Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic.
Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic.
Nucleic Acids Res. 2024 May 8;52(8):4604-4626. doi: 10.1093/nar/gkae081.
Bacteria have evolved structured RNAs that can associate with RNA polymerase (RNAP). Two of them have been known so far-6S RNA and Ms1 RNA but it is unclear if any other types of RNAs binding to RNAP exist in bacteria. To identify all RNAs interacting with RNAP and the primary σ factors, we have established and performed native RIP-seq in Bacillus subtilis, Corynebacterium glutamicum, Streptomyces coelicolor, Mycobacterium smegmatis and the pathogenic Mycobacterium tuberculosis. Besides known 6S RNAs in B. subtilis and Ms1 in M. smegmatis, we detected MTS2823, a homologue of Ms1, on RNAP in M. tuberculosis. In C. glutamicum, we discovered novel types of structured RNAs that associate with RNAP. Furthermore, we identified other species-specific RNAs including full-length mRNAs, revealing a previously unknown landscape of RNAs interacting with the bacterial transcription machinery.
细菌已经进化出能够与 RNA 聚合酶（RNAP）结合的结构 RNA。到目前为止，已经知道了两种-6S RNA 和 Ms1 RNA，但尚不清楚细菌中是否存在其他类型与 RNAP 结合的 RNA。为了鉴定与 RNAP 和主要 σ 因子相互作用的所有 RNA，我们已经在枯草芽孢杆菌、谷氨酸棒杆菌、链霉菌、耻垢分枝杆菌和致病性结核分枝杆菌中建立并进行了天然 RIP-seq。除了枯草芽孢杆菌中的已知 6S RNA 和耻垢分枝杆菌中的 Ms1 外，我们还在结核分枝杆菌的 RNAP 上检测到了 Ms1 的同源物 MTS2823。在谷氨酸棒杆菌中，我们发现了与 RNAP 结合的新型结构 RNA。此外，我们还鉴定了其他具有物种特异性的 RNA，包括全长 mRNA，揭示了与细菌转录机制相互作用的 RNA 的先前未知图谱。
