Escherichia coli sRNA

Escherichia coli contains a number of small RNAs located in intergenic regions of its genome. The presence of at least 55 of these has been verified experimentally.[1] 275 potential sRNA-encoding loci were identified computationally using the QRNA program. These loci will include false positives, so the number of sRNA genes in E. coli is likely to be less than 275.[2] A computational screen based on promoter sequences recognised by the sigma factor sigma 70 and on Rho-independent terminators predicted 24 putative sRNA genes, 14 of these were verified experimentally by northern blotting. The experimentally verified sRNAs included the well characterised sRNAs RprA and RyhB. Many of the sRNAs identified in this screen, including RprA, RyhB, SraB and SraL, are only expressed in the stationary phase of bacterial cell growth.[3] A screen for sRNA genes based on homology to Salmonella and Klebsiella identified 59 candidate sRNA genes. From this set of candidate genes, microarray analysis and northern blotting confirmed the existence of 17 previously undescribed sRNAs, many of which bind to the chaperone protein Hfq and regulate the translation of RpoS (Sigma 38).[4] UptR sRNA transcribed from the uptR gene is implicated in suppressing extracytoplasmic toxicity by reducing the amount of membrane-bound toxic hybrid protein.[5]

Cell motility enhancing sRNA named Esr41, was discovered in intergenic region of pathogenic enterohemorrhagic E.coli (EHEC) O157:H7 Sakai. Esr41 sequence is not present in nonpathogenic E. coli K12, but the sRNA can induce cell motility in K12 as well, suggesting that target genes controlled by Esr41 are present in both E.coli.[6]

Trans-encoded small RNA RalA has 16 nucleotides complementary to coding region of toxin RalR mRNA. RalA functions as an antitoxin by preventing translation of RalR (a non-specific endonuclease that cleaves methylated and unmethylated DNA). Its activity requires RNA chaperone Hfq. RalR and RalA form a type I toxin-antitoxin (TA) system. RalR/RaLA TA locus is responsible for resistance to the antibiotic fosfomycin in E.coli.[7]

Deep sequencing of RNA expressed during chemical stress and high cell density fermentation discovered 253 novel intergenic transcripts adding to roughly 200 intergenic sRNAs previously described in E. coli. Several of the sRNAs exhibited specific expression patterns during high cell density fermentation and are differentially expressed in the presence of multiple chemicals, suggesting they may play roles during stress conditions. The novel sRNAs showing differential expression in several stress conditions were: ES003, ES036, ES056, ES098, ES173, ES180, ES205, ES220, ES222, ES239.[8]

Esre sRNA, for "essential small RNA in E. coli", is located in 3′ moiety of yigP gene[9] (also known as ubiJ), which is involved in coenzyme Q8 biosynthesis in Escherichia coli and Salmonella enterica serovar Typhimurium.

AgrB antisense RNA (arsR-gov region gene B) is transcribed opposite of dinQ (translates into a toxic single transmembrane peptide) with 30 complementary nucleotides. AgrB appears to repress accumulation of dinQ by RNA interference and counteracts its toxicity.[10]

* Mycobacterium tuberculosis sRNA
* Pseudomonas sRNA
* Bacillus subtilis BSR sRNAs
* Caenorhabditis elegans sRNA
* Bacteroides thetaiotaomicron sRNA
* List of RNA structure prediction software

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Gallery of E.coli small RNA secondary structure images

* sraA: Secondary structure taken from the Rfam database. Family RF02029

* tp2: Secondary structure taken from the Rfam database. Family RF02030

* tpke11: Secondary structure taken from the Rfam database. Family RF02031

## References

1. ↑ "A survey of small RNA-encoding genes in Escherichia coli". Nucleic Acids Research 31 (7): 1813–1820. April 2003. doi:10.1093/nar/gkg297. PMID 12654996.
2. ↑ "Computational identification of noncoding RNAs in E. coli by comparative genomics". Current Biology 11 (17): 1369–1373. September 2001. doi:10.1016/S0960-9822(01)00401-8. PMID 11553332. Bibcode: 2001CBio...11.1369R.
3. ↑ "Novel small RNA-encoding genes in the intergenic regions of Escherichia coli". Current Biology 11 (12): 941–950. June 2001. doi:10.1016/S0960-9822(01)00270-6. PMID 11448770. Bibcode: 2001CBio...11..941A.
4. ↑ "Identification of novel small RNAs using comparative genomics and microarrays". Genes & Development 15 (13): 1637–1651. July 2001. doi:10.1101/gad.901001. PMID 11445539.
5. ↑ "Oversynthesis of a new Escherichia coli small RNA suppresses export toxicity of DsbA'-PhoA unfoldable periplasmic proteins". Journal of Bacteriology 183 (4): 1147–1158. February 2001. doi:10.1128/JB.183.4.1147-1158.2001. PMID 11157926.
6. ↑ "A novel small regulatory RNA enhances cell motility in enterohemorrhagic Escherichia coli". The Journal of General and Applied Microbiology 60 (1): 44–50. 2014-01-01. doi:10.2323/jgam.60.44. PMID 24646762.
7. ↑ "RalR (a DNase) and RalA (a small RNA) form a type I toxin-antitoxin system in Escherichia coli". Nucleic Acids Research 42 (10): 6448–6462. June 2014. doi:10.1093/nar/gku279. PMID 24748661.
8. ↑ "Differential expression of small RNAs under chemical stress and fed-batch fermentation in E. coli". BMC Genomics 16. December 2015. doi:10.1186/s12864-015-2231-8. PMID 26653712. 50x50px This article contains quotations from this source, which is available under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.
9. ↑ "Esre: a novel essential non-coding RNA in Escherichia coli". FEBS Letters 586 (8): 1195–1200. April 2012. doi:10.1016/j.febslet.2012.03.010. PMID 22575655. Bibcode: 2012FEBSL.586.1195C.
10. ↑ "Single transmembrane peptide DinQ modulates membrane-dependent activities". PLOS Genetics 9 (2). 2013. doi:10.1371/journal.pgen.1003260. PMID 23408903.

## Further reading

* "A computational approach to identify genes for functional RNAs in genomic sequences". Nucleic Acids Research 29 (19): 3928–3938. October 2001. doi:10.1093/nar/29.19.3928. PMID 11574674.
* "A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome". Bio Systems 65 (2–3): 157–177. 2002. doi:10.1016/S0303-2647(02)00013-8. PMID 12069726. Bibcode: 2002BiSys..65..157C.
* "Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays". Nucleic Acids Research 30 (17): 3732–3738. September 2002. doi:10.1093/nar/gkf505. PMID 12202758.
* "How to find small non-coding RNAs in bacteria". Biological Chemistry 386 (12): 1219–1238. December 2005. doi:10.1515/BC.2005.140. PMID 16336117.
* "Genome-wide detection of novel regulatory RNAs in E. coli". Genome Research 21 (9): 1487–1497. September 2011. doi:10.1101/gr.119370.110. PMID 21665928.

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