Genome-Wide Detection of Small Regulatory RNAs in Deep-Sea Bacterium Shewanella piezotolerans WP3.
Genome-Wide Detection of Small Regulatory RNAs in Deep-Sea Bacterium Shewanella piezotolerans WP3.
复制标题
深海细菌希瓦氏菌 WP3 中小调节 RNA 的全基因组检测
DOI：
10.3389/fmicb.2017.01093
复制
发表时间：
2017
影响因子：
5.2
通讯作者：
Wang F
中科院分区：
文献类型：
--
作者：
Nawaz MZ;Jian H;He Y;Xiong L;Xiao X;Wang F
希瓦氏菌是深海中最丰富的变形菌之一，以其多功能的电子接受能力而闻名。它们适应多样化和极端环境的分子机制尚不清楚。众所周知，小非编码 RNA (sRNA) 可在转录和转录后水平调节基因表达，从而在微生物适应中发挥关键作用。为了了解 sRNA 在希瓦氏菌适应深海环境中的潜在作用，本文采用计算机模拟方法检测希瓦氏菌压电耐受性 WP3（一种耐压和耐冷的深海铁还原细菌）基因组中的 sRNA。在扫描了 3673 组直系同源基因的 5' 和 3' UTR 后，在 S. piezotolerans WP3 中高度可信地鉴定出 209 个 sRNA 候选物。这些假定的 sRNA 中约 92%（209 个中的 193 个）属于反式编码 RNA 类，表明反式调节 RNA 是 S. piezotolerans WP3 中的主要 sRNA 类。其余 16 个顺式调节 RNA 通过定量聚合酶链式反应进行了验证。进一步证明五种顺式 sRNA 可以充当冷调节 sRNA。我们的研究在转录水平上提供了额外的证据，以破译微生物对极端环境条件的适应机制。
Shewanella are one of the most abundant Proteobacteria in the deep-sea and are renowned for their versatile electron accepting capacities. The molecular mechanisms involved in their adaptation to diverse and extreme environments are not well understood. Small non-coding RNAs (sRNAs) are known for modulating the gene expression at transcriptional and posttranscriptional levels, subsequently playing a key role in microbial adaptation. To understand the potential roles of sRNAs in the adaptation of Shewanella toward deep-sea environments, here an in silico approach was utilized to detect the sRNAs in the genome of Shewanella piezotolerans WP3, a piezotolerant and psychrotolerant deep-sea iron reducing bacterium. After scanning 3673 sets of 5′ and 3′ UTRs of orthologous genes, 209 sRNA candidates were identified with high confidence in S. piezotolerans WP3. About 92% (193 out of 209) of these putative sRNAs belong to the class trans-encoded RNAs, suggesting that trans-regulatory RNAs are the dominant class of sRNAs in S. piezotolerans WP3. The remaining 16 cis-regulatory RNAs were validated through quantitative polymerase chain reaction. Five cis-sRNAs were further shown to act as cold regulated sRNAs. Our study provided additional evidence at the transcriptional level to decipher the microbial adaptation mechanisms to extreme environmental conditions.