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.

中文翻译：

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全基因组检测深海细菌希瓦氏菌WP3中的小调节RNA。

希瓦氏菌是深海中最丰富的变形杆菌之一，并以其多功能的电子接受能力而闻名。它们适应多种多样和极端环境所涉及的分子机制尚未得到很好的理解。众所周知，小的非编码RNA（sRNA）可在转录和转录后水平上调节基因表达，随后在微生物适应中发挥关键作用。为了了解sRNA在Shewanella适应深海环境中的潜在作用，这里采用了计算机方法来检测Shewanella piezotolerans WP3（一种耐压和抗精神病的深海铁还原细菌）基因组中的sRNA。在扫描了3673套直系同源基因的5'和3'UTR序列后，鉴定出209个对S具有高度信心的sRNA候选物。耐压性WP3。这些推定的sRNA中约有92％（209个中的193个）属于反式编码RNA类，这表明反调节性RNA是S.zozotolerans WP3中sRNA的主要类别。通过定量聚合酶链反应验证了其余16个顺式调控RNA。进一步显示了五个顺式-sRNA充当冷调节的sRNA。我们的研究在转录水平上提供了其他证据，以破译微生物对极端环境条件的适应机制。还显示了五个顺式-sRNA充当冷调节的sRNA。我们的研究在转录水平上提供了其他证据，以破译微生物对极端环境条件的适应机制。进一步显示了五个顺式-sRNA充当冷调节的sRNA。我们的研究在转录水平上提供了其他证据，以破译微生物对极端环境条件的适应机制。