Global discovery of small RNAs in the fish pathogen Edwardsiella piscicida: key regulator of adversity and pathogenicity
Global discovery of small RNAs in the fish pathogen Edwardsiella piscicida: key regulator of adversity and pathogenicity
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全球发现鱼类病原体爱德华氏菌 (Edwardsiella piscicida) 中的小 RNA：逆境和致病性的关键调节因子。
DOI：
10.1186/s13567-018-0613-z
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发表时间：
2018-12-11
影响因子：
4.4
通讯作者：
Hu, Yong-hua
中科院分区：
文献类型：
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作者：
Du, He-he;Zhou, Hai-Zhen;Hu, Yong-hua
最近，细菌小RNA(SRNA)被证明是应激反应中的一个关键调节因子。水生爱德华氏菌是一种重要的水生病原菌，其sRNA的特征至今还不是很清楚。在本研究中，利用RNA-seq技术，我们在全球范围内发现并鉴定了在正常的LB介质、酸压力、缺铁胁迫和氧化压力下生长的鱼腥藻表达的sRNA候选序列。通过对Rfam数据库的搜索，共发现148个sRNA，包括19个先前注释的sRNA和129个新的sRNA候选序列。与正常条件下相比，3个应激样本中103个sRNAs(DEsRNA，差异表达的sRNA)和1615个mRNAs(DEmRNAs，差异表达的mRNAs)的表达有显著差异。根据IntaRNA的预测和DEsRNAs与DEmRNAs之间的关系分析，预测了103个DEsRNAs调控769个靶mRNAs。靶标DEmRNAs的多效性表明，sRNAs广泛参与多种生理过程，包括对逆境的反应和致病性，后者被感染实验进一步证实。在sRNAs的靶基因中出现了大量的转录因子，这表明sRNAs可能深入地交织在鱼腥藻复杂的基因调控网络中。此外，本研究还鉴定了49个与HfQ相关的sRNAs。综上所述，我们在全球范围内首次在鱼类病原菌中发现了sRNAs，我们的发现表明，在鱼类对环境胁迫和致病性的适应中，sRNAs具有重要的作用。这些结果也为破译与生理反应和致病性相关的基因表达调控机制提供了线索。
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.