Global discovery of small RNAs in the fish pathogen Edwardsiella piscicida: key regulator of adversity and pathogenicity

Abstract

Recently, bacterial small RNA (sRNA) has been shown to be involved as a key regulator in stress responses. sRNAs of Edwardsiella piscicida, an important aquatic pathogen, are not well characterized to date. In this study, using RNA-seq technology, we globally found and identified sRNA candidates expressed from E. piscicida grown in normal LB medium, acid pressure, iron deficiency stress, and oxidation pressure. A total of 148 sRNAs were found, including 19 previously annotated sRNAs and 129 novel sRNA candidates by searching against the Rfam database. Compared in normal condition, the expression of 103 sRNAs (DEsRNA, differentially expressed sRNA) and 1615 mRNAs (DEmRNAs, differentially expressed mRNA) showed significant differences in three stress sample. Based on the prediction by IntaRNA and relational analysis between DEsRNAs and DEmRNAs, 103 DEsRNAs were predicted to regulate 769 target mRNAs. Pleiotropic function of target DEmRNAs indicated that sRNAs extensively participated in a variety of physiological processes, including response to adversity and pathogenicity, the latter was further confirmed by infection experiment. A large number transcription factors appeared in target genes of sRNAs, which suggested that sRNAs likely deeply interlaced within complex gene regulatory networks of E. piscicida. Moreover, 49 Hfq-associated sRNAs were also identified in this study. In summary, we globally discovered sRNAs for the first time in pathogenic bacteria of fish, and our findings indicated that sRNAs in E. piscicida have important roles in adaptation to environmental stress and pathogenicity. These results also provide clues for deciphering regulation mechanism of gene expression related to physiological response and pathogenicity.Electronic supplementary materialThe online version of this article (10.1186/s13567-018-0613-z) contains supplementary material, which is available to authorized users.

Edwardsiella piscicida: A versatile emerging pathogen of fish

“…The regulation of esrB links the stress conditions and virulence expression level during the progression of infection in E. piscicida and other phylogenetically related pathogens such as Salmonella species [89]. Hfq is another global regulator of an mRNA/sRNA chaperon associated with pathogenesis and interacts with~49 sRNA in E. piscicida; there were~148 sRNAs including 129 novel sRNAs that were associated with regulation of adversity adaptation and pathogenicity [90]. Although the distinct sRNAs and targeted mRNAs remain unknown, preliminary data in E. pisicicida suggested that Hfq is involved in T3SS/T6SS expression and in vivo pathogenesis (Wang QY et al, unpublished communication).…”

Type II toxin–antitoxin system, RatAB, contributes to oxidative resistance, biofilm formation and virulence of Edwardsiella piscicida

“…The interaction E . piscicida and host cells were studied as reported previously (Du et al, 2018). Briefly, FG cells and Hela cells were cultured to a single layer in a 48‐well cell plate and infected with TX01, TX01Δ rat A, TX01Δ rat AB, TX01Δ rat AC and TX01Δ rat ABC strains at a multiplicity of infection (MOI) of 50: 1.…”

Acid resistance system CadBA is implicated in acid tolerance and biofilm formation and is identified as a new virulence factor of Edwardsiella tarda

“…The interaction of E . tarda and host cells was studied as reported previously [ 38 ]. Briefly, E. tarda TX01, TX01Δ cadA , TX01Δ cadB , TX01Δ cadBA , TX01Δ cadA C, and TX01Δ cadB C strains were grown in LB broth at 30 °C and then transferred into DMEM without shaking until the optical density at 600 nm reached 1.0.…”