Liu Guiyang, Yang Xu, Yan Wenjin, Wang Yiqun, Yu Feng, Zheng Jianting
State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.
Nucleic Acids Res. 2025 Apr 22;53(8). doi: 10.1093/nar/gkaf339.
In bacteria, principal σ factors (σ70 or σA) transcribe housekeeping genes required for cell viability. Although most principal σ genes are transcribed by the RNA polymerase (RNAP) holoenzyme containing the principal σ factor itself, an extracytoplasmic function (ECF) σ factor (σShbA) governs transcription of the principal σ factor gene (hrdB) in two model Streptomycetes. Here, we employed a combination of cryo-electron microscopy (cryo-EM) and bioinformatics to decipher how σShbA-RNAP holoenzymes govern the transcription of hrdB genes in Streptomyces. A cryo-EM structure of Streptomyces coelicolor σShbA-RNAP-promoter open (RPo) complex was solved at 2.97 Å resolution. In combination with in vitro transcription assays, we demonstrate the unique structural features used by the σShbA to recognize the hrdB promoter and form a transcription bubble. All Streptomyces genomes (603) tagged as 'reference' were retrieved from NCBI Datasets. The conserved protein sequences and genomic neighborhoods, as well as the promoter consensus sequences of σShbA and σHrdB homologs, support that the principal σHrdB being governed by the ECF σShbA is a common feature in Streptomyces. Overall, these results provide detailed molecular insights into the transcription of the principal σHrdB gene and pave the way for globally modulating Streptomyces cell viability.
在细菌中，主要的σ因子（σ70或σA）转录细胞生存所需的管家基因。尽管大多数主要的σ基因由包含主要σ因子自身的RNA聚合酶（RNAP）全酶转录，但在两种模式链霉菌中，一种胞外功能（ECF）σ因子（σShbA）控制主要σ因子基因（hrdB）的转录。在此，我们结合冷冻电子显微镜（cryo-EM）和生物信息学来解析σShbA-RNAP全酶如何控制链霉菌中hrdB基因的转录。天蓝色链霉菌σShbA-RNAP-启动子开放（RPo）复合物的冷冻电镜结构以2.97 Å的分辨率解析出来。结合体外转录分析，我们展示了σShbA用于识别hrdB启动子并形成转录泡的独特结构特征。从NCBI数据集检索了所有标记为“参考”的链霉菌基因组（603个）。σShbA和σHrdB同源物的保守蛋白质序列、基因组邻域以及启动子共有序列表明，主要的σHrdB受ECF σShbA控制是链霉菌的一个共同特征。总体而言，这些结果为主要σHrdB基因的转录提供了详细的分子见解，并为全局调节链霉菌细胞活力铺平了道路。
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