State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
PLoS One. 2013 Sep 11;8(9):e74495. doi: 10.1371/journal.pone.0074495. eCollection 2013.
Small non-coding RNAs (sRNAs) facilitate host-microbe interactions. They have a central function in the post-transcriptional regulation during pathogenic lifestyles. Hfq, an RNA-binding protein that many sRNAs act in conjunction with, is required for Y. pestis pathogenesis. However, information on how Yersinia pestis modulates the expression of sRNAs during infection is largely unknown.
We used RNA-seq technology to identify the sRNA candidates expressed from Y. pestis grown in vitro and in the infected lungs of mice. A total of 104 sRNAs were found, including 26 previously annotated sRNAs, by searching against the Rfam database with 78 novel sRNA candidates. Approximately 89% (93/104) of these sRNAs from Y. pestis are shared with its ancestor Y. pseudotuberculosis. Ninety-seven percent of these sRNAs (101/104) are shared among more than 80 sequenced genomes of 135 Y. pestis strains. These 78 novel sRNAs include 62 intergenic and 16 antisense sRNAs. Fourteen sRNAs were selected for verification by independent Northern blot analysis. Results showed that nine selected sRNA transcripts were Hfq-dependent. Interestingly, three novel sRNAs were identified as new members of the transcription factor CRP regulon. Semi-quantitative analysis revealed that Y. pestis from the infected lungs induced the expressions of six sRNAs including RyhB1, RyhB2, CyaR/RyeE, 6S RNA, RybB and sR039 and repressed the expressions of four sRNAs, including CsrB, CsrC, 4.5S RNA and sR027.
This study is the first attempt to subject RNA from Y. pestis-infected samples to direct high-throughput sequencing. Many novel sRNAs were identified and the expression patterns of relevant sRNAs in Y. pestis during in vitro growth and in vivo infection were revealed. The annotated sRNAs accounted for the most abundant sRNAs either expressed in bacteria grown in vitro or differentially expressed in the infected lungs. These findings suggested these sRNAs may have important functions in Y. pestis physiology or pathogenesis.
小非编码 RNA（sRNA）促进宿主与微生物的相互作用。它们在致病性生活方式中的转录后调控中具有核心功能。Hfq 是一种 RNA 结合蛋白，许多 sRNA 与之结合发挥作用，是鼠疫耶尔森氏菌发病所必需的。然而，关于鼠疫耶尔森氏菌如何在感染过程中调节 sRNA 的表达的信息在很大程度上尚不清楚。
我们使用 RNA-seq 技术鉴定了在体外生长和感染小鼠肺部的鼠疫耶尔森氏菌中表达的 sRNA 候选物。通过在 Rfam 数据库中搜索，共发现 104 个 sRNA，包括 26 个先前注释的 sRNA 和 78 个新的 sRNA 候选物。来自鼠疫耶尔森氏菌的这些 sRNA 中约有 89%（93/104）与它的祖先假结核耶尔森氏菌共有。这些 sRNA 中有 97%（101/104）在 135 株鼠疫耶尔森氏菌的 80 多个测序基因组中共有。这 78 个新的 sRNA 包括 62 个基因间和 16 个反义 sRNA。选择了 14 个 sRNA 通过独立的 Northern blot 分析进行验证。结果表明，9 个选定的 sRNA 转录本依赖于 Hfq。有趣的是，三个新的 sRNA 被鉴定为 CRP 调控因子转录物的新成员。半定量分析显示，来自感染肺部的鼠疫耶尔森氏菌诱导了包括 RyhB1、RyhB2、CyaR/RyeE、6S RNA、RybB 和 sR039 在内的六种 sRNA 的表达，并抑制了包括 CsrB、CsrC、4.5S RNA 和 sR027 在内的四种 sRNA 的表达。
本研究首次尝试对感染鼠疫耶尔森氏菌的样本中的 RNA 进行直接高通量测序。鉴定了许多新的 sRNA，并揭示了在体外生长和体内感染过程中相关 sRNA 在鼠疫耶尔森氏菌中的表达模式。在体外培养的细菌中表达或在感染肺部中差异表达的最丰富的 sRNA 是注释的 sRNA。这些发现表明这些 sRNA 可能在鼠疫耶尔森氏菌的生理或发病机制中具有重要功能。
