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.{{cite journal | vauthors = Hershberg R, Altuvia S, Margalit H | title = A survey of small RNA-encoding genes in Escherichia coli | journal = Nucleic Acids Research | volume = 31 | issue = 7 | pages = 1813–1820 | date = April 2003 | pmid = 12654996 | pmc = 152812 | doi = 10.1093/nar/gkg297 }} 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.{{cite journal | vauthors = Rivas E, Klein RJ, Jones TA, Eddy SR | title = Computational identification of noncoding RNAs in E. coli by comparative genomics | journal = Current Biology | volume = 11 | issue = 17 | pages = 1369–1373 | date = September 2001 | pmid = 11553332 | doi = 10.1016/S0960-9822(01)00401-8 | s2cid = 5243194 | doi-access = free }} 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.{{cite journal | vauthors = Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S | title = Novel small RNA-encoding genes in the intergenic regions of Escherichia coli | journal = Current Biology | volume = 11 | issue = 12 | pages = 941–950 | date = June 2001 | pmid = 11448770 | doi = 10.1016/S0960-9822(01)00270-6 | doi-access = free }} 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).{{cite journal | vauthors = Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S | title = Identification of novel small RNAs using comparative genomics and microarrays | journal = Genes & Development | volume = 15 | issue = 13 | pages = 1637–1651 | date = July 2001 | pmid = 11445539 | pmc = 312727 | doi = 10.1101/gad.901001 }} UptR sRNA transcribed from the uptR gene is implicated in suppressing extracytoplasmic toxicity by reducing the amount of membrane-bound toxic hybrid protein.{{cite journal | vauthors = Guigueno A, Dassa J, Belin P, Boquet PL | title = Oversynthesis of a new Escherichia coli small RNA suppresses export toxicity of DsbA'-PhoA unfoldable periplasmic proteins | journal = Journal of Bacteriology | volume = 183 | issue = 4 | pages = 1147–1158 | date = February 2001 | pmid = 11157926 | pmc = 94987 | doi = 10.1128/JB.183.4.1147-1158.2001 }}

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.{{cite journal | vauthors = Sudo N, Soma A, Muto A, Iyoda S, Suh M, Kurihara N, Abe H, Tobe T, Ogura Y, Hayashi T, Kurokawa K, Ohnishi M, Sekine Y | title = A novel small regulatory RNA enhances cell motility in enterohemorrhagic Escherichia coli | journal = The Journal of General and Applied Microbiology | volume = 60 | issue = 1 | pages = 44–50 | date = 2014-01-01 | pmid = 24646762 | doi = 10.2323/jgam.60.44 | doi-access = free }}

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.{{cite journal | vauthors = Guo Y, Quiroga C, Chen Q, McAnulty MJ, Benedik MJ, Wood TK, Wang X | title = RalR (a DNase) and RalA (a small RNA) form a type I toxin-antitoxin system in Escherichia coli | journal = Nucleic Acids Research | volume = 42 | issue = 10 | pages = 6448–6462 | date = June 2014 | pmid = 24748661 | pmc = 4041452 | doi = 10.1093/nar/gku279 }}

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.{{cite journal | vauthors = Rau MH, Bojanovič K, Nielsen AT, Long KS | title = Differential expression of small RNAs under chemical stress and fed-batch fermentation in E. coli | journal = BMC Genomics | volume = 16 | pages = 1051 | date = December 2015 | pmid = 26653712 | pmc = 4676190 | doi = 10.1186/s12864-015-2231-8 | doi-access = free }} 50x50px This article contains quotations from this source, which is available under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.

Esre sRNA, for "essential small RNA in E. coli", is located in 3′ moiety of yigP gene{{cite journal | vauthors = Chen Z, Wang Y, Li Y, Li Y, Fu N, Ye J, Zhang H | title = Esre: a novel essential non-coding RNA in Escherichia coli | journal = FEBS Letters | volume = 586 | issue = 8 | pages = 1195–1200 | date = April 2012 | pmid = 22575655 | doi = 10.1016/j.febslet.2012.03.010 | s2cid = 43271507 }} (also known as ubiJ), which is involved in coenzyme Q8 biosynthesis in Escherichia coli and Salmonella enterica serovar Typhimurium.

AgrB antisene 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.{{cite journal | vauthors = Weel-Sneve R, Kristiansen KI, Odsbu I, Dalhus B, Booth J, Rognes T, Skarstad K, Bjørås M | title = Single transmembrane peptide DinQ modulates membrane-dependent activities | journal = PLOS Genetics | volume = 9 | issue = 2 | pages = e1003260 | date = 2013 | pmid = 23408903 | pmc = 3567139 | doi = 10.1371/journal.pgen.1003260 | doi-access = free }}

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| Image:sraA_secondary_structure.jpg|sraA: Secondary structure taken from the [https://archive.today/20121205022142/http://rfam.org/ Rfam] database. Family [http://rfam.org/family/RF02029 RF02029]

| Image:tp2_secondary_structure.jpg |tp2: Secondary structure taken from the [https://archive.today/20121205022142/http://rfam.org/ Rfam] database. Family [http://rfam.org/family/RF02030 RF02030]

| Image:tpke11_secondary_structure.jpg |tpke11: Secondary structure taken from the [https://archive.today/20121205022142/http://rfam.org/ Rfam] database. Family [http://rfam.org/family/RF02031 RF02031]

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Escherichia coli sRNA

References

Further reading