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Comparative genomics provides structural and functional insights into Bacteroides RNA biology
Molecular Microbiology ( IF 3.6 ) Pub Date : 2021-08-11 , DOI: 10.1111/mmi.14793
Gianluca Prezza 1 , Daniel Ryan 1 , Gohar Mädler 2 , Sarah Reichardt 1 , Lars Barquist 1, 3 , Alexander J Westermann 1, 2
Affiliation  

Bacteria employ noncoding RNA molecules for a wide range of biological processes, including scaffolding large molecular complexes, catalyzing chemical reactions, defending against phages, and controlling gene expression. Secondary structures, binding partners, and molecular mechanisms have been determined for numerous small noncoding RNAs (sRNAs) in model aerobic bacteria. However, technical hurdles have largely prevented analogous analyses in the anaerobic gut microbiota. While experimental techniques are being developed to investigate the sRNAs of gut commensals, computational tools and comparative genomics can provide immediate functional insight. Here, using Bacteroides thetaiotaomicron as a representative microbiota member, we illustrate how comparative genomics improves our understanding of RNA biology in an understudied gut bacterium. We investigate putative RNA-binding proteins and predict a Bacteroides cold-shock protein homolog to have an RNA-related function. We apply an in silico protocol incorporating both sequence and structural analysis to determine the consensus structures and conservation of nine Bacteroides noncoding RNA families. Using structure probing, we validate and refine these predictions and deposit them in the Rfam database. Through synteny analyses, we illustrate how genomic coconservation can serve as a predictor of sRNA function. Altogether, this work showcases the power of RNA informatics for investigating the RNA biology of anaerobic microbiota members.

中文翻译:

比较基因组学为拟杆菌属 RNA 生物学提供结构和功能见解

细菌在广泛的生物过程中使用非编码 RNA 分子,包括搭建大分子复合物、催化化学反应、抵御噬菌体和控制基因表达。已经确定了模型好氧细菌中大量非编码小 RNA (sRNA) 的二级结构、结合伙伴和分子机制。然而,技术障碍在很大程度上阻碍了厌氧肠道微生物群的类似分析。虽然正在开发实验技术来研究肠道共生体的 sRNA,但计算工具和比较基因组学可以提供即时的功能洞察力。在这里,使用Bacteroides thetaiotaomicron作为一个有代表性的微生物群成员,我们说明了比较基因组学如何提高我们对研究不足的肠道细菌中 RNA 生物学的理解。我们调查推定的 RNA 结合蛋白并预测拟杆菌属冷休克蛋白同源物具有 RNA 相关功能。我们应用结合序列和结构分析的计算机方案来确定九种拟杆菌的共有结构和保守性非编码 RNA 家族。使用结构探测,我们验证和完善这些预测并将它们存储在 Rfam 数据库中。通过同线性分析,我们说明了基因组共保守如何作为 sRNA 功能的预测因子。总而言之,这项工作展示了 RNA 信息学在研究厌氧微生物群成员的 RNA 生物学方面的力量。
更新日期:2021-08-11
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