Set up repository

+import fileinput
+import re
+import sys
+
+if ( len( sys.argv ) < 3 ):
+    sys.stderr.write( "E: usage: " +sys.argv[0] + " <input_file> <output_file> \n" )
+    sys.stderr.flush();
+
+    exit( 2 );
+else:
+    print("Ok.")
+
+#LEER ARCHIVO INPUT
+text_file = open( sys.argv[1], "r" )
+dato = text_file.read().splitlines()
+text_file.close()
+
+
+#QUITA EXTENSION DE NOMBRE DE ARCHIVO
+split_line = sys.argv[2]
+split_line = split_line[:-4]
+file_name=""
+file_name = split_line + ".san"
+open( file_name , 'w').close()
+
+#ESCRIBIR REGEX EN ARGV 2
+for line in dato:
+    line = re.sub('[\(][^\(|^\)]*\s[0-9]+\s[^\(|^\)]*[\)]', '', line.rstrip()) #elimina (_num_)
+    line = re.sub('[\(][^\(|^\)]*\s[0-9]+\.[0-9]+\s[^\(|^\)]*[\)]', '', line.rstrip()) #elimina (_num.num_)
+    line = re.sub('[\[][^\(|^\)]*\s[0-9]+\s[^\(|^\)]*[\]]', '', line.rstrip()) #elimina [_num_]
+    line = re.sub('[\[][^\(|^\)]*\s[0-9]+\.[0-9]+\s[^\(|^\)]*[\]]', '', line.rstrip()) #elimina [_num.num_]
+    line = re.sub('[\(][^\(|^\)]*\s(fig\s\.|figure|e\s\.\sg\s\.|table)\s[^\(|^\)]*[\)]', '', line.rstrip(), flags=re.I) #
+    #print(line)
+
+
+    save_file = open( file_name, "a" )
+    save_file.write(line)
+    save_file.write("\n")
+    save_file.close()

+The results of the present study extend these observations and show that the MetR protein also stimulates the in-vitro expression of metH and that both the MetE and MetH proteins synthesized in-vitro are enzymatically active .

+In spite of this , MarA ( E89A ) activation was greater than that of WT MarA for inaA , sodA , and ybjC ; it was comparable to that of WT MarA for micF and less than that of WT MarA for fumC , mdaB , nfsB , and ybhW  .

+Although the cocrystal structure of MarA with the marRAB marbox DNA  indicates no interaction between the two molecules at this position  , we considered the possibility that steric hindrance between the marbox DNA and MarA could limit activation by MarA when position 12 is not a T residue ( see the Discussion for a fuller treatment ) .

+In contrast , the E89D variant was less active than WT MarA for fpr and completely inactive ( indistinguishable from the control plasmid ) for mdtG .

+E89G was approximately twice as active as WT MarA for fpr and 4-fold more active for mdtG although for both promoters it was considerably less active than E89A .

+( The activations shown here are greater than those apparent in Table 2 because the expression of the plasmids carrying MarA , SoxS , and their mutants is not entirely shut off by lacI q so that the increases expressed in Table 2 appear smaller .

+If , as outlined above and presented in greater detail in the Discussion , steric interference with the phosphate between positions 12 and 13 and the glutamic-acid side chain at position 89 is responsible for the very poor activation of promoters such as fpr , then it would be predicted that binding of WT MarA to the fpr marbox would be enhanced if that phosphate were absent .

+We therefore compared the binding affinity of WT MarA to either a 36-bp double-stranded DNA containing the marbox sequence of fpr or with dsDNA of the same sequence and length but prepared so that the phosphate linkage between positions 12 and 13 of the marbox was eliminated ( see Materials and Methods ) .

+Again  , MarA bound very poorly to the fpr marbox  .

+Of the seven class I promoters examined , MarA ( Q91A ) activated the acrAB , marRAB , and zwf promoters to similar extents as WT MarA but activated acnA , fpr , mdtG , and poxB to only 60 % or less of MarA WT levels  .

+For the nine class II promoters , MarA ( Q91A ) significantly reduced the activation of fumC , inaA , micF , pqiA , and ybjC but had no significant effect on nfsB , mdaB , sodA , oryhbW .

+Indeed , nfsB and sodA are among the promoters that Q91A activated to the same extent as WT MarA .

+Among the class I promoters that exhibited measurable binding to MarA , MarA ( Q91A ) showed no greater binding or activation for acrAB , a modest reduction in activation and binding for mdtG and zwf , and a reduction in binding but not in activation for marRAB .

+Although not observed in these experiments , a more detailed analysis of the binding of MarA ( Q91A ) to the micF marbox  showed a very small reduction in binding concomitant with the reduced ability of MarA ( Q91A ) to activate the class II micF promoter  .

+We have shown here that the MarA glutamic-acid residue E89 is responsible for decreasing the binding of WT MarA relative to SoxS for the class I marbox promoters , acnA , mdtG , fpr , and zwf , thereby decreasing the relative activation of these promoters and hence the resistance engendered to superoxides by MarA .

+x First published online 19 November 2009 Competitive activation of the Escherichia coli argO gene coding for an arginine exporter by the transcriptional regulators Lrp and ArgPmmi 6950 1513 .

+This shows that whereas both NagC and ChbR appear to act as repressors for the chbB operon in the absence of the inducing sugar chitobiose , ChbR is necessary for induction and so behaves as a dual-function repressor -- activator .

+Identification of the DNAbinding domain of the OmpR protein required for transcriptional activation of the ompF and ompC genes of Escherichia coli by in-vivo DNA footprinting .

+MelR is a member of the AraC-XylS family of bacterial gene regulatory proteins  and our previous studies have shown that MelR , together with the cyclic AMP receptor protein , CRP , regulates expression of the melAB operon that encodes products essential for melibiose metabolism  .

+For example , the nitrate reductase genes narGHJI are regulated exclusively by NarL and are not responsive to NarP as observed here for cydD , while nitrate induction of the fdnGHI operon is regulated predominantly by NarL but is also responsive in part to NarP  .

+Under identical experimental conditions as for argO , the regulatory regions of the other ArgP-regulated genes ( asd , dapB , dapD , gdhA , lysA , lysC , and lysP ) were also bound by ArgP , with apparent K d s ranging from 55 nM to 170 nM ; in all these cases ( unlike the situation with argO ) , the addition of Lys was associated with an increase in the apparent K d , indicating that ArgP binding in these instances is Lys-sensitive .

+Given that the activation by full-length , chromosomally expressed RhaS at rhaBAD is approximately 33-fold higher than that of chromosomally expressed RhaR at rhaSR , comparable efficiencies of activation by the CTDs to their full-length counterparts would have resulted in His 6-RhaR-CTD activating rhaSR by approximately 30-fold .

+This observation not only allows us to understand how a modest mutation in O NC2 can affect fimB expression whereas the D3 mutation does not , but it also supports our prior assertion that NanR activates fimB expression without NagC  .

+These latter results , together with the experiments described here showing that MetJ binds to this region of DNA , strongly suggest that the-8 to + 27 region is involved in metE repression .

+Thus , it appears that NarL and NarP adopt overlapping mechanisms to inhibit ydhY -- T expression .

+Some of these operons are regulated by the NarL protein alone , such as the narG and frdA operons , whereas expression of the nirB ( encoding NADH-dependent nitrite reductase ) , nrfA and fdnG operons is controlled by both the NarL and NarP proteins .

+The ArgP protein enhances the expression of the argK gene To test the biological activity of the ArgP protein on the arginine transport system , the amounts of mRNA synthesized by a 502 bp KpnI-EcoRV DNA fragment containing the N terminus and the control region of the argK gene was investigated .

+RESULTS Oligomerization of DnaA Protein to the dnaA Promoter -- Sequence-specific DNA binding of DnaA protein to the dnaA promoter region  was studied in detail using a combined gel-shift and chemical footprinting assay to determine the extent of DNA binding to the region flanking the consensus DNA-binding site , the DnaA box .

+An alternative explanation is that repression occurs by the ' roadblock ' mechanism described for PurR repression of the purB promoter  .

+The experiments in Fig. 2a -- c suggest that the binding of Rob to the robboxes of the fumC , micF , and inaA promoters occludes the binding of 70 R4 to the 35 hexamer of these class II promoters , as is also the case during SoxS-dependent activation of the fumC and micF promoters .

+ß-Galactosidase activity Promoter Mutated site minus NO 3 plus NO 3 Fold induction ogt100 93 + 1 439 + 12 4.7 ogt102 NarL I 92 + 5 107 + 6 1.2 ogt104 NarL II 56 + 2 87 + 3 1.6 the yeaR promoter is repressed by the binding of NsrR to a target that overlaps the 10 hexamer element  [ 12,31,32 ] .

+Besides , MarA activates fumC , fpr , nfo and other genes possibly involved in response to the oxidative-stress .

+Nitrate-and nitrite-mediated expression of the hcp is dependent on NarL and NarP Sequence analysis of the hcp regulatory region suggested that it contains a binding site for FNR and also binding sites for nitrite-and nitrate-activated regulators , NarL and NarP  .

+Therefore , arafl is essential for both repression and activation and acts as a switch to allow both the repressor and the activator forms of the AraC protein to control the araBAD promoter .

+As hmpA and ytfE encode a nitric-oxide reductase and a mechanism to repair iron-sulfur centers damaged by nitric-oxide , the demonstration that hcp-hcr , hmpA , and ytfE are the three transcripts most tightly regulated by NsrR highlights the possibility that the hybrid cluster protein , HCP , might also be part of a defense mechanism against reactive nitrogen stress .

+3901-3905 , June 1987 Microbiology The narL gene product activates the nitrate reductase operon and represses the fumarate reductase and trimethylamine N-oxide reductase operons in Escherichia coli ( frd gene/tor gene/regulation ) S. Thus the D3 region is not apparently required for NanR to activate fimB expression in the wildtype background , and it could contain specific sequences that inhibit this .

+Another example is the NarL/NarP-and FNR-stimulated expression of nirB and nrf genes , which are repressed by Fis and IHF  .

+These results show that constitutive and inducible expression of the chromosomal MarA was able to upregulate nfnB expression in contrast with the lack of activation mediated by constitutive expression of the chromosomal SoxS and Rob proteins .

+Transcription activation at the Escherichia coli melAB promoter : interactions of MelR with its DNA target site and with domain 4 of the RNA polymerase sigma subunit .

+Orientation of MelR bound at site R Wade et al.  showed that MelR-binding site R is essential for MelR-dependent repression of the melR A MelR RNA-1 B TB23 TB23 TB22 TB22 MelR + + % Relative Intensity 150 100 50 0 TB23 MelR + MelR TB22 Figure 2 .

+Similar to the results of metE expression , MetR greatly stimulates the synthesis of MetH using plasmid pQN1011 as template  .

+Separate contributions of UhpA and CAP to activation of transcription of the uhpT promoter of Escherichia coli .

+Summary Expression from the Escherichia coli nrfA promoter ( pnrfA ) is activated by both the FNR protein ( an anaerobically triggered transcription activator ) and the NarL or NarP proteins ( transcription activators triggered by nitrite and nitrate ) .

+One obvious difference between the synthetic promoter and the napF operon promoter is that transcription from the latter is also activated by the NarP protein bound to a site centered at position 44.5 .

+NarL-mediated repression of the frdA promoter is achieved by NarL binding over a large region centred near the transcription start site and including the FNR site  .

+The microarray data for the other promoters that are apparently activated by NsrR must be evaluated cautiously , however , because few of these transcripts encode proteins known or suspected to be involved in the response to RNS , and most of the differences were much smaller ( typically two-to threefold apparent activation ) than the 30-fold repression of ytfE , the 14-fold repression of hmpA , and the up-to-15-fold repression of hcp .

+As at the yeaR promoter , nitrate-dependent induction can be repressed by Fis that binds to a single site overlapping the upstream DNA site for NarL .

+This was indeed suggested by Détiollaz et al.  on the basis that IHF sites replacing CAP sites allowed activation of the malT promoter , albeit less than with CAP .

+It accepts a methyl group from methylphosphotriesters and then acts as a transcriptional activator of the ada operon AdiY Escherichia coli SP : P33234 Transcriptional activator of the adiA gene for 253 32 , 237 biodegradative acid-induced arginine decarboxylase AfrR Escherichia coli TE : Q07681 Probable transcriptional activator of the 272 258 afrABRS operon for expression of AF/R1 fimbria in E. coli RDEC-1 , a rabbit pathogen AggR Escherichia coli SP : P43464 Transcriptional activator of the aggA gene for 265 183 aggregative adherence fimbria I ( AAF/I ) expression in enteroaggregative E. coli strains AppY Escherichia coli SP : P05052 Transcriptional activator of the cyxAB , hyaAB-243 12 , 131 CDEF and appA operons during the deceleration phase of growth AraC Citrobacter freundii SP : P11765 Regulator of several operons involved in the 281 30 transport and catabolism of L-arabinose ( similar to E. coli AraC ) AraC Escherichia coli SP : P03021 Activator of the expression of the araBAD , 292 174 , 238 , 248 , 266 araFGH and araE operons , which are involved in the transport and catabolism of L-arabinose .

+The NarL and NarP proteins are each able to activate expression of the nirB and nrfA operons by interaction with common DNA-binding sites .

+The NarL/NarP protein binding sites required for activation of the nirB and nrfA operons are located further upstream  than that of the aeg-46 .5 operon  .

+Coeffectors of ArgP in yggA regulation .

+The identification of NagC as an activator of fimB expression indicated that the expression of the recombinase would be inhibited by GlcNAc .

+In conclusion , MelR and CRP bind to the melAB promoter co-operatively to adjacent sites in order to activate transcription in a co-dependent manner .

+Like MalE-SoxS , MarA ( i ) activated the transcription of zwf , fpr , fumC , micF , nfo , and sodA ; ( ii ) required a 21-bp '' soxbox '' sequence to activate zwf transcription ; and ( iii ) was '' ambidextrous , '' i. e. , required the C-terminal domain of the a subunit of RNA polymerase for activation of zwf but not fumC or micF .

+Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP ( cAMP ) - cAMP receptor protein complex .

+They demonstrated that acnA has two promoters , P1 and P2 , the latter being regulated by SoxS , FNR , CRP and ArcA .

+This domain alone could activate transcription of araBAD up to 15 % as well as full-length AraC when alone or to the same level as fulllength AraC when fused to an unrelated dimerization domain  .

+We found that Rob ( i ) activates the transcription of zwf , fpr , fumC , micF , nfo , and sodA , ( ii ) requires a 21-bp soxbox-marbox-robbox sequence to activate zwf transcription , ( iii ) protects the soxbox/marbox/robbox from attack by DNase I , ( iv ) is ambidextrous , i. e. , requires the C-terminal domain of the a subunit of RNA polymerase for activation of zwf but not fumC or micF , ( v ) bends zwf and fumC DNA , and ( vi ) binds zwf and fumC DNA as a monomer .

+These indicate that DnaA and IciA proteins independently bind to their respective binding sites on the dnaA # 1996 Blackwell Science Ltd , Molecular Microbiology , 19 , 389 -- 396392 Y. Schematic representation of regulation of araBAD and araC promoters by CAP , P1 , and P2 .

+This work is a first step in studying the mechanism ( s ) by which AraC regulates transcription at the araE promoter , p E , and at p FGH .

+Together with a bioinformatic analysis of other Enterobacteriaceae species , these data identify a conserved AraC regulon that includes 7 previously described AraC-regulated genes ( araB , araA , araD , araE , araF , araG , and araH ) as well as three novel targets identified in this work ( ytfQ , araT , and araU ) .

+The mechanism of transcriptional activation of micF and ompC by OmpR as well as a role of IHF in this activation need to be better understood .

+At the same time , it is noteworthy that two of the genes that are most prominently regulated by ArgP , argO and lysP , are both also regulated by the leucineresponsive general transcriptional regulator Lrp  .

+The Rob homologs MarA and SoxS can activate transcription of a broad range of genes in-vivo  , including sodA , fumC , micF , zwf , and inaA , suggesting broadly overlapping activities of these three regulators .

+ Systematic mutagenesis of the DNA binding sites for SoxS in the zwf and fpr promoters of Escherichia coli : identifying nucleotides required for DNA binding and transcription activation .

+Although a similar arrangement of sites around the transcription initiation regions of other genes of the gal regulon might have suggested that they all are regulated by a similar mechanism to galE  , the results presented in this paper demonstrate that repression of the galP gene , is mediated by a distinctly different nucleoprotein complex involving NagC as well as GalR and GalS and including at least 280 bp of DNA .

+These data clearly indicate that the hcp promoter is activated by FNR and repressed by NsrR .

+Transcriptional repression of the dnaA gene of Escherichia coli by DnaA protein .

+We identified eight genes and confirmed that seven are transcriptionally activated by normal expression of Rob from the chromosomal rob gene ( inaA , marR , aslB , ybaO , mdlA , yfhD , and ybiS ) .

+Thus , the dmsA promoter is repressed by NarL binding to multiple sites spread across 80 bp covering the entire promoter  .

+We conclude that RhaR positively regulates transcription from the promoters pl , p2 and p3 , and that RhaS may regulate p1 and p3 weakly .

+The shaded boxes denote 22 bp DNA sites for CRP : one site centered at position 241.5 is responsible for the activation of the melR promoter , while the other , centered at position 2155.5 is involved in activation of the melAB promoter .

+For example , the galETK operon is regulated by three factors GalR , CAP and the nucleoid-associated protein HU .

+Research Article J Mol Microbiol Biotechnol 2003 ; 6 : 41 -- 56 DOI : 10.1159 / 000073407 Dual Control by Regulators , GntH and GntR , of the GntII Genes for Gluconate Metabolism in Escherichia coli Ryouichi Tsunedomi Hanae Izu Takuya Kawai Mamoru Yamada Department of Biological Chemistry , Faculty of Agriculture , Yamaguchi University , Yamaguchi , Japan Key Words Gluconate metabolism W Gntll W gntR W gntH W Divergent promoter W Expressional regulation Abstract Escherichia coli possesses two systems , GntI and GntII , for gluconate uptake and catabolism , whose genes are regulated by GntR as a repressor and GntH as an activator , respectively .

+Plasmids overproducing either the NagC protein or the Mlc protein repress the expression of manX , but the effect of the Mlc protein is stronger .

+In vitro , ArgP binds the lysP regulatory region with a K d of around 55 nM and the binding affinity is diminished upon the addition of Lys  , suggesting that Lys represses lysP in-vivo by engendering the loss of ArgP binding to the lysP operator region .

+For the nirBDC and nrfABCDEFG operons , Fnr protein , bound near position 41.5 , activates transcription maximally only when phospho-NarL or-NarP protein is bound further upstream to block inhibition by other proteins  .

+These results indicated that ArgP is responsible for the transcriptional activation of lysP in the absence of lysine .

+In our previous study  , we reported that repression of the melR promoter by MelR was unaffected by point mutations in either site 1 or site 1 0 .

+ FNR dependent activation of the class II dmsA and narG promoters of Escherichia coli requires FNR-activating regions 1 and 3 .

+Expression of acrZ is coregulated with acrAB and tolC by the MarA , Rob , and SoxS transcription factors .

+Moreover , a common inverted repeat sequence coincided with the defined here NsrR recognition motif was shown to be involved in NsrR-mediated repression of the ytfE gene .

+At the nirB promoter ( pnirB ) , it has been shown that IHF and Fis drive the promoter DNA into an inhibitory architecture , which represses FNR-dependent transcription .

+An isorepressor , GalS , has also been identified as © 2008 The Authors Journal compilation © 2008 Blackwell Publishing LtdNagC , GalR and GalS repression at galP 147 Fig. 1 .

+Deletion of crp  resulted in a level of expression from each fusion that was similar to the expression from ( rhaS-lacZ ) 90 in the crp strain background , supporting our hypothesis that full rhaSR activation requires CRP .

+This suggests that Fnr and NarP may act synergistically to activate napF operon expression .

+Negative regulation of aeg-46 .5 operon expression by the NarL protein In addition to its function as a transcriptional activator , the NarL protein negatively regulates expression of the frdA , dmsA and nrfA operons in response to nitrate availability .

+Lysine represses transcription of the Escherichia coli dapB gene by preventing its activation by the ArgP activator .

+Our analysis revealed that inaA , marRAB , aslB , ybaO , mdlA , yfhD , and ybiS were transcriptionally activated by constitutive levels of Rob , while galT expression was repressed .

+NarL-phosphate must bind to multiple upstream sites to activate transcription from the narG promoter of Escherichia coli .

+However , narG and frdA operon expression is regulated by the NarL protein alone  , suggesting that the NarL binding sites in these control regions are not efficiently recognized by the NarP protein .

+Furthermore , as NagC binding to O NC1 prevents CRP-dependent activation of nanC  , this study should enhance our understanding of the regulation of this gene as well .

+The Escherichia coli Ada protein can interact with two distinct determinants in the 70 subunit of RNA polymerase according to promoter architecture : identification of the target of Ada activation at the alkA promoter .

+Also , DnaA protein functions as a transcriptional repressor for the expression of other genes including rpoH  , mioC  , the guaBA operon  , and uvrB  , while the expression of the nrd gene appeared to be enhanced by DnaA protein  .

+Transposon mutagenesis experiments aimed at defining the Rob regulon revealed eight Rob-regulated targets , namely inaA , marRAB , aslB , ybaO , mdlA , yfhD , ybiS , and galT  , some of which are also known members of the mar and sox regulons  .

+Results illustrated in Figure 5B show that MelR-dependent repression of the melR promoter is unaffected when CRP binding at this target is prevented .

+Northern blotting analysis indicated that RbsR represses the purHD operon for de novo synthesis of purine nucleotide but activates the add and udk genes involved in the salvage pathway of purine nucleotide synthesis .