INTRODUCTION
The Csr (carbon storage regulator) or Rsm (repressor of stationary-phase metabolites) system is a widely conserved bacterial posttranscriptional regulatory system (
1–3). Its components, their functions, and the mechanisms by which the central regulator of this system, CsrA or RsmA, affects gene expression have been studied primarily in
Gammaproteobacteria (
4–6). The sequence-specific RNA binding protein CsrA regulates translation, stability, and/or transcription or elongation of numerous target mRNAs. CsrA regulates the expression of genes involved in lifestyle transitions. In
Escherichia coli, CsrA activates glycolysis and central carbon pathways (
7–13) and motility (
14,
15). Conversely, it represses gluconeogenesis (
7), glycogen biosynthesis (
16–20), biofilm formation (
21–24), the stringent response (
25), and expression of genes involved in other stress resistance and stationary-phase processes, e.g.,
cstA,
hfq,
cel,
sdiA, and
nhaR (
24,
26–30). Its effects on pathogenesis are complex. For example, CsrA both positively and negatively affects expression of enteropathogenic
E. coli (EPEC) pathogenicity island genes (
31,
32). CsrA was found to copurify with over 700 different mRNAs in
E. coli K-12 (
25) and to affect the expression of hundreds of genes (
33).
Consistent with its extensive regulatory role, CsrA activity is tightly controlled. In
E. coli,
csrA is transcribed from five promoters using two different sigma factors (
34). Furthermore, CsrA directly represses its own translation while indirectly activating its transcription (
34). CsrA activity is antagonized by the noncoding small RNAs (sRNAs) CsrB and CsrC, which contain multiple CsrA binding sites that allow them to sequester this protein (
35,
36). Fluctuations in the levels of these RNAs regulate CsrA activity in response to the environment. Transcription of both
csrB and
csrC (
csrB/
C) is activated by the BarA-UvrY two-component signal transduction system (TCS) in response to carboxylic acids such as formate and acetate (
3,
36–41). CsrA indirectly activates transcription of CsrB and CsrC through its effects on BarA-UvrY, creating a negative-feedback loop within the Csr circuitry (
37,
38,
42). CsrB/C turnover requires the GGDEF-EAL domain protein CsrD, which is necessary for cleavage by RNase E and turnover (
42,
43). Therefore, CsrD affects the expression of CsrA-regulated genes and processes. Recent studies showed that glucose availability activates CsrB/C decay. The unphosphorylated form of EIIA
Glc of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS), which predominates during glucose transport, binds to the EAL domain of CsrD (
44). We previously proposed a model for the influence of carbon nutrition on the workings of the Csr system based on these observations. The elimination of a preferred carbon source and the buildup of carboxylic acid products of metabolism together facilitate CsrB/C sRNA accumulation, inhibit CsrA activity, and promote the physiological switch from the exponential phase to the stationary phase of growth and a stress-resistant phenotype (
43,
44).
Noteworthy among the many
E. coli mRNAs that copurified with CsrA were transcripts for global regulatory factors such as
relA and
dksA of the stringent response system and
crp and
cyaA of the catabolite repression system (
25). Reciprocal regulatory interactions between the Csr and stringent response systems permit the Csr system to posttranscriptionally reinforce the transcriptional effects of DksA and (p)ppGpp on the expression of genes that are coregulated by these systems (
25). Details of the interactions between the Csr and catabolite repression regulatory systems were not previously determined and are the subject of the present study.
The genes
crp and
cyaA encode the cyclic AMP (cAMP) receptor protein (CRP) and the enzyme that synthesizes cAMP, adenylate cyclase, respectively. The cAMP-CRP complex regulates transcription in response to the availability of a preferred carbon source, e.g., glucose (
45–47). Under conditions of carbon limitation, the PTS proteins, including the glucose-specific protein EIIA
Glc, are predominantly phosphorylated. In this form, P-EIIA
Glc binds to adenylate cyclase and activates cAMP synthesis (
48). Transport and phosphorylation of glucose or other PTS sugars leads to dephosphorylation of EIIA
Glc and loss of its ability to activate cAMP synthesis. The cAMP-CRP complex mediates hierarchical utilization of nonpreferred carbon sources, referred to as carbon catabolite repression (CCR), by activating the expression of genes required for the transport and utilization of alternative carbon sources (
49). cAMP-CRP also influences the expression of genes not directly involved in carbon metabolism such as those encoding ribosomal proteins, tRNAs, amino acid biosynthesis enzymes, heat shock proteins, sRNAs, and perhaps as many as 70 transcription factors (
45–47,
50–55). cAMP levels and cAMP-CRP regulatory functions have been suggested to respond to both the carbon status and the nitrogen status of the cell, leading to reorganization of the proteome (
56).
cAMP-CRP is a bifunctional protein that can activate or repress transcription (
57). As a transcriptional activator, cAMP-CRP binds to a sequence located upstream from (class I activation) or close to (class II activation) promoter DNA and participates in protein-protein interactions leading to transcription initiation by RNA polymerase (
58). Activation using CRP binding sites positioned farther upstream from the promoter requires cAMP-CRP to work in conjunction with other regulatory proteins and may involve protein-protein interactions and/or DNA bending. DNA binding mechanisms similar to those observed in activation are employed when cAMP-CRP acts as a repressor (
57).
Bioinformatics analysis for potential cAMP-CRP binding sites in the
E. coli genome identified the coding region of
syd, the gene immediately upstream from
csrB, as a possible target (
47). In addition, an online tool (Virtual Footprint [
www.prodoric.de/vfp]) for predicting the binding sequences of regulatory proteins identified potential CRP binding sites in
csrB,
csrC,
csrA,
csrD, and
uvrY. Also, possible reciprocal regulatory interactions between cAMP-CRP and the Csr system prompted us to undertake the present study. We provide evidence that cAMP-CRP inhibits the transcription of
csrC directly and that of
csrB indirectly, while CsrA modestly and conditionally activates
crp expression. The implications of this new circuitry for determining the complex global regulatory response of
E. coli to its carbon nutritional environment are discussed.
MATERIALS AND METHODS
Bacterial strains and growth conditions.
The strains, plasmids, and bacteriophage used in this study are listed in
Table 1. Oligonucleotides are listed in
Table 2. Unless otherwise indicated, bacteria were grown at 37°C, with shaking at 250 rpm, in Luria-Bertani (LB) medium (
59), LB medium buffered with 0.1 M MOPS (3-morpholinopropane-1-sulfonic acid) (LB-MOPS) and with or without an added carbon source, or Kornberg (KB) medium (1.1% K
2HPO
4, 0.85% KH
2PO
4, 0.6% yeast extract containing 0.5% glucose for liquid medium). Media were supplemented with antibiotics at the following concentrations or as indicated otherwise: kanamycin at 100 μg/ml; ampicillin at 100 μg/ml; chloramphenicol at 25 μg/ml, and tetracycline at 10 μg/ml. P1
vir transductions were performed as previously described (
59).
Construction of lacZ reporter fusions.
Single-copy, chromosomally integrated transcriptional and translational fusions to
lacZ were constructed using the CRIM system (
60) with plasmid vectors pLFX and pLFT, derived from pAH125 (
25), and integrated into the chromosome at the λ
att site, and single integrants were confirmed by PCR, as described previously (
60).
For constructing csrB-lacZ and csrC-lacZ transcriptional fusions, 502 (−500 to +2 with respect to the csrB transcription initiation site)-nucleotide (nt) and 304 (−301 to +3 with respect to the csrC transcription initiation site)-nt regions of csrB and csrC were amplified by PCR from E. coli MG1655 genomic DNA using primer pairs csrB lacZ Fwd/csrB lacZ Rev and csrC lacZ Fwd/csrC lacZ Rev. PCR products were gel purified, digested with PstI and KpnI, ligated to PstI- and KpnI-digested and dephosphorylated plasmid pLFX, and electroporated into DH5αλpir cells. Sequence-verified plasmids pLFXcsrB-lacZ and pLFXcsrC-lacZ were integrated into the λ att site of E. coli MG1655 ΔlacZ, using helper plasmid pPFINT.
For constructing the crp′-′lacZ translational fusion, the primer pair crp trsln Fwd/crp trsln Rev was used to amplify a 677-nucleotide region (nucleotides −667 to +10 with respect to the translational start site) of crp from MG1655. The resulting PCR product was gel purified, digested with PstI and EcoRI, ligated to PstI- and EcoRI-digested, dephosphorylated plasmid pLFT, and electroporated into DH5αλpir cells. Primer pair cyaA trsln Fwd/cyaA trsln Rev was used to amplify a 497-nucleotide region (nucleotides −438 to +59 with respect to the cyaA translational start site) of cyaA from MG1655, gel purified, digested with PstI and BamHI, ligated to PstI- and BamHI-digested, dephosphorylated plasmid pLFT, and electroporated into DH5αλpir cells. The sequence-verified plasmids, pLFTcrp′-′lacZ and pLFTcyaA′-′lacZ, were integrated into the λ att site of E. coli MG1655 ΔlacZ using helper plasmid pPFINT.
β-Galactosidase and protein assays.
Assays to examine the effects of
csrA on expression of
cyaA′-′
lacZ and
crp′-′
lacZ translational fusions were performed as described previously (
19). Assays to examine the effects of cAMP-CRP on
csrB-lacZ and
csrC-lacZ transcriptional fusions were conducted as described previously (
61) with minor modifications (
25). Total cell protein was measured after precipitation with 10% trichloroacetic acid, using the bicinchoninic acid assay (Pierce Biotechnology) with bovine serum albumin as a protein standard. Purified proteins were quantified similarly but without trichloroacetic acid precipitation.
Northern blotting.
Total RNA was isolated using a RiboPure-Bacteria kit (Ambion) or by phenol-chloroform extraction. Phenol-chloroform extraction was performed following the Gross Lab protocol (
http://derisilab.ucsf.edu/microarray/pdfs/Total_RNA_from_Ecoli.pdf) for isolation of total RNA from
E. coli. For Northern blotting, 2 μg of total RNA was mixed with 2 volumes of loading buffer (50% [vol/vol] deionized formamide; 6% [vol/vol] formaldehyde; 1× MOPS [20 mM]; 5 mM sodium acetate [NaOAc]; 2 mM EDTA [pH 7.0]; 10% [vol/vol] glycerol; 0.05% [wt/vol] bromophenol blue; 0.01% [wt/vol] ethidium bromide), denatured by heating at 75°C for 5 min, chilled on ice, and separated by electrophoresis on a 7 M urea–5% polyacrylamide gel. RNA was transferred overnight to a positively charged nylon membrane (Roche) in 1× Tris-borate-EDTA (TBE) buffer and fixed to the membrane by UV cross-linking. The rRNA that was transferred was stained with methylene blue and imaged using a Gel-Doc, and its signal intensity was quantified using Quantity One software. CsrB or CsrC RNAs were detected with DIG-labeled RNA probes according to a digoxigenin (DIG) Northern starter kit manual (Roche), and the signals were captured with a ChemiDoc XRS+ system (Bio-Rad, Hercules, CA).
Construction of a carboxy-terminal FLAG-tagged UvrY protein.
A strain expressing a recombinant UvrY protein containing a 3× FLAG tag at the carboxy terminus from the native
uvrY locus was constructed as described earlier (
62). The recombinant UvrY
FLAG protein appeared to be fully functional, as determined by its ability to activate the synthesis of CsrB and CsrC RNAs relative to the results seen with the wild-type (WT) UvrY protein (data not shown).
Western blotting of CsrA and UvrY-FLAG.
For Western blotting, cultures were grown with shaking at 37°C at 250 rpm and harvested throughout the growth curve. Cells were mixed with 2× sample buffer (4% [wt/vol] SDS; 0.16 M Tris; 1.5% [vol/vol] β-mercaptoethanol; 20% [vol/vol] glycerol; 0.02% [wt/vol] bromophenol blue, pH 6.0) and lysed by sonication and then by boiling. Samples (1 to 5 μg of total cellular protein) were subjected to SDS-PAGE, transferred to 0.2 μM polyvinylidene difluoride (PVDF) membranes, and detected using polyclonal anti-CsrA, monoclonal anti-FLAG (for UvrY-FLAG), or anti-RpoB (for RpoB) antibodies as described previously (
62). Unphosphorylated UvrY was resolved from phosphorylated UvrY (P-UvrY) on SDS gels containing Phos-Tag reagent, as described previously (
62).
Electrophoretic gel mobility shift assays (EMSA) for RNA binding.
Binding of CsrA to
crp and
cyaA transcripts was determined by EMSA with
in vitro-synthesized
crp and
cyaA transcripts (MAXIscript SP6/MEGAshortscript kit; Ambion) and recombinant CsrA-His
6 (
2). The template DNA for
in vitro transcription of
crp and
cyaA was generated by PCR from MG1655 genomic DNA, using oligonucleotide pairs crp WT Fwd SP6/crp P1 Rev (
crp WT) and cyaA WT Fwd T7/cyaA WT Rev T7 (
cyaA WT). WT
crp transcripts (178 nt, consisting of 167 nt of the noncoding mRNA leader and 11 nt of the coding region) and
cyaA transcripts (201 nt, consisting of 154 nt of the noncoding mRNA leader and 47 nt of the coding region) were gel purified, treated with Antarctic phosphatase (NEB), and radiolabeled at the 5′ end using [γ-
32P]ATP and T4 polynucleotide kinase. Binding reaction mixtures contained 0.6 nM RNA, 10 mM MgCl
2, 100 mM KCl, 32.5 ng total yeast RNA, 20 mM dithiothreitol (DTT], 7.5% glycerol, 4 U SUPERasin (Ambion), and various concentrations of CsrA (0 to 640 nM) and were incubated at 37°C for 30 min. Reaction mixtures were separated on 9% native polyacrylamide gels using 1× TBE buffer as the electrophoresis buffer, and labeled RNA was analyzed using a phosphorimager equipped with Quantity One software, as described previously (
25).
Purification of native CRP protein.
The
E. coli crp coding region was PCR amplified from MG1655 genomic DNA using the primer pair crp Fwd Exp/crp Rev Exp. The resulting PCR product was gel purified, digested with EcoRI and XhoI, ligated to EcoRI and XhoI digested, dephosphorylated pET24a(+), and transformed into DH5α cells. The resulting clone pET24a(+)
crp was verified by sequencing and transformed into the expression host, BL21(λDE3). Shaking cultures of BL21(λDE3) pET24a(+)
crp were grown in LB (300 ml) containing kanamycin at 37°C for 3 h, and expression of
crp was induced for 3 h with 1 mM isopropyl-β-
d-thiogalactopyranoside (IPTG). Cells were collected by centrifugation, resuspended in 30 ml of binding buffer (20 mM Tris-HCl [pH 7.9]; 500 mM NaCl; 20 mM imidazole), lysed using a French press, and centrifuged to remove cell debris from the cell lysate. The native CRP protein was fractionated using HisTrap column chromatography (
63). The cell lysate was loaded onto a His-Trap column (HisTrap HP; GE Healthcare), rinsed with binding buffer (20 mM Tris-HCl [pH 7.9]; 500 mM NaCl; 20 mM imidazole), and eluted with a gradient of binding buffer and elution buffer (20 mM Tris-HCl [pH 7.9]; 500 mM NaCl; 500 mM imidazole). CRP-containing fractions were pooled and dialyzed against a buffer containing 50 mM Tris-HCl (pH 7.6], 200 mM KCl, 10 mM MgCl
2, 0.1 mM EDTA, 1 mM DTT, and 10% glycerol. The final CRP solution was adjusted to 50% glycerol and stored at −20°C. Purity was estimated to be ≥98% by SDS-PAGE.
Purification of carboxy-terminal His-tagged UvrY protein.
His
6-tagged UvrY protein was purified from a strain expressing the recombinant protein as described previously (
3).
In vitro phosphorylation of UvrY.
UvrY protein was phosphorylated by incubation with 100 mM lithium potassium acetyl-phosphate (Sigma-Aldrich) for 60 min at room temperature in a buffer containing 50 mM HEPES, 100 mM NaCl, and 10 mM MgCl
2 as described previously (
40).
Electrophoretic gel mobility shift assays for DNA binding.
For DNA gel shift assays, the regions from nt −400 to −1 and nt −200 to −1, with respect to the transcriptional start sites of csrB and csrC, respectively, were amplified by PCR from MG1655 genomic DNA and subjected to end labeling with [γ-32P]ATP using T4 polynucleotide kinase. Binding reaction mixtures (10 μl) contained 0.5 nM end-labeled DNA, 20 mM Tris HCl (pH 7.5), 10% (vol/vol) glycerol, 50 mM KCl, 3 mM MgCl2, 1 mM dithiothreitol, 100 μg/ml bovine serum albumin, and, as indicated, cAMP, CRP, and/or P-UvrY. Reaction mixtures were incubated for 30 min at 37°C degrees, and then 1 μl xylene cyanol was added and samples were separated by electrophoresis on 6% native polyacrylamide gels with 0.5× TBE buffer as the running buffer. The gels were dried, and radioactive signals were captured by phosphorimaging and analyzed using Quantity One software.
DNase I footprinting.
DNA of csrB and csrC regions, extending from nt −420 to +46 and nt −319 to +100 relative to the respective transcriptional start sites, was amplified by PCR from MG1655 to generate the csrB and csrC templates for footprinting. To label the 5′ end of the nontemplate or template strand, a 32P end-labeled forward or reverse primer, respectively, was used in the PCR and the resulting PCR product was gel purified. Binding reaction mixtures (10 μl) contained labeled DNA (0.5 nM), 20 mM Tris HCl (pH 7.5), 10% (vol/vol) glycerol, 50 mM KCl, 3 mM MgCl2, 1 mM dithiothreitol, 100 μg/ml BSA, 200 μM cAMP, and CRP or P-UvrY. Reaction mixtures were incubated for 30 min at 37°C and cooled on ice. Then, a solution containing 0.025 U of DNase I (Roche) and CaCl2 (1 mM final concentration) was added, and the contents were gently mixed by pipetting and incubated in a 37°C water bath for 1 min. Thereafter, DNase I was heat inactivated at 75°C for 10 min, samples were chilled on ice, and 2 vol of loading buffer was added. The DNA was denatured by heating at 95°C for 5 min and separated by electrophoresis on a 7 M urea–6% polyacrylamide gel. After electrophoresis, the gel was dried and radioactive signals were collected by phosphorimaging and quantified using Quantity One software. Sequencing ladders were prepared with the use of a ThermoSequenase cycle sequencing kit (Affymetrix, USB; catalog no. 78500), as recommended by the manufacturer.
In vitro coupled transcription-translation.
Coupled transcription-translational assays for expression of pLFXcsrC-lacZ were performed with S-30 extracts prepared from a
uvrY-deficient strain (CF7789
uvrY::
cam) as described previously (
38,
61), except that the reaction mixtures were assembled to reach 32 μl and contained 0.5 U
E. coli RNA polymerase holoenzyme and 3 μl of [
35S]methionine (1,175 Ci/mmol). Radiolabeled proteins were separated by electrophoresis through Bis-Tris SDS-PAGE. Gels were stained, destained, and dried, and radioactive signals were detected by phosphorimaging and quantified using Quantity One Software.
DISCUSSION
These studies were inspired by observations suggestive of regulatory connections between the catabolite repression and Csr systems. For example, (i)
crp and
cya mRNAs copurified with the CsrA protein (
25), (ii) potential cAMP-CRP binding sites were identified upstream of the
csrB gene by bioinformatics analysis (
47), and (iii) a number of genes and processes have been reported to be regulated by both CsrA and cAMP-CRP (
14,
18,
21,
66) (
Fig. 10). In addition, the phosphorylation state of the PTS protein EIIA
Glc serves as the key sensory mechanism for cAMP synthesis and catabolite repression control and for the turnover pathway of CsrB/C sRNAs (
43,
44,
48). Our present data establish direct and apparently indirect connections between these two important global regulatory systems.
We determined that cAMP-CRP represses the synthesis of
E. coli CsrB and CsrC sRNAs using a combination of molecular genetics and biochemical evidence. Levels of these sRNAs and
csrB-lacZ and
csrC-lacZ expression were elevated in strains unable to produce cAMP-CRP (
Fig. 1 to
3). While both CsrB and CsrC responded positively to cAMP-CRP
in vivo, only
csrC DNA was a target of specific, high-affinity
in vitro binding by cAMP-CRP (
Fig. 5 to
8). Thus, cAMP-CRP uses distinct mechanisms for regulating
csrB versus
csrC expression. Consistent with this finding, cAMP-CRP had little or no effect on the cellular levels of P-UvrY and CsrA, which are known to activate both
csrB and
csrC expression (
Fig. 4). Integration host factor IHF is the only factor known to differentially activate
csrB transcription without affecting
csrC (
3,
41). However, the
ihfA and
ihfB genes, which encode the IHF subunits, were not among the
E. coli genes found to contain cAMP-CRP binding sites by genomic SELEX analyses (
47). Thus, IHF seems unlikely to mediate the effects of cAMP-CRP on
csrB.
The Csr regulon is broad in scope and includes many genes involved in carbon and energy metabolism. Not surprisingly, the carbon nutritional status influences the workings of the Csr system. The BarA-UvrY (-SirA) TCS of
E. coli and
Salmonella activates
csrB expression in response to end products of bacterial carbon metabolism that accumulate in the mammalian large intestine, such as formate, acetate, and propionate (
39,
67). Furthermore, chromatin immunoprecipitation-exo (ChIP-exo) studies have shown that P-UvrY (P-SirA) binds primarily to
csrB and
csrC DNA
in vivo in these bacteria, indicating that activation of
csrB and
csrC transcription is the main function of BarA-UvrY (
3). In contrast, citrate accumulation in
Vibrio fischeri (
68) and other tricarboxylic acid cycle intermediates in
Pseudomonas fluorescens (
69) are correlated with the function of this TCS, also referred to as GacS-GacA. The biochemical mechanisms involved in these sensory processes remain to be determined. In
E. coli, CsrA positively regulates several enzymes of glycolysis, in particular, the enzyme phosphofructokinase A, which drives metabolic flux beyond the upper trunk of the glycolysis pathway (
7,
13). By inference, products of carbon metabolism downregulate CsrA activity and glycolytic flux through the Embeden-Meyerhof-Parnas pathway, while they activate gluconeogenesis, glycogen synthesis, synthesis of the biofilm exopolysaccharide dPNAG, and pathways and processes favoring stress resistance and survival, which are repressed by CsrA (
Fig. 10) (
7,
17,
18,
22,
24,
33).
The Csr system is also regulated in complex ways by the availability of preferred carbon substrate for growth (
Fig. 10). Transport of glucose by the PTS pathway leads to dephosphorylation of EIIA
Glc, which binds to CsrD and activates the decay pathway for CsrB/C in
E. coli (
43,
44). This kind of regulatory pathway may function in most
Enterobacteriaceae,
Vibrionaceae, and
Shewanellaceae species and yet is absent in the majority of gammaproteobacterial families, the members of which lack a
csrD homolog (
42,
43). Furthermore, cAMP-CRP modestly inhibits CsrB/C decay (
Fig. 2). Therefore, EIIA
Glc and P-EIIA
Glc relay complementary information to CsrD and adenylate cyclase, respectively, favoring CsrB/C decay when glucose is present. Together,
csrB/
C transcription, which is stimulated by end products of carbon metabolism, and CsrB/C decay, which is activated by glucose, have the potential to reinforce each other's effects on CsrB/C. Both pathways should drive CsrB/C accumulation when preferred carbon resources have been expended and end products have accumulated, promoting the physiological switch from glycolytic growth to stationary-phase metabolism (
9,
44).
Our new observations present a twist on the role of carbon substrate in the Csr system. cAMP-CRP formation, which is inhibited by the effect of glucose on EIIA
Glc phosphorylation, leads to repression of
csrB/
C transcription (
Fig. 1). Thus, the presence of glucose has the potential to activate both the synthesis and turnover of CsrB/C, through its effects on the phosphorylation state of EIIA
Glc (
Fig. 10). How might these conflicting effects of glucose be of benefit to
E. coli? When a preferred carbon source is present and metabolic end products such as formate or acetate are accumulating, both the synthesis and turnover of CsrB/C should occur. We propose that this may lead to accelerated responses to cues or stimuli affecting the Csr system, as described in general for the behavior of incoherent feedback loops (
53,
70). In support of this hypothesis, results of modeling studies with genes of the Csr system suggest that the CsrD-dependent decay pathway for CsrB/C sRNAs enhances rates of Csr response to signals, although the involvement of glucose or carbon metabolites in this process has not been demonstrated (
71). In view of the hundreds of genes and numerous pathways and processes that are controlled by CsrA (
13,
25,
33), the proposed operation of a futile cycle of CsrB/C synthesis and turnover when a preferred carbon source is available may be a small price to pay to poise the Csr system for rapid response.
We demonstrated that cAMP-CRP directly represses
csrC expression by binding to
csrC DNA (
Fig. 5,
6, and
8), while
csrB appears to be repressed indirectly (
Fig. 5 and
7). Repression by cAMP-CRP can be accomplished in a number of ways. For example, CRP can bind at a location close to the promoter and directly interfere with transcription initiation or elongation (
57,
72). Alternatively, CRP can prevent binding of an activator (
52) or can activate transcription from a promoter and indirectly lead to repression of transcription from an overlapping divergent promoter (
73,
74). Our results suggest that repression of
csrC expression by cAMP-CRP acts in conjunction with P-UvrY-dependent activation. DNase I footprinting experiments show that cAMP-CRP and P-UvrY compete for binding in a region far upstream of the
csrC promoter (
Fig. 6). We should emphasize that cAMP-CRP binds even more tightly at a location immediately downstream of the P-UvrY binding site (
Fig. 6). Whether repression is mediated by direct competition of cAMP-CRP with P-UvrY for binding to
csrC DNA or is a consequence of cAMP-CRP binding to the downstream site and inhibiting the productive interaction of bound P-UvrY with RNA polymerase or other regulatory elements for
csrC transcription remains to be seen.
The Csr system appears to be conserved in all
Gammaproteobacteria species, but details such as the number of CsrA paralogs and Csr sRNAs produced by a given species can differ (
6,
44,
75,
76). Not surprisingly, even among closely related
Enterobacteriaceae species, the links between Csr and catabolite repression circuitry differ. In
Yersinia pseudotuberculosis, cAMP-CRP exerts indirect and opposite regulatory effects on
csrB and
csrC (
77). Furthermore, while
csrB expression in
Y. pseudotuberculosis depends on BarA-UvrY,
csrC expression is directly activated by the PhoP-PhoQ TCS (
78).
Salmonella enterica was reported to somehow activate expression of the
uvrY ortholog,
sirA, via cAMP-CRP, with positive downstream effects on
csrB-lacZ and
csrC-lacZ gene fusions (
79). In addition, CLIP-seq studies in
Salmonella revealed binding of CsrA to
crp (
cap) leader mRNA at two locations (
80), one of which is related in sequence to
E. coli BS2 (
Fig. 8A). Additional studies will be required to unravel the biological significance of such variations in the Csr and catabolite repression networks.