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])

Function

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]

House-keeping

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. 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.^[15]

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][16][17]

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.^[18][19][20] 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.^[18][21]

Virulence

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.^[22] 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.^[23][24]

Database

BSRD (kwanlab.bio.cuhk.edu.hk/BSRD) is a repository for published sRNA sequences with multiple valuable annotations and expression profiles.^[25]

See also

• Escherichia coli sRNA
• Mycobacterium tuberculosis sRNA
• Bacillus subtilis BSR sRNAs
• Non-coding RNA
• Xanthomonas sRNA

References