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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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Organization of the glmY and glmZ genes in Enterobacteriaceae. (A) Diagram illustrating gene synteny of the glmY and glmZ regions in Enterobacteriaceae. The gene cluster glmY-glrK-yfhG-glrR-glnB is conserved in Enterobacteriacea, but in some species e.g. Yersinia and Photorhabdus, gene nadE is inserted between glrR and glnB. Upstream of glmY, genes mltF and purL are present except for Providencia sp. Small orfs of unknown function are interspersed between purL and glmY in Yersinia, Photorhabdus and other species. Gene glmZ clusters with the downstream located and divergently orientated hemCDXY cluster, while the region upstream is variable. (B) Organization of enterobacterial glmY and glmZ promoters. Sequence alignments of the glmY and glmZ promoter regions from 39 enterobacterial genomes classified the species into three groups, for which Y. pseudotuberculosis, S. typhimurium and E. coli are representatively shown (for details, see Supplementary Figures S3 and S4). Yersinia possesses the sequences for a σ54-promoter (labeled in red) and three GlrR binding sites upstream of both sRNA genes, while overlapping σ70-promoters appear to be absent. GlrR binding sites and σ54-promoters are also detectable upstream of both sRNA genes in Salmonella, but in addition putative σ70-promoters (labeled in blue) that overlap the σ54-promoters, are detectable. This arrangement is also found upstream of E. coli glmY. However, E. coli glmZ appears to be transcribed from a single σ70-promoter. The sequence alignment also detected two putative IHF binding sites that coincide with the occurrence of σ54-promoters.
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Figure 1: Organization of the glmY and glmZ genes in Enterobacteriaceae. (A) Diagram illustrating gene synteny of the glmY and glmZ regions in Enterobacteriaceae. The gene cluster glmY-glrK-yfhG-glrR-glnB is conserved in Enterobacteriacea, but in some species e.g. Yersinia and Photorhabdus, gene nadE is inserted between glrR and glnB. Upstream of glmY, genes mltF and purL are present except for Providencia sp. Small orfs of unknown function are interspersed between purL and glmY in Yersinia, Photorhabdus and other species. Gene glmZ clusters with the downstream located and divergently orientated hemCDXY cluster, while the region upstream is variable. (B) Organization of enterobacterial glmY and glmZ promoters. Sequence alignments of the glmY and glmZ promoter regions from 39 enterobacterial genomes classified the species into three groups, for which Y. pseudotuberculosis, S. typhimurium and E. coli are representatively shown (for details, see Supplementary Figures S3 and S4). Yersinia possesses the sequences for a σ54-promoter (labeled in red) and three GlrR binding sites upstream of both sRNA genes, while overlapping σ70-promoters appear to be absent. GlrR binding sites and σ54-promoters are also detectable upstream of both sRNA genes in Salmonella, but in addition putative σ70-promoters (labeled in blue) that overlap the σ54-promoters, are detectable. This arrangement is also found upstream of E. coli glmY. However, E. coli glmZ appears to be transcribed from a single σ70-promoter. The sequence alignment also detected two putative IHF binding sites that coincide with the occurrence of σ54-promoters.

Mentions: In E. coli, transcription of glmY is controlled by overlapping σ70- and σ54-dependent promoters. Activity of the σ54-promoter is governed by the TCS GlrR/GlrK, which is encoded downstream of glmY (22). To investigate, whether this unusual promoter architecture is conserved in other bacteria and to increase our understanding of regulation of glmZ transcription, we compared the promoter sequences of glmY and glmZ from a comprehensive number of genomes. To retrieve these sequences, we used the sRNA sequences of Escherichia coli K12 (strain MG1655) as queries in NCBI Blast analyses. This search generated a list of species, all belonging to the Enterobacteriaceae family, which coincidently contained both sRNA genes. Inspection of gene synteny using the MicrobesOnline tool (28) and the KEGG database (29) revealed conserved localization of glmZ downstream of the divergently orientated hemCDXY operon encoding enzymes involved in tetrapyrrole synthesis, whereas the region upstream of glmZ is variable and may carry insertion elements (Figure 1A and Supplementary Figure S1). Gene glmY is always located upstream of the gene cluster glrK-yfhG-glrR (Figure 1A and Supplementary Figure S2). Collectively, these observations suggest that sRNA genes glmY and glmZ are elements of the core genome conserved in Enterobacteriaceae. The conserved co-localization of glmY with the genes encoding the sensor kinase GlrK and the response regulator GlrR suggests that regulation of glmY expression by this TCS might be likewise conserved.Figure 1.


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)

Organization of the glmY and glmZ genes in Enterobacteriaceae. (A) Diagram illustrating gene synteny of the glmY and glmZ regions in Enterobacteriaceae. The gene cluster glmY-glrK-yfhG-glrR-glnB is conserved in Enterobacteriacea, but in some species e.g. Yersinia and Photorhabdus, gene nadE is inserted between glrR and glnB. Upstream of glmY, genes mltF and purL are present except for Providencia sp. Small orfs of unknown function are interspersed between purL and glmY in Yersinia, Photorhabdus and other species. Gene glmZ clusters with the downstream located and divergently orientated hemCDXY cluster, while the region upstream is variable. (B) Organization of enterobacterial glmY and glmZ promoters. Sequence alignments of the glmY and glmZ promoter regions from 39 enterobacterial genomes classified the species into three groups, for which Y. pseudotuberculosis, S. typhimurium and E. coli are representatively shown (for details, see Supplementary Figures S3 and S4). Yersinia possesses the sequences for a σ54-promoter (labeled in red) and three GlrR binding sites upstream of both sRNA genes, while overlapping σ70-promoters appear to be absent. GlrR binding sites and σ54-promoters are also detectable upstream of both sRNA genes in Salmonella, but in addition putative σ70-promoters (labeled in blue) that overlap the σ54-promoters, are detectable. This arrangement is also found upstream of E. coli glmY. However, E. coli glmZ appears to be transcribed from a single σ70-promoter. The sequence alignment also detected two putative IHF binding sites that coincide with the occurrence of σ54-promoters.
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Related In: Results  -  Collection

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Figure 1: Organization of the glmY and glmZ genes in Enterobacteriaceae. (A) Diagram illustrating gene synteny of the glmY and glmZ regions in Enterobacteriaceae. The gene cluster glmY-glrK-yfhG-glrR-glnB is conserved in Enterobacteriacea, but in some species e.g. Yersinia and Photorhabdus, gene nadE is inserted between glrR and glnB. Upstream of glmY, genes mltF and purL are present except for Providencia sp. Small orfs of unknown function are interspersed between purL and glmY in Yersinia, Photorhabdus and other species. Gene glmZ clusters with the downstream located and divergently orientated hemCDXY cluster, while the region upstream is variable. (B) Organization of enterobacterial glmY and glmZ promoters. Sequence alignments of the glmY and glmZ promoter regions from 39 enterobacterial genomes classified the species into three groups, for which Y. pseudotuberculosis, S. typhimurium and E. coli are representatively shown (for details, see Supplementary Figures S3 and S4). Yersinia possesses the sequences for a σ54-promoter (labeled in red) and three GlrR binding sites upstream of both sRNA genes, while overlapping σ70-promoters appear to be absent. GlrR binding sites and σ54-promoters are also detectable upstream of both sRNA genes in Salmonella, but in addition putative σ70-promoters (labeled in blue) that overlap the σ54-promoters, are detectable. This arrangement is also found upstream of E. coli glmY. However, E. coli glmZ appears to be transcribed from a single σ70-promoter. The sequence alignment also detected two putative IHF binding sites that coincide with the occurrence of σ54-promoters.
Mentions: In E. coli, transcription of glmY is controlled by overlapping σ70- and σ54-dependent promoters. Activity of the σ54-promoter is governed by the TCS GlrR/GlrK, which is encoded downstream of glmY (22). To investigate, whether this unusual promoter architecture is conserved in other bacteria and to increase our understanding of regulation of glmZ transcription, we compared the promoter sequences of glmY and glmZ from a comprehensive number of genomes. To retrieve these sequences, we used the sRNA sequences of Escherichia coli K12 (strain MG1655) as queries in NCBI Blast analyses. This search generated a list of species, all belonging to the Enterobacteriaceae family, which coincidently contained both sRNA genes. Inspection of gene synteny using the MicrobesOnline tool (28) and the KEGG database (29) revealed conserved localization of glmZ downstream of the divergently orientated hemCDXY operon encoding enzymes involved in tetrapyrrole synthesis, whereas the region upstream of glmZ is variable and may carry insertion elements (Figure 1A and Supplementary Figure S1). Gene glmY is always located upstream of the gene cluster glrK-yfhG-glrR (Figure 1A and Supplementary Figure S2). Collectively, these observations suggest that sRNA genes glmY and glmZ are elements of the core genome conserved in Enterobacteriaceae. The conserved co-localization of glmY with the genes encoding the sensor kinase GlrK and the response regulator GlrR suggests that regulation of glmY expression by this TCS might be likewise conserved.Figure 1.

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