Systematic analysis of the role of bacterial Hfq-interacting sRNAs in the response to antibiotics

Kim, Taeyeon; Bak, Geunu; Lee, Juyeon; Kim, Kwang-sun

doi:10.1093/jac/dkv042

Cited by 61 publications

(54 citation statements)

References 47 publications

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“…Conversely, over-expression of SdsR renders E. coli cells more susceptible to levofloxacin and several other antibiotics (90,91). Repression of the tolC mRNA (Figure 3D), encoding part of a large multiple drug efflux pump (92), by SdsR is a key factor for this phenotype, however, regulation of additional target genes seems to matter as well (91).…”

Section: Discussionmentioning

confidence: 99%

The target spectrum of SdsR small RNA inSalmonella

et al. 2016

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Model enteric bacteria such as Escherichia coli and Salmonella enterica express hundreds of small non-coding RNAs (sRNAs), targets for most of which are yet unknown. Some sRNAs are remarkably well conserved, indicating that they serve cellular functions that go beyond the necessities of a single species. One of these ‘core sRNAs’ of largely unknown function is the abundant ∼100-nucleotide SdsR sRNA which is transcribed by the general stress σ-factor, σS and accumulates in stationary phase. In Salmonella, SdsR was known to inhibit the synthesis of the species-specific porin, OmpD. However, sdsR genes are present in almost all enterobacterial genomes, suggesting that additional, conserved targets of this sRNA must exist. Here, we have combined SdsR pulse-expression with whole genome transcriptomics to discover 20 previously unknown candidate targets of SdsR which include mRNAs coding for physiologically important regulators such as the carbon utilization regulator, CRP, the nucleoid-associated chaperone, StpA and the antibiotic resistance transporter, TolC. Processing of SdsR by RNase E results in two cellular SdsR variants with distinct target spectra. While the overall physiological role of this orphan core sRNA remains to be fully understood, the new SdsR targets present valuable leads to determine sRNA functions in resting bacteria.

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Section: Discussionmentioning

confidence: 99%

The target spectrum of SdsR small RNA inSalmonella

et al. 2016

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“…TolC was also identified as one of a large number of targets of SdsR in Salmonella, using microarray analysis (K. S. Fröhlich, K. Haneke, K. Papenfort, and J. Vogel, personal communication). In another study published while the current work was being prepared for publication, the same plasmid library as that used here was screened for effects on sensitivity or resistance to a panel of antibiotics, and the overexpression of SdsR was found to increase sensitivity to multiple antibiotics, in particular, quinolones (29). Based on that observation and target prediction, the authors predicted tolC as a possible target, and a decrease in tolC mRNA was confirmed by reverse transcription-quantitative PCR (qRT-PCR) analysis after overexpression of the sRNA (29).…”

Section: Discussionmentioning

confidence: 99%

“…Although the exact functions of SdsR remain unclear, previous studies have suggested it has a role in modulating susceptibility to quinolone antibiotics. The overexpression of SdsR reduced resistance to quinolone antibiotics, such as levofloxacin, nalidixic acid, and norfloxacin, in multiple-drug-resistant strains of E. coli and Salmonella (29). In addition, SdsR was reported to contribute to an increase in the mutagenesis rate in E. coli cells treated with subinhibitory levels of ampicillin, presumably via its interaction with mutS (30).…”

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confidence: 99%

Small RNA Regulation of TolC, the Outer Membrane Component of Bacterial Multidrug Transporters

Parker

Gottesman

2016

J Bacteriol

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Bacteria use multidrug efflux pumps to export drugs and toxic compounds out of the cell. One of the most important efflux pumps in Escherichia coli is the AcrAB-TolC system. Small regulatory RNAs (sRNAs) are known to be major posttranscriptional regulators that can enhance or repress translation by binding to the 5= untranslated region (UTR) of mRNA targets with the help of a chaperone protein, Hfq. In this study, we investigated the expression of acrA, acrB, and tolC translational fusions using 27 Hfq-dependent sRNAs overexpressed from plasmids. No significant sRNA regulation of acrA or acrB was detected. SdsR (also known as RyeB), an abundant and well-conserved stationary-phase sRNA, was found to repress the expression of tolC, the gene encoding the outer membrane protein of many multidrug resistance efflux pumps. This repression was shown to be by direct base pairing occurring upstream from the ribosomal binding site. SdsR overexpression and its regulation of tolC were found to reduce resistance to novobiocin and crystal violet. Our results suggest that additional targets for SdsR exist that contribute to increased antibiotic sensitivity and reduced biofilm formation. In an effort to identify phenotypes associated with single-copy SdsR and its regulation of tolC, the effect of a deletion of sdsR or mutations in tolC that should block SdsR pairing were investigated using a Biolog phenotypic microarray. However, no significant phenotypes were identified. Therefore, SdsR appears to modulate rather than act as a major regulator of its targets. IMPORTANCEAcrAB-TolC is a major efflux pump present in E. coli and Gram-negative bacteria used to export toxic compounds; the pump confers resistance to many antibiotics of unrelated classes. In this study, we found that SdsR, a small RNA expressed in stationary phase, repressed the expression of tolC, resulting in increased sensitivity to some antibiotics. This extends the findings of previous studies showing that sRNAs contribute to the regulation of many outer membrane proteins; manipulating or enhancing their action might help in sensitizing bacteria to antibiotics.

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“…As it has been proposed before (Gruber and Sperandio 2015;Kim et al 2015;Peng et al 2015), computational analysis of the sRNAs' targets is an excellent starting point toward understanding their physiological roles in the cell. Here, we used TargetRNA2 as a target predictor for being the algorithm with the best correlation of targets predicted and actually confirmed, among the programs widely used for this purpose (Kery et al 2014).…”

Section: Discussionmentioning

confidence: 99%

A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

Rossi

Bossé

et al. 2016

RNA

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Bacterial regulatory small RNAs (sRNAs) play important roles in gene regulation and are frequently connected to the expression of virulence factors in diverse bacteria. Only a few sRNAs have been described for Pasteurellaceae pathogens and no in-depth analysis of sRNAs has been described for Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, responsible for considerable losses in the swine industry. To search for sRNAs in A. pleuropneumoniae, we developed a strategy for the computational analysis of the bacterial genome by using four algorithms with different approaches, followed by experimental validation. The coding strand and expression of 17 out of 23 RNA candidates were confirmed by Northern blotting, RT-PCR, and RNA sequencing. Among them, two are likely riboswitches, three are housekeeping regulatory RNAs, two are the widely studied GcvB and 6S sRNAs, and 10 are putative novel trans-acting sRNAs, never before described for any bacteria. The latter group has several potential mRNA targets, many of which are involved with virulence, stress resistance, or metabolism, and connect the sRNAs in a complex gene regulatory network. The sRNAs identified are well conserved among the Pasteurellaceae that are evolutionarily closer to A. pleuropneumoniae and/or share the same host. Our results show that the combination of newly developed computational programs can be successfully utilized for the discovery of novel sRNAs and indicate an intricate system of gene regulation through sRNAs in A. pleuropneumoniae and in other Pasteurellaceae, thus providing clues for novel aspects of virulence that will be explored in further studies.

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Systematic analysis of the role of bacterial Hfq-interacting sRNAs in the response to antibiotics

Abstract: Our data indicate that Hfq-associated sRNAs potentially enable bacteria to adapt to antibiotic challenges via multifaceted approaches. Therefore, sRNA-based applications will form a new antibiotic arsenal for combating the rise in antibiotic resistance.

Cited by 61 publications

References 47 publications

The target spectrum of SdsR small RNA inSalmonella

The target spectrum of SdsR small RNA inSalmonella

Small RNA Regulation of TolC, the Outer Membrane Component of Bacterial Multidrug Transporters

A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

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