Defining the Transcriptional and Post-transcriptional Landscapes of Mycobacterium smegmatis in Aerobic Growth and Hypoxia
Defining the Transcriptional and Post-transcriptional Landscapes of Mycobacterium smegmatis in Aerobic Growth and Hypoxia
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DOI：
10.3389/fmicb.2019.00591
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发表时间：
2019-03-26
影响因子：
5.2
通讯作者：
Shell, Scarlet S.
中科院分区：
文献类型：
--
作者：
Martini, M. Carla;Zhou, Ying;Shell, Scarlet S.
结核分枝杆菌在人肺中感染、增殖和长期存活的能力在很大程度上取决于对基因表达的严格控制。全转录组分析是理解全球范围内基因调控的关键。在这里，我们将联合收割机5 '末端定向库与RNaseq表达库结合起来，以深入了解分枝杆菌在对数生长期和缺氧（一种生理相关的应激条件）下的转录组组织和转录后mRNA切割景观。使用模式生物耻垢分枝杆菌，我们确定了6，090转录起始位点（TSS）在对数生长期具有高置信度，其中67%被归类为注释基因的主要TSS，其余的根据其基因组背景被归类为内部，反义或孤儿。有趣的是，超过25%的RNA转录物缺乏前导序列，并且在具有前导序列的编码序列中，53%缺乏强一致的Shine-Dalgarno位点。这表明，像M。结核分枝杆菌（M.包皮垢可以通过多种机制启动翻译。我们的方法还使我们能够识别出3,000多个RNA切割位点，这些位点发生在一个新的序列基序上。据我们所知，这是分枝杆菌中转录组范围内RNA切割位点图的首次报道。切割位点显示出对mRNA调控区的位置偏好，突出了转录后调控在基因表达中的重要性。我们发现，在低氧条件下，与感染过程中的宿主环境，分枝杆菌改变其转录谱和核酸内切酶的RNA裂解显着减少，这表明了以前的报告增加mRNA半衰期的机制解释，以应对压力。此外，一些TSS在缺氧中被触发，其中56个在其启动子区域中含有σ因子SigF的结合基序。这表明SigF对低氧挑战的分枝杆菌中的转录组重塑有直接贡献。总而言之，我们的数据为进一步研究分支杆菌的转录和转录后调节提供了基础。
The ability of Mycobacterium tuberculosis to infect, proliferate, and survive during long periods in the human lungs largely depends on the rigorous control of gene expression. Transcriptome-wide analyses are key to understanding gene regulation on a global scale. Here, we combine 5'-end-directed libraries with RNAseq expression libraries to gain insight into the transcriptome organization and post-transcriptional mRNA cleavage landscape in mycobacteria during log phase growth and under hypoxia, a physiologically relevant stress condition. Using the model organism Mycobacterium smegmatis, we identified 6,090 transcription start sites (TSSs) with high confidence during log phase growth, of which 67% were categorized as primary TSSs for annotated genes, and the remaining were classified as internal, antisense, or orphan, according to their genomic context. Interestingly, over 25% of the RNA transcripts lack a leader sequence, and of the coding sequences that do have leaders, 53% lack a strong consensus Shine-Dalgarno site. This indicates that like M. tuberculosis, M. smegmatis can initiate translation through multiple mechanisms. Our approach also allowed us to identify over 3,000 RNA cleavage sites, which occur at a novel sequence motif. To our knowledge, this represents the first report of a transcriptome-wide RNA cleavage site map in mycobacteria. The cleavage sites show a positional bias toward mRNA regulatory regions, highlighting the importance of post-transcriptional regulation in gene expression. We show that in low oxygen, a condition associated with the host environment during infection, mycobacteria change their transcriptomic profiles and endonucleolytic RNA cleavage is markedly reduced, suggesting a mechanistic explanation for previous reports of increased mRNA half-lives in response to stress. In addition, a number of TSSs were triggered in hypoxia, 56 of which contain the binding motif for the sigma factor SigF in their promoter regions. This suggests that SigF makes direct contributions to transcriptomic remodeling in hypoxia-challenged mycobacteria. Taken together, our data provide a foundation for further study of both transcriptional and posttranscriptional regulation in mycobacteria.