| GcvB RNA | |
|---|---|
 Predicted
secondary structure and
sequence conservation of GcvB | |
| Identifiers | |
| Symbol | GcvB |
| Rfam | RF00022 |
| Other data | |
| RNA type | Gene |
| Domain(s) | Bacteria |
| SO | SO:0000379 |
| PDB structures | PDBe |
The gcvB RNA gene encodes a small non-coding RNA involved in the regulation of a number of amino acid transport systems as well as amino acid biosynthetic genes. The GcvB gene is found in enteric bacteria such as Escherichia coli. GcvB regulates genes by acting as an antisense binding partner of the mRNAs for each regulated gene. This binding is dependent on binding to a protein called Hfq. Transcription of the GcvB RNA is activated by the adjacent GcvA gene and repressed by the GcvR gene. [1] A deletion of GcvB RNA from Y. pestis changed colony shape as well as reducing growth. [2] It has been shown by gene deletion that GcvB is a regulator of acid resistance in E. coli. GcvB enhances the ability of the bacterium to survive low pH by upregulating the levels of the alternate sigma factor RpoS. [3] A polymeric form of GcvB has recently been identified.[ citation needed] Interaction of GcvB with small RNA SroC triggers the degradation of GcvB by RNase E, lifting the GcvB-mediated mRNA repression of its target genes. [4]
Targets of GcvB
GcvB has been shown to regulate a large number of genes in E. coli and Salmonella species. GcvB was shown to bind to Oppa and DppA which transport oligopeptides and dipeptides respectively. [5] [6] It has been shown to also regulate gltL, argT, STM, livK, livJ, brnQ, sstT and cycA which are involved in uptake of a variety of amino acids. [7] [8] [9] GcvB RNA also is involved in regulating a variety of genes involved in amino acid biosynthesis such as ilvC, gdhA, thrL and serA. [10] GcvB RNA binds PhoPQ mRNA, which encodes a two-component system involved in magnesium homeostasis. [11]
Polymerisation
There is evidence that E. coli GcvB can form polymers. Native polyacrylamide gel electrophoresis was used to show a higher molecular weight band corresponding to a potential polymer. [12] Transmission electron microscopy was then used to identify a filamentous structure for the polymer. However, the authors suggest that these long filaments are unlikely to be physiologically relevant. It was shown that a construct containing only the first 61 nucleotides including the first stem-loop was sufficient for polymerisation. Similar results were recently shown for the DsrA RNA. [13] The physiological relevance of polymerisation is not known.
Species distribution
The GcvB RNA is found in a range of bacteria including: [14]
- Escherichia coli
- Yersinia pestis [2]
- Haemophilus influenzae
- Vibrio cholerae
- Shigella dysenteriae
- Salmonella typhimurium
- Klebsiella pneumoniae
- Photorhabdus luminescens
- Pasteurella multocida [15]
References
- ^ Urbanowski, ML; Stauffer LT; Stauffer GV (2000). "The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli". Mol Microbiol. 37 (4): 856–868. doi: 10.1046/j.1365-2958.2000.02051.x. PMID 10972807. S2CID 811119.
- ^ a b McArthur SD, Pulvermacher SC, Stauffer GV (2006). "The Yersinia pestis gcvB gene encodes two small regulatory RNA molecules". BMC Microbiol. 6: 52. doi: 10.1186/1471-2180-6-52. PMC 1557403. PMID 16768793.
- ^ Jin Y, Watt RM, Danchin A, Huang JD (2009). "Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli". BMC Genomics. 10: 165. doi: 10.1186/1471-2164-10-165. PMC 2676305. PMID 19379489.
- ^ Miyakoshi, Masatoshi; Chao, Yanjie; Vogel, Jörg (2015-06-03). "Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA". The EMBO Journal. 34 (11): 1478–1492. doi: 10.15252/embj.201490546. ISSN 1460-2075. PMC 4474525. PMID 25630703.
- ^ Urbanowski ML, Stauffer LT, Stauffer GV (August 2000). "The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli". Mol. Microbiol. 37 (4): 856–868. doi: 10.1046/j.1365-2958.2000.02051.x. PMID 10972807. S2CID 811119.
- ^ Pulvermacher SC, Stauffer LT, Stauffer GV (January 2009). "Role of the Escherichia coli Hfq protein in GcvB regulation of oppA and dppA mRNAs". Microbiology. 155 (Pt 1): 115–123. doi: 10.1099/mic.0.023432-0. PMID 19118352.
- ^ Sharma CM, Darfeuille F, Plantinga TH, Vogel J (November 2007). "A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites". Genes Dev. 21 (21): 2804–2817. doi: 10.1101/gad.447207. PMC 2045133. PMID 17974919.
- ^ Pulvermacher SC, Stauffer LT, Stauffer GV (January 2009). "The small RNA GcvB regulates sstT mRNA expression in Escherichia coli". J. Bacteriol. 191 (1): 238–248. doi: 10.1128/JB.00915-08. PMC 2612445. PMID 18952787.
- ^ Pulvermacher SC, Stauffer LT, Stauffer GV (January 2009). "Role of the sRNA GcvB in regulation of cycA in Escherichia coli". Microbiology. 155 (Pt 1): 106–114. doi: 10.1099/mic.0.023598-0. PMID 19118351.
- ^ Vogel J (January 2009). "A rough guide to the non-coding RNA world of Salmonella". Mol. Microbiol. 71 (1): 1–11. doi: 10.1111/j.1365-2958.2008.06505.x. hdl: 11858/00-001M-0000-000E-C124-A. PMID 19007416. S2CID 205366563.
- ^ Coornaert, A; Chiaruttini, C; Springer, M; Guillier, M (Jan 2013). "Post-Transcriptional Control of the Escherichia coli PhoQ-PhoP Two-Component System by Multiple sRNAs Involves a Novel Pairing Region of GcvB". PLOS Genetics. 9 (1): e1003156. doi: 10.1371/journal.pgen.1003156. PMC 3536696. PMID 23300478.
- ^ Busi F, Cayrol B, Lavelle C, LeDerout J, Piétrement O, Le Cam E, Geinguenaud F, Lacoste J, Régnier P, Arluison V (2009). "Auto-assembly as a new regulatory mechanism of noncoding RNA". Cell Cycle. 8 (6): 952–954. doi: 10.4161/cc.8.6.7905. PMID 19221499.
- ^ Cayrol B, Geinguenaud F, Lacoste J, et al. (2009). "Auto-assembly of E. coli DsrA small noncoding RNA: Molecular characteristics and functional consequences". RNA Biol. 6 (4): 434–445. doi: 10.4161/rna.6.4.8949. PMID 19535898.
- ^ Pulvermacher SC, Stauffer LT, Stauffer GV (April 2008). "The role of the small regulatory RNA GcvB in GcvB/mRNA posttranscriptional regulation of oppA and dppA in Escherichia coli". FEMS Microbiol. Lett. 281 (1): 42–50. doi: 10.1111/j.1574-6968.2008.01068.x. PMID 18312576.
- ^ Gulliver, Emily L.; Wright, Amy; Lucas, Deanna Deveson; Mégroz, Marianne; Kleifeld, Oded; Schittenhelm, Ralf B.; Powell, David R.; Seemann, Torsten; Bulitta, Jürgen B. (May 2018). "Determination of the small RNA GcvB regulon in the Gram-negative bacterial pathogen Pasteurella multocida and identification of the GcvB seed binding region". RNA. 24 (5): 704–720. doi: 10.1261/rna.063248.117. ISSN 1469-9001. PMC 5900567. PMID 29440476.
Further reading
- Busi F, Le Derout J, Cerciat M, Régnier P, Hajnsdorf E (July 2010). "Is the secondary putative RNA-RNA interaction site relevant to GcvB mediated regulation of oppA mRNA in Escherichia coli?". Biochimie. 92 (10): 1458–1461. doi: 10.1016/j.biochi.2010.06.020. PMID 20603180.
- Stauffer LT, Stauffer GV (January 2005). "GcvA interacts with both the alpha and sigma subunits of RNA polymerase to activate the Escherichia coli gcvB gene and the gcvTHP operon". FEMS Microbiol. Lett. 242 (2): 333–338. doi: 10.1016/j.femsle.2004.11.027. PMID 15621456.
- Yang, Q; Figueroa-Bossi, N; Bossi, L (Jan 2014). "Translation Enhancing ACA Motifs and Their Silencing by a Bacterial Small Regulatory RNA". PLOS Genetics. 10 (1): e1004026. doi: 10.1371/journal.pgen.1004026. PMC 3879156. PMID 24391513.
External links
| GcvB RNA | |
|---|---|
|
Predicted
secondary structure and
sequence conservation of GcvB | |
| Identifiers | |
| Symbol | GcvB |
| Rfam | RF00022 |
| Other data | |
| RNA type | Gene |
| Domain(s) | Bacteria |
| SO | SO:0000379 |
| PDB structures | PDBe |
The gcvB RNA gene encodes a small non-coding RNA involved in the regulation of a number of amino acid transport systems as well as amino acid biosynthetic genes. The GcvB gene is found in enteric bacteria such as Escherichia coli. GcvB regulates genes by acting as an antisense binding partner of the mRNAs for each regulated gene. This binding is dependent on binding to a protein called Hfq. Transcription of the GcvB RNA is activated by the adjacent GcvA gene and repressed by the GcvR gene. [1] A deletion of GcvB RNA from Y. pestis changed colony shape as well as reducing growth. [2] It has been shown by gene deletion that GcvB is a regulator of acid resistance in E. coli. GcvB enhances the ability of the bacterium to survive low pH by upregulating the levels of the alternate sigma factor RpoS. [3] A polymeric form of GcvB has recently been identified.[ citation needed] Interaction of GcvB with small RNA SroC triggers the degradation of GcvB by RNase E, lifting the GcvB-mediated mRNA repression of its target genes. [4]
Targets of GcvB
GcvB has been shown to regulate a large number of genes in E. coli and Salmonella species. GcvB was shown to bind to Oppa and DppA which transport oligopeptides and dipeptides respectively. [5] [6] It has been shown to also regulate gltL, argT, STM, livK, livJ, brnQ, sstT and cycA which are involved in uptake of a variety of amino acids. [7] [8] [9] GcvB RNA also is involved in regulating a variety of genes involved in amino acid biosynthesis such as ilvC, gdhA, thrL and serA. [10] GcvB RNA binds PhoPQ mRNA, which encodes a two-component system involved in magnesium homeostasis. [11]
Polymerisation
There is evidence that E. coli GcvB can form polymers. Native polyacrylamide gel electrophoresis was used to show a higher molecular weight band corresponding to a potential polymer. [12] Transmission electron microscopy was then used to identify a filamentous structure for the polymer. However, the authors suggest that these long filaments are unlikely to be physiologically relevant. It was shown that a construct containing only the first 61 nucleotides including the first stem-loop was sufficient for polymerisation. Similar results were recently shown for the DsrA RNA. [13] The physiological relevance of polymerisation is not known.
Species distribution
The GcvB RNA is found in a range of bacteria including: [14]
- Escherichia coli
- Yersinia pestis [2]
- Haemophilus influenzae
- Vibrio cholerae
- Shigella dysenteriae
- Salmonella typhimurium
- Klebsiella pneumoniae
- Photorhabdus luminescens
- Pasteurella multocida [15]
References
- ^ Urbanowski, ML; Stauffer LT; Stauffer GV (2000). "The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli". Mol Microbiol. 37 (4): 856–868. doi: 10.1046/j.1365-2958.2000.02051.x. PMID 10972807. S2CID 811119.
- ^ a b McArthur SD, Pulvermacher SC, Stauffer GV (2006). "The Yersinia pestis gcvB gene encodes two small regulatory RNA molecules". BMC Microbiol. 6: 52. doi: 10.1186/1471-2180-6-52. PMC 1557403. PMID 16768793.
- ^ Jin Y, Watt RM, Danchin A, Huang JD (2009). "Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli". BMC Genomics. 10: 165. doi: 10.1186/1471-2164-10-165. PMC 2676305. PMID 19379489.
- ^ Miyakoshi, Masatoshi; Chao, Yanjie; Vogel, Jörg (2015-06-03). "Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA". The EMBO Journal. 34 (11): 1478–1492. doi: 10.15252/embj.201490546. ISSN 1460-2075. PMC 4474525. PMID 25630703.
- ^ Urbanowski ML, Stauffer LT, Stauffer GV (August 2000). "The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli". Mol. Microbiol. 37 (4): 856–868. doi: 10.1046/j.1365-2958.2000.02051.x. PMID 10972807. S2CID 811119.
- ^ Pulvermacher SC, Stauffer LT, Stauffer GV (January 2009). "Role of the Escherichia coli Hfq protein in GcvB regulation of oppA and dppA mRNAs". Microbiology. 155 (Pt 1): 115–123. doi: 10.1099/mic.0.023432-0. PMID 19118352.
- ^ Sharma CM, Darfeuille F, Plantinga TH, Vogel J (November 2007). "A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites". Genes Dev. 21 (21): 2804–2817. doi: 10.1101/gad.447207. PMC 2045133. PMID 17974919.
- ^ Pulvermacher SC, Stauffer LT, Stauffer GV (January 2009). "The small RNA GcvB regulates sstT mRNA expression in Escherichia coli". J. Bacteriol. 191 (1): 238–248. doi: 10.1128/JB.00915-08. PMC 2612445. PMID 18952787.
- ^ Pulvermacher SC, Stauffer LT, Stauffer GV (January 2009). "Role of the sRNA GcvB in regulation of cycA in Escherichia coli". Microbiology. 155 (Pt 1): 106–114. doi: 10.1099/mic.0.023598-0. PMID 19118351.
- ^ Vogel J (January 2009). "A rough guide to the non-coding RNA world of Salmonella". Mol. Microbiol. 71 (1): 1–11. doi: 10.1111/j.1365-2958.2008.06505.x. hdl: 11858/00-001M-0000-000E-C124-A. PMID 19007416. S2CID 205366563.
- ^ Coornaert, A; Chiaruttini, C; Springer, M; Guillier, M (Jan 2013). "Post-Transcriptional Control of the Escherichia coli PhoQ-PhoP Two-Component System by Multiple sRNAs Involves a Novel Pairing Region of GcvB". PLOS Genetics. 9 (1): e1003156. doi: 10.1371/journal.pgen.1003156. PMC 3536696. PMID 23300478.
- ^ Busi F, Cayrol B, Lavelle C, LeDerout J, Piétrement O, Le Cam E, Geinguenaud F, Lacoste J, Régnier P, Arluison V (2009). "Auto-assembly as a new regulatory mechanism of noncoding RNA". Cell Cycle. 8 (6): 952–954. doi: 10.4161/cc.8.6.7905. PMID 19221499.
- ^ Cayrol B, Geinguenaud F, Lacoste J, et al. (2009). "Auto-assembly of E. coli DsrA small noncoding RNA: Molecular characteristics and functional consequences". RNA Biol. 6 (4): 434–445. doi: 10.4161/rna.6.4.8949. PMID 19535898.
- ^ Pulvermacher SC, Stauffer LT, Stauffer GV (April 2008). "The role of the small regulatory RNA GcvB in GcvB/mRNA posttranscriptional regulation of oppA and dppA in Escherichia coli". FEMS Microbiol. Lett. 281 (1): 42–50. doi: 10.1111/j.1574-6968.2008.01068.x. PMID 18312576.
- ^ Gulliver, Emily L.; Wright, Amy; Lucas, Deanna Deveson; Mégroz, Marianne; Kleifeld, Oded; Schittenhelm, Ralf B.; Powell, David R.; Seemann, Torsten; Bulitta, Jürgen B. (May 2018). "Determination of the small RNA GcvB regulon in the Gram-negative bacterial pathogen Pasteurella multocida and identification of the GcvB seed binding region". RNA. 24 (5): 704–720. doi: 10.1261/rna.063248.117. ISSN 1469-9001. PMC 5900567. PMID 29440476.
Further reading
- Busi F, Le Derout J, Cerciat M, Régnier P, Hajnsdorf E (July 2010). "Is the secondary putative RNA-RNA interaction site relevant to GcvB mediated regulation of oppA mRNA in Escherichia coli?". Biochimie. 92 (10): 1458–1461. doi: 10.1016/j.biochi.2010.06.020. PMID 20603180.
- Stauffer LT, Stauffer GV (January 2005). "GcvA interacts with both the alpha and sigma subunits of RNA polymerase to activate the Escherichia coli gcvB gene and the gcvTHP operon". FEMS Microbiol. Lett. 242 (2): 333–338. doi: 10.1016/j.femsle.2004.11.027. PMID 15621456.
- Yang, Q; Figueroa-Bossi, N; Bossi, L (Jan 2014). "Translation Enhancing ACA Motifs and Their Silencing by a Bacterial Small Regulatory RNA". PLOS Genetics. 10 (1): e1004026. doi: 10.1371/journal.pgen.1004026. PMC 3879156. PMID 24391513.