Escherichia Coli SRNA
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Escherichia coli ''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly fo ...
'' contains a number of small RNAs located in
intergenic region An intergenic region is a stretch of DNA sequences located between genes. Intergenic regions may contain functional elements and junk DNA. Properties and functions Intergenic regions may contain a number of functional DNA sequences such as p ...
s of its
genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
. The presence of at least 55 of these has been verified experimentally. 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. A computational screen based on promoter sequences recognised by the
sigma factor A sigma factor (σ factor or specificity factor) is a protein needed for initiation of Transcription (biology), transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to g ...
sigma 70 and on
Rho Rho (; uppercase Ρ, lowercase ρ or ; or ) is the seventeenth letter of the Greek alphabet. In the system of Greek numerals it has a value of 100. It is derived from Phoenician alphabet, Phoenician letter resh . Its uppercase form uses the same ...
-independent terminators predicted 24 putative sRNA genes, 14 of these were verified experimentally by
northern blotting The northern blot, or RNA blot,Gilbert, S. F. (2000) Developmental Biology, 6th Ed. Sunderland MA, Sinauer Associates. is a technique used in molecular biology research to study gene expression by detection of RNA (or isolated mRNA) in a sample.Ke ...
. 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. A screen for sRNA genes based on homology to ''
Salmonella ''Salmonella'' is a genus of bacillus (shape), rod-shaped, (bacillus) Gram-negative bacteria of the family Enterobacteriaceae. The two known species of ''Salmonella'' are ''Salmonella enterica'' and ''Salmonella bongori''. ''S. enterica'' ...
'' and ''
Klebsiella ''Klebsiella'' is a genus of Gram-negative, oxidase-negative, rod-shaped bacteria with a prominent polysaccharide-based capsule. ''Klebsiella'' is named after German-Swiss microbiologist Edwin Klebs (1834–1913). Carl Friedlander described ' ...
'' identified 59 candidate sRNA genes. From this set of candidate genes,
microarray A microarray is a multiplex (assay), multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of biological interactions. It is a two-dimensional array on a Substrate (materials science), solid substrate—usu ...
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). UptR sRNA transcribed from the ''uptR'' gene is implicated in suppressing extracytoplasmic toxicity by reducing the amount of membrane-bound toxic hybrid protein. 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''. ''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 In molecular biology, endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain (namely DNA or RNA). Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically (with regard to sequence), while man ...
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''. 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. ''Esre'' sRNA, for "essential small RNA in ''E. coli''", is located in 3′ moiety of ''yigP'' gene (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 RNA interference (RNAi) is a biological process in which RNA molecules are involved in sequence-specific suppression of gene expression by double-stranded RNA, through translational or transcriptional repression. Historically, RNAi was known by ...
and counteracts its toxicity. * ''Mycobacterium tuberculosis'' sRNA * ''Pseudomonas'' sRNA * ''Bacillus subtilis'' BSR sRNAs * ''Caenorhabditis elegans'' sRNA * ''Bacteroides thetaiotaomicron'' sRNA *
List of RNA structure prediction software This list of RNA structure prediction software is a compilation of software tools and web portals used for RNA structure prediction. Single sequence secondary structure prediction. Single sequence tertiary structure prediction Comparative met ...


References


Further reading

* * * * * {{refend Non-coding RNA