GcvB RNA

Last updated
GcvB RNA
RF00022.jpg
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]

Related Research Articles

Bacterial translation is the process by which messenger RNA is translated into proteins in bacteria.

<i>trp</i> operon Operon that codes for the components for production of tryptophan

The trp operon is a group of genes that are transcribed together, encoding the enzymes that produce the amino acid tryptophan in bacteria. The trp operon was first characterized in Escherichia coli, and it has since been discovered in many other bacteria. The operon is regulated so that, when tryptophan is present in the environment, the genes for tryptophan synthesis are repressed.

The gene rpoS encodes the sigma factor sigma-38, a 37.8 kD protein in Escherichia coli. Sigma factors are proteins that regulate transcription in bacteria. Sigma factors can be activated in response to different environmental conditions. rpoS is transcribed in late exponential phase, and RpoS is the primary regulator of stationary phase genes. RpoS is a central regulator of the general stress response and operates in both a retroactive and a proactive manner: it not only allows the cell to survive environmental challenges, but it also prepares the cell for subsequent stresses (cross-protection). The transcriptional regulator CsgD is central to biofilm formation, controlling the expression of the curli structural and export proteins, and the diguanylate cyclase, adrA, which indirectly activates cellulose production. The rpoS gene most likely originated in the gammaproteobacteria.

fis E. coli gene

fis is an E. coli gene encoding the Fis protein. The regulation of this gene is more complex than most other genes in the E. coli genome, as Fis is an important protein which regulates expression of other genes. It is supposed that fis is regulated by H-NS, IHF and CRP. It also regulates its own expression (autoregulation). Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions.

<span class="mw-page-title-main">OmrA-B RNA</span>

The OmrA-B RNA gene family is a pair of homologous OmpR-regulated small non-coding RNA that was discovered in E. coli during two large-scale screens. OmrA-B is highly abundant in stationary phase, but low levels could be detected in exponentially growing cells as well. RygB is adjacent to RygA a closely related RNA. These RNAs bind to the Hfq protein and regulate gene expression by antisense binding. They negatively regulate the expression of several genes encoding outer membrane proteins, including cirA, CsgD, fecA, fepA and ompT by binding in the vicinity of the Shine-Dalgarno sequence, suggesting the control of these targets is dependent on Hfq protein and RNase E. Taken together, these data suggest that OmrA-B participates in the regulation of outer membrane composition, responding to environmental conditions.

<span class="mw-page-title-main">Sib RNA</span>

Sib RNA refers to a group of related non-coding RNA. They were originally named QUAD RNA after they were discovered as four repeat elements in Escherichia coli intergenic regions. The family was later renamed Sib when it was discovered that the number of repeats is variable in other species and in other E. coli strains.

<span class="mw-page-title-main">RprA RNA</span>

The RprA RNA gene encodes a 106 nucleotide regulatory non-coding RNA. Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site.

<span class="mw-page-title-main">RyhB</span> 90 nucleotide RNA

RyhB RNA is a 90 nucleotide RNA that down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur.

<span class="mw-page-title-main">Spot 42 RNA</span>

Spot 42 (spf) RNA is a regulatory non-coding bacterial small RNA encoded by the spf gene. Spf is found in gammaproteobacteria and the majority of experimental work on Spot42 has been performed in Escherichia coli and recently in Aliivibrio salmonicida. In the cell Spot42 plays essential roles as a regulator in carbohydrate metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP complex.

<span class="mw-page-title-main">MicA RNA</span>

The MicA RNA is a small non-coding RNA that was discovered in E. coli during a large scale screen. Expression of SraD is highly abundant in stationary phase, but low levels could be detected in exponentially growing cells as well.

<span class="mw-page-title-main">ArcZ RNA</span>

In molecular biology the ArcZ RNA is a small non-coding RNA (ncRNA). It is the functional product of a gene which is not translated into protein. ArcZ is an Hfq binding RNA that functions as an antisense regulator of a number of protein coding genes.

<span class="mw-page-title-main">GlmZ RNA</span> Small non-coding RNA (ncRNA)

GlmZ is a small non-coding RNA (ncRNA). It is the functional product of a gene which is not translated into protein.

<span class="mw-page-title-main">SroB RNA</span> Non-coding RNA gene

The sroB RNA is a non-coding RNA gene of 90 nucleotides in length. sroB is found in several Enterobacterial species but its function is unknown. SroB is found in the intergenic region on the opposite strand to the ybaK and ybaP genes. SroB is expressed in stationary phase. Experiments have shown that SroB is a Hfq binding sRNA.

<span class="mw-page-title-main">GlmY RNA</span>

The GlmY RNA family consists of a number of bacterial RNA genes of around 167 bases in length. The GlmY RNA gene is present in Escherichia coli, Shigella flexneri, Yersinia pestis and Salmonella species, where it is found between the yfhK and purL genes. It was originally predicted in a bioinformatic screen for novel ncRNAs in E. coli.

<span class="mw-page-title-main">Hfq protein</span>

The Hfq protein encoded by the hfq gene was discovered in 1968 as an Escherichia coli host factor that was essential for replication of the bacteriophage Qβ. It is now clear that Hfq is an abundant bacterial RNA binding protein which has many important physiological roles that are usually mediated by interacting with Hfq binding sRNA.

<span class="mw-page-title-main">Hok/sok system</span>

The hok/sok system is a postsegregational killing mechanism employed by the R1 plasmid in Escherichia coli. It was the first type I toxin-antitoxin pair to be identified through characterisation of a plasmid-stabilising locus. It is a type I system because the toxin is neutralised by a complementary RNA, rather than a partnered protein.

Bacterial small RNAs are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops. Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a number of bacterial species including Escherichia coli, the model pathogen Salmonella, the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti, marine cyanobacteria, Francisella tularensis, Streptococcus pyogenes, the pathogen Staphylococcus aureus, and the plant pathogen Xanthomonas oryzae pathovar oryzae. Bacterial sRNAs affect how genes are expressed within bacterial cells via interaction with mRNA or protein, and thus can affect a variety of bacterial functions like metabolism, virulence, environmental stress response, and structure.

<span class="mw-page-title-main">FnrS RNA</span>

FnrS RNA is a family of Hfq-binding small RNA whose expression is upregulated in response to anaerobic conditions. It is named FnrS because its expression is strongly dependent on fumarate and nitrate reductase regulator (FNR), a direct oxygen availability sensor.

<span class="mw-page-title-main">TisB-IstR toxin-antitoxin system</span> Biochemical process related to DNA damage

The TisB-IstR toxin-antitoxin system is the first known toxin-antitoxin system which is induced by the SOS response in response to DNA damage.

<span class="mw-page-title-main">LdrD-RdlD toxin-antitoxin system</span>

RdlD RNA is a family of small non-coding RNAs which repress the protein LdrD in a type I toxin-antitoxin system. It was discovered in Escherichia coli strain K-12 in a long direct repeat (LDR) named LDR-D. This locus encodes two products: a 35 amino acid peptide toxin (ldrD) and a 60 nucleotide RNA antitoxin. The 374nt toxin mRNA has a half-life of around 30 minutes while rdlD RNA has a half-life of only 2 minutes. This is in keeping with other type I toxin-antitoxin systems.

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.

Further reading