Bacterial small RNA
Bacterial small RNAs are
Origin
In the 1960s, the abbreviation sRNA was used to refer to "soluble RNA," which is now known as
The first bacterial sRNA was discovered and characterized in 1984.[16] MicF in E. coli was found to regulate the expression of a key structural gene that makes up the outer membrane of the E. coli cell.[17] Shortly after, the Staphylococcus aureus sRNA RNAIII was found to act as a global regulator of S. aureus virulence and toxin secretion.[17] Since these initial discoveries, over six thousand bacterial sRNAs have been identified, largely through RNA-sequencing experiments.[18]
Techniques
Several laboratory and bioinformatic techniques can be used to identify and characterize sRNA transcripts.[3]
- RNA-sequencing, or RNA-seq, is used to analyze expression levels of all transcripts in a genome, including sRNAs.[19]
- Microarrays use complementary DNA probes to bind to possible sRNA loci in intergenic regions.[3]
- Northern blotting can reveal possible sRNA transcript size and expression levels by running a mixed RNA sample on an agarose gel and probing for a desired sRNA.[3]
- Target prediction software can predict possible interactions between sRNAs and mRNA by finding regions of complementarity within sRNA and mRNA target sequences.[20]
Function
Bacterial sRNAs have a wide variety of regulatory mechanisms. Generally, sRNAs can bind to
sRNAs that interact with mRNA can also be categorized as
House-keeping
Amongst the targets of sRNAs are a number of house-keeping genes. The 6S RNA binds to
Stress response
Many sRNAs are involved in stress response regulation.
Regulation of RpoS
The RpoS gene in E. coli encodes
Regulation of outer membrane proteins
The
Virulence
In some bacteria sRNAs regulate virulence genes. 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.[25] The FasX sRNA is the only well-characterized regulatory RNA known to control the regulation of several virulence factors in Streptococcus pyogenes, including both cell-surface associated adhesion proteins as well as secreted factors.[36][37][38][39]
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.[40][41]
Biofilm Formation
Biofilm is a type of bacterial growth pattern where multiple layers of bacterial cells adhere to a host surface. 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] The P. aeruginosa sRNA SbrA was found to be necessary for full biofilm formation and pathogenicity.[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. aeruginosa.[42]
Antibiotic Resistance
Several bacterial sRNAs are involved in the regulation of genes that confer
Target prediction
In order to understand an sRNA's function one primarily needs to describe its targets. Here, target predictions represent a 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,
Databases
- BSRD (kwanlab.bio.cuhk.edu.hk/BSRD) is a repository for published sRNA sequences with multiple annotations and expression profiles.[18]
- SRD (srd.genouest.org/) is a database of Staphylococcus aureus sRNAs with sequences, predicted structures, and genome start and end sites.[50]
- sRNAdb (http://srnadb.fb11.uni-giessen.de/sRNAdb) is a database of sRNAs from Gram-positive bacterial species with sequence annotation.[51]
See also
- 5 prime ureB sRNA
- Aar small RNA, an sRNA produced by species of Acinetobacter
- AfaR small RNA, a small RNA produced by the bacterium Escherichia coli.
- Bacillus subtilis BSR sRNAs
- Escherichia coli sRNA
- Mycobacterium tuberculosis sRNA
- Bacteroides thetaiotaomicron sRNA
- Non-coding RNA
- Xanthomonas sRNA
- Brucella sRNA
- Anti small RNA
- Riboswitches
- Streptococcus sRNA
- MicF, the first characterized chromosomal sRNA
- RNAIII, the first characterized bacterial sRNA found to influence virulence
- VR-RNA, a small RNA produced by Clostridium perfringens.
References
- ^ PMID 17574901.
- PMID 18981732.
- ^ PMID 11445539.
- PMID 12654996.
- S2CID 5243194.
- ^ PMID 11448770.
- ^ S2CID 205366563.
- PMID 20398411.
- PMID 16168080.
- PMID 21067590.
- PMID 23762235.
- ^ PMID 21423670.
- PMID 21276262.
- PMID 5969078.
- ^ PMID 22922465.
- PMID 6201848.
- ^ PMID 27337442.
- ^ PMID 23203879.
- PMID 28756649.
- ^ PMID 16717284.
- PMID 27836995.
- ^ PMID 19239884.
- PMID 24348246.
- PMID 17383220.
- ^ ISBN 978-3-540-28129-0.
- PMID 25389522.
- PMID 34043736.
- PMID 20227418.
- PMID 26870012.
- PMID 12753181.
- PMID 20393591.
- ^ PMID 17055775.
- PMID 11601842.
- PMID 15466019.
- PMID 19411843.
- PMID 21143309.
- PMID 22882718.
- PMID 25586884.
- PMID 26391206.
- PMID 15242645.
- PMID 21453446.
- ^ PMID 28771593.
- ^ PMID 28529506.
- PMID 23980183.
- ^ PMID 24838564.
- PMID 18940824.
- PMID 28472523.
- PMID 21672960.
- PMID 27044921.
- PMID 25805861.
- PMID 22883983.