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.
Highlights
Edwardsiella piscicida [1, 2], one family member of Enterobacteriaceae, is a Gram-negative, motile, rod-shaped bacterium
Sequencing of RNA from E. piscicida To identify globally small RNA (sRNA) and investigate the sRNA transcriptome profiles of E. piscicida, total RNA was separately isolated from bacteria grown in normal media (Con) and three adverse conditions, i.e., acidic condition (Ac), iron deficiency (Dp), and oxidation pressure (Pe)
The results showed that 19 sRNAs expression were significantly upregulated and 30 sRNAs expressions were significantly downregulated when Hfq was inactivated (Figure 6). qRT-PCR was conducted to examine the mRNA levels of 5 upregulated sRNAs and 14 downregulated sRNAs
Summary
Edwardsiella piscicida (formerly included in E. tarda) [1, 2], one family member of Enterobacteriaceae, is a Gram-negative, motile, rod-shaped bacterium. The majority of sRNAs function as regulators of gene expression at the post-transcriptional level and play critical regulatory roles in major biological processes, such as adaptation to various environmental stresses, quorum sensing, biofilm formation, motility, and pathogenicity [17,18,19,20,21,22,23,24]. Bacterial sRNA can be divided into two types: cis-encoded and trans-encoded sRNA The former is expressed from the same locus as their sole target with which they share full complementarity. Deleting Hfq, which has pleiotropic effects on the stability of several sRNAs, results in numerous phenotypes, including resistance to environmental stresses and pathogenicity [31, 32]. Our previous study showed that Hfq played an important role in responding to adversity and pathogenicity of E. piscicida [13], but its mechanism remains unknown
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