GcvB RNA

Last updated
GcvB RNA
RF00022.jpg
Predicted secondary structure and sequence conservation of GcvB
Identifiers
SymbolGcvB
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]

Contents

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]

References

  1. ↑ 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.
  2. 1 2 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.
  3. ↑ 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.
  4. ↑ 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.
  5. ↑ 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.
  6. ↑ 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.
  7. ↑ 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.
  8. ↑ 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.
  9. ↑ 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.
  10. ↑ 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.
  11. ↑ 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.
  12. ↑ 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.
  13. ↑ 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.
  14. ↑ 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.
  15. ↑ 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.

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