Novel small RNA (sRNA) landscape of the starvation-stress response transcriptome of Salmonella enterica serovar typhimurium
Novel small RNA (sRNA) landscape of the starvation-stress response transcriptome of Salmonella enterica serovar typhimurium
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DOI：
10.1080/15476286.2016.1144010
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发表时间：
2016-03-03
期刊：
影响因子：
4.1
通讯作者：
Borchert, Glen M.
中科院分区：
文献类型：
--
作者：
Amin, Shivam V.;Roberts, Justin T.;Borchert, Glen M.
小RNA（sRNA）是短的（类似于50-200个核苷酸）非编码RNA，调节细菌的细胞活动。饥饿的碳能源（C）来源的肠道沙门氏菌经历了广泛称为饥饿应激反应（SSR）的遗传和生理变化。在试图确定新的sRNA有助于SSR控制，我们增长的对数期，5小时C-饥饿和24小时C-饥饿培养的毒性沙门氏菌肠道亚种肠道血清型鼠伤寒沙门氏菌菌株SL 1344和全面测序其小RNA转录组。引人注目的是，采用一种新的战略sRNA发现的基础上确定动态转录本所产生的“基因空”的地区，我们确定了58个完全未描述的沙门氏菌sRNA基因可能调节SSR平均类似的1,000倍的变化，在对数期和C饥饿的细胞之间的表达。重要的是，通过综合转录组分析和选择候选物的北方印迹证实了单个sRNA基因座的表达。值得注意的是，我们发现43个候选sRNA与其他细菌中的特征sRNA具有显著的序列同一性，并且类似于我们的sRNA的70%可能呈现特征sRNA结构构象。此外，我们发现我们的58个候选sRNA中的53个与相邻的mRNA位点重叠或与SL 1344基因组中其他地方转录的mRNA共享显著的序列互补性，这强烈表明它们通过反义碱基配对调节转录物的表达。最后，除了鉴定出58个可能参与SSR的全新肠道沙门氏菌基因外，我们还发现了证据表明sRNA比目前所认识的要普遍得多，沙门氏菌sRNA实际上可能有数千个。
Small RNAs (sRNAs) are short (similar to 50-200 nucleotides) noncoding RNAs that regulate cellular activities across bacteria. Salmonella enterica starved of a carbon-energy (C) source experience a host of genetic and physiological changes broadly referred to as the starvation-stress response (SSR). In an attempt to identify novel sRNAs contributing to SSR control, we grew log-phase, 5-h C-starved and 24-h C-starved cultures of the virulent Salmonella enterica subspecies enterica serovar Typhimurium strain SL1344 and comprehensively sequenced their small RNA transcriptomes. Strikingly, after employing a novel strategy for sRNA discovery based on identifying dynamic transcripts arising from "gene-empty" regions, we identify 58 wholly undescribed Salmonella sRNA genes potentially regulating SSR averaging an similar to 1,000-fold change in expression between log-phase and C-starved cells. Importantly, the expressions of individual sRNA loci were confirmed by both comprehensive transcriptome analyses and northern blotting of select candidates. Of note, we find 43 candidate sRNAs share significant sequence identity to characterized sRNAs in other bacteria, and similar to 70% of our sRNAs likely assume characteristic sRNA structural conformations. In addition, we find 53 of our 58 candidate sRNAs either overlap neighboring mRNA loci or share significant sequence complementarity to mRNAs transcribed elsewhere in the SL1344 genome strongly suggesting they regulate the expression of transcripts via antisense base-pairing. Finally, in addition to this work resulting in the identification of 58 entirely novel Salmonella enterica genes likely participating in the SSR, we also find evidence suggesting that sRNAs are significantly more prevalent than currently appreciated and that Salmonella sRNAs may actually number in the thousands.