Bacterial small RNA
[1][2] Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq[3] in a number of bacterial species including Escherichia coli,[4][5][6] the model pathogen Salmonella,[7] the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti,[8] marine cyanobacteria,[9] Francisella tularensis (the causative agent of tularaemia),[10] Streptococcus pyogenes[11], the pathogen Staphylococcus aureus[12], and the plant pathogen Xanthomonas oryzae pathovar oryzae.
[3][6] However, a class of sRNAs are shown to be derived from the 3'-UTR of mRNAs by independent transcription or nucleolytic cleavage.
[17] Since these initial discoveries, over six thousand bacterial sRNAs have been identified, largely through RNA-sequencing experiments.
Levels of OxyS are increased in response to oxidative stress, therefore inhibiting RpoS under these conditions.
The expression of OmpC and OmpF is regulated by the sRNAs MicC and MicF in response to stress conditions.
In Salmonella, the pathogenicity island encoded InvR RNA represses synthesis of the major outer membrane protein OmpD; another co-activated DapZ sRNA from 3'-UTR represses abundant membrane Opp/Dpp transporters of oligopeptides;[15] and SgrS sRNA regulates the expression of the secreted effector protein SopD.
[7] In Staphylococcus aureus, RNAIII regulates a number of genes involved in toxin and enzyme production and cell-surface proteins.
[36][37][38][39] In Vibrio species, the Qrr sRNAs and the chaperone protein Hfq are involved in the regulation of quorum sensing.
This mode of growth is often found in pathogenic bacteria, including Pseudomonas aeruginosa, which can form persistent biofilm within the respiratory tract and cause chronic infection.
[42] A mutant P. aeruginosa strain with SbrA deleted formed a 66% smaller biofilm and its ability to infect a nematode model was reduced by nearly half when compared to wildtype P.
[48] It has been shown that target prediction for enterobacterial sRNAs can benefit from transcriptome wide Hfq-binding maps.
