Cold adaptation regulated by cryptic prophage excision in Shewanella oneidensis.
Cold adaptation regulated by cryptic prophage excision in Shewanella oneidensis.
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希瓦氏菌奥尼登斯 (Shewanella oneidensis) 中隐性前噬菌体切除调节的冷适应。
DOI：
10.1038/ismej.2016.85
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发表时间：
2016-12
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--
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在细菌所经历的环境压力中，温度变化是最重要的之一。在本研究中，我们发现了一种新的冷适应机制，这种冷适应机制发生在DNA水平上，并受隐蔽的原噬菌体切除的调控。以往对细菌耐冷性的研究主要集中在细胞膜结构的变化以及在RNA和蛋白质水平上的变化。基因组变化是否也能对这一过程做出贡献还没有被探索过。在这里，我们使用了全基因组深度测序的方法来探索DNA水平上的变化，在一个模式的嗜冷菌菌株。我们发现，温度下降导致一种新的P4类隐蔽原噬菌体的切除增加了10000倍。重要的是，尽管原噬菌体切除只发生在相对较少的细菌种群中，但它能够促进生物膜的形成，并促进整个种群的生存。这种原噬菌体切除通过破坏编码转移信使RNA(TmRNA)的关键基因来影响细胞生理学。此外，我们还发现组蛋白样核结构蛋白(H-NS)在温热条件下可以通过与假定的切除酶基因的启动子结合来抑制原噬菌体的切除。在低温下，H-NS水平降低，导致原噬菌体切除的抑制。综上所述，我们的结果表明，隐蔽的原噬菌体切除作为一种调节开关，通过控制tmRNA的活性和生物膜的形成，使宿主能够在低温下生存。
Among the environmental stresses experienced by bacteria, temperature shifts are one of the most important. In this study, we discovered a novel cold adaptation mechanism in Shewanella oneidensis that occurs at the DNA level and is regulated by cryptic prophage excision. Previous studies on bacterial cold tolerance mainly focus on the structural change of cell membrane and changes at the RNA and protein levels. Whether or not genomic change can also contribute to this process has not been explored. Here we employed a whole-genome deep-sequencing method to probe the changes at DNA level in a model psychrotrophic bacteria strain. We found that temperature downshift induced a 10 000-fold increase of the excision of a novel P4-like cryptic prophage. Importantly, although prophage excision only occurred in a relatively small population of bacteria, it was able to facilitate biofilm formation and promote the survival of the entire population. This prophage excision affected cell physiology by disrupting a critical gene encoding transfer-messenger RNA (tmRNA). In addition, we found that the histone-like nucleoid-structuring protein (H-NS) could silence prophage excision via binding to the promoter of the putative excisionase gene at warm temperatures. H-NS level was reduced at cold temperatures, leading to de-repression of prophage excision. Collectively, our results reveal that cryptic prophage excision acts as a regulatory switch to enable the survival of the host at low temperature by controlling the activity of tmRNA and biofilm formation.
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