any ?-sheet .
The mazEF system causes a programmed-cell-death response-to-stresses including starvation and antibiotics .
Binding of NO to the GAF-domain relieves intramolecular repression of the central-domain , leading to the activation of the ATPase activity and interaction-with-?54 RNA polymerase .
Based on a computational rod model of the DNA-LacI complex , the looping of both linear DNA and supercoiled DNA minicircles over a broad range of DNA interoperator lengths was analyzed .
An iron-sulfur cluster and a metal cofactor ( possibly a similar metal or formate ) have been proposed as the signals sensed by HyfR .
Accordingly , this transcriptional repressor family protein is composed of two domains : a conserved N-terminal domain which contains the DNA-binding region , and the carboxy-terminal domain , which is involved in effector-binding and dimerization .
The AR1 region contacts with the ? subunit , the AR2 region makes contact with the ?70 , and the AR3 contacts the ? NTD of the RNA polymerase .
RutR can bind upstream of the nemRA operon ; however , it does not play an important role in regulation of nemRA expression in vivo .
A microarray analysis for ModE of E. coli was done by .
The catalytic AAA + domain is necessary and sufficient to activate ?54 transcription in vivo and in vitro .
However , based on nickel enrichment DNA microarrays and additional gel shift assays , it was identified as a transcriptional repressor of mcbR , which regulates biofilm-formation and mucoidity by repressing expression of mcbA ( ybiM ) .
In addition , a recent microarray-based global transcriptional profiling study suggested that the DcuR regulon could comprise at least 39 genes , including some involved in lipopolysaccharide-biosynthesis and some involved in anaerobic nitrate and nitrite respiration .
This sRNA binds to FhlA mRNA and inhibits translation by interfering with the binding of the mRNA and the ribosome .
The expression of bolA is regulated at the transcriptional level and at posttranscriptional levels .
Distinct forms of DPD constitute the interconverting molecules family generally called autoinducer 2 ( AI-2 ) .
As a member of the DeoR/GlpR family of transcriptional regulators .
FruR belongs to the GalR-LacI family of transcriptional regulators , which are helix-turn-helix DNA-binding proteins .
Phosphorylated OmpR controls the transcriptional expression of several genes and operons whose products are involved in adaptation to changes in osmolarity , such as major outer membrane porins , and negatively regulates the expression of flagella promotes biofilm-formation increases curli genes expression increases expression of several drug exporter genes and confers increased beta-lactam resistance among other effects .
In the presence of L - and meso-tartrate , Dan stimulates expression of the divergently transcribed ttdABT operon , encoding L-tartrate dehydratase and the L-tartrate : succinate antiporter .
It is a DNA-binding protein with similarity to StpA and these two proteins can have similar functions .
Through a cascade of events NtrC appears to regulate as much as 2 % of the genome , and many of these genes encode transport systems for nitrogen-containing compounds .
Under glucose-limited conditions , this double mutant exhibits an increase of biomass of only 13 % .
PhoB consists of two functional domains , the N-terminal receiver-domain , which is phosphorylated , and the C-terminal output domain , which binds to DNA and interacts-with-the-?70-subunit of RNA polymerase to activate transcription .
The transcription factor ModE , for Molybdenum , is the principal regulator that controls the transcription of operons involved in the transport of molybdenum and synthesis of molybdoenzymes and molybdate-related functions , among others .
A dominant negative form of StpA can disrupt H-NS activity and vice versa , and H-NS can interact with StpA at two distinct domains to form heterodimers in vitro ; also there exists evidence that some of these proteins can form homodimers .
The biotin repressor , BirA , coordinately represses transcription of the divergent genes that are necessary for the synthesis of biotin .
In the absence of inductor , this repressor binds in tandem to inverted repeat sequences that consist of 20-nucleotide-long DNA target sites .
This regulator is comprised of two domains : the carboxy-terminal domain , which is similar to cupin-superfamily-proteins , and the amino-terminal domain , which has high similarity to regulators of the HTH-XRE-family .
RtcR belongs to the group of ?54-dependent transcriptional regulators , which contain three domains : the sensory-domain located in the N-terminus , the central-domain involved in ATP-hydrolysis and interaction-with-?54 , and the C-terminal domain , which contains a helix-turn-helix motif .
In addition , Rhee et al. identified the DNA-binding properties of the C-terminal of OmpR based on chemical shift changes and analysis of amino acid substitutions and base pair substitutions .
It was demonstrated in Salmonella enterica serovar Typhimurium that LsrR directly senses and binds the molecule 4,5-dihydroxy-2 ,3 - pentanedione ( DPD ) , phosphorylated and dephosphorylated .
LeuO is part of the RpoS/H-NS/Hfq / LeuO/DsrA RNA regulatory cascade that controls the bglGFH operon and translation of rpoS , particularly at low temperatures .
Based on an alanine-scanning mutagenesis approach , it was shown that the inducer maltotriose binds inside the cavity of the tetratricopeptide-like sensor domain of MalT , a bacterial STAND transcription factor .
Although PspA appears to regulate transcription of the psp regulon , it does not bind to DNA , but it is necessary for repressing this regulon .
GadW is one of the regulators in the acid resistance system and is encoded by the unusual gadXW operon , which is located in the region called the acid fitness island .
However , footprinting analyses showed that the dimers of CytR are flanked or sandwiched by two dimers of CRP .
HipB forms dimers in solution .
Reviews : .
This allows OxyR to regulate as many as 40 additional gene products indirectly by affecting mRNA stability or translation efficiency .
Gene induction occurs when the physiological inducer , l-rhamnose , binds to RhaR and when cellular cyclic AMP levels are high .
tdc : threonine dehydratase .
It forms a stable multimer ( most likely a tetramer ) and binds to two adjacent inverted repeats within the murR/murQ operator region , preventing recruitment of RNA polymerase .
The crystal structure of the native NanR has been solved .
Overproduction of AcrR improves organic solvent tolerance ( OTS ) through regulation of the SoxS regulon .
On the other hand , it does not appear to be autoregulated .
Solution and crystal structures of MqsA have been solved .
Mutations at position 15 in the N-terminal arm of AraC do not activate transcription in the presence of arabinose , and this was confirmed by using a molecular dynamic ( MD ) simulation , which revealed that preservation of the shape of the arm is critical to inducibility .
Three-dimensional models of the N-terminus of FadR and NanR show topological similarities and a ~ 26 % sequence identity between them .
UlaR binds to four inverted repeat motifs in the divergent intergenic region ulaG-ulaA and overlaps its target promoters to repress transcription by blocking the interaction of the RNA polymerase with ulaGp and ulaAp .
In the absence of rapidly metabolizable carbon sources , such as glucose , EIIAGlc is phosphorylated and activates adenylate cyclase , resulting in an elevated level of cAMP .
Xylose regulator , XylR , is a transcription factor involved in d-xylose degradation .
Iwig and colleagues showed that RcnR is not directly related to other proteins that use nickel , although they showed that RcnA , as the exporter of excess ions , has direct participation .
Based on crystal structure and mutation analyses , it was determined that the K64 and R65 residues are crucial for the NikR functions on the nikAp1 promoter in vivo .
The regulatory activity of this protein has been suggested by analogy with FNR ; this activity might be modulated by a sensory iron-sulfur cluster or by reversible disulfide-bond formation .
The exact position and sequence that SdaR binds to in DNA have not been yet determined .
CsgD belongs to the FixJ/LuxR/UhpA-family , which is characterized by a C-terminal domain that contains a potential helix-turn-helix DNA-binding motif and a receiver-domain in the N-terminal region .
The aporepressor is activated as a DNA-binding protein by noncooperative binding of two L-tryptophan molecules to the homodimer .
Synthesis of alsR and rpiB genes is induced when Escherichia coli is grown on d-allose in the absence of glucose .
QseB and QseC of enterohemorrhagic E. coli ( EHEC ) and of E. coli K-12 are almost identical ; there are only three amino acid differences in QseB and only eight amino acid differences in QseC between these strains .
D5P is converted into its hydrated form to create strong H-bonds with the carboxyl group of D243 .
at the amino acid level .
Maltotriose plays a dual role in signal-transduction by MalT ; it triggers nucleotide-binding oligomerization domain ( NOD ) opening and renders the MalT multimeric platform competent for downstream signaling .
As a consequence , adenylate cyclase is not activated , resulting in a reduced level of cAMP .
DgsA , better known as Mlc , makes large colonies , is a transcriptional dual regulator that controls the expression of a number of genes encoding enzymes of the Escherichia coli phosphotransferase ( PTS ) and phosphoenolpyruvate ( PEP ) systems .
Biotinyl-5 ' - adenylate and biotin stimulate dimerization and DNA-binding .
Lrp belongs to the Lrp/AsnC-family of transcriptional regulatory proteins , which is widely distributed throughout the eubacterial and archaeal domains .
Detailed analysis of the role of the C7 and the C3 regions of PspF has been presented with respect to ATP-hydrolysis , protein-oligomerization , binding to the ?54 holoenzyme , and transcription-activation .
BolA is a member of the BolA-family , which is widely distributed among proteobacteria and eukaryotes .
These regulators form homodimers and heterodimers in vivo .
For this reason the FruR regulator is implicated in the expression of a large number of operons that encode enzymes which comprise central pathways of carbon metabolism .
Reviews : 24097899 -RSB- .
The Cys-106 residue , which is conserved among NemR homologs , has been identified as a trigger for the NemR RCS-sensing mechanism .
OxyR recognizes a motif comprised of ATAGnt elements spaced at 10-bp intervals .
It is activated in response to the presence of peptides or amino acids .
LacI is negatively autoregulated when it binds to two DNA-binding sites , one located downstream of the lacI gene and the other one located in the coding sequence for the C-terminus of LacI .
Association of the enzyme with the membrane is dependent on reduction of the FAD cofactor , which induces a change in the conformation of the protein .
This reaction converts the Ada protein into a strong transcriptional activator of several genes .
It has been identified as global repressor of carbon oxidation pathways .
CytR senses and binds cytidine , and when this happens the cooperativity of CytR and CRP is interrupted and the expression of genes is induced .
It is activated during exponential growth in acidified minimal medium and enables the cell to survive gastric acidity .
This regulator is involved in the degradation of sugar acids and is subject to catabolic repression in the presence of glucose and at low levels of cyclic AMP .
TdcA probably interacts with TdcR to activate transcription and they appear to function together with CRP and IHF , proteins that bend the DNA , for this activation .
The arabinose regulator , AraC , is a transcription factor that regulates transcription of several genes and operons involved in arabinose-catabolism and transport .
Presently , the nemRA operon is the unique member of the NemR regulon .
HyfR shows 46 % identity to FhlA , a member of the same group .
The DNA-binding domain is very highly conserved among FadR-containing bacteria , whereas the C-terminal acyl-CoA-binding domain shows only weak conservation .
FadR activates the fabH promoter in the absence of long-chain-fatty-acids .
The N-terminal domain is required for oligomerization and it is involved in protein-protein interactions , while the purified C-terminal domain is involved in DNA-binding .
By making use of micro arrays analysis , Constantinidou et al concluded that FNR represses cspA gene-expression , but it is not know which of the two promoters ( cspAp1 , cspA2 ) is affected .
YiaJ shows high homology to the IclR-family of regulators ; it is composed of two domains , an amino-terminal domain that contains a potential helix-turn-helix DNA-binding motif and a carboxy-terminal region featuring a second motif of unknown function .
H-NS functions almost exclusively as a transcriptional repressor , although there is no clear evidence that this regulator is an activator .
It is known that SlyA recognizes a short palindromic DNA sequence of 12 bp .
The hexuronate regulator , UxuR , is a transcriptional factor .
The protein when bound to these sites forms a loop that inhibits the transcription elongation , thus producing truncated proteins that are tagged for degradation by the small peptide SsrA .
MhpR is necessary to recruit CRP to the regulatory region of the mhp operon , where both proteins activate transcription .
Regulation by heteromeric transcription factors is a rare event in the bacterial word .
CRP binds to a 22-bp symmetrical site and induces a severe bend upon binding , with an angle of & sim ; 80 ° .
Zinc mediates the Mlc repressor function .
The wild-type Ebg enzyme , encoded by the ebg operon , is not efficient enough to permit growth on lactose .
Transcription of this operon is induced when E. coli is grown during acetate accumulation in the exponential phase .
For this reason , there is the possibility that these regulators bind the same sites with different affinities .
L-Ascorbate-6-P weakens the affinity of UlaR for DNA and displaces the UlaR oligomer state from a transcription-silencing tetrameric form to a transcription-activating dimeric form .
The norR gene is transcribed divergently from norVW and autoregulated .
The dcuSR operon contains two promoters , an external one that transcribes both genes and an internal one that only transcribes to dcuR and that is activated by CRP .
Accordingly , this transcriptional repressor family protein is composed of two domains : a conserved N-terminal domain which contains the DNA-binding region , and the carboxy-terminal domain , which is involved in oligomerization and binding of the inducer .
CitB/DpiA shows 47 % similarity to the CitB protein from K. pneumoniae , which also controls the citrate fermentation process .
When only CRP is bound to this promoter , it functions as an activator , and then , when CytR binds to DNA and to CRP , the activation is repressed because CytR masks an activating region of CRP that otherwise would contact the RNA polymerase to activate transcription .
PhoB is a response regulator and belongs to the two-component system PhoR/PhoB .
Trehalose repressor , TreR , acts as a repressor of operons involved in trehalose-transport and degradation under osmotic stress .
McbR carries a helix-turn-helix DNA-binding motif ( aa 37-56 ) and represses transcription of mcbA by binding to the promoter region of mcbA .
In cells with three clusters , the additional cluster tends to appear in the middle .
The transcription factor CsiR , for Carbon starvation induced Regulator , is a finely modulate repressor that controls the transcription of genes involved in the degradation and transport of 4-aminobutyrate for utilization as a source of nitrogen .
This reaction is specific , that is , NarL-P is only desphosphorylated by NarX .
RutR regulates genes directly or indirectly involved in the complex pathway of pyrimidine-metabolism and also plays a role in regulation of the genes for degradation of purines and genes for maintenance of pH homeostasis .
FUR is a sensor of the concentration of intracellular iron , and the genetic repression occurs when the physiological inducer , iron ( Fe2 + ) , binds to FUR .
LrhA , LysR homologue A , regulates the transcription of genes involved in the synthesis of type 1 fimbriae .
This proposal was not unexpected , because the identity and similarity of the C-terminal domains are 41 % and 66 % , respectively .
This promoter includes a -10 hexamer and different elements located at -14 T / -13 C , -12 T , and -7 T. Based on mutational analyses , it was shown that the upstream TC constitutes an extended -10 motif and is recognized by R108 ( which recognizes both 14T and 13C ) , a residue in the ?-helix of FliZ .
IHF acts mostly as an accessory factor , stabilizing a correct nucleoprotein complex .
In the presence of Dha , DhaL : : ADP displaces DhaK or blocks the association of the DhaK/DhaR complex and DhaR activates the transcription of the Dha operon .
Upon removal of the inducer ( salicylate ) , MarA is degraded by the Lon-protease and the binding of MarA with DNA or RNA polymerase protects it from degradation .
It activates soxS transcription when oxidized soxS is regulated only by its intracellular concentration .
It shows a potential helix-turn-helix motif in the carboxyl-terminal domain , which has 48 % identity and 70 % similarity to the corresponding domain of the RcsB protein .
resolution and also has been solved by NMR spectroscopy .
The activity of AcrR , which belongs to the TetR family , appears to be regulated by ligands such as rhodamine 6G , ethidium , and proflavin .
FruR has been observed to be predominantly a tetrameric structure in solution .
It binds to four operator sites with the conserved inverted repeat sequence motif TATCCN8GGATA , and its binding occurs cooperatively and almost simultaneously on the same face of the DNA helix .
MhpR is able to bind to its DNA-binding site even in the absence of inducer ; however , increasing concentrations of inducer improve the binding strength of MhpR .
In the three-dimensional structure of an XapR homolog ( CysB from Klebsiella aerogenes ) , these two regions appear close to each other , forming one signal-binding-site .
ArcA represses and activates transcription solely by binding DNA , and it activates only indirectly when its binding interferes with the binding and repression of another transcriptional repressor .
It coregulates with another transcriptional regulator , CRP ; both are transcription factors involved in l-arabinose-degradation .
The PspF-PspA complex is mainly located in the nucleoid ; however , this complex is able to frequently travel from the nucleoid to the membrane to sense changes in the membrane that result from some types of stress .
Furthermore , a consensus sequence has been proposed for RcdA sites .
The consensus sequence for the NagC-binding site has been determined via combination of native site comparisons , operator mutagenesis , and selection of DNA-binding fragments , .
Glyoxylate and pyruvate have been identified as effectors of IclR and show antagonistic effects .
Although little is known about the mechanism of regulation of the YiaJ regulator , recently it has been demonstrated to act as a repressor by binding to cis-acting elements that overlap yiaKp .
MngR belongs to the GntR-family of transcriptional regulators and has a helix-turn-helix motif in the N-terminal domain and a UbiC-transcription-regulator-associated-domain that is predicted to be a sensor for small molecules .
In Escherichia coli there are two separate direct repair mechanisms for the reversal of these types of alkylating lesions through the involvement of two methyltransferases , Ada and Ogt .
Both of these transcription units appears to be repressed by HNS .
Reviews : .
A dinJ-yafQ deletion mutant is impaired in biofilm-formation .
Its crystal structure reveals that the sugar molecule is bound within a ?-barrel , buried by the N-terminal arm of the protein .
They share a regulatory region that contains two sites of 21 bp each , one with two direct repeat sequences of 10 bp that are bound by MngR .
SoxR belongs to the MerR-family and is a homodimer in solution .
l-idonate regulator , IdnR , is a transcription factor that regulates genes involved in l-idonate metabolism , which are organized in two coordinately regulated transcription units .
Overproduction of LeuO causes the phenotype Bgl + , since LeuO can unsilence the bglGFB operon , which is silenced ( phenotypically Bgl ) under laboratory conditions .
Therefore , the NarL and NarP regulons overlap .
The FlhD and FlhC proteins are transcriptional factors and can form homodimers independently ( FlhD2 and FlhC2 ) and the assembly of these homodimers results in the formation of heterotetramers ( FlhD2C2 ) .
These regulators bind cooperatively to activate transcription of operons involved in transport and catabolism of d-xylose .
The rcnR gene is encoded divergently to the rcnA gene , which encodes an efflux protein that is involved in nickel and cobalt homeostasis it removes an excess of ions .
When PaaX is overexpressed , it causes elevated levels of mutations in the genome ; therefore , it is a candidate to regulate DNA-replication , recombination , or repair .
These proteins have an N-terminal sensory-domain , a C-terminal helix-turn-helix DNA-binding domain , and a dimerization motif in between .
It has been suggested that BaeS senses envelope disorder Indole and zinc have been used as inducers of this disorder .
The regulatory effect of ModE is induced when E. coli is grown under anaerobic growth conditions and when the physiological inducer , molybdenum , binds to ModE and promotes the dimerization of the ModE-Mo complex .
Expression of the allS gene is negligible under aerobic conditions and is increased under anaerobic conditions in the presence of glyoxylate or allantoin .
BetI forms a complex with DNA in the presence of choline , binding to a 20-bp-long sequence with dyad symmetry that overlaps betTp and betIp simultaneously .
Expression of asnC is regulated by nitrogen availability ; under nitrogen-limiting conditions , Nac represses asnC .
Two types of DNA-binding sites have been described for IscR : type 1 and type 2 .
OxyR , oxidative stress regulator , is the transcriptional dual regulator for the expression of antioxidant genes in response-to-oxidative-stress , in particular , elevated levels of hydrogen peroxide .
The amino acid sequence of AdiY shows homology to members of the XylS/AraC-family of transcriptional regulators .
The Gluconate repressor , GntR , is a transcription factor that negatively regulates the operon involved in the catabolism of d-gluconate via the Entner-Doudoroff pathway and also represses genes involved in two different systems related to d-gluconate uptake : gluconate I and gluconate II .
In addition , the receiver may make protein-protein contacts necessary for transcription-activation .
The Rhamnose regulator , RhaS , is a transcription factor involved in l-rhamnose-degradation and transport .
Members of this family have two domains , an N-terminal domain with a helix-turn-helix DNA-binding motif and a C-terminal domain with dimerization and effector-binding motifs .
Cys-21 could play the more critical role in the RclR redox response .
HyfR , hydrogenase four regulator , controls the expression of genes responsible for the proton-translocating formate hydrogenase system and for formate-transport under anaerobiosis , low pH , and post-exponential growth conditions .
Based on site-directed mutagenesis , Asp275 and Asp278 in LysP and Arg265 and Arg268 in CadC were identified as residues for the stimulus-dependent interaction between them .
This operon is induced under anaerobiosis , at low pH , and under fermentative conditions by formate , and it is subject to catabolite repression .
In some of these residues , NemR is controlled by alkylation .
The active conformation of Zur is observed when it is in a reduced form and when it is bound to Zn ( II ) .
The C-terminal domain of the ? subunit ( ? CTD ) is required for the recruitment of RNA polymerase .
Review : .
Although it has been shown that NanR can form homodimers in solution , its DNA-binding stoichiometry is unknown .
For full expression of arcA both FNR and ArcA are required .
Transcription of these operons is induced when E. coli is grown in the absence of glucose and when the physiological inducer , l-arabinose , binds to the AraC regulator .
Dimerization of ArsR is required for DNA-binding and its ability to act as a transcriptional repressor .
BasS functions as a membrane-associated protein kinase that phosphorylates BasR in response to elevated levels of Fe ( III ) which can permeabilize the outer membrane and result in cell-death .
Induction of the cre regulon during pyruvate growth is entirely CreC dependent .
CreB functions as a transcriptional activator by recruiting RNA polymerase , whereas the binding of CreB to the cre tag represses transcription through promoter occlusion .
Therefore , under conditions when Fe-S cluster assembly becomes rate limiting , levels of -LSB- 2Fe-2S -RSB- - containing IscR may decrease due to a lower rate of its synthesis , thus relieving repression of the iscRSUA operon for the biogenesis of the iron-sulfur cluster .
Homology and genomic organization of similar antitoxin/toxin systems among bacteria has been reviewed .
The output domain belongs to the winged-helix-turn-helix family of transcription factors .
The BaeSR , PhoBR , and CreBC two-component systems have been shown to interact in the regulation-of-gene-expression .
The binding targets for AgaR consist of 24-nucleotide-long repeat sequences that possess conserved motifs .
The operator site 5 ' of yefM-yoeB comprises adjacent long ( L ) and short ( S ) palindromes with core 5 ' - TGTACA-3 ' motifs with a center-to-center distance of 12 bp which was suggested to be crucial for the correct stable positioning of YefM-YoeB at the two repeats .
When DNA is damaged , the RecA coprotease binds to the single-stranded DNA in the damaged region to form a filament .
On the other hand Dyszel et al. showed that the SdiA protein is partially dependent upon a diffusible molecule -LSB- N - ( 3-oxo-hexanoyl ) - L-homoserine lactone -RSB- .
Purification of -LSB- 4Fe-4S -RSB- - FNR in an O2-free environment has been described .
Accordingly , this transcriptional repressor family protein is composed of two domains : a conserved N-terminal domain which contains the DNA-binding region , and the carboxy-terminal domain , which is involved in effector-binding and oligomerization .
In the absence of lysine , LysP regulates CadC negatively .
The structure of the MazE-MazF complex is presented at 1.7 A resolution .
Therefore , it has been suggested that MqsA and the MqsA-MqsR complex negatively autoregulate expression of the mqsRA operon .
In the presence of iron , FUR binds in tandem to possible inverted repeat sequences in the intergenic region to repress transcription by overlapping the -35 box of the regulated promoter .
Regulation has been described .
Protein structure and allosteric activation .
Under anaerobic growth conditions , transcription of the fnr gene is negatively autoregulated .
Zhang et al. ( 2012 ) showed that L1 is multifunctional , since it interacts with three elements important for isomerization from RPc to RPo ( the RNAP closed and open complexes , respectively ) .
AsnC belongs to the AsnC-family of regulatory proteins whose members are widely distributed in archaea and bacteria .
As nickel levels depend on the Nik uptake system ( NikR regulator , NikABCDE transporter ) and nickel is highly used during anaerobic growth by the Ni-Fe hydrogenase isozyme , the additional participation of RcnR and RcnA in nickel homeostasis changes the previous understanding of the cell 's nickel processing .
Autophosphorylation of DcuS is stimulated by C4-dicarboxylates such as fumarate or succinate , and the phosphate group is transferred to DcuR , which is converted to a dimeric form .
MurR carries a so-called SIS-domain in its C-terminal which is involved in MurNAc-6-P binding .
AscG also regulates prpBC for propionate-catabolism .
The full operon is repressed by nitrate acting through the NarXL regulatory system , so that E.coli will use nitrate as a respiratory electron acceptor before fumarate .
Protein-protein interactions in the MazE-MazF complex are discussed .
The dimer-interface has been structurally characterized .
CRP is a homodimer and consists of two domains connected by a short hinge region .
PutA : proline utilization .
This protein composed of two domains , an amino-terminal domain that contains a potential helix-turn-helix DNA-binding motif and a carboxy-terminal domain involved in co-inducer-recognition and dimerization .
The repressor CytR and the activator CRP , two dimeric proteins , interact to form a complex repressor nucleoprotein in the intergenic region .
The ClpXP and Lon-proteases degrade ZntR , but the regulator is protected against proteolysis when it is bound to zinc and DNA .
The crystal structure of the unphosphorylated dimeric form of BaeR has been determined .
FlhD and FlhC are part of the unusual flhDC operon that encodes two transcriptional regulators .
MalT subunits consist of four domains : the C-terminal DNA-binding domain , the N-terminal ATP-binding domain , and two domains ( DT2 and DT3 ) involved in effector-recognition ( maltotriose ) .
Although HipA does not bind the Hip regulatory region , it plays an indirect role via its binding to HipB .
In the absence of L-lactate and under anaerobic conditions , this regulator repressed the transcription of the lldPRD operon .
Golding et al. showed that GalR is the major repressor of the gal operon .
ttdR ( dan gene ) is repressed by FNR and the nitrate and nitrite two-component systems NarXL and NarPQ .
Eleven possible targets were predicted to be under PgrR control .
It also regulates transcription of many other genes that participate in a variety of cellular functions , including genes involved in the following processes or responses : biogenesis of flagella transcription control of the type I fimbria structural genes acid resistance the functional glutamic acid-dependent system osmotically inducible genes the glutamate decarboxylase-dependent acid resistance system osmotic control the type-II-secretion pathway carbon sources genes involved in the RNA component of the small subunit ( 30S subunit ) and proteases among others .
ArgP , arginine protein , controls the transcription of genes involved in the arginine-transport system and genes involved in DNA-replication .
Oxidation of HypT is reversed by the presence of the methionine sulfoxide reductases MsrA and MsrB , resulting in an inactive protein .
In the presence of nitrate or nitrite NarL or NarP binds to a target site upstream of the binding sites for FNR , IHF , and Fis , counteracting the effect of IHF but not that of Fis .
The C-terminal 270 residues of RbsR are homologous to the ribose-binding protein RbsB .
The toxin MqsR functions as an mRNA interferase , that is , it possesses endoribonuclease activity and cleaves mRNA at the specific sequence GCU , 5 ' or 3 ' of the G. Elevated levels of free MqsR result in programmed-cell-death due to the degradation of mRNA and concomitant inhibition of protein-synthesis .
FliZ and FliY were originally proposed to be cell-density responsive regulators of ?F .
Synthesis of this operon is induced when E. coli is grown in the absence of glucose or glycerol .
Taken together these data suggest that PhoB is activated through an intermolecular mechanism .
Many iron acquisition genes are derepressed in the mntR mutant .
In addition , Yamada et al. suggested that the regulators GutM and GutR have contrary effects ; in the absence of glucitol , GutR represses transcription of the gut operon , and in the presence of glucitol , GutR interacts with this carbohydrate to dissociate from DNA , causing increases of GutM in sufficient amounts to increase transcription of the gut operon .
Overproduction of KdpE causes a drug-resistance phenotype .
It was suggested that AtoC oligomerizes , but the stoichiometry is unknown .
No LeuO consensus binding sequence is known .
A linear recognition element which can be recognized by YoeB was identified using peptide array technology .
The yefM gene is upregulated during growth in biofilms and yefM-yoeB is upregulated in persister cells it is probable that derepression of yefM-yoeB autoregulation occurs in these circumstances in response to an as-yet-unknown environmental or cell-cycle signal ( s ) that interferes with the YefM-YoeB-operator interaction .
The specific AppY binding site has not yet been identified .
In addition , Mlc regulates expression of the MalT transcriptional regulator , the activator of the maltose regulon .
The FhlA-binding sites are represented by an inverted 14-bp repeat motif .
In this way , RhaS activates transcription of l-rhamnose gene clusters .
A negative autoregulation network motif increases the input dynamic range of the arabinose system by coupling the transcription factor protein level to the input signal .
This regulator is a member of the two-component regulatory system ZraS/ZraR .
The N-terminal region has a helix-turn-helix domain , and a C-terminal helix is implicated in EIICBGlc binding .
This reaction is specific , that is , NarP-P is only dephosphorylated by NarQ .
This repressor binds in tandem to inverted repeat sequences that are 16 nucleotides long and possess conserved motifs ; each dimer binds to one of these conserved sequences .
Previously , MngR , also called FarR , for fatty acyl-responsive regulator , had been proposed to regulate genes involved in the citric-acid-cycle in response to fatty acids , which release MngR from its DNA-binding site .
Independently , each repressor binds to DNA separately .
However , it was experimentally shown that SdiA does not respond to indole , although it can inhibit SdiA activity .
Titration showed that trehalose-6-phosphate binds more strongly than trehalose .
During activation , three activating regions ( AR ) are surface exposed for contact with the polymerase and promote transcription .
agaR : N-acetylglactosamine-degradation .
According to microarray analysis , the mannosyl-d-glycerate regulator , MngR , regulates only two genes , mngA and mngB , involved in 2-O-?-mannosyl-D-glycerate utilization .
There is evidence for the existence of two types of interactions between SoxS and ?70 R4 , with one type being able to occur off-DNA ( within a SoxS-RNAP binary complex that scans the chromosome for SoxS-dependent promoters ) and with the other one occurring on-DNA ( within a SoxS-RNAP binary complex residing at a SoxS-dependent promoter ) .
PspA , PspB , and PspC form a complex , and PspC is required for PspA to bind to PspB PspA , PspB , and PspC are not observed to cross-link with PspD .
The model predicts that MarA increases the rate of transcription initiation while decreasing the overall presence of the transcription machinery at the promoter .
The physiological inducer is unknown .
In a specific way and with high binding affinity , this regulator recognizes and binds to sites that have closely related sequences .
Binding of NO relieves intramolecular repression and activates the ATPase activity of the central AAA + domain .
Tramonti et al. speculated that GadW binds in tandem to two directed repeat sequences , in the same orientation , in the intergenic regions to activate or repress the transcription of the genes regulated .
Transcription of this operon is induced when E. coli is grown in the absence of glucose and when the physiological inducer D-ribose binds to the RbsR repressor .
This inhibition is through intramembrane and perisplasmic contacts under noninducing conditions .
This box sequence , TAGACCnnnnGGTCTA , is close to the recognition sequence , TTGACCAnnTGGTCAA , of RutR ( the RutR box ) .
This protein belongs to the DtxR-family .
It is a DNA-binding protein with similarity to H-NS and these two proteins can have similar functions .
However , the majority of these sites are not functional because they are not in the proper orientation or distance relative to the promoter .
Activity of PdhR is controlled by pyruvate .
-RSB- .
The transcriptional dual regulator CRP , cAMP receptor protein , also called CAP , catabolite gene activator protein , regulates the expression of over 180 genes in E. coli .
Overproduction of MraZ during the early logarithmic phase showed that 23 % of the genes were differentially regulated .
This regulator binds in tandem to sequences that are 20 nucleotides long and possess conserved motifs composed of two 10-bp direct repeat subsites ; each dimer binds to one of these conserved sequences .
AHLs might control the transcriptional-activity of SdiA by enhancing its stability rather than by directly affecting its DNA-binding affinity .
UhpA has two modules : the receiver module , which contains the putative site of phosphorylation in the N-terminal domain and the activation module , which contains a helix-turn-helix motif for DNA-binding in the C-terminal domain .
Reviews : .
The crystal structure of an N-terminally truncated fragment of ZntR bound to zinc was solved at a resolution of 19 Å .
YehU/YehT and YpdA/YpdB two-component systems are activated and expression of the corresponding target genes was found to occur at the same time as the onset of the stationary phase .
Expression of the arnBCADTEF operon increased during growth with elevated FeSO4 or FeCl3 and was dependent upon the BasSR two-component signal-transduction-system .
A new interaction that also occurs via prerecruitment between ?70 R4 of RNA .
Lrp-regulated promoters commonly contain multiple adjacent binding sites for the protein with low sequence specificity .
Lrp forms a mixture of octamers and hexadecamers .
Although , the majority of the LexA-regulated genes have only one SOS box , some have two or three boxes which sometimes overlap .
A single mutation , W220F , in the inducer-binding site of the LacI repressor reduces leakiness .
Rob , MarA , and SoxS bind as monomers to the same DNA site , a degenerate 20-bp sequence known as the Mar-Sox-Rob box , which has to be in a specific orientation and distance relative to the -35 and -10 boxes of the promoter .
PaaX contains a helix-turn-helix motif for DNA-binding that is similar to the motif found in the N-terminal of members of the GntR-family of transcriptional regulators .
HypT belongs to the large family of LTTRs and is conserved in ? - , ? - , and ?-proteobacteria and eukaryotes ( Xenopus tropicalis ) , which suggests conservation of the HOCl response in evolution and its maintenance throughout the kingdoms .
MlrA is a regulator of curli production in an avian pathogenic Escherichia coli strain and in Salmonella enterica serovar Typhimurium .
ZraR , zinc resistance-associated regulator , controls the expression of genes involved in tolerance to high zinc concentrations .
Members of this family have two domains , an N-terminal domain with a helix-turn-helix DNA-binding motif and a large C-terminal domain .
The araBAD operon is located upstream of araC and in the opposite direction .
H-NS is a direct activator of the flhDC operon and represses transcription of hdfR .
These clusters are located near the one-quarter and three-quarter positions along the long axis of the cell .
?-Keto-acids inhibit cAMP production .
It is activated in the absence of oxygen and by nitrite under anaerobic conditions .
In addition , in the presence of unphosphorylated EIIAGlc , inducer is transported into the cell , leading to the inactivation of the corresponding repressor molecules -LSB- Magasanik70 * -RSB- .
Expression of YafQ alone reduces protein-synthesis and inhibits growth , and coexpression of DinJ alleviates that phenotype , acting as the antitoxin .
It is composed of two domains : the carboxy-terminal domain , which contains the DNA-binding region , and the amino-terminal domain , which is responsible for dimerization and l-arabinose binding .
NarP is 44 % homologous to NarL , the structure of which has been solved by X-ray crystallography .
However , a potential mechanism for the phosphorylation-mediated activation of OmpR-regulated transcription follows the same pattern as with other members of the OmpR/PhoB family of response regulators ( RRs ) .
Like HU , IHF plays a role in polyamine-dependent DNA condensation .
Two directly repeated hexameric DNA sequences that are highly enriched in A/T residues have been proposed to be the sites recognized by a DcuR dimer .
The crystal structure of the DNA-binding domain has been determined at 1.95 - ?
DcuR regulates several genes involved in C4-dicarboxylate-metabolism .
Activation of the YehU/YehT signaling-cascade , which results in YjiY production , suppresses YpdA/YpdB-mediated yhjX induction , whereas activation of the YpdA/YpdB signaling-cascade , as well as inducing the synthesis of YhjX , promotes expression of yjiY .
At high concentrations of K + , the kinase activity of KdpD is inhibited .
GadX is highly homologous to GadW ( 42 % ) , and apparently both are capable of cross talk to regulate expression of the genes of this system .
Deletion of basSR resulted in acid sensitivity during growth at elevated iron concentrations .
It consists of two helix-turn-helix regions connected by an ?-helix .
Additional genes might be identified by high-throughput analysis .
Binding of GntR to DNA is diminished in the presence of the inducer d-gluconate .
Gene induction occurs when the physiological inducer , d-allose , binds to AlsR , liberating the repression effect caused by this protein .
Both genes glnG , encoding the response regulator ( NtrC , also called NRI ) , and glnL , encoding the sensor kinase ( NtrB , also called NRII ) , are organized in the operon glnALG .
These three monomer proteins bind to the same DNA site , a degenerate 19-bp sequence known as the sox-mar-rob box , which has to be in a specific orientation and distance relative to the -35 and -10 boxes of the promoter .
Although little is known about the regulating mechanism of GadX , Tucker et al. proposed that this regulator and GadW have distinct molecular mechanisms .
GntR is closely homologous to IdnR ARRAY ( 0x15c3fc0 ) and belongs to the LacI/GalR family of transcriptional regulators .
Wang et al. ( 2011 ) reported that H-NS clusters could thus serve as anchoring points for numerous DNA loci distributed throughout the genome , creating DNA loops connecting the anchored loci .
The functions of these 33 genes are involved in different processes , such as persistence , metabolism , transcriptional regulation , mismatch-repair , membrane proteins , transporter proteins , and inner membrane proteins .
N-acetylgalactosamine repressor , AgaR , negatively controls the expression of the aga gene cluster , which is involved in transport and catabolism of N-acetylgalactosamine and d-galactosamine .
The expression of the flhDC master operon is multirregulated by several systems including those that respond to high osmolarity catabolic repression quorum-sensing synthesis of type 1 fimbriae the histone-like nucleoid protein heat shock , etc. .
Homologs of FabR are found exclusively in ?-protobacteria .
Catabolite repression and inducer exclusion .
HypT is specifically activated by HOCl by methionine oxidation , protecting the cells from the detrimental effects of HOCl ) .
This proposal was not unexpected , because the identity and similarity of the C-terminal domains are 41 % and 66 % , respectively .
The investigators showed that in this model OmpR-P binds differentially and cooperatively to regulatory regions of the genes ompF and ompC .
BolA regulates the transcription of genes involved in the morphology of the cell to confer protection to the cell , specifically under stress conditions and during stationary phase .
Both the M3 motif and the intervening spacer could be stabilizers for the YehT : DNA complex .
It negatively regulates its own transcription independently of cyanate .
Homology with PaaX has been found in other bacteria , such as Pseudomonas putida , Bacillus halodurans , and Arthrobacter sp. , among others .
The transcriptional repressor DeoR , for Deoxyribose Regulator , is involved in the negative expression of genes related to transport and catabolism of deoxyribonucleoside nucleotides .
In some species the arrangement of these genes in the genome is different than in Escherichia coli .
The gene that codes for it is the 11th in the hyf operon , which contains 12 genes that are not expressed at significant levels .
Two N-terminal domains intertwine to form a dimeric DNA-binding ribbon-helix-helix ( RHH ) domain .
It is probable that McbR binds DNA as a dimer .
Although the C-terminal domain and the central-domain from RtcR are similar to those of other members of this group , its N-terminal domain is not .
This interdomain linker is protected from proteolytic digestion in the presence of CRP .
A basRG53V ( constitutive ) mutant is resistant to polymyxin B and colistin , sensitive to the anionic agent deoxycholic acid , and expresses eptA , arnB , and yibD at high levels .
As rcnR expression is induced in response to iron even in the absence of Fur it is possible that RcnR responds to iron ions directly .
The expression of galR is increased only in the presence of inducer .
The synthesis of this regulon is induced when Escherichia coli is grown under different extracytoplasmic stress conditions and upon infection by filamentous phage ( phage-shock ) .
The C-terminal domain shows similarity to aldehyde-dehydrogenases , indicating that the true substrate for the second enzymatic activity may be ?-glutamic semialdehyde , which is thought to spontaneously equilibrate with P5C .
BirA-bio-5 ' - AMP has been observed to be predominantly monomeric in solution whereas more recent studies indicate that dimerization occurs before DNA-binding .
This consensus sequence shows a core binding site of 9 bp , TTGTgtACA , with inverted repeat symmetry .
The crystal structures of CueR dimers bound to Cu + , Ag + , or Au + have been solved .
Trucker et al. provided evidence that GadW can work as a coactivator of GadX or it can inhibit the GadX-dependent activation , along with evidence of more target genes for GadX/GadW regulation .
In addition , MalK inhibits maltotriose binding by MalT ; interestingly , however , MalK interacts directly with MalT in the absence of maltotriose but not in the presence of maltotriose .
YdfH is not a global repressor , and few genes are repressed by YdfH .
TdcR has a helix-turn-helix motif that shows 25 % and 35 % identity to the same motifs of the transcriptional regulators NtrC and Fis , respectively .
Crystal structures of the amino-terminal proline dehydrogenase domain have been reported , and site-directed mutants in various active site residues have been characterized .
As a member of the RpiR/YebK/YfhH family of transcriptional regulators , AlsR features an N-terminal domain containing a helix-turn-helix motif .
SdiA has been shown to increase transcription from the P2 promoter of the ftsQAZ operon by facilitating RNA polymerase binding to the promoter region .
As a member of the AraC/XylS-family , this transcription factor is composed of two domains : the C-terminal domain ( 60 % homologous to the C-terminal of GadW ) , which contains two potential helix-turn-helix DNA-binding motifs in the DNA-binding region , and the amino-terminal domain ( 30 % homologous to the N-terminal of GadW ) , which is responsible for dimerization .
Among these predicted targets of RcdA , six genes correspond to transcription regulators ( AppY , CsgD , FimB , RcdA , Sxy , and YcgF ) .
LeuO is a dual transcriptional regulator that regulates genes involved in leucine-biosynthesis , genes involved in the utilization of certain ?-glucosides and genes encoding LuxR-type transcription factors .
The NagC , N-acetylglucosamine , transcriptional dual regulator participates in regulating the phosphotransferase system ( PTS ) .
Proline-dehydrogenase activity requires the presence of an electron acceptor ; in vivo , it is thought that the reduced FADH <SUB> 2 </SUB> transfers electrons to the quinone pool in the cytoplasmic membrane , and finally to oxygen via the respiratory chain .
This site is conserved in some NadR ortholog target genes in some enterobacteria , and it was also identified upstream of the nadR gene itself in E. carotovora , S. marcescens , Y. pestis , and Y. enterocolitica , but not in Escherichia coli .
In the presence of any of these ions , ZntR activates transcription of zntA by a DNA distortion mechanism that makes the promoter a better substrate for RNA polymerase .
Gmr functions as a connector and a trigger enzyme in local c-di-GMP signaling ; its direct inhibition of YdaM is relieved when it binds and degrades c-di-GMP , allowing YdaM to activate the transcription factor MlrA .
Transcription of puuA was induced in a puuR deletion mutant .
Lrp appears to be very well conserved in members of the ?-proteobacteria .
in Hebrew .
A mutation in the tdcA gene of enterohemorrhagic Escherichia coli O157 : H7 causes the expression of OmpA protein which is involved , among several other processes , in cellular adherence .
When phosphate is in excess , autophosphorylation of PhoR is inhibited and PhoB-P is dephosphorylated .
showed that GadX alone activates the gadA and gadB promoters .
The crystal structure of intact SdiA has been determined .
The gatYZABCD operon is expressed constitutively due to an insertion of IS3E into the gatR gene .
There are four AsnC sites in the divergent regulatory regions of asnA and asnC , and they are separated by 18 bp .
The binding targets for DeoR consist of 16-nucleotide inverted repeat sequences that possess conserved motifs .
The group amino acids Thr-118 with Ser-187 ; Lys-49 with Lys50 ; and Asp86 and Ile81 with Gly-85 are important for AR1 , AR2 , and AR3 , respectively , to make contact with the RNA polymerase .
Activation by RcsB-BglJ occurs both at non-HNS-repressed promoters as well as at promoters repressed by HNS and/or StpA .
This transcription factor is a regulator that belongs to the LacI/GalR family ( specifically , to the HutC subfamily ) .
The RelE toxin inhibits protein-translation by catalyzing cleavage of mRNA in the A site of the ribosome .
Under anaerobic conditions ArcA is phosphorylated in a phosphorelay reaction that involves phosphotransfer from the autophosphorylated transmitter domain of ArcB to the receiver and Hpt domain of ArcB and finally to the receiver-domain of ArcA .
YqhC belongs to the AraC/XylS transcriptional activator family , as it shows 13.6 % amino acid identity with AraC .
EmrR belongs to the MarR-family of transcriptional regulators which respond to a variety of phenolic compounds and are found in gram-positive and gram-negative species as well as in mycobacteria .
The dimer recognizes and binds to a 12-2-12 inverted repeat but the binding of arsenic or antimonite to ArsR causes a conformational change in it , leading to dissociation from DNA and hence derepression .
This regulator belongs to the LysR-family .
Oxidation is significantly faster than reduction , allowing for transient activation in a reducing environment .
NarL-binding heptamers are found as single copies , inverted repeats , or direct repeats at positions between +20 and -200 relative to the transcriptional start sites .
RstA belongs to the two-component system RstA/RstB .
AR1 recruits ?-CTD to the DNA region upstream of the bound CRP dimer , while AR2 interacts with ?-NTD of RNAP .
BirA is a bifunctional protein that possesses both regulatory and enzymatic activities : it acts as the DNA-binding transcriptional repressor of the biotin operon and also exhibits biotin ligase activity .
AlpA expression leads to increased synthesis of IntA , which results in excision of the CP4-57 cryptic prophage .
It regulates several genes upon hypochlorite stress , which increases cellular viability by reducing the intracellular iron levels .
Gluconate I is considered the main system for transport of d-gluconate and contains genes that encode high - and low-affinity gluconate-transporters .
In addition , a hybrid protein , in which the receiver-domain has been replaced by a leucine-zipper , is active in vivo as a transcriptional activator .
At class I promoters , AR1 of the downstream subunit of the CRP dimer interacts with the ?-CTD of RNAP , thereby increasing the affinity of RNAP for the promoter DNA .
This protein acts as a pleiotropic transcriptional factor with a strong preference for horizontally acquired genes among the 250 loci to which it binds .
RstA overproduction causes drug-resistance .
This regulator belongs to the IclR-family of repressors .
However , MntR lacks the SH3-like domain .
It coregulates with CRP , a global transcriptional regulator .
CusR belongs to the two-component system CusS/CusR , which responds to increases in the copper concentration .
The transcription factor NhaR , for Na + / H + antiporter Regulator , is dependent on Na + and it controls the transcription of the gene involved in adaptation to Na + and alkaline pH response to adverse conditions and biofilm-formation .
Neither of these two promoters is regulated by DcuR .
On the other hand , site 2 overlaps the -35 and -10 boxes of the sutRp promoter .
McbR belongs to the group of DNA-binding proteins of the GntR/FadR family of bacterial regulators .
HU binds DNA without sequence specificity and with low affinity , but at low concentrations HU induces bends and at high concentrations HU induces the formation of rigid filaments .
KdpE is a member of the OmpR/PhoB subfamily of response regulators and binds a 23-bp recognition sequence .
Each monomer consists of three domains , an N-terminal DNA-binding domain carrying two helix-turn-helix motifs , a central dimerization domain , and a C-terminal metal-binding domain .
For activation of pfl , a functional interaction between the ArcA and Fnr protein has been suggested .
The analysis showed that three successive TGGGN direct repeats are separated by two consecutive 5-nt spacers .
A gene encoding a potential nucleoside hydrolase and transcribed divergently from yeiL has also been suggested to be subject to YeiL regulation .
AdiY is a positive DNA-binding transcriptional regulator that controls the arginine decarboxylase ( adi ) system , which is strongly induced in rich medium , under anaerobic conditions , and at low pH. Several proteins are involved in the induction of the adi system .
The proteins with greatest similarity to AppY are CfaD of enterotoxigenic Escherichia coli and VirF of Shigella flexneri .
Members of this family share similar N-terminal DNA-binding domains but are classified into four subfamilies according to their divergence in their C-terminal domains , which are involved in effector-binding and oligomerization .
This protein is an envelope-protein that contains a putative membrane-spanning region , and as for the members of the family of transcriptional regulators ( AraC/XylS ) that it pertains to it also contains a helix-turn-helix motif for DNA-binding in the C-terminal region .
Based on gel filtration experiments and in analogy to other bacterial toxin-antitoxin systems , it has been proposed that the MqsA-MqsR complex consists of one MqsA dimer and two MqsR dimers .
However , Xu et al. ( 2001 ) reported that homologies to CAP and the Tet repressor based on structure are more relevant and they have categorized FadR as a chimera of two motifs .
In the complex , one C-terminus in the YefM homodimer is unfolded and the other one shows an ?-helical conformation and conceals the endoribonuclease fold of YoeB .
The operon containing both genes , citB ( dpiA ) , encoding the response regulator , and citA ( dpiB ) , encoding the sensor kinase , is transcribed divergently to the citCDEFXGT operon .
Based on DNA footprinting assay results , two regions for SutR were identified in the ydcO-sutR spacer sequence .
EvgA is a member of the NarL subfamily of response regulators , consisting of an N-terminal receiver-domain and a C-terminal helix-turn-helix DNA-binding domain .
It has been proposed that NadR recognizes and binds to two palindromic sequences of 6 bp separated by six less conserved nucleotides .
Based on the site identified on the csgDp1 promoter , sites for another four genes were identified , two of which are transcriptional regulators .
The cellular concentration of FNR is similar under both anaerobic and aerobic growth , but its activity is regulated directly by oxygen .
HU forms high-affinity complexes with DNA containing sharp bends , kinks , branched and bulged structures , or single-strand breaks and loops .
The xapR gene is located downstream of the genes it regulates and in the same direction , but in an independent transcription unit that appears to be expressed constitutively .
RprA is a small RNA that regulates positively the translation of rpoS .
Parts of the C-terminal domain may function as a lid that covers the internal substrate-channeling cavity .
Two binding sites for CadC , Cad1 and Cad2 , have been determined in the cadBA operon .
FNR is the primary transcriptional regulator that mediates the transition from aerobic to anaerobic growth through the regulation of hundreds of genes .
On the other hand , genes involved in iron acquisition and homeostasis upon hypochlorite stress are downregulated by YjiE .
FNR was named for the mutant defect in fumarate and nitrate reduction .
murR and murQ are unique and now well-known genes that are regulated by MurR .
Accordingly , this family protein is composed of two domains : a conserved C-terminal domain which contains the DNA-binding region and the N-terminal domain , which is involved in effector-binding .
The gene malT is located upstream of the operon malPQ and in the opposite direction .
The binding targets for GadX consist of 21-nucleotide-long directed repeat sequences that possess conserved motifs , called the GAD box , which is proposed to be the binding site for GadX and GadW .
NarL , nitrate/nitrite-response-regulator - NarL , is a transcriptional dual regulator of many anaerobic electron transport and fermentation-related genes in the response to the availability of high concentrations of nitrate or nitrite .
Thymine deprivation also represses mazEF transcription .
CreBC is considered a global regulator that is positioned at the heart of metabolic control .
The adaptability and plasticity of a regulatory network were determined by using an in vivo system that was developed to identify variants of helix-turn-helix transcription for the MarA transcriptional regulator .
NagC is displaced from its DNA targets by interacting with GlcNAc-6-P .
The flagellar regulator is conformed by two FlhD subunits and two FlhC subunits , as a heterotetramer while FlhD is constituted by two domains : the N-terminal domain is responsible for dimerization and the C-terminal is a highly flexible domain contain the DNA-binding ( helix-turn-helix motif ) region .
YeiL , the third member of the CRP/FNR family , has the main structural elements conserved in Crp and Fnr , such as a sensory-domain , an ?-helix that serves as a dimer-interface , and a DNA-recognition helix also found in Fnr .
These regulators bind cooperatively to activate transcription of five operons related to transport , catabolism , and autoregulation of l-arabinose .
It has been shown that SoxS binds to the C-terminal domain of the ?-subunit of RNA polymerase ( ?-CTD ) , in particular , it interacts with amino acid residues lying in or near the DNA-binding determinant of ?-CTD .
Under nitrogen ( N ) - limiting conditions , the NtrC transcriptional dual regulator regulates genes involved in the assimilation of nitrogen and in the minimization of the slow growth caused by the N-limited condition .
BaeR belongs to the BaeS/BaeR two-component system .
In addition , the receiver may make protein-protein contacts necessary for transcription-activation .
Based on differential gene-expression analysis comparing the WT to a mraZ mutant , 100 genes under the control of MraZ were identified .
The YpdA/YpdB system stimulates expression of the yjiY gene , the target of the YehU/YehT system , which suggests an interconnectivity between the two systems .
The C-terminal domain contains the determinants for oligomerization and two redox-active cysteines , Cys199 and Cys208 .
On the other hand , in an arcA mutant , the TCA-cycle flux was increased 4.4 times above that of the wild type in the presence of nitrates , and the intracellular ATP/ADP ratio increased approximately 2-fold above that of the wild-type strain .
It was proposed that these proteins bind to their target sites by a mechanism named DNA scanning or prerecruitment .
Such conserved localization with genes of metal-related functions suggests that these homologs are likely to play a regulatory role in metal homeostasis .
YdfH belongs to the GntR transcription factor family for which the consensus sequence is reported to be tnGTnnnACna .
However , only the ArgP-arginine complex can produce transcripts , whereas ArgP-lysine appears to inhibit transcription .
The 3D structure of apo-MntR has been solved .
Each dimer binds to one of these conserved sequences .
In the presence of proline , PutA is associated with the cytoplasmic membrane and acts a bifunctional enzyme catalyzing both reactions of the proline-degradation pathway : the oxidation of proline by proline dehydrogenase and subsequent oxidation to glutamate by pyrroline-5-carboxylate ( P5C ) dehydrogenase .
This protein has a DNA-binding domain with a helix-turn-helix motif in the N-terminus and an effector-binding C-terminal domain .
Under aerobic conditions , the autokinase activity of ArcB is inhibited by quinone electron carriers and unphosphorylated ArcB promotes the dephosphorylation of ArcA-P by a reverse phosphorelay reaction .
MraZ is a transcriptional repressor involved in the control of cell-division and cell wall genes .
The N-terminal domain is involved in the protein-protein interaction , while the purified C-terminal domain alone promotes annealing of RNA oligonucleotides and trans-splicing in vitro .
In the presence of leucine the octamer configuration is favored .
RclR ( formerly YkgD ) is a redox-sensitive transcriptional activator that belongs to the AraC-family , whose highly conserved cysteine residues are highly specifically sensitive to oxidation by reactive chlorine species ( RCS ) .
The Cold shock protein A , CspA , is a major cold shock protein and was shown to be detected only during early-log-phase growth at 37 ° C and during log phase after a shift from 37 ° C to 10 ° C. However , studies have shown that although the expression of cspA is reduced during stationary phase , cspA mRNA and CspA are detectable during all growth phases .
The YqjI regulator is structurally related to the PadR-family , which is characterized by a winged-helix-turn-helix ( WHTH ) motif .
Tramonti et al. speculated that GadX binds in tandem to two directed repeat sequences , in the same orientation , in the intergenic regions to activate or represses the transcription of the genes regulated .
The solution structure of the C-terminal DNA-binding domain has been solved .
The following genes were identified via chromatin immunoprecipitation ( ChIP ) in vivo : sutR , cysE , and fliZ .
The sensor kinase EvgS carries an N-terminal periplasmic domain and three cytoplasmic domains , a transmitter , a receiver , and a phosphotransfer ( HPt ) domain .
This protein also may have an undetermined role in metal metabolism , because qseBC deletion mutants show hypersensitivity to several toxic cations .
This regulator is located in the unusual gut operon , which contains two glucitol-specific transcription factors , GutR and GutM , that regulate this operon negatively and positively , respectively ; both regulators control transcription of glucitol PTS permease .
Its N-terminal domain shares 49 % identity with MarA and SoxS .
This helix plays a central role in the allosteric activation of CRP .
SutR ( formely YdcN ) regulates a set of genes involved in the utilization of sulfur .
CRP is activated as a DNA-binding protein by binding of its allosteric effector , cAMP .
CRP activates a gene potentially related to persistence .
NarP , nitrate/nitrite-response-regulator - NarP , is a transcriptional dual regulator of many anaerobic electron transport and fermentation - related genes in the response to the availability of high concentrations of nitrate or nitrite .
The region of 30 bp that NanR binds to is close to a Dam methylation site ( GATC ) that appears to be necessary for induction of some genes of the NanR regulon .
YdeO is an AraC-like transcriptional activator for at least 12 operons , including the gadE-mdtE-mdtF operon .
H-NS binds to intergenic regions as well as regions within genes , but not all genes that bind H-NS are affected by this protein , a fact that is in agreement with the primary role assigned to HN-S in maintenance of nucleoid structure .
Although little is known about the regulating mechanism of GadW , Tucker et al. proposed that this regulator and GadX have distinct molecular mechanisms .
The dimerization domain contains a 10-turn ?-helix that forms an antiparallel coiled-coil with the helix of the other monomer .
FeaR belongs to the AraC/XylS-family of transcriptional regulators .
In the absence of its repressor , AllR , allS is expressed under nitrogen-limiting growth conditions , but its induction is independent of the regulators Nac and NtrC , which are active under these conditions .
GalS belongs to the GalR/LacI-family of transcriptional regulators .
In the presence of arabinose , this regulator activates transcription by overlapping the -35 box of the core promoters , and the central position of the binding site is located near bp -41.5 .
The activated FNR conformation is able to bind a specific palindromic sequence of DNA with the consensus sequence TTGATNNNNATCAA .
Review : .
This protein is homologous to some other proteins , such as MtrR of Neisseria gonorrhoeae , TcmR of Streptomyces glaucescens , JadR2 from Streptomyces venezuelae , and AcrR from Escherichia coli .
The glucitol repressor , GutR , is a DNA-binding transcription factor that represses an operon ( gut ) involved in transport and utilization of glucitol .
Therefore , with nitrite , NarP-P is the major regulator , and with nitrate both NarL and NarP are functional .
FlhC is constituted by two domains ; arrangement of the domains is unique in the FlhC-family .
The majority of ArcA-binding sites overlap the ?70 promoter recognition elements .
However , it is probable that YqhC does not interact directly with inducers but responds to a physiological effect of aldehydes .
MntR , Mn2 + transport regulator , the primary sensor and transducer of manganese abundance , is a dual regulator that senses manganese and negatively or positively controls the transcription of different genes involved in manganese-homeostasis .
FadR is a global regulator of lipid-metabolism , as it activates multiple operons responsible for fatty-acid-synthesis .
Class I - and class II-dependent promoters require one cAMP-CRP for activation and have a single DNA-binding site located upstream of the RNAP-binding site , centered near position -93 , -83 , -72 , or -62 of class I promoters and overlapping the RNAP-binding site of class II promoters .
FruR acts as an activator of genes encoding gluconeogenic Krebs-cycle and glyoxylate shunt enzymes , and the negative effect on genes encoding Entner-Doudoroff pathway and glycolytic enzymes .
Gene induction occurs when the physiological inducer , melibiose , binds to the MelR regulator and when cellular cyclic AMP levels are high .
Resequencing of multiple isolates of the MG1655 strain has identified several genetic variations compared to the reference sequence , including a 1-bp deletion in glpR in strain ATCC700926 .
SoxS is now the first example of an Escherichia coli transcriptional activator that uses a single positive control surface to make specific protein-protein contacts with two different subunits of RNAP .
atoC , encoding the response regulator , and atoS , encoding the sensor kinase , are located in the genome upstream of the atoDAEB operon .
This protein has two Zn ( II ) - binding sites : site A , which only binds to Zn ( II ) , and site B ( the sensor site ) , which binds to Zn ( II ) and Co ( II ) with high and low affinities , respectively .
Currently , there are different models for the formation of DNA-H-NS-DNA bridges which show that this protein binds in tandem to sequences in the genome , forming multimers .
HipB is the antitoxin of the HipAB toxin-antitoxin system .
On other hand , Jiang et al. in 1997 demonstrated that CspA acts as an RNA chaperone that prevents secondary structure formation of RNA at low temperatures cspA mRNA is very unstable at 37 ° C and rapidly disappears as the cell density and RNase activity increase .
Based on genomic SELEX analysis , of a total of 688 Dan-binding sites , 504 were located within intergenic noncoding regions and 184 were within coding regions .
These promoter islands are associated with genes acquired horizontally .
Apparently , SoxS functions as a co-sigma factor and redirects RNA polymerase to promoters carrying a SoxS-binding site .
PspC is essential for this activation , whereas PspB is not strictly required .
In addition , the operons regulated are induced when Escherichia coli is grown in the presence of inductor , glycerol , or glycerol-3-phosphate ARRAY ( 0x15b6280 ) , and the absence of glucose .
Then , the phosphate group is transferred from AtoS to the D55 residue of AtoC to activate this protein .
The opposite regulatory actions of MatA on mat and on flhDC promoters advance the adaptation of E. coli from a planktonic to an adhesive lifestyle .
The affinity of MetJ to this site is enhanced by S-adenosyl methionine ( AdoMet ) which is the end product of methionine-biosynthesis and which binds MetJ to act as a corepressor .
The deletion of the fruR gene causes a reduction in cellular-growth .
QseB , quorum-sensing E. coli regulator B , is the response regulator component of the QseB-QseC two-component system , which is one component of the quorum-sensing regulatory cascade involved in the positive regulation of flagella and motility genes by activating transcription of flhDC , an operon that encodes the master regulator of these genes .
YgiV had been predicted as a transcriptional regulator .
In the presence of hypochlorite , HypT becomes active due to oxidation of three methionines ( Met123 , Met206 , and Met230 ) .
CadC is an integral membrane protein that belongs to the ToxR-like family of transcriptional activators .
ArgP is also called IciA ( for inhibitor of chromosome initiation ) .
SoxS shares 49 % identity with MarA and the N-terminal domain of Rob .
In the absence of arabinose , AraC is unable to activate araBp , but it regulates its own expression by repressing araCp and araBp simultaneously .
The binding site for RhaS overlaps the -35 region of both rhaBp and rhaTp promoters in 4 bp .
FadR belongs to the GntR-family .
DhaR belongs to the family of bacterial enhancer-binding proteins which contain three domains : the sensing-domain located in the N-terminus , the central AAA + domain , and the C-terminal domain , which contains a helix-turn-helix motif involved in the interaction-with-DNA .
TreR occurs as a homodimer and is composed of two domains : an amino-terminal domain that contains a potential helix-turn-helix DNA-binding motif , and a carboxy-terminal domain involved in effector-recognition .
However , transcriptome analyses have shown that this protein not only regulates this operon but also upregulates or downregulates 11 and 32 genes , respectively , that are involved in flagellar synthesis .
However , they have different specificities for select binding sites .
This transcription factor binds to two 12-bp-long direct repeat nucleotide sequences in tandem , overlapping the malXp and malIp simultaneously .
DhaR is inactivated when DnaK binds to the sensing-domain of this regulator , in the absence of Dha .
MraZ and MraW have antagonistic functions .
The differential regulation of these genes might be caused by the degeneracy of their DNA-binding sites .
The DNA sequence which the proteins of the family recognize and to which they bind are also well-conserved among genomes .
This effect could be due to the inhibition of the osmoprotectant producing the genes , betA , betB , and betT .
The transcriptional-activity of SdiA is affected not only by quorum signaling but also by other environmental factors , such as oxidation .
MqsR has a toxic effect on Escherichia coli bacterial growth , which is partially reduced by the ygiV mutation .
In this ring there is contact of the receiver-domain of one subunit with the ATPase domain of a second one .
The antitoxin MqsA has two functions .
The crystal structures of the monomeric full-length protein and of the dimeric output domain bound to DNA have been solved .
In systematic studies of oligomerization , it was shown that some members of the LysR-family , like NhaR , interact with other members of the family to form heterodimers , but the physiological significance of this is unknown .
The majority of work concerning PaaX has been done in E. coli W , in which has been found the DNA-binding sites for PaaX , including a site upstream of the paaXY operon .
On the other hand , MatA controls the expression of the flhDC operon , with higher affinity to flhDp , repressing flagellum biosynthesis , motility , and taxis .
Review : .
On the other hand , CRP alone is unable to activate transcription of rha operons in the absence of RhaS .
However , when asparagine is present the activation of asnA is turned off .
MqsA recognizes two palindromic sites located between the promoter and the start codon of mqsR .
Zn2 + inhibits growth of a basR mutant slightly .
The H-NS protein , for Histone-like nucleoid structuring protein , is a nucleoid-associated multifunctional protein that is capable of condensing and supercoiling DNA .
Transcriptome analyses have been performed .
Hexamerization is required for this function and does not require ATP , DNA , or the DNA-binding domain .
The 23-bp palindrome consensus sequence for Zur-binding sites of gamma-proteobacteria , including Escherichia coli , has been determined by computational analysis .
Review : .
The analysis showed that the most stable loops for linear DNA occur when LacI adopts the extended conformation .
Holo-CueR binds more strongly to DNA than apo-CueR and with a higher conformational flexibility Both holo - and apo-CueR bend DNA .
The HU protein has been shown to be involved in DNA-replication and the formation of transcription foci and it modulates the binding of IHF to oriC and stabilizes the DnaA oligomer bound to oriC .
The gene adiY is located downstream of adiA and in the same orientation .
glnA encodes a glutamine synthetase .
The C-terminal region of proteins from this family features a helix-turn-helix motif .
FabR directly influences membrane lipid homeostasis .
Although in both Salmonella enterica serovar Typhimurium and Escherichia coli the OmpR transcriptional dual regulator is identical , its expression is regulated differently in the two bacterial species , and there are very large differences in the composition of the OmpR regulon .
These regulators bind cooperatively to activate transcription of the operon involved in transport and catabolism of melibiose .
The same sequence is also recognized by the transcriptional repressor AcrR .
Induction occurs when the physiological inducer , allolactose , binds to the lac repressor , preventing it from binding to the operator .
BaeR : bacterial adaptive response , response-regulator .
Subsequent transfer of the phosphate group to PhoB results in activation of PhoB .
A total of 140 genes were found to be under LeuO control , based on genomic SELEX screening ; 133 of these genes are related to the stress response , pathogenesis expression , and fimbrial genes for biofilm-formation and are under the control of an antagonistic interplay between LeuO and H-NS .
This protein , together with the proteins HNS , EvgA , and GadE , pertains to a specific regulatory circuit that is functional in exponential-phase cells growing in minimal medium .
The consensus sequence TGTCGnnnnTGACA is in agreement with alignments determined by the curator for these upstream regions and with the corresponding evidence obtained in the bibliography of every operon , including similarity to the consensus sequence and the data from footprinting assays , computational analysis , and profiling of FhlA-dependent gene-expression .
Based on genome scanning and microarray analysis , it has been determined that yhjX is the sole target gene regulated by the YpdA/YpdB system , and it is modulated by the sequence-dependent structure of the surrounding DNA .
MurR N-acetyl muramic acid repressor , represses genes involved in the catabolism of cell wall sugars .
MazE : ma-ze tr .
On the other hand H-NS also may form heterotrimeric complexes with Hha and YdgT .
Binding occurs in vitro in both the presence and the absence of copper ions .
The mntR gene is transcribed divergently from the mngAB operon .
The interaction of ZntR with Zn ( II ) has been characterized but its interaction with other ions has not been described .
It was found that the promoter islands , which are regions of DNA containing multiple transcription start sites , are recognized and inactivated by HNS .
The family to which DicA belongs has not been established ; it is a protein of 15 kDa with a hypothetical DNA-binding domain in the N-terminal domain .
The transcription factor IclR , for Isocitrate-lyase Regulator , is negatively autoregulated and it regulates the expression of the glyoxylate-bypass operon .
The binding of PaaX to DNA is inhibited by phenylacetyl-CoA , which is the product of the first catabolic step in PA degradation .
UlaR activity is also controlled by homotypic tetramer-dimer transitions regulated by L-ascorbate-6-P .
Although little is known about the mechanism of regulation of the LysR transcription factor , Stragier et al. demonstrated that its regulator acts as an activator by binding to cis-acting elements , inverted repeat sequences that are not well-conserved , near the promoter .
CsgD might activate transcription through two different mechanisms , as suggested by the different locations of its binding sites in the regulatory regions of the genes it activates .
Lrp can act as a repressor or activator for its target genes .
GadE also controls the expression of two transcription factors related to acid resistance , GadW and GadX , and for this reason it is considered the central activator of the acid response system .
The SgrR protein is a member of a novel family of regulators and contains an N-terminal which is characteristic of winged-helix DNA-binding transcriptional regulators and a predicted C-terminal solute-binding domain .
Dependent on the localization of its binding site , CRP functions by a class I or class II mechanism at class III promoters or by a more complex mechanism which can involve direct interactions with the second activator , or CRP exerts its function by DNA bending .
On the other hand , in the presence of acetoacetate , AtoC regulates the transcription of the atoDAEB operon whose products are involved in catabolism of short-chain fatty acids .
Review : .
Analysis of the crystal structures of the tetrameric Mlc/EIIB complex shows a molecular mechanism of Mlc inactivation by membrane sequestration , in which Mlc loss its DNA-binding ability in vivo due to the conformational obstruction by EIIB molecules .
Tramonti et al. .
This protein consists of two domains , an amino-terminal domain that contains a potential helix-turn-helix DNA-binding motif and a carboxy-terminal domain involved in the oligomerization and the recognition of a possible co-inducer .
Binding of these agents interferes with the ability of EmrR to bind DNA .
SoxR induces soxS expression , and SoxS , in turn , activates transcription of genes of the regulon .
The activation effect of DsdC on this operon is enhanced by CRP , but CRP can not act alone on the operon .
Currently , no DNA-binding sites for this regulator have been reported in the literature , and although little is known about the regulating mechanism of ExuR , it has been shown to act as a repressor that binds to a putative inverted repeat sequence .
When overexpressed in E. coli , it destabilizes plasmid inheritance , represses transcription of appY , encoding a regulator of anaerobic metabolism , and induces the SOS-response by competing with DnaA and DnaB in binding to A/T-rich sequences at the replication origin .
It binds and thereby inhibits the endoribonuclease activity of MqsR .
This operon encodes two transcriptional regulators , GadX and GadW , both of which are members of the AraC/XylS-family of transcriptional regulators .
Review : .
This regulator is located in the unusual gut operon , which contains two glucitol-specific transcription factors , GutR and GutM , that regulate this operon negatively and positively , respectively ; both regulators control transcription of glucitol PTS permease .
The consensus sequence for TrpR is described as two symmetrically arranged half-sites with the sequence GNACT separated by a spacer of 8 bp .
This regulation is known as the SOS-response .
HU is a heterodimer formed by an ?-subunit and a ?-subunit , which are encoded by the hupA and hupB genes , respectively and are differentially stimulated during cold shock .
The oxidized form of Zur does not bind to DNA or zinc .
L-Ascorbate-6-P is the effector of the UlaR transcriptional repressor , and when this small molecule binds to UlaR , it severely impairs the formation of UlaR cognate operator sites , since they form a stable complex .
This induction requires dpiBA .
A preliminary analysis of the crystal structure of MraZ has been published .
This regulator activates the transcription of the psp regulon , and it is negatively autoregulated and coordinately activated by transcription of the divergent operon psp .
As another example , IHF stimulates transcription at ?54-dependent promoters .
Betaine inhibitor , BetI , acts as a repressor of glycine-betaine-synthesis-from-choline .
The 3D structure has been solved for the receiver-domain and two constitutively active mutants of this domain as well as that for the output domain .
In systematic studies of oligomerization , it was shown that some members of the LysR-family , like LysR , interact with other members of the family to form heterodimers , but the physiological significance of this is unknown .
Its overexpression produces round-shaped cells , alters elongation and cell septation induces biofilm-formation impairs cell-growth rate , and alters the properties of the outer membrane .
There is intensive cross-regulation with the paralogous two-component system NarQ-NarP .
A model of regulation by CreBC was proposed by Cariss et al. ( 2008 ) in which CreC responds to changes in the growth medium and/or signal and autophosphorylates ; later , its phosphate is passed on to CreB , which binds to cre tag sequences .
A direct repeat GCGT motif of the SutR box was found in the yfiC , ydcO , and sutR genes , which are associated with group A spacers , and the palindromic sequence of GCGT ( Nn ) ACGC was identified for yfiC , thiI , ydcO , and sutR genes .
ArgR is also essential for a site-specific recombination reaction that resolves plasmid ColE1 multimers to monomers and is necessary for plasmid stability .
GcvA also activates transcription of the gcv genes , via interaction with the ? or ? subunits of RNA polymerase .
Based on transcriptome analysis , expression levels of a set of genes regulated by Fur change substantially in response-to-antibiotic treatment .
Zur is able to form dimers , even in the absence of zinc .
This negative regulation requires in addition to PhoR an intact Pst system and PhoU .
The complex is hexameric and is comprised of a MazE homodimer sandwiched between MazF homodimers .
In accordance with this , the CynR regulatory domain is sufficient for dimerization , whereas the full-length protein behaves as a higher-order oligomer .
Currently , no inducer for this regulator has been reported in the literature , although Reush et al. proposed that this regulator can form a complex with a short chain of polyhydroxybutyrate .
The FabR consensus sequence has been identified as a palindromic sequence with a length of 18 bp .
The MazE-MazF system mediates the toxicity of guanosine 3 ' ,5 ' - bispyrophosphate ( rapid relA induction ) , which is associated with amino acid deprivation ; cell-death caused by the antibiotics rifampicin , chloramphenicol , and spectinomycin ; and the thymineless death ( TLD ) response to thymine starvation .
In the presence of poly ( P ) , HupA is efficiently degraded by Lon .
Currently , no DNA-binding sites for this regulator have been reported in the literature .
BetI belongs to the TetR/AcrR-family of transcriptional regulators .
NarP acts as a repressor or activator of gene-expression , or it interferes with other regulatory proteins bound near the promoter .
Review : .
In vivo studies detected crosswise stimulus-dependent alterations in the expression of their respective target genes , and mutational analyses revealed that deletion of any of the components of the signal-transduction cascade affects the function of the other .
The Nag regulon consists of two divergent operons , nagE and nagBACD .
Reviews : .
The transcriptional regulators of E. coli that show higher similarity to EnvR are AppY and AdiY .
The YefM protein appears to lack secondary structure , and its native conformation is proposed to be unfolded .
LldR is a protein that belongs to the GntR-family and , accordingly , this transcriptional repressor family protein is composed of two domains : a conserved N-terminal domain which contains the DNA-binding region , and the carboxy-terminal domain , which is involved in effector-binding and oligomerization .
Although little is known about the regulating mechanism of UxuR , it has been shown to act as a repressor , binding to a putative inverted repeat sequence from the uid operon in a cooperative process with UidR .
Class III promoters require multiple activator molecules , that is , either two or more CAP dimers or one CRP dimer and additional activator proteins synergistically activate transcription .
The AraC regulator belongs to the AraC/XylS-family and occurs as both a monomer and a homodimer .
More specifically , Dan belongs to the group II nucleoid proteins , which include Fis , Rob ( CbpB ) , CbpA , and IciA and show irregular distribution within the nucleoid .
FhlA shows 46 % identity to the HyfR protein , a member of the same group .
This transcription factor is composed of two domains , a C-terminal domain that contains two potential helix-turn-helix DNA-binding motifs and an N-terminal domain involved in l-rhamnose binding and dimerization of the protein .
LeuO activates transcription of the divergent leuLABCD operon .
There are more than 10,000 such binding sites per genome .
This operon is transcribed divergently on the opposite strand , under the control of ?38 ( RpoS ) RNA polymerase .
When bound to DNA , oxidized OxyR stimulates transcription by interacting with the C-terminal domain of the ?-subunit of RNA polymerase .
YoeB enhances the interaction with YefM by affecting the YefM conformation to one that is more favorable for DNA-binding and/or by stabilizing the nucleoprotein complex at the operator site and reducing basal expression of the yefM-yoeB operon .
It is negatively autoregulated and coordinately represses transcription of the divergent gene rpiB , encoding an enzyme in the pentose pathway .
Review : .
As a subset of the class I promoters , the Mar-Sox-Rob box is separated by ~ 30 bp from the -10 hexamer but can be functional in either orientation .
The strictly conserved TT/AA motif , located in both ends of the center of symmetry , is probably the major recognition point for NagC .
LexA is widely distributed in bacteria , and it appears that it emerged from the gram-positive group .
Mutational studies carried out to define interactions between RhaS and ?70 suggest the existence of two interaction regions in both .
This interaction appears to be affected by a mutation in the interdomain linker .
This regulator forms a complex with DNA in the absence of nickel , binding to a 20-bp-long sequence with an imperfect palindromic sequence .
The monomer of this transcription factor contains two domains : the N-terminal domain is responsible for binding DNA and the dimerization and also contains a winged-helix-turn-helix motif .
In addition , SdiA also affects the expression of a number of genes , including a decrease in expression of several motility and chemotaxis genes , a pleiotropic effect over the expression of genes involved in cell-division , drug sensitivity , DNA-replication and repair , macromolecular metabolism genes involved in the glutamate-dependent acid resistance systems ( AR-2 ) and an increase in the expression of the AcrAB multidrug efflux pump proteins .
EbgR diverged from other repressors shortly after the divergence of the Gram positive from the Gram negative eubacteria , approximately 2.2 billion years ago .
SutR is a small transcription factor with a helix-turn-helix ( HTH ) motif and belongs to the Cro-C1-type superfamily .
During induction by fuculose 1-phosphate , FucR binds to DNA , positively autoregulating itself and simultaneously activating transcription of the divergent fucAO operon .
A mraZ deletion mutant is more sensitive to nalidixic acid and kasugamycin than the wild type .
ZraS and ZraR show considerable homology with the proteins NtrB and NtrC , respectively .
Genes related to the stress response proteins and fatty-acid-biosynthetic pathways are upregulated by FadR .
Overproduction of DcuR causes a drug-resistance phenotype .
By using a computational model of transcriptional activation it was proposed that at the class I promoter of mar MarA increases the binding of RNA polymerase but not the occupancy .
Two N-terminal segments of YefM form a symmetrical dimer within the YefM2-YoeB heterotrimeric complex and do not contact YoeB directly .
It was previously suggested that MraZ is an inhibitor of the RsmH methyltransferase , but this report has since been retracted .
Presumably the hexamer is further stabilized by additional DNA wrapped around the ring .
Expression of gadE is controlled by an unusually large 798-bp upstream intergenic region , termed the sensory integration locus .
Based on these findings , it was proposed that these proteins activate the transcription by a mechanism named DNA scanning or prerecruitment , which consists of the formation of the complex RNA polymerase transcriptional regulator in the absence of DNA , and then this complex scans the DNA to bind to appropriate sites .
There are more than 10,000 such binding sites per genome .
In this way , RhaS activates transcription of l-rhamnose gene clusters .
It has been demonstrated that SlyA increases expression of hemolysin E by antagonizing the negative effects of H-NS .
The tertiary structure of the YoeB toxin and the YefM2-YoeB complex has been described .
Nonphysiological analogs , such as thiogalactosides , can function as inducers too .
It may also have the capability to respond to starvation and high cell density and positively controls ?S expression .
The metal ion is bound with a linear coordination to two conserved cysteine residues .
Due to the autoregulation of crp , cAMP-CRP levels decrease .
It could have a major impact on in vitro verification of the vast numbers of previously unrecognized genes in the FNR regulon , especially in genomic studies .
In Klebsiella pneumoniae , Nac functions as a dimer , and for some sites it can bind as a tetramer ; it recognizes long and short sites in the absence of a coeffector .
YqjI is inactivated under conditions of elevated nickel levels , and the presence of this divalent metal prevents its binding to the target gene .
As with other members of the family , the possibility exists of that this regulator activates dependent promoters of ?70 instead of dependent promoters of ?54 .
In the absence of nitrate and nitrite , NarX and NarQ stimulate the dephosphorylation of NarL-P and NarP-P .
In the presence of nitrate both sensors phosphorylate NarL and NarP to the same extent .
The operon containing both genes zraR , encoding the response regulator , and zraS , encoding the sensor kinase , is located next to and in the opposite direction to zraP , a gene regulated by ZraR .
These studies resulted in a detailed picture of the mechanism of the redox-dependent structural changes of the protein and identified Y540 as an important substrate specificity determinant .
The membrane-associated form of PutA does not bind put promoter DNA ; thus , the enzymatic and DNA-binding activities of PutA are mutually exclusive .
The Mlc monomer is composed of three domains : a DNA-binding motif ( D-domain ) , an EIICBGlc-binding motif ( E-domain ) , and an oligomerization domain ( O-domain ) .
It has been suggested that the three AcrR ligands bind to distinct overlapping sites and that two of them ( ethidium and proflavin ) can be simultaneously bound in the cavity .
RutR recognizes and binds a 16-bp ( 7-2-7 ) inverted repeat consensus sequence where the central A/T nucleotide in each half-site appears to be the most important for the site .
It was proposed that these proteins bind to their target sites by a mechanism named DNA scanning or prerecruitment .
A 3D model has been proposed for the major I2 conformation of EcHU?2 .
The rutR gene , which is autorepressed is transcribed divergently from the RutR-regulated rutABCDEFG operon .
Currently , the GadW/GadX-dependent circuit , involved in the GAD system , is under discussion and study .
The regulatory protein for uptake of hexose phosphates , UhpA activates the transcription of a gene that codes for UhpT , a protein that transports many phosphorylated sugars into the cell .
However , the cysteines at positions 21 and 116 have been determined as essential in sensing electrophiles in vivo and in vitro .
These sites act as enhancer-binding sites for transcriptional activation by NorR .
MazF exhibits RNase activity toward tmRNA , and tmRNA is involved in release of MazF-mediated cell-growth inhibition .
Activation by LysR requires the presence of diaminopimelic acid .
MazE is an antitoxin that counteracts the MazF toxin .
UhpB unphosphorylated is able to dephosphorylate to UhpA .
The expression of the operon containing both genes qseB , encoding the response regulator , and qseC , encoding the sensor kinase , is regulated by a quorum-sensing system , and the regulatory region of the operon is 99.6 % identical to the regulatory region of the same operon in EHEC .
mdtEF encodes a multidrug efflux pump , and gadE encodes the master regulator for glutamate-dependent acid resistance .
YqjI is a local transcription regulator that represses expression of the divergent operon , yqjH-yqjI , related to its autorepression and the synthesis of an NADPH-dependent ferric reductase .
More than 50 % of the sites have additional DR elements , and the majority of ArcA-binding sites contain three to five DR elements , predominantly at a CTC spacing of 11 bp .
It is a global transcriptional silencer of genes with high AT content regulates 5 % of all Escherichia coli genes and plays a key role in global chromosome-organization in bacteria .
The conformational flexibility of unbound LexA is the key element in establishing a coordinated SOS-response .
The Mar-Sox-Rob box contains an invariant A at position 1 , two recognition elements , the RE1 at position 4-7 and RE2 at position 15-18 , and a 7-bp A/T-rich spacer separating these elements .
mdtNOP ( sdsRQP ) is involved in sensitivity control against sulfa drugs .
Some proteins , such as SufB , IscU , EprA , and IscA , are involved in the assembly and transfer of the -LSB- 2Fe-2S -RSB- cluster to IscR .
Both dcuR , encoding the response regulator , and dcuS , encoding the sensor kinase , are organized in an operon that is located upstream of the dcuB-fumB operon , whose expression is activated by DcuR .
TdcA belongs to the LysR-family of transcriptional regulators , and like the other members of this family , it has a helix-turn-helix motif in the N-terminal domain for DNA-binding .
MatA binds more weakly to pfliA and to pfliC , and their levels are equal to those observed for matB .
Additionally , synthesis of rha operons is induced when E. coli is grown on l-rhamnose in the absence of glucose and when cellular cyclic AMP levels are high .
Comparison of both structures reveals that oxidation is accompanied by a significant structural change in the regulatory domain .
The N-terminus determines metal-specific responses in the recognition of cognate and noncognate metals .
The LysP-CadC interaction is mediated via trans-membrane and periplasmic contacts .
Therefore , it is possible that this protein regulates genes involved in DNA-replication , recombination , or repair .
Although it has not been possible to test the ligand binding to FeaR , these data and those of others suggest that it is a substrate or intermediate of the TynA/FeaB pathway , as it is more likely that an aldehyde ( tyramine ) is the direct inducer for the PEA catabolic pathway and a likely coeffector of FeaR .
The pho promoters contain functional -10 sequences but lack the consensus -35 sequence .
The transcriptional repressor HipB , for High persistence , is negatively autoregulated and controls the transcription of a critical persistence factor .
This domain is found in proteins such as UbiC from Escherichia coli , TreR from Bacillus subtilis , and HutC from Pseudomonas aeruginosa .
NtrC belongs to the two-component system NtrB/NtrC and is a member of the ?54-dependent activator family , whose homologues are widely distributed in bacteria .
It was therefore predicted to play a role in the heat shock response .
The AAA + domain may directly contact DNA while promoting-open-complex-formation .
When this protein is repressing transcription , it overlaps the whole promoter region .
On the other hand , in an in vivo single-molecule assay , the sliding process for the LacI TF was determined .
This transcription factor is composed of two domains , a C-terminal domain that contains two potential helix-turn-helix DNA-binding motifs and an N-terminal domain involved in l-rhamnose binding and dimerization of the protein .
In the presence of bio-5 ' - AMP , BirA binds to 40-nucleotide-long DNA target sites in the bioA/bioBFCD intergenic region to coordinately repress transcription of bioAp and bioBp .
At high levels of magnesium the phospho-PhoP phosphatase activity of the sensor protein is induced .
Under aerobic conditions , H-NS represses the cadBA operon .
A crystal structure of AsnC complexed with the ligand l-asparagine has been solved at 2.4 - Å resolution .
SutR , for regulator of sulfur-utilization .
Also , the 3D structures of the output domain without DNA and in complex with its target DNA have been solved .
Review : .
The proline-dehydrogenase-activity resides in the amino-terminal 669 amino acids of PutA ; a truncated protein retains proline dehydrogenase and DNA-binding activity but lacks membrane association and 1-pyrroline-5-carboxylate-dehydrogenase-activity .
Dihydroxyacetone Regulator , DhaR , is negatively autoregulated and coordinately activates transcription of the divergent Dha operon ( dhaKLM ) , which encodes three subunits of the dihydroxyacetone ( Dha ) kinase .
Glycine cleavage A , GcvA , is a repressor of the glycine cleavage enzyme system , which is a secondary pathway for production of C1 units .
NtrC interacts with ?54-RNA polymerase through auxiliary DNA-binding proteins , such as FIS , via DNA looping .
ArsR negatively controls the expression of the genes involved in arsenical and antimonite metals resistance whose expression is induced in the presence of these metals .
On the other hand , D'Autr % e ' ; aux et al. showed that nitric oxide , a radical that is potentially toxic , inhibits the DNA-binding of this repressor .
AraC binds to the less-conserved site ( -42.5 ) with less strength ; this binding occurs only in the presence of arabinose , and it is absolutely required for expression of araBp .
This operon encodes two transcriptional regulators , GadX and GadW , both of which are members of the AraC/XylS-family of transcriptional regulators .
Binding of BluF to BluR is stimulated by blue light .
In addition , there is a linker that connects both the N-terminal and C-terminal .
The YpdA/YpdB two-component system is widespread among proteobacteria and show a high degree of conservation in gammaproteobacteria .
The specific inducer for NagC is GlcNAc-6-P , the product of GlcNAc transport by the PTS .
Microcins are low-molecular-weight polypeptide antibiotics .
In the presence of nitrite , autophosphorylation of NarX is low and NarX acts primarily as a phosphatase for NarL-P .
The crystal structure of BirA has been determined by X-ray crystallography to a resolution of 2.3 Å and that of a BirA-biotin complex has been solved by several research groups .
YehT belongs to the LytTR response regulator ( RR ) of the two-component system that is involved in the stationary-phase control network .
Based on saturation transfer difference NMR , it was shown that both trehalose-6-phosphate and trehalose bind to TreR with similar affinities .
Trucker et al. gave evidence that GadW can work as a coactivator of GadX or it can inhibit the GadX-dependent activation ; they also provided evidence of more target genes for GadX/GadW regulation .
In addition , it was found that 2-O-?-mannosyl-d-glycerate ( MG ) can induce the SdaR regulon MG has been recognized as a protective osmolyte in hyperthermophylic prokaryotes and as a carbon source for Escherichia coli .
It also regulates genes involved in the uptake of glucose .
As a member of this family FruR contains two functional domains : an N-terminal domain which contains a helix-turn-helix motif for DNA-binding , and the effector-binding domain located in the C-terminus , which is homologous to the periplasmic sugar-binding protein for ribose , arabinose , and galactose .
The building block of HypT is likely a dimer ; similar to other LTTRs , it forms unusually large oligomers , as dodecameric ring-like structures , in vitro that undergo large DNA-induced conformational changes to form dimers and tetramers .
In addition , Lrp affects nearly three-fourths of the genes induced upon entry into stationary phase .
Binding of GlpR to DNA is diminished in the presence of the inducers glycerol or G3P .
MurR is a member of the RpiR/AlsR family of transcriptional regulators , whose members contain two domains , a highly conserved N-terminal HTH domain and a C-terminal SIS ( sugar phosphate isomerase/sugar phosphate-binding ) domain .
FadR coordinately regulates fatty-acid-biosynthesis and fatty-acid-degradation at the level of transcription .
Subsequently , the phosphate group is transferred from KdpD to Asp-52 of KdpE leading to the dimerization and activation of KdpE .
For example , RstA is a suppressor of a lesion in yjeE , a gene essential for cell-growth and whose cellular function is unknown .
The lsrR gene is transcribed together with lsrK in an operon , and this last gene encodes a protein that phosphorylates to DPD .
The redox state of the iron-sulfur cluster regulates SoxR activity .
CueR binds to a 19-bp sequence containing two 7-bp inverted repeats separated by a 7-bp spacer .
These proteins are dissimilar in their N-terminal regions , which in FhlA recognizes formate .
PhoP belongs to the OmpR/PhoB subfamily of response regulators characterized by a winged-helix DNA-binding domain .
In addition it is a DNA-binding protein , as is the case for other bacterial antitoxins .
Its regulator represses transcription by overlapping the promoters puuAp and puuDp , and the binding targets for PuuR consist of 15 nucleotides , with the following recognition sequence : AAAATATAATGAACA .
It is composed of an N-terminal CheY-like receiver-domain and a C-terminal LytTR-like effector domain with DNA-binding affinity .
One of them that was identified , the strongest SutR-binding site , is called site 1 , and it represses ydcO and activates sutR expression ; it is a direct repeat , GCGT , separated by 4 bp .
In addition Tramonti et al. provided evidence that the transcription of the gadXW operon is regulated to a posttranscriptional level by a gadY small RNA .
Currently there are different interpretations and models to explain how FUR could overlap inverted repeats in tandem .
ArsR belongs to the ArsR/SmtB family of transcriptional regulators that respond to a variety of metals .
Overproduction of YehT is associated with moderate resistance to growth-inhibiting agents , such as crystal violet and deoxycholate .
The glycolytic flux is determined by the concentration of the metabolite fructose-1 ,6 - bisphosphate , which is the molecular effector of Cra .
Zur is not autoregulated .
In the absence of proline , PutA binds to operator sequences in the putA-putP intergenic region and represses transcription , most likely by keeping RNA polymerase from binding to the putA promoter .
Mlc has a high homology with the NagC transcriptional dual regulator ( 40 % identity and 80 % similarity ) .
It is negatively autoregulated and coordinately represses transcription of the divergent agaZVWEFA operon , which is related to transport and degradation of N-acetylgalactosamine .
Expression of gutR is activated in the presence of glucitol and in the absence of glucose .
On the other hand , UxuR is highly similar to ExuR ( 49 % identity ) , and apparently both act together , capable of cross talk to regulate expression of the uxuR regulon .
Its activity is silenced by the receiver-domain , and phosphorylation relieves inhibition .
NanR regulates transcription when it binds to a region of ~ 30 bp that contains three conserved motifs in tandem .
The transcriptional activator GadX , for Glutamic acid decarboxylase , is positively autoregulated and controls the transcription of pH-inducible genes , including the principal acid resistance system is glutamate dependent ( GAD ) , is also referred to as the GAD system , and its genes are involved in multidrug efflux .
The variations in the number , spacing , location , and predicted strength of DR elements within the chromosomal ArcA-binding regions suggest plasticity in the architecture of ArcA-binding sites for either repressed or activated operons .
If glucose is available , EIIAGlc is predominantly dephosphorylated .
Autophosphorylation of ArcB is stimulated by effectors such as d-lactate , pyruvate , and acetate .
A consensus recognition sequence has been described .
In systematic studies of oligomerization , it was shown that some members of the LysR-family , like CynR , interact with other members of the family to form heterodimers , but the physiological significance of this is unknown .
The members of this family exhibit two domains , an amino-terminal domain involved in coinducer-recognition and dimerization and a carboxy-terminal domain that contains a potential helix-turn-helix DNA-binding motif .
It has been suggested that NarL is responsible for nitrate-mediated repression and NarP is responsible for nitrite-mediated repression of ydh , and both compete with RNA polymerase for binding at the promoter .
In contrast , for the regulation of promoters containing type 2 sites , such as PsufA , the -LSB- 2Fe-2S -RSB- cluster of IscR is dispensable .
MraZ overproduction is lethal and perturbs cell-division .
hns is induced by high hydrostatic pressure and DNA-synthesis .
Weight matrices for the DNA-binding site for ArcA-P have been obtained .
Zur , which belongs to the Fur-family , appears to have a DNA-binding site in the N-terminal domain , around residue 65 , and a signal-recognition site in the C-terminal domain .
The structure of Lrp from Escherichia coli bound to DNA as an octamer has been solved .
These proteins are dissimilar in their N-terminal regions , which in FhlA recognizes formate .
StpA appears to be a backup for Hns in the regulation of a set of nonessential and recently acquired genes .
Melibiose triggers MelR-dependent activation of melAp and relieves MelR-dependent repression of melRp .
SlyA belongs to the MarR-family of transcriptional regulators .
Changes in the external pH activate the adiA gene .
Like CitB from K. pneumoniae , CitB/DpiA from E. coli contains a helix-turn-helix DNA-binding motif in the C-terminal domain and three well-conserved residues , two aspartates ( positions 13 and 57 ) and one lysine ( position 107 ) , in the N-terminal domain .
It was shown that most ArcA-binding sites contain additional direct repeat ( DR ) elements as well as the two required for binding an ArcA dimer , and this finding provided a novel insight into how ArcA accomplish global regulation-of-gene-expression .
The sensor proteins YedW , UhpB , and YedV , which also belong to two-component systems , can activate CusR via signal cross talk .
AdiY may function directly or indirectly with CysB to increase expression of adiA .
YiaJ is a transcriptional repressor that negatively controls the expression of genes involved in the catabolism of the rare pentose l-lyxose .
The intracellular concentration of Mlc is very limited .
Tentatively , this transcription factor is classified as a member of the LysR-family .
Its transcription is induced under stationary phase and under different stress conditions , such as carbon starvation , osmotic stress , heat shock , acidic stress , and oxidative stress .
Proteins with antizyme activity have been found in several organisms , from plants to eubacteria .
MalT is monomeric in solution , but in the presence of maltodextrin and ATP it forms multiple complexes ( oligomers ) in its target promoters and activates transcription by overlapping the -35 box of promoters .