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Common and divergent features in transcriptional control of the homologous small RNAs GlmY and GlmZ in Enterobacteriaceae.

Göpel Y, Lüttmann D, Heroven AK, Reichenbach B, Dersch P, Görke B - Nucleic Acids Res. (2010)

Bottom Line: However, in a subset of species such as E. coli this relationship is partially lost in favor of σ(70)-dependent transcription.In addition, we show that activity of the σ(54)-promoter of E. coli glmY requires binding of the integration host factor to sites upstream of the promoter.Finally, evidence is provided that phosphorylation of GlrR increases its activity and thereby sRNA expression.

View Article: PubMed Central - PubMed

Affiliation: Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstrasse 8, 37077 Göttingen, Germany.

ABSTRACT
Small RNAs GlmY and GlmZ compose a cascade that feedback-regulates synthesis of enzyme GlmS in Enterobacteriaceae. Here, we analyzed the transcriptional regulation of glmY/glmZ from Yersinia pseudotuberculosis, Salmonella typhimurium and Escherichia coli, as representatives for other enterobacterial species, which exhibit similar promoter architectures. The GlmY and GlmZ sRNAs of Y. pseudotuberculosis are transcribed from σ(54)-promoters that require activation by the response regulator GlrR through binding to three conserved sites located upstream of the promoters. This also applies to glmY/glmZ of S. typhimurium and glmY of E. coli, but as a difference additional σ(70)-promoters overlap the σ(54)-promoters and initiate transcription at the same site. In contrast, E. coli glmZ is transcribed from a single σ(70)-promoter. Thus, transcription of glmY and glmZ is controlled by σ(54) and the two-component system GlrR/GlrK (QseF/QseE) in Y. pseudotuberculosis and presumably in many other Enterobacteria. However, in a subset of species such as E. coli this relationship is partially lost in favor of σ(70)-dependent transcription. In addition, we show that activity of the σ(54)-promoter of E. coli glmY requires binding of the integration host factor to sites upstream of the promoter. Finally, evidence is provided that phosphorylation of GlrR increases its activity and thereby sRNA expression.

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Model illustrating the roles of the TCS GlrR/GlrK, σ54 and IHF for transcription of sRNA genes glmY and glmZ in Enterobacteriaceae. Histidine kinase GlrK phosphorylates response regulator GlrR, which stimulates binding of GlrR to its target sites on the DNA. GlrR binds to three activator binding sites present upstream of σ54-dependent promoters that control the expression of sRNA genes glmY in all species and glmZ in a subset of species. GlrR, which contains a σ54 interaction domain, is absolutely required for activity of these σ54-promoters. In addition, promoter activity depends on IHF, which might facilitate interaction of GlrR with the σ54-RNA polymerase by binding-induced bending of the promoter DNA. In Y. pseudotuberculosis, transcription of glmY and glmZ is directed by single σ54-promoters that require activation by GlrR. Hence, glmY and glmZ compose a regulon controlled by GlrR and σ54. A similar arrangement is found in S. typhimurium, but σ70-promoters that overlap the σ54-promoters additionally contribute to glmY and glmZ expression. Overlapping σ54- and σ70-promoters also direct expression of the E. coli glmY gene, while expression of glmZ is achieved from a single constitutively active σ70-promoter. Sequence alignment analyses suggest that these three different arrangements might also apply to other enterobacterial species as shown in the Figure.
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Figure 8: Model illustrating the roles of the TCS GlrR/GlrK, σ54 and IHF for transcription of sRNA genes glmY and glmZ in Enterobacteriaceae. Histidine kinase GlrK phosphorylates response regulator GlrR, which stimulates binding of GlrR to its target sites on the DNA. GlrR binds to three activator binding sites present upstream of σ54-dependent promoters that control the expression of sRNA genes glmY in all species and glmZ in a subset of species. GlrR, which contains a σ54 interaction domain, is absolutely required for activity of these σ54-promoters. In addition, promoter activity depends on IHF, which might facilitate interaction of GlrR with the σ54-RNA polymerase by binding-induced bending of the promoter DNA. In Y. pseudotuberculosis, transcription of glmY and glmZ is directed by single σ54-promoters that require activation by GlrR. Hence, glmY and glmZ compose a regulon controlled by GlrR and σ54. A similar arrangement is found in S. typhimurium, but σ70-promoters that overlap the σ54-promoters additionally contribute to glmY and glmZ expression. Overlapping σ54- and σ70-promoters also direct expression of the E. coli glmY gene, while expression of glmZ is achieved from a single constitutively active σ70-promoter. Sequence alignment analyses suggest that these three different arrangements might also apply to other enterobacterial species as shown in the Figure.

Mentions: In this study we addressed the transcriptional regulation of two sRNA genes, glmY and glmZ, which are conserved in Enterobacteriaceae. Our analysis reveals three different scenarios of control of glmY and glmZ expression operative in enterobacterial species as described for Y. pseudotuberculosis, S. typhimurium and E. coli. Sequence alignment analyses (Supplementary Figures S3 and S4) suggest that these species are representatives for other species showing similar glmY and glmZ promoter architectures, respectively (Figure 8). Most importantly, our results suggest that in most species expression of both sRNAs is controlled by σ54 and the response regulator GlrR (Figure 8). This adds two sRNA genes to the regulon governed by σ54 in Enterobacteriaceae. The glmY and glmZ genes of Y. pseudotuberculosis exhibit all features of canonical σ54-dependent genes. Their expression depends on σ54 (Figures 2 and 3) and on binding of the activator protein GlrR to ABS present upstream of the σ54-promoter, as demonstrated for Y. pseudotuberculosis glmZ (Figure 4 and Supplementary Figure S8). In conclusion, transcription is initiated from single σ54-promoters that require activation by GlrR and the same may also hold true for species of the genera Arsenophonus, Dickeya, Erwinia, Pectobacterium, Photorhabdus, Proteus and Serratia (Figure 8). A somewhat different scenario is operative in the case of S. typhimurium glmY and glmZ. The corresponding promoter regions also contain three ABS and a σ54-promoter. Accordingly, GlrR specifically binds to these regions and stimulates transcription (Figures 2 and 3). However, both genes are still expressed in mutants lacking σ54, which is at first glance incompatible with the properties of genuine σ54-dependent genes. The expression in the absence of σ54 is explained by additional σ70-promoters that overlap the σ54-promoters and can potentially start transcription at the same site. According to the sequence alignment, such overlapping σ70- and σ54-promoters may also exist in Citrobacter, Cronobacter and Enterobacter species (Figure 8). We have recently shown that in E. coli transcription of glmY is controlled by a similar mechanism (22). In contrast, E. coli glmZ is not controlled by GlrR or σ54 and accordingly GlrR does not bind the E. coli glmZ promoter (Figure 3). A single constitutively active σ70-promoter directs expression of glmZ in E. coli (Figure 5) and presumably also in Klebsiella and other Escherichia species (including Shigella) (Figure 8). In sum, our work suggests that glmY and glmZ transcription is controlled by σ54 and the TCS GlrR/GlrK in most Enterobacteria, but in a subset of species this relation is gradually lost in favor of unregulated σ70-dependent transcription.Figure 8.


Common and divergent features in transcriptional control of the homologous small RNAs GlmY and GlmZ in Enterobacteriaceae.

Göpel Y, Lüttmann D, Heroven AK, Reichenbach B, Dersch P, Görke B - Nucleic Acids Res. (2010)

Model illustrating the roles of the TCS GlrR/GlrK, σ54 and IHF for transcription of sRNA genes glmY and glmZ in Enterobacteriaceae. Histidine kinase GlrK phosphorylates response regulator GlrR, which stimulates binding of GlrR to its target sites on the DNA. GlrR binds to three activator binding sites present upstream of σ54-dependent promoters that control the expression of sRNA genes glmY in all species and glmZ in a subset of species. GlrR, which contains a σ54 interaction domain, is absolutely required for activity of these σ54-promoters. In addition, promoter activity depends on IHF, which might facilitate interaction of GlrR with the σ54-RNA polymerase by binding-induced bending of the promoter DNA. In Y. pseudotuberculosis, transcription of glmY and glmZ is directed by single σ54-promoters that require activation by GlrR. Hence, glmY and glmZ compose a regulon controlled by GlrR and σ54. A similar arrangement is found in S. typhimurium, but σ70-promoters that overlap the σ54-promoters additionally contribute to glmY and glmZ expression. Overlapping σ54- and σ70-promoters also direct expression of the E. coli glmY gene, while expression of glmZ is achieved from a single constitutively active σ70-promoter. Sequence alignment analyses suggest that these three different arrangements might also apply to other enterobacterial species as shown in the Figure.
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Figure 8: Model illustrating the roles of the TCS GlrR/GlrK, σ54 and IHF for transcription of sRNA genes glmY and glmZ in Enterobacteriaceae. Histidine kinase GlrK phosphorylates response regulator GlrR, which stimulates binding of GlrR to its target sites on the DNA. GlrR binds to three activator binding sites present upstream of σ54-dependent promoters that control the expression of sRNA genes glmY in all species and glmZ in a subset of species. GlrR, which contains a σ54 interaction domain, is absolutely required for activity of these σ54-promoters. In addition, promoter activity depends on IHF, which might facilitate interaction of GlrR with the σ54-RNA polymerase by binding-induced bending of the promoter DNA. In Y. pseudotuberculosis, transcription of glmY and glmZ is directed by single σ54-promoters that require activation by GlrR. Hence, glmY and glmZ compose a regulon controlled by GlrR and σ54. A similar arrangement is found in S. typhimurium, but σ70-promoters that overlap the σ54-promoters additionally contribute to glmY and glmZ expression. Overlapping σ54- and σ70-promoters also direct expression of the E. coli glmY gene, while expression of glmZ is achieved from a single constitutively active σ70-promoter. Sequence alignment analyses suggest that these three different arrangements might also apply to other enterobacterial species as shown in the Figure.
Mentions: In this study we addressed the transcriptional regulation of two sRNA genes, glmY and glmZ, which are conserved in Enterobacteriaceae. Our analysis reveals three different scenarios of control of glmY and glmZ expression operative in enterobacterial species as described for Y. pseudotuberculosis, S. typhimurium and E. coli. Sequence alignment analyses (Supplementary Figures S3 and S4) suggest that these species are representatives for other species showing similar glmY and glmZ promoter architectures, respectively (Figure 8). Most importantly, our results suggest that in most species expression of both sRNAs is controlled by σ54 and the response regulator GlrR (Figure 8). This adds two sRNA genes to the regulon governed by σ54 in Enterobacteriaceae. The glmY and glmZ genes of Y. pseudotuberculosis exhibit all features of canonical σ54-dependent genes. Their expression depends on σ54 (Figures 2 and 3) and on binding of the activator protein GlrR to ABS present upstream of the σ54-promoter, as demonstrated for Y. pseudotuberculosis glmZ (Figure 4 and Supplementary Figure S8). In conclusion, transcription is initiated from single σ54-promoters that require activation by GlrR and the same may also hold true for species of the genera Arsenophonus, Dickeya, Erwinia, Pectobacterium, Photorhabdus, Proteus and Serratia (Figure 8). A somewhat different scenario is operative in the case of S. typhimurium glmY and glmZ. The corresponding promoter regions also contain three ABS and a σ54-promoter. Accordingly, GlrR specifically binds to these regions and stimulates transcription (Figures 2 and 3). However, both genes are still expressed in mutants lacking σ54, which is at first glance incompatible with the properties of genuine σ54-dependent genes. The expression in the absence of σ54 is explained by additional σ70-promoters that overlap the σ54-promoters and can potentially start transcription at the same site. According to the sequence alignment, such overlapping σ70- and σ54-promoters may also exist in Citrobacter, Cronobacter and Enterobacter species (Figure 8). We have recently shown that in E. coli transcription of glmY is controlled by a similar mechanism (22). In contrast, E. coli glmZ is not controlled by GlrR or σ54 and accordingly GlrR does not bind the E. coli glmZ promoter (Figure 3). A single constitutively active σ70-promoter directs expression of glmZ in E. coli (Figure 5) and presumably also in Klebsiella and other Escherichia species (including Shigella) (Figure 8). In sum, our work suggests that glmY and glmZ transcription is controlled by σ54 and the TCS GlrR/GlrK in most Enterobacteria, but in a subset of species this relation is gradually lost in favor of unregulated σ70-dependent transcription.Figure 8.

Bottom Line: However, in a subset of species such as E. coli this relationship is partially lost in favor of σ(70)-dependent transcription.In addition, we show that activity of the σ(54)-promoter of E. coli glmY requires binding of the integration host factor to sites upstream of the promoter.Finally, evidence is provided that phosphorylation of GlrR increases its activity and thereby sRNA expression.

View Article: PubMed Central - PubMed

Affiliation: Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstrasse 8, 37077 Göttingen, Germany.

ABSTRACT
Small RNAs GlmY and GlmZ compose a cascade that feedback-regulates synthesis of enzyme GlmS in Enterobacteriaceae. Here, we analyzed the transcriptional regulation of glmY/glmZ from Yersinia pseudotuberculosis, Salmonella typhimurium and Escherichia coli, as representatives for other enterobacterial species, which exhibit similar promoter architectures. The GlmY and GlmZ sRNAs of Y. pseudotuberculosis are transcribed from σ(54)-promoters that require activation by the response regulator GlrR through binding to three conserved sites located upstream of the promoters. This also applies to glmY/glmZ of S. typhimurium and glmY of E. coli, but as a difference additional σ(70)-promoters overlap the σ(54)-promoters and initiate transcription at the same site. In contrast, E. coli glmZ is transcribed from a single σ(70)-promoter. Thus, transcription of glmY and glmZ is controlled by σ(54) and the two-component system GlrR/GlrK (QseF/QseE) in Y. pseudotuberculosis and presumably in many other Enterobacteria. However, in a subset of species such as E. coli this relationship is partially lost in favor of σ(70)-dependent transcription. In addition, we show that activity of the σ(54)-promoter of E. coli glmY requires binding of the integration host factor to sites upstream of the promoter. Finally, evidence is provided that phosphorylation of GlrR increases its activity and thereby sRNA expression.

Show MeSH
Related in: MedlinePlus