Petushkov Ivan, Esyunina Daria, Kulbachinskiy Andrey
Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
Molecular Biology Department, Biological Faculty, Moscow State University, Moscow 119991, Russia.
Nucleic Acids Res. 2017 Apr 7;45(6):3006-3016. doi: 10.1093/nar/gkw1213.
Transcription initiation by bacterial RNA polymerase (RNAP) requires a variable σ subunit that directs it to promoters for site-specific priming of RNA synthesis. The principal σ subunit responsible for expression of house-keeping genes can bind the transcription elongation complex after initiation and induce RNAP pausing through specific interactions with promoter-like motifs in transcribed DNA. We show that the stationary phase and stress response σ38 subunit can also induce pausing by Escherichia coli RNAP on DNA templates containing promoter-like motifs in the transcribed regions. The pausing depends on σ38 contacts with the DNA template and RNAP core enzyme and results in formation of backtracked transcription elongation complexes, which can be reactivated by Gre factors that induce RNA cleavage by RNAP. Our data suggest that σ38 can bind the transcription elongation complex in trans but likely acts in cis during transcription initiation, by staying bound to RNAP and recognizing promoter-proximal pause signals. Analysis of σ38-dependent promoters reveals that a substantial fraction of them contain potential pause-inducing motifs, suggesting that σ38-depended pausing may be a common phenomenon in bacterial transcription.
细菌RNA聚合酶（RNAP）的转录起始需要一个可变的σ亚基，该亚基将其引导至启动子以进行RNA合成的位点特异性引发。负责管家基因表达的主要σ亚基在起始后可与转录延伸复合物结合，并通过与转录DNA中类似启动子的基序的特异性相互作用诱导RNAP暂停。我们发现，稳定期和应激反应σ38亚基也可在转录区域含有类似启动子基序的DNA模板上诱导大肠杆菌RNAP暂停。这种暂停取决于σ38与DNA模板和RNAP核心酶的接触，并导致形成回溯的转录延伸复合物，该复合物可被诱导RNAP进行RNA切割的Gre因子重新激活。我们的数据表明，σ38可以反式结合转录延伸复合物，但在转录起始期间可能顺式起作用，即通过与RNAP保持结合并识别启动子近端的暂停信号。对依赖σ38的启动子的分析表明，其中很大一部分含有潜在的暂停诱导基序，这表明依赖σ38的暂停可能是细菌转录中的常见现象。
