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Bacterial small RNA

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Title: Bacterial small RNA  
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Subject: AfaR small RNA, 5 prime ureB sRNA, SR1 RNA, Xanthomonas sRNA, Bacillus subtilis BSR sRNAs
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Bacterial small RNA

Bacterial small RNAs (sRNA) are small (50-250 nucleotide) non-coding RNA molecules produced by bacteria; they are highly structured and contain several stem-loops.[1][2] Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as microarrays and Northern blotting in a number of bacterial species including Escherichia coli, the nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti, marine cyanobacteria, Francisella tularensis (the causative agent of tularaemia) and the plant pathogen Xanthomonas oryzae pathovar oryzae.[3][4][5][6][7][8][9][10]

In the 1960s, the abbreviation sRNA was used to refer to "soluble RNA," which is now known as transfer RNA or tRNA (for an example of the abbreviation used in this sense, see.[11])


sRNAs can either bind to protein targets, and modify the function of the bound protein, or bind to mRNA targets and regulate gene expression. Antisense sRNAs can be categorised as cis-encoded sRNAs, where there is an overlap between the antisense sRNA and the target gene, and trans-encoded sRNAs, where the antisense sRNA gene is separate from the target gene.[1][12]


Amongst the targets of sRNAs are a number of house-keeping genes. The 6S RNA binds to RNA polymerase and regulates transcription, tmRNA has functions in protein synthesis, including the recycling of stalled ribosomes, 4.5S RNA regulates signal recognition particle (SRP), which is required for the secretion of proteins and RNase P is involved in maturing tRNAs.[13][14]

Stress response

Many sRNAs are involved in stress response regulation.[15] They are expressed under stress conditions such as cold shock, iron depletion, onset of the SOS response and sugar stress.[14] The small RNA nitrogen stress-induced RNA 1 (NsiR1) is produced by Cyanobacteria under conditions of nitrogen deprivation.[16]

Regulation of RpoS

The RpoS gene in E. coli encodes sigma 38, a sigma factor which regulates stress response and acts as a transcriptional regulator for many genes involved in cell adaptation. At least three sRNAs, DsrA, RprA and OxyS, regulate the translation of RpoS. DsrA and RprA both activate RpoS translation by base pairing to a region in the leader sequence of the RpoS mRNA and disrupting formation of a hairpin which frees up the ribosome loading site. OxyS inhibits RpoS translation. DsrA levels are increased in response to low temperatures and osmotic stress, and RprA levels are increased in response to osmotic stress and cell-surface stress, therefore increasing RpoS levels in response to these conditions. Levels of OxyS are increased in response to oxidative stress, therefore inhibiting RpoS under these conditions.[14][17][18]

Regulation of outer membrane proteins

The outer membrane of gram negative bacteria acts as a barrier to prevent the entry of toxins into the bacterial cell, and plays a role in the survival of bacterial cells in diverse environments. Outer membrane proteins (OMPs) include porins and adhesins. Numerous sRNAs regulate the expression of OMPs. The porins OmpC and OmpF are responsible for the transport of metabolites and toxins. The expression of OmpC and OmpF is regulated by the sRNAs MicC and MicF in response to stress conditions.[19][20][21] The outer membrane protein OmpA anchors the outer membrane to the murein layer of the periplasmic space. Its expression is downregulated in the stationary phase of cell-growth. In E. coli the sRNA MicA depletes OmpA levels, in Vibrio cholerae the sRNA VrrA represses synthesis of OmpA in response to stress.[19][22]


In some bacteria sRNAs regulate virulence genes. In Salmonella the InvR RNA represses synthesis of the major outer membrane protein OmpD, and SgrS sRNA regulates the expression of the secreted effector protein SopD.[23] In Staphylococcus aureus, RNAIII regulates a number of genes involved in toxin and enzyme production and cell-surface proteins.[14] The FasX and Pel sRNAs in Streptococcus pyogenes are encoded in loci associated with virulence. Pel RNA activates synthesis of surface-associated and secreted proteins.[14]

Quorum sensing

In Vibrio species, the Qrr sRNAs and the chaperone protein Hfq are involved in the regulation of quorum sensing. Qrr sRNAs regulate the expression of several mRNAs including the quorum-sensing master regulators LuxR and HapR.[24][25]

Target prediction

In order to understand an sRNA's function one primarily needs to describe its targets. Here, target predictions represent a sensible, fast and free method for initial characterization of putative targets, given that the sRNA actually exerts its function via direct base pairing with a target RNA. Examples are CopraRNA,[26][27] IntaRNA,[27][28] TargetRNA[29] and RNApredator.[30]


BSRD ( is a repository for published sRNA sequences with multiple valuable annotations and expression profiles.[31]

See also


  1. ^ a b Vogel J, Wagner EG (June 2007). "Target identification of small noncoding RNAs in bacteria". Curr. Opin. Microbiol. 10 (3): 262–70.  
  2. ^ Viegas SC, Arraiano CM (2008). "Regulating the regulators: How ribonucleases dictate the rules in the control of small non-coding RNAs". RNA Biol 5 (4): 230–43.  
  3. ^ Hershberg R, Altuvia S, Margalit H (April 2003). "A survey of small RNA-encoding genes in Escherichia coli". Nucleic Acids Res. 31 (7): 1813–20.  
  4. ^ Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (July 2001). "Identification of novel small RNAs using comparative genomics and microarrays". Genes Dev. 15 (13): 1637–51.  
  5. ^ Argaman L, Hershberg R, Vogel J, et al. (June 2001). "Novel small RNA-encoding genes in the intergenic regions of Escherichia coli". Curr. Biol. 11 (12): 941–50.  
  6. ^ Rivas E, Klein RJ, Jones TA, Eddy SR (September 2001). "Computational identification of noncoding RNAs in E. coli by comparative genomics". Curr. Biol. 11 (17): 1369–73.  
  7. ^ Schlüter JP, Reinkensmeier J, Daschkey S, et al. (2010). "A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti". BMC Genomics 11: 245.  
  8. ^ Axmann IM, Kensche P, Vogel J, Kohl S, Herzel H, Hess WR (2005). "Identification of cyanobacterial non-coding RNAs by comparative genome analysis". Genome Biol. 6 (9): R73.  
  9. ^ Postic G, Frapy E, Dupuis M, et al. (2010). "Identification of small RNAs in Francisella tularensis". BMC Genomics 11: 625.  
  10. ^ Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX, Jia YT (2011). "Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae". BMC Genomics 12: 87.  
  11. ^ Crick F (1966). "Codon–anticodon pairing: the wobble hypothesis". J Mol Biol 19 (2): 548–55.  
  12. ^ Cao Y, Wu J, Liu Q, et al. (November 2010). "sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments". RNA 16 (11): 2051–7.  
  13. ^ Wassarman KM (April 2007). "6S RNA: a small RNA regulator of transcription". Curr. Opin. Microbiol. 10 (2): 164–8.  
  14. ^ a b c d e Christian Hammann; Nellen, Wolfgang (2005). Small RNAs:: Analysis and Regulatory Functions (Nucleic Acids and Molecular Biology). Berlin: Springer.  
  15. ^ Caswell CC, Oglesby-Sherrouse AG, Murphy ER (October 2014). "Sibling rivalry: related bacterial small RNAs and their redundant and non-redundant roles". Front Cell Infect Microbiol 2014 (4): 151.  
  16. ^ Ionescu, D; Voss, B; Oren, A; Hess, WR; Muro-Pastor, AM (Apr 30, 2010). "Heterocyst-specific transcription of NsiR1, a non-coding RNA encoded in a tandem array of direct repeats in cyanobacteria.". Journal of Molecular Biology 398 (2): 177–88.  
  17. ^ Repoila F, Majdalani N, Gottesman S (May 2003). "Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm". Mol. Microbiol. 48 (4): 855–61.  
  18. ^ Benjamin JA, Desnoyers G, Morissette A, Salvail H, Massé E (March 2010). "Dealing with oxidative stress and iron starvation in microorganisms: an overview". Can. J. Physiol. Pharmacol. 88 (3): 264–72.  
  19. ^ a b Vogel J, Papenfort K (December 2006). "Small non-coding RNAs and the bacterial outer membrane". Curr. Opin. Microbiol. 9 (6): 605–11.  
  20. ^ Delihas N, Forst S (October 2001). "MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors". J. Mol. Biol. 313 (1): 1–12.  
  21. ^ Chen S, Zhang A, Blyn LB, Storz G (October 2004). "MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli". J. Bacteriol. 186 (20): 6689–97.  
  22. ^ Song T, Wai SN (July 2009). "A novel sRNA that modulates virulence and environmental fitness of Vibrio cholerae". RNA Biol 6 (3): 254–8.  
  23. ^ Vogel J (January 2009). "A rough guide to the non-coding RNA world of Salmonella". Mol. Microbiol. 71 (1): 1–11.  
  24. ^ Lenz DH, Mok KC, Lilley BN, Kulkarni RV, Wingreen NS, Bassler BL (July 2004). "The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae". Cell 118 (1): 69–82.  
  25. ^ Bardill JP, Zhao X, Hammer BK (April 2011). "The Vibrio cholerae quorum sensing response is mediated by Hfq-dependent sRNA/mRNA base-pairing interactions". Mol Microbiol 80 (5): 1381–94.  
  26. ^ Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013). "Comparative genomics boosts target prediction for bacterial small RNAs.". Proc Natl Acad Sci U S A 110 (37): E3487–E3496.  
  27. ^ a b Wright PR, Georg J, Mann M, Sorescu DA, Richter AS, Lott S, Kleinkauf R, Hess WR, Backofen R (2014). "CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains.". Nucleic Acids Res 42 (Web Server): W119–23.  
  28. ^ Busch A, Richter AS, Backofen R (2008). "IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions.". Bioinformatics 24 (24): 2849–56.  
  29. ^ Tjaden B, Goodwin SS, Opdyke JA, et al. (2006). "Target prediction for small, noncoding RNAs in bacteria". Nucleic Acids Res. 34 (9): 2791–802.  
  30. ^ Eggenhofer F, Tafer H, Stadler PF, Hofacker IL (2011). "RNApredator: fast accessibility-based prediction of sRNA targets". Nucleic Acids Res 39 (Web Server): W149–54.  
  31. ^ Li, L; Kwan, HS (January 2013). "BSRD: a repository for bacterial small regulatory RNA.". Nucleic Acids Research 41 (Database issue): D233–8.  
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