A transcriptional silencer downstream of the promoter in the osmotically controlled proU operon of Salmonella typhimurium ABSTRACT The proU operon of Salmonella typhimurium is induced by conditions of high osmolalit .
The cis-acting sequences that mediate osmotic control of transcription were characterized by deletion analysis .
The nucleotide sequence between -60 and +274 ( relative to the transcription start point ) is sufficient for normal osmotic control .
Deletions that removed sequences upstream of position +274 but left the promoter intact resulted in greatly increased expression from the proU promoter in the absence of osmotic-stress .
Thus , the transcription control region of the proU operon consists of two discrete components : ( i ) the promoter and ( it ) a negatively acting site that overlaps the coding sequence of the first structural gene of the operon , proV .
That this negative regulatory element is a transcriptional terminator or mRNA processing site was ruled out .
Our results suggest that the negative regulatory element behaves as a transcriptional silencer that inhibits transcription initiation at the proU promoter in me-dium of low osmolality by some action at a distance .
We propose several possible mechanisms for the function of this regulatory site .
Organisms generally respond to increases in the osmolality of their environment by elevating the intracellular concentrations of a few species of low-molecular-weight compounds , which regulate osmolality of the cells ( 1 ) .
In bacteria , proline and glycine betaine are two of the prominent solutes at high concentrations under conditions of osmotic-stress .
In Sal-monella typhimurium and Escherichia coli , these two compounds are accumulated in medium of high osmolality via two permeases , the constitutive ProP system and the osmotically inducible ProU system ( 1 ) .
The proteins of the latter system are encoded in the proV , proW , and proX genes , which make up the proU operon ( 2 , 3 ) .
Transcription of this operon is increased > 100-fold by conditions of high osmolality ( 1 ) .
Previously , we found that the proU promoter of S. typhi-murium was expressed at a very high , unregulated level from a fragment that contained 320 nucleotides upstream and 32 nucleotides downstream of the transcription start site ( 4 ) .
This result indicated that the proU operon is under negative control that operates at site ( s ) located outside of this region .
Here we show that an important transcriptional regulatory element is located downstream from the proU promoter , within the first structural gene of the operon .
MATERIALS AND METHODS Recombinant DNA Manipulations .
Recombinant DNA procedures and nuclease S1 analysis of mRNAs were done as described ( 4 ) .
The low-copy lac expression vector pDO182 ( Fig. 1 ) consists of a 4.0-kilobase-pair ( kbp ) Pst I-EcoRI fragment from pHJS21 ( 6 ) , carrying a gene for spectinomycin resistance and the pSC101 origin of replication , an EcoRI-HindIII-BamHI linker ( 5 ' - GAATTCCCGAAGCTTCGGG - The publication costs of this article were defrayed in part by page charge payment .
This article must therefore be hereby marked `` advertisement '' in accordance with 18 U.S.C. § 1734 solely to indicate this fact .
GATCC-3 ' ) , and a 6.3-kbp BamHI-Sal I fragment from pRS415 ( 7 ) , which carries the promoterless lacZYA operon ; the Pst I site derived from pHJS21 and the Sal I site from pRS415 were converted to blunt ends and ligated together .
Plasmid pTAT13 34-1 contains , in the following order : the tacll promoter , the phoA ' gene , Xba I , Sac I , Stu I , and Bgl II cloning sites , and the lacZ gene ; it is similar to pTAT7 ( 8 ) , except for the cloning sites between the phoA and lacZ genes ( N. Franklin , personal communication ) .
According to the usual convention , the nucleotide of the proU operon that specifies the start site of the major species of proU mRNA is designated as + 1 , with nucleotides downstream of this position being denoted by positive numbers and nucleotides upstream denoted by negative numbers .
This notation a change from our previous numbering represents ( 4 ) : the nucleotide position previously designated as 596 is now referred to as + 1 .
This start point for transcription of the proU operon agrees well with that determined by others ( 3 , 9 , 10 ) .
The translation start site of the proV gene is at position +65 .
The cloned proU promoter region we used had been derived from an S. typhimurium strain carrying the proU1872 : : Mud-1 insertion ( 4 ) .
Because of the long inverted repeat within the right ( lac ) end of the phage ( 5 ) , we were unable to unequivocally determine the exact site of the proU1872 : : Mud-l insertion .
According to our best estimate , this insertion is approximately at position + 1170 of the proU operon and will be denoted position + 1.2 kbp hereafter .
All of the proU promoter fragments were analyzed on both the pSC101-derived pDO182 and the ColEl-derived pRS415 lac expression vectors .
We obtained consistent results with the two sets of plasmids and therefore , we present only the data for the low-copy , pDO182-based plasmids .
Details of the construction of the plasmids used for deletion analysis of the proU transcriptional control region are as described ( 11 ) ; here we present only the main features of the plasmids .
Deletions upstream ( 5 ' ) or downstream ( 3 ' ) of the proU promoter were generated by exonuclease Bal-31 digestion .
The upstream deletions originated from a HindIII site located at position -595 ; the ends generated were ligated to HindIII or EcoRI linkers , and the proU fragments were placed upstream of the lacZ gene in pDO182 ( Fig. 1 ) .
The downstream deletions originated from an Sst II site at position + 308 ; the ends were ligated to HindIII orBamHI linkers , and the proU promoter fragments were inserted into pDO182 ( Fig. 2 ) .
The precise endpoints of the 5 ' and 3 ' deletions were established by sequence determination .
Plasmid pDO244 carries proU sequences from position -320 to position +274 , but with a BamHI linker ( 5 ' - GGGGGATCCGGCGC-17-bp CCC-3 ' ) inserted into a Taq I site , between positions +31 and +32 ( Fig. 2 ) .
Abbreviations : IPTG , isopropyl f3-D-thiogalactoside ; kilobase pairs ( kbp ) .
* Present address : Department of Biochemistry , A-312 College of Medicine West , The University of Illinois at Chicago , IL 60612 .
tTo whom reprint requests should be addressed .
RESULTS The proU Transcriptional Control Region Is Between Nucleotide Positions -60 and +274 .
On plasmid pDO185 , which carries proU sequences from -595 to +1.2 kbp , the proU promoter was induced 90-fold by 0.5 M NaCl ( Fig. 1 ) .
Nucleotides upstream of position -60 are dispensable for the transcriptional control of the proU operon because on plasmids pDO186 , pDO187 , pDO188 , pDO190 , and pDO191 the deletion of the sequences between positions -595 and -60 , did not substantially affect osmotic induction ( Fig. 1 ) .
There was a marked decrease in expression of the reporter lacZ gene upon deletion of the region normally present upstream of position -34 ( plasmid pDO193 ) ; this deletion could have removed part of the -35 sequence of the promoter or some other positively acting control site .
The proU promoter on a fragment that carries sequences from positions -508 to +308 ( pDO178 ) was induced 130-fold fragments , including the one carrying positions -320 to +32 ( pDO208 ) , the proU promoter exhibited a residual induction by high osmolality ( Fig. 2 ) .
Therefore , other sequences near or upstream of the promoter may participate in the osmotic control .
Conceivably , the deletions that resulted in increased constitutive expression of the lacZ gene may have generated or unmasked a new promoter .
To test this , we determined by nuclease S1-mapping the transcription start sites of proU mRNAs synthesized in-vivo from three plasmids carrying proU inserts from -508 to +48 , from -60 to + 117 , and from -320 to +32 .
With all three plasmids , the constitutively synthesized proU mRNAs were initiated at the correct transcription start point of the proU operon ( data not shown ) .
To test whether the downstream regulatory site in the proU operon has a trans-acting function , we introduced plasmids carrying various combinations of the proU promoter and the downstream regulatory element into a strain that harbored a chromosomal proU : : TnphoA fusion .
The presence or absence of the downstream regulatory site on the plasmids had no effect on the osmotic control of expression of the chromosomal pro U : : TnphoA fusion ( data not shown ) , indicating that the regulatory element acts only in cis to modulate expression of the proU promoter .
A 17-bp Insertion Between the Promoter and the Downstream Regulatory Site Does Not Abolish Osmotic Regulation .
Plasmid pDO244 carries a 17-bp insertion between proU positions +31 and +32 , but nevertheless the proU promoter on this plasmid exhibited nearly normal osmotic control ( Fig. 2 ) .
Therefore , a 17-bp increase in the distance and an -220 ° change in the phasing angle between the promoter and the regulatory site can be tolerated for the osmotic control of proU operon expression .
The Downstream Regulatory Site Is Not a General Transcription Terminator .
Transcriptional control at sites downstream of the promoter could entail environmentally regulated termination or pausing oftranscription or degradation of mRNA .
To ascertain whether such mechanisms function in the proU operon , we used nuclease S1 to determine whether a promoter-proximal part of the proU mRNA is synthesized constitutively in cells grown in medium of low osmolality .
The probe carriedproU sequences from -57 to +137 and was labeled at the 5 ' end of the strand complementary to the proU mRNA ; although we could detect a protected fragment of 137 nucleotides in length with RNA isolated from wild-type cells grown under high-osmolality conditions , we were unable to resolve a protected fragment with RNA isolated from cells grown in low osmolality ( data not shown ) .
This result , whic agrees with the primer-extension analysis of Stirling et al. ( 10 ) , indicates that not even a 5 ' portion of the proU mRNA is synthesized in the low-osmolality medium , and therefore the proU operon is probably regulated at the level of transcription initiation .
However , it is possible that we were unable to detect a short , terminated proU mRNA because of its rapid turnover .
We conducted a second experiment to test the possibility that the downstream regulatory element in the proU operon is an osmotically regulated transcriptional polarity site .
We placed this element between the tac promoter and the IacZ gene on the transcription termination assay vector pTAT13 34-1 and determined whether it would confer osmotic regulation on transcription originating at the tac promoter ( Fig. 3 ) .
In low osmolality without isopropyl P-D-thiogalactoside ( IPTG ) , the ( 3-galactosidase specific activity obtained with plasmid pDO223 ( proU insert : -60 to +274 ) was 19-fold lower than with plasmid pDO225 ( proU insert : -60 to +95 ) .
This result , which was obtained with high-copy , ColEl-based plasmids , corroborates our conclusion that there is a negative regulatory element downstream of the proU promoter .
This regulatory element , however , had < 2.5-fold effect on the IPTG-inducible transcription of the lacZ gene from the tac promoter ( Fig. 3 ; compare the ( 3-galactosidase activity obtained with plasmid pDO225 with that obtained with plasmids pDO223 , pDO229 , and pDO227 in the medium of low osmolality plus IPTG ) .
Thus , the negative regulatory element does not function as a general transcriptional polarity site .
DISCUSSION We found a negative regulatory element in the proU operon of S. typhimurium , downstream of the promoter , between positions +33 and + 274 .
As the translation start site of the proV gene is at position +65 , osmotic regulation of proU operon expression could entail some form of translational control .
This hypothesis can be ruled out because increased basal expression of the proU operon occurred with deletions that did not excise the translation start site of the proV gene and with deletions that removed it .
Moreover , the lacZ gene on plasmids pDO182 and pTAT13 34-1 has its own translation start site ( 7 , 8 ) and , at least for pDO182 , is preceded by nonsense codons in all three reading frames ( 7 ) .
Lucht and Bremer ( 9 ) reported the isolation of an IS1 insertion into the proU promoter of E. coli that generated a new promoter with a -35 sequence from the IS1 and the -10 sequence of proU .
Although the hybrid promoter was expressed at a much lower level than the proU promoter , it still responded to osmotic control with almost normal induction ratio .
This result supports our inference that the osmotic control of the proU operon is mediated at sites downstream of the promoter and , combined with our observations , suggests that the -35 element of the proU promoter and sequences upstream from it are not crucial for proper osmotic regulation .
Genetic control at the mRNA level could be exerted at four points : ( i ) initiation , ( ii ) elongation , ( iii ) termination of transcription , or ( iv ) mRNA degradation .
That the downstream regulatory element did not diminish transcriptional efficiency of the tac promoter ( Fig. 3 ) indicates that the downstream regulatory element is not a generalized transcription termination or pausing site or the target for mRNA degradation .
However , sequences adjacent to promoters can modulate the ability of RNA polymerase to read-through various terminators ( 13-15 ) , and therefore the downstream regulatory element might be an osmotically controlled transcriptional terminator that is recognized only by transcription complexes emanating from the proU promoter .
Although we can not completely rule out this possibility , the failure to detect any synthesis of the 5 ' end of the proU mRNA in cells grown in low osmolality by S1-nuclease-mapping ( see above ) and primer-extension ( 10 ) provides some evidence against it .
Furthermore , there is no apparent terminator structure in the + 1 to +274 region of the proU operon .
For these reasons , it is more likely that the downstream regulatory site is a transcriptional silencer that controls transcription initiation by some action at a distance .
Examples for this mode of transcriptional regulation exist in both eukaryotes ( 16-18 ) and prokaryotes ( 19-21 ) .
The gal operon of E. coli is tranfrom scribed two promoters which are flanked by a pair of binding sites for the repressor proteins ( 19 ) .
Repressor protein complexes bound to these sites also bind each other and form a DNA loop , which blocks productive transcription by some unknown mechanism .
Every bacterial operon that has a negatively acting site downstream of the promoter thus far described also contains a second binding site upstream of the promoter , with the repression being effected by a DNA loop formed by multimers of a single species of protein ( 21 ) .
However , the -60 to +274 nucleotide region of the proU operon does not contain an obvious tandemly repeated sequence of sufficient length to suggest this type of mechanism for the proU operon .
It is possible though , that a DNA loop could be held together by heterologous proteins bound to two different sequences or by a single protein that can bind to two different sequences on the DNA , as seen with the Int protein of phage A ( 22 ) .
However , other repression mechanisms could be envisioned in which the regulatory protein binds to only one site on the DNA and transmits the regulatory signal to the promoter by some means other than a DNA loop .
The regulatory site downstream of the promoter could be the binding site for a protein that influences some threedimensional feature of the promoter , such as supercoiling or conversion to the Z-DNA structure .
In this model , the proU promoter would be inherently a strong promoter , but in medium of low osmolality it would be incapacitated because of the action of a protein at the downstream regulatory site .
It is also conceivable that the downstream regulatory site could be the binding site for a scaffold protein that under conditions of low osmolality wraps neighboring DNA into a nucleosome-like structure and buries the promoter , as proposed for transcriptional control by chromatin in eukaryotes ( 23 ) .
The osmotic control of transcription of the proU operon is not disrupted by a 17-bp insertion between the proU promoter and the downstream regulatory element , but the downstream regulatory element can not act on the tac promoter at a distance of 1.8 kbp ( Fig. 3 ) .
The pleiotropic OsmZ ( Hns ) DNA-binding protein , which is required for full repression of the proU operon in low osmolality ( 24 ) , may be part of the regulatory apparatus that acts at the downstream regulatory site .
To distinguish among possible models , it will be important to determine whether there are any constraints on the relative order , distance , or phasing of the proU promoter and the downstream element for proper osmotic control of transcription .
Also , it will be important to identify the regulatory protein ( s ) acting at the downstream regulatory site .
During the review of this manuscript , Dattanada et al. ( 25 ) also reported a negative regulatory site within the transcribed region of the proU operon of E. coli .
We thank Drs. N. Franklin and C. Turnbough for stimulating discussions ; Dr. N. Franklin for plasmid pTAT13 34-1 before its publication ; and Drs. V. DiRita , S. Gelvin , J. Hamer , and S. Kustu for helpful comments on the manuscript .
This work was supported by the U.S. Public Health Service Grant R01-GM3194401 .
Csonka , L. N. & Hanson , A. D. ( 1991 ) Annu .
Dattanada , C. S. & Gowrishankar , J. ( 1989 ) J. Bacteriol .
Gowrishankar , J. ( 1989 ) J. Bacteriol .
Overdier , D. G. , Olson , E. R. , Erickson , B. D. , Ederer , M. M. & Csonka , L. N. ( 1989 ) J. Bacteriol .
Metcalf , W. W. , Steed , P. M. & Wanner , B. L. ( 1990 ) J. Bacteriol .
Schreier , H. J. , Brown , S. W. , Hirshi , H. D. , Nomellini , J. F. & Sonenshein , A. L. ( 1989 ) J. Mol .
Simons , R. W. , Houman , F. & Kleckner , N. ( 1987 ) Gene 53 , 85-96 .
Franklin , N. C. ( 1989 ) Plasmid 21 , 31-42 .
Lucht , J. & Bremer , ( 1991 ) J. 10 .
Stirling , D. A. , Hulton , C. S. J. , Waddell , L. , Park , S. F. , Stewart , G. S. A. B. , Booth , I. R. & Higgins , C. F. ( 1989 ) Mol .
Overdier , D. G. ( 1990 ) Ph.D. thesis ( Purdue Univ. , West Lafayette , IN ) .
Brickman , E. & Beckwith , J. ( 1975 ) J. Mol .
Telesnitsky , A. P. W. & Chamberlin , M. J. ( 1989 ) J. Mol .
Goliger , J. A. , Yang , X. , Guo , H.-C .
& Roberts , J. W. ( 1989 ) J. Mol .
Holben , W. E. & Morgan , E. A. ( 1984 ) Proc .
Licht , J. D. , Grossel , M. J. , Figge , J. & Hansen , U. M. ( 1990 ) Nature ( London ) 346 , 76-79 .
Brand , A. H. , Breeden , L. , Abraham , J. , Sternglanz , R. & K. Nasmyth , ( 1985 ) Cell 41 , 41-48 .
Levine , M. & Manley , J. L. ( 1989 ) Cell 59 , 405-408 .
Huo , L. , Martin , K. J. & Schleif , R. ( 1988 ) Proc .
Gralla , J. D. ( 1989 ) Cell 57 , 193-195 .
Moitoso de Vargas , L. , Kim , S. & Landy , A. ( 1989 ) Science 244 , 1457-1461 .
Pederson , D. S. , Thoma , F. & Simpson , R. T. ( 1986 ) Annu .
Hulton , C. S. J. , Seirafi , A. , Hinton , J. C. D. , Sidebotham , J. M. , Waddell , L. , Pavitt , G. D. , Owen-Hughes , T. , Spassky , A. , Buc , H. & Higgins , C. F. ( 1990 ) Cell 63 , 631-642 .
Dattanada , C. S. , Rajkumari , K. & Gowrishankar , J. ( 1991 ) J. Bacteriol .