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Journal of Bacteriology, May 2006, p. 3175-3181, Vol. 188, No. 9
0021-9193/06/$08.00+0 doi:10.1128/JB.188.9.3175-3181.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
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Thomas J. Silhavy*
Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
Received 7 December 2005/ Accepted 20 February 2006
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In E. coli, LrhA expression decreases the levels of RpoS, thus preventing the accumulation of the sigma factor and the transcription of hundreds of stationary-phase genes (10). There are multiple factors that affect RpoS expression, and they work at every possible level of control, including transcription, translation, protein stability, and activity (26). Many environmental conditions influence rpoS translation, and most of these require the sRNA chaperone Hfq. It has been suggested that LrhA affects RpoS stability by stimulating the activity of SprE (RssB), the adaptor protein for RpoS degradation (6, 10). This was intriguing, since it was one of only a few factors affecting SprE activity, whose regulation is the sole mechanism for RpoS accumulation upon carbon starvation (24, 27, 36). Similar models involving LrhA and SprE homologs in E. carotovora and Photorhabdus temperata have been invoked but never tested (14, 25).
Another global regulator of RpoS and flagellar synthesis is the RcsCDB system. This phosphorelay consists of a membrane-bound sensor kinase (RcsC), a phosphorelay protein (RcsD), and a response regulator (RcsB) with an auxiliary protein (RcsA) (22). Although it was first characterized for its role in capsule synthesis, many additional genes in its regulon overlap those found in the RpoS regulon, including katE, osmC, osmB, and ftsZ (11, 22). Moreover, this regulatory system activates RpoS translation in a manner that partially requires the sRNA (noncoding RNA) RprA (20, 23). Most of the genes known to be controlled by Rcs are activated by this system, the only case of repression being the flhDC master regulator (9). The actual signals triggering RcsC are not known, but disruptions in the cell surface, such as loss of lipopolysaccharides or periplasmic glucans, activate the system (22).
In this paper, we show that LrhA represses rpoS translation by a mechanism that requires the sRNA chaperone Hfq. In addition, we identify a signaling mechanism that controls lrhA expression. In particular, we demonstrate that lrhA synthesis is repressed by the RcsCDB phosphorelay system.
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TABLE 1. Strains used in this study
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Media and growth conditions. Lactose MacConkey agar and Luria-Bertani (LB) broth and agar were prepared as described previously (31). Bacteria were grown at 37°C unless otherwise noted.
Western blot analysis.
One-milliliter samples were prepared from exponentially growing cells (optical density at 600 nm [OD600]
0.4 to 0.5). Whole cells were pelleted and immediately resuspended in sodium dodecyl sulfate (SDS) loading buffer (31) in a volume equal to OD600/10. After boiling for 10 min, equal volumes were loaded onto 12% SDS-polyacrylamide gels (17). After electrophoresis, proteins were transferred onto nitrocellulose membranes and probed with a 1:6,000 dilution of anti-RpoS antibody (our laboratory stock). For secondary antibody, donkey anti-rabbit immunoglobulin G-horseradish peroxidase conjugate (Amersham Pharmacia Biotech) was used at a dilution of 1:6,000. The bands were detected using the ECL antibody detection kit (Amersham Pharmacia Biotech) and XAR film (Kodak).
ß-Galactosidase assays. Cultures of strains grown in LB overnight were subcultured 1:100 into fresh LB broth and grown with aeration at 37°C until the OD600 was 0.4 to 0.5. ß-Galactosidase assays were performed as previously described (32) Relative ß-galactosidase units were determined by the rate (in OD420 units per minute) divided by the OD600 times the volume assayed (in milliliters). Each figure depicts an individual experiment, and all experiments were repeated at least three times.
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The lrhA49::cam allele has an inserted transposon located 571 base pairs upstream from the lrhA start codon and causes lrhA transcription to be upregulated (10). This overexpression of lrhA causes RpoS levels to decrease compared to an otherwise isogenic wild-type strain (10). Conversely, a strain carrying lrhA::spc, a null allele of lrhA, has only slightly increased RpoS levels (10).
To examine whether LrhA affects RpoS levels solely by activating the degradation pathway, we tested whether there was any phenotype with these lrhA alleles in a background in which RpoS is not degraded. In the sprE::tet background, which abolishes RpoS degradation but has no effect on its translation (27), RpoS levels were decreased in the presence of the lrhA49::cam allele (Fig. 1, compare lanes 1 and 2). RpoS levels were marginally higher with the lrhA::spc allele than with lrhA+ (Fig. 1, lanes 1 and 3). Likewise, in the clpX::kan background, RpoS levels were lower in cells carrying the lrhA49::cam allele and slightly higher in lrhA::spc cells than in wild-type lrhA cells (Fig. 1, lanes 4, 5, and 6). Thus, the effect of LrhA on RpoS is not disrupted by the absence of RpoS degradation. This indicates that LrhA affects RpoS levels in a manner that is independent of protein stability.
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FIG. 1. Western blotting for RpoS shows that lrhA mutations are additive with mutations in sprE and clpX. The lrhA49::cam allele contains a transposon inserted in the chromosome upstream of the lrhA promoter, which causes LrhA levels to increase and RpoS levels to decrease (6, 10). The lrhA::spc allele is a null mutation that has been shown to slightly increase RpoS levels. Lanes 1 to 3 (CNP58, CNP110, and CNP112, respectively) show the effect of the lrhA mutations in the absence of the RpoS degradation adaptor protein SprE, and lanes 4 to 6 (CNP115, CNP113, and CNP114, respectively) show the effect in the absence of the RpoS protease chaperone ClpX. Removing either sprE or clpX has no effect on RpoS translation (29). All Western blot samples were collected from cells growing exponentially in LB medium.
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FIG. 2. LrhA represses rpoS translation. (A) The rpoS'-lacZ+ operon fusion (CNP118) reports only rpoS transcription. The lrhA alleles found in CNP120 and CNP121 have a negligible influence on this transcriptional fusion. (B) The rpoS477'-'lacZ (CNP125) reports rpoS translation and transcription but does not affect RpoS stability. The lrhA49::cam allele (CNP127) strongly represses this fusion, whereas the lrhA::spc allele (CNP128) does not have a strong effect. Samples were collected from cells growing logarithmically in LB medium and processed for ß-galactosidase assays as described in Materials and Methods.
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FIG. 3. The sRNA chaperone Hfq is necessary for LrhA repression of rpoS translation. In the hfq::kan background, the lrhA49::cam allele (CNP213) did not reduce RpoS levels compared to those found in the lrhA+ background (CNP215), as determined by Western blotting. However, the lrhA::spc allele (CNP214) still had a positive effect on RpoS levels. A sprE::tet background was used for these experiments to increase the overall levels of RpoS, since the hfq mutation has a negative effect on RpoS synthesis and lowers its levels to below the detection threshold in wild-type cells. All samples were collected from cells growing exponentially in LB rich medium.
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FIG. 4. (A) LrhA represses rprA synthesis. The overexpression allele of lrhA (lrhA49::cam) in CNP267 reduces rprA'-lacZ ß-galactosidase activity compared to the lrhA+ allele in CNP170. The null allele of lrhA (lrhA::spc) in CNP268 does not have a large effect on rprA'-lacZ+ ß-galactosidase activity. (B) Epistasis tests with LrhA and RprA. The lrhA49::cam allele still reduces rpoS'-'lacZ activity compared to the lrhA+ allele in the rprA::kan background (CNP166 and CNP205). Thus, LrhA represses RpoS in an RprA-independent fashion. All samples were collected from exponentially growing cells in LB medium.
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dsrA background (data not shown), where the RprA effect on RpoS levels is more pronounced (20). In summary, LrhA represses RprA translation threefold. Although this may contribute to the reduction of RpoS levels under certain conditions, our data indicate that LrhA mostly controls rpoS translation in an RprA-independent fashion. RcsCDB decreases synthesis of LrhA. To better understand the signals to which LrhA responds, we sought to identify genes that affect its synthesis and activity. To this end, we performed a minitransposon mutagenesis screen in a strain carrying an lrhA'-'lacZ fusion. LysR regulators, such as LrhA, often bind ligands which regulate their activity (30). Since LrhA regulates itself (10, 18), our transposon mutagenesis screen in the lrhA'-'lacZ fusion strain could identify genes that regulated either LrhA activity or its expression, and knowledge of such factors could provide insight into the nature of the signals sensed by LrhA. Over 26,000 transposon-mutated colonies were screened for changes in LacZ activity on both X-Gal (5-bromo-4-chloro-3-indolyl-ß-D-galactopyranoside) LB agar and lactose MacConkey agar, and linkage to the transposon was confirmed using standard techniques.
An insertion in the rcsD (yojN) gene that decreased the LacZ activity of the lrhA'-'lacZ fusion was identified. RcsD is a member of the Rcs system which responds to cell envelope stress. It is a phosphorelay protein, and upon activation of the system, it phosphorylates the response regulator RcsB, which, in turn, directs synthesis of capsule and other gene products (22). RcsD also has a phosphatase activity; therefore, rcsD null mutants have increased levels of phosphorylated RcsB, since this protein can be phosphorylated by small-molecule donors (22).
ß-Galactosidase assays were performed on samples taken from exponentially growing cultures of the wild type and the rcsD::cam mutant. The rcsD::cam insertion decreased the lrhA'-'lacZ fusion activity fivefold (Fig. 5A). To confirm that the rcsD mutation affected lrhA synthesis through the Rcs pathway, a mutation was introduced in rcsB. Without RcsB, rcsD::cam did not repress lrhA expression (Fig. 5A). Both the double mutant and an rcsB::kan single mutant had only a very modest and insignificant increase in lrhA synthesis compared to wild-type strains (Fig. 5A). Thus, we predict that the phosphorylated form of RcsB, which accumulates in the rcsD mutant, negatively regulates the lrhA'-'lacZ fusion.
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FIG. 5. The Rcs phosphorelay represses lrhA synthesis. (A) ß-Galactosidase assays show that the rcsD::cam mutant found in our screen decreases lrhA'-'lacZ expression fivefold (TC15 and TC132). This repression is abolished in an rcsB rcsD double mutant (CNP265), while the single mutation rcsB (CNP264) does not have a strong phenotype. (B) RcsD represses LrhA synthesis rather than affecting LrhA activity. In the absence of wild-type LrhA (TC18), synthesis of lrhA'-'lacZ is still affected by a mutation in rcsD (VC16). The lower levels of lrhA'-'lacZ activity in the lrhA::spc strain (TC18 compared to TC15) confirm that LrhA positively autoregulates itself (18). All samples were taken from exponentially growing cells and processed as described in Materials and Methods.
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15%) in lrhA synthesis (data not shown). Thus, RcsA does not contribute to repression of lrhA. To see if the rcsD mutation affects LrhA activity or synthesis, we tested if rcsD::cam still had an effect on the activity of the lrhA'-'lacZ fusion in the absence of LrhA. If it affected LrhA activity, then it would have no influence on the fusion in cells lacking LrhA. Replacing wild-type lrhA with the null allele caused lrhA'-'lacZ fusion activity to decrease (Fig. 5B). There have been conflicting reports on the nature of the LrhA autoregulation (10, 18), and these results confirm that LrhA a has positive feedback loop. The rcsD mutant affected lrhA'-'lacZ in both the wild-type and the lrhA::spc backgrounds. Therefore, the Rcs pathway represses lrhA synthesis rather than LrhA activity.
FtsK reduces synthesis of lrhA. Another transposon insertion found in the screen for mutations affecting expression of the lrhA'-'lacZ fusion was in the ftsK gene, which encodes a protein involved in DNA translocation. Mutants that contained disruptions of this gene showed an increase of lrhA'-'lacZ activity compared to otherwise wild-type strains (Fig. 6A). To test if this mutation affected LrhA activity or synthesis, ß-galactosidase assays were performed with a strain containing both the ftsK::tet and lrhA::spc alleles. Despite the absence of LrhA, there was still an increase in lrhA'-'lacZ levels in the ftsK mutant compared to those in the wild type. This suggests that FstK decreases LrhA levels by decreasing its synthesis.
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FIG. 6. A mutation in ftsK increases lrhA expression. (A) ß-Galactosidase assays show that the ftsK::tet mutant found in our screen stimulates lrhA'-'lacZ expression (TC46 compared to TC15). This effect persists in the lrhA::spc background (VC4 compared to TC18), indicating that the mutation affects lrhA expression rather than LrhA activity. (B) The ftsK effect on RpoS levels requires wild-type LrhA. It had previously been shown that ftsK mutants reduce RpoS levels owing to posttranscription control (7). In this Western blot, the double mutant with ftsK::tet and lrhA::spc alleles (VC4) does not have any attenuation of RpoS levels in stationary phase.
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Many environmental stresses affecting RpoS do so at the level of translation. LrhA also regulates rpoS translation and appears to be involved in the cell's response to membrane perturbations through the Rcs system. Control of rpoS translation frequently includes one or more sRNAs, and we think that the LrhA pathway is no exception. LrhA represses synthesis of the sRNA RprA and most likely affects another sRNA(s) as well. It is likely that there are multiple sRNAs that regulate RpoS in addition to those already characterized. Finding the other sRNAs can be difficult in genetic screens because they are sometimes highly redundant (19) and because they are small targets for transposons. Note that in the hfq mutant the effect of lrhA overexpression was abolished but that of the lrhA null allele persisted. Accordingly, we speculate that LrhA may repress a positively regulating sRNA in addition to RprA. In the absence of LrhA, the concentration of this sRNA would increase to a level where it could affect RpoS without the aid of Hfq. There are several examples of similar sRNAs which can affect their target mRNAs without Hfq if they are overexpressed (29, 33).
Activation of the Rcs pathway represses LrhA which, in turn, increases rpoS translation. Whether the RcsB effect on LrhA is direct or indirect is not yet apparent. It has previously been reported that stimulation of the Rcs pathway activates RpoS expression, in a manner that was partly dependent on RprA. An additional three- to fivefold induction of RpoS by the Rcs system occurred independently of RprA (23). We believe that the RprA-independent activation of RpoS by the Rcs system involves the LrhA pathway (Fig. 7).
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FIG. 7. Model of how LrhA and the Rcs phosphorelay affect RpoS translation. LrhA represses the sRNA RprA, which is an activator of RpoS translation. LrhA also regulates RpoS translation in an RprA-independent manner by an unidentified sRNA(s), which could act either positively or negatively, as indicated by heavy lines. This additional mechanism accounts for most of the effect of LrhA on RpoS translation in exponentially growing cells in LB. The Rcs system represses LrhA synthesis, and tests of epistasis demonstrate that the effect of LrhA on RpoS is independent of RcsB (data not shown). Thus, Rcs can activate RpoS translation in at least two ways: by directly stimulating RprA and by repressing LrhA synthesis.
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T.J.S. was supported by a grant from NIGMS (GM065216).
Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02319. ![]()
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S level in starving Escherichia coli cells increases solely as a result of its increased stability, despite decreased synthesis. Mol. Microbiol. 24:643-651.[CrossRef][Medline]This article has been cited by other articles:
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