Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.
PLoS One. 2013;8(2):e55156. doi: 10.1371/journal.pone.0055156. Epub 2013 Feb 15.
The prevalence and characteristics of small regulatory RNAs (sRNAs) have not been well characterized for Bacillus subtilis, an important model system for Gram-positive bacteria. However, B. subtilis was recently found to synthesize many candidate sRNAs during stationary phase. In the current study, we performed deep sequencing on Hfq-associated RNAs and found that a small subset of sRNAs associates with Hfq, an enigmatic RNA-binding protein that stabilizes sRNAs in Gram-negatives, but whose role is largely unknown in Gram-positive bacteria. We also found that Hfq associated with antisense RNAs, antitoxin transcripts, and many mRNA leaders. Several new candidate sRNAs and mRNA leader regions were also discovered by this analysis. Additionally, mRNA fragments overlapping with start or stop codons associated with Hfq, while, in contrast, relatively few full-length mRNAs were recovered. Deletion of hfq reduced the intracellular abundance of several representative sRNAs, suggesting that B. subtilis Hfq-sRNA interactions may be functionally significant in vivo. In general, we anticipate this catalog of Hfq-associated RNAs to serve as a resource in the functional characterization of Hfq in B. subtilis.
枯草芽孢杆菌（Bacillus subtilis）是革兰氏阳性菌的重要模式生物，但目前尚未很好地描述其小调控 RNA（sRNA）的流行程度和特征。然而，最近发现枯草芽孢杆菌在静止期合成许多候选 sRNA。在本研究中，我们对 Hfq 相关 RNA 进行了深度测序，发现一小部分 sRNA 与 Hfq 相关，Hfq 是一种神秘的 RNA 结合蛋白，在革兰氏阴性菌中稳定 sRNA，但在革兰氏阳性菌中的作用在很大程度上尚不清楚。我们还发现 Hfq 与反义 RNA、抗毒素转录本和许多 mRNA 前导区结合。通过这种分析还发现了几个新的候选 sRNA 和 mRNA 前导区。此外，与 Hfq 相关的 mRNA 片段与起始或终止密码子重叠，而相对较少的全长 mRNA 被回收。hfq 缺失减少了几种代表性 sRNA 的细胞内丰度，这表明枯草芽孢杆菌 Hfq-sRNA 相互作用在体内可能具有功能意义。总的来说，我们预计这个 Hfq 相关 RNA 目录将作为枯草芽孢杆菌中 Hfq 功能特征的资源。
