A transposon-derived small RNA regulates gene expression in Salmonella Typhimurium

Ellis, Mary; Trussler, Ryan S.; Charles, Onella; Haniford, David B.

doi:10.1093/nar/gkx094

Cited by 29 publications

(34 citation statements)

References 68 publications

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“…The irvA 5’ UTR base pairs with gbpC mRNA and prevents its degradation by an RNase J2-mediated pathway (89). Another example is the sRNA derived from the 5’ UTR of the IS200 transposase mRNA (tnpA) , which base pairs with and represses the mRNA encoding a transcriptional regulator (invF) required for the expression of several genes encoding type III secretion system SPI1 effector proteins (90). …”

Section: Other Types Of Multifunctional Srnas/mrnasmentioning

confidence: 99%

Dual-Function RNAs

et al. 2018

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Bacteria are known to use RNA, either as mRNAs encoding proteins or as non-coding small RNAs (sRNAs), to regulate numerous biological processes. However, a few sRNAs have two functions: they act as base pairing RNAs and encode a small protein with additional regulatory functions. Thus, these so called “dual-function” sRNAs can serve as both a riboregulator and an mRNA. In some cases, these two functions can act independently within the same pathway while in other cases, the base-pairing function and protein function act in different pathways. Here, we discuss the five known dual-function sRNAs: SgrS from enteric species, RNAIII and Psm-mec from Staphylococcus aureus, Pel RNA from Streptococcus pyogenes, and SR1 from Bacillus subtilis, and review their mechanisms of action and roles in regulating diverse biological processes. We also discuss the prospect of finding additional dual-function sRNAs and future challenges in studying the overlap and competition between the functions.

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Section: Other Types Of Multifunctional Srnas/mrnasmentioning

confidence: 99%

Dual-Function RNAs

et al. 2018

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“…Small regulatory RNAs contribute to bacterial response to environmental stress, maintenance of cell homeostasis (Updegrove et al 2015;Wagner and Romby 2015), and the modulation of bacterial virulence (Ellis et al 2017;Heidrich et al 2017). Small RNAs (sRNAs) act by pairing with partly or fully complementary sequences in regulated mRNAs to affect their transcription, translation, or stability (Bobrovskyy and Vanderpool 2016;Hao et al 2016;Sedlyarova et al 2016;Chao et al 2017;Gorski et al 2017).…”

Section: Introductionmentioning

confidence: 99%

The binding of Class II sRNA MgrR to two different sites on matchmaker protein Hfq enables efficient competition for Hfq and annealing to regulated mRNAs

Kwiatkowska

Wróblewska

Johnson

et al. 2018

RNA

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MgrR is an Hfq-dependent sRNA, whose transcription is controlled by the level of Mg ions in MgrR belongs to Class II sRNAs because its stability in the cell is affected by mutations in Hfq differently than canonical, Class I sRNAs. Here, we examined the effect of mutations in RNA binding sites of Hfq on the kinetics of the annealing of MgrR to two different target mRNAs, and , by global data fitting of the reaction kinetics monitored by gel electrophoresis of intermediates and products. The data showed that the mutation on the rim of the Hfq ring trapped MgrR on Hfq preventing the annealing of MgrR to either mRNA. The mutation in the distal face slowed the ternary complex formation and affected the release of MgrR-mRNA complexes from Hfq, while the mutation in the proximal face weakened the MgrR binding to Hfq and in this way affected the annealing. Moreover, competition assays established that MgrR bound to both faces of Hfq and competed against other sRNAs. Further studies showed that uridine-rich sequences located in less structurally stable regions served as Hfq binding sites in each mRNA. Overall, the data show that the binding of MgrR sRNA to both faces of the Hfq ring enables it to efficiently anneal to target mRNAs. It also confers on MgrR a competitive advantage over other sRNAs, which could contribute to efficient cellular response to changes in magnesium homeostasis.

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“…Logically, the encoding of sRNAs and mRNAs at intersecting loci should affect the retention and evolution of these genetic elements in the genome. For example, TnpA, a transposable element-derived sRNA in Salmonella , shares its promoter with an mRNA, which may have resulted in increased selective pressure to maintain the transposon within which it is encoded (64). It stands to reason that even if its target mRNA is lost, the sRNA may persist long enough to acquire a new target.…”

Section: Modes and Consequences Of Srna Lossmentioning

confidence: 99%

Origin, Evolution, and Loss of Bacterial Small RNAs

Dutcher

Raghavan

2018

Microbiol Spectr

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Despite the central role of bacterial non-coding small RNAs (sRNAs) in posttranscriptional regulation, little is understood about their evolution. Here, we compile what has been studied to date and trace a life cycle of sRNAs—from their mechanisms of emergence, through processes of change and frequent neofunctionalization, to their loss from bacterial lineages. Because they possess relatively unrestrictive structural requirements, we find that sRNA origins are varied, and include de novo emergence as well as formation from pre-existing genetic elements via duplication events and horizontal gene transfer. The need for only partial complementarity to their mRNA targets facilitates apparent rapid change, which also contributes to significant challenges in tracing sRNAs across broad evolutionary distances. We document that recently-emerged sRNAs in particular evolve quickly, mirroring dynamics observed in microRNAs, their functional analogs in eukaryotes. Mutations in mRNA-binding regions, transcriptional regulator or sigma factor binding sites, and protein-binding regions are all likely sources of shifting regulatory roles of sRNAs. Finally, using examples from the few evolutionary studies available, we examine cases of sRNA loss, and describe how these may be the result of adaptive in addition to neutral processes. We highlight the need for more comprehensive analyses of sRNA evolutionary patterns as a means to improve novel sRNA detection, enhance genome annotation, and deepen our understanding of regulatory networks in bacteria.

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A transposon-derived small RNA regulates gene expression in Salmonella Typhimurium

Cited by 29 publications

References 68 publications

Dual-Function RNAs

Dual-Function RNAs

The binding of Class II sRNA MgrR to two different sites on matchmaker protein Hfq enables efficient competition for Hfq and annealing to regulated mRNAs

Origin, Evolution, and Loss of Bacterial Small RNAs

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