Small Non-coding RNA RyhB Mediates Persistence to Multiple Antibiotics and Stresses in Uropathogenic Escherichia coli by Reducing Cellular Metabolism

Shanshan Zhang,Ying Zhang,Youhua Yuan,Shuang Liu,Wenhong Zhang,Nan Wu

doi:10.3389/fmicb.2018.00136

Shanshan Zhang, Ying Zhang + Show 4 more

Open Access

https://doi.org/10.3389/fmicb.2018.00136

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Abstract

As dormant phenotypic variants of bacteria, persisters account for many chronic infections affecting human health. Despite numerous studies, the role of small non-coding RNA (sRNA) in bacterial persistence has not been reported. To investigate the role of Hfq-interacting sRNA in persistence, we constructed the deletion mutants of 20 Hfq-interacting sRNAs (RyhB, GcvB, MgrR, RybB, MicF, SgrS, RprA, DicF, SsrS, FnrS, GadY, DsrA, OmrB, ArcZ, RyeB, RydC, OmrA, MicA, MicC, and ChiX) to assess their persistence capacity in uropathogenic Escherichia coli strain UTI89 and identified a new sRNA RyhB being involved in persister formation. The ryhB-knockout mutant had significant defect in persistence to a diverse range of antibiotics (levofloxacin, cefotaxime, gentamicin) and stresses (hyperosmosis, acid, and heat) in both exponential phase and stationary phase. In addition, the effect of RyhB on persistence was synergistic with ppGpp and Fur protein. RNA-Seq analysis indicated that the ryhB-knockout mutant had a hyperactive metabolic state compared with the parent strain. Interestingly, increased adenosine triphosphate (ATP) levels and altered NAD+/NADH ratios were observed in the ryhB-knockout mutant. Our findings represent a new level of persistence regulation via sRNA and may provide novel therapeutic targets for interventions.

Highlights

Persisters represent a small number of metabolically quiescent bacteria that survive exposure to bactericidal drugs and stresses while remaining susceptible to drugs and stresses under appropriate conditions (Lewis, 2010; Zhang, 2014)
Many studies on persistence mechanisms have been performed in Escherichia coli (E. coli), with multiple genes and pathways small non-coding RNA (sRNA) RyhB Is Involved in Persister Formation being identified as involved in persister formation, including toxin-antitoxins (TA), SOS response, and DNA repair, signal transduction, membrane stress, energy production, phosphate metabolism, and protein degradation (Zhang, 2014; Harms et al, 2016)
To explore the role of sRNA in persistence, we constructed the knockout-mutant strains of 20 known Hfq-binding sRNAs (RyhB, GcvB, MgrR, RybB, MicF, SgrS, RprA, DicF, SsrS, FnrS, GadY, DsrA, OmrB, ArcZ, RyeB, RydC, OmrA, MicA, MicC, and ChiX; Mandin and Gottesman, 2010; Kim et al, 2015) in E. coli urinary tract infections (UTIs) strain UTI89 and exposed the mutants to bactericidal antibiotic levofloxacin (5 μg/mL) in the stationary phase

Summary

Introduction

Persisters represent a small number of metabolically quiescent bacteria that survive exposure to bactericidal drugs and stresses while remaining susceptible to drugs and stresses under appropriate conditions (Lewis, 2010; Zhang, 2014). Many studies on persistence mechanisms have been performed in Escherichia coli (E. coli), with multiple genes and pathways sRNA RyhB Is Involved in Persister Formation being identified as involved in persister formation, including toxin-antitoxins (TA), SOS response, and DNA repair, signal transduction, membrane stress, energy production, phosphate metabolism, and protein degradation (Zhang, 2014; Harms et al, 2016) These findings indicate that persistence is a very complex phenomenon with redundant mechanisms and that there may be other more important potential mechanisms that remain unknown. Whether the role of Hfq in persistence has anything to do with the Hfq-interacting sRNAs remains unknown

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