Department of Biology, University of South Alabama , Mobile , AL , USA.
Department of Food Science, University of Campinas , Campinas , Brazil.
RNA Biol. 2019 Nov;16(11):1643-1657. doi: 10.1080/15476286.2019.1653680. Epub 2019 Aug 15.
Noncoding RNA (ncRNA) modulation of gene expression has now been ubiquitously observed across all domains of life. An increasingly apparent role of ncRNAs is to coordinate changes in gene expressions in response to environmental stress. , a common food-born pathogen, is known for its striking ability to survive, adapt, and thrive in various unfavourable environments which makes it a particularly difficult pathogen to eliminate as well as an interesting model in which to study ncRNA contributions to cellular stress response. Mounting evidence now suggests that small RNAs (sRNAs) represent key regulators of stress adaptation. Approximately 50-500 nucleotides in length, sRNAs regulate gene expression through complementary base pairing with molecular targets and have recently been suggested to outnumber protein-coding genes in bacteria. In this work, we employ small RNA transcriptome sequencing to characterize changes in the sRNA profiles of in response to desiccation. In all, we identify 102 previously annotated sRNAs significantly differentially expressed during desiccation; and excitingly, 71 novel sRNAs likewise differentially expressed. Small transcript northern blotting and qRT-PCRs confirm the identities and expressions of several of our novel sRNAs, and computational analyses indicate the majority are highly conserved and structurally related to characterized sRNAs. Predicted sRNA targets include several proteins necessary for desiccation survival and this, in part, suggests a role for desiccation-regulated sRNAs in this stress response. Furthermore, we find individual knock-outs of two of the novel sRNAs identified herein, either sRNA1320429 or sRNA3981754, significantly impairs the ability of to survive desiccation, confirming their involvements (and suggesting the potential involvements of other sRNAs we identify in this work) in the response to desiccation.
非编码 RNA（ncRNA）对基因表达的调控现在已经在所有生命领域中被普遍观察到。ncRNA 的一个越来越明显的作用是协调基因表达的变化，以响应环境压力。作为一种常见的食源性病原体，它以惊人的能力在各种不利环境中生存、适应和茁壮成长而闻名，这使得它成为一种特别难以消除的病原体，也是研究 ncRNA 对细胞应激反应贡献的有趣模型。越来越多的证据表明，小 RNA（sRNA）是应激适应的关键调节剂。sRNA 的长度约为 50-500 个核苷酸，通过与分子靶标互补配对来调节基因表达，最近有人提出，在细菌中，sRNA 的数量超过了编码蛋白的基因数量。在这项工作中，我们采用小 RNA 转录组测序来描述 应对干燥时 sRNA 谱的变化。总共，我们确定了 102 个先前注释的 sRNA 在干燥过程中显著差异表达；令人兴奋的是，还有 71 个新的 sRNA 也同样差异表达。小转录本Northern 印迹和 qRT-PCR 证实了我们几个新的 sRNA 的身份和表达，计算分析表明，大多数 sRNA 高度保守，并且与已鉴定的 sRNA 结构相关。预测的 sRNA 靶标包括一些对干燥生存至关重要的蛋白质，这部分表明，干燥调节的 sRNA 在这种应激反应中起作用。此外，我们发现本文鉴定的两个新的 sRNA 中的两个，sRNA1320429 或 sRNA3981754 的敲除，显著降低了 对干燥的生存能力，证实了它们（并暗示了我们在这项工作中鉴定的其他 sRNA 的潜在参与）在 对干燥的反应中的参与。
