Structural insights into the transcription activation mechanism of the global regulator GlnR from actinobacteria

• Published in: Proceedings of the National Academy of Sciences - PNAS 2023-05, Vol.120 (22), p.e2300282120-e2300282120
• Main Authors: Shi, Jing, Feng, Zhenzhen, Xu, Juncao, Li, Fangfang, Zhang, Yuqiong, Wen, Aijia, Wang, Fulin, Song, Qian, Wang, Lu, Cui, Hong, Tong, Shujuan, Chen, Peiying, Zhu, Yejin, Zhao, Guoping, Wang, Shuang, Feng, Yu, Lin, Wei
• Format: Article
• Language: English
• Subjects: Actinobacteria - genetics; Actinobacteria - metabolism; Aldehydes; Bacterial Proteins - metabolism; Binding sites; Crystal structure; Deoxyribonucleic acid; DNA; DNA structure; DNA-directed RNA polymerase; Domains; Gene expression; Gene Expression Regulation, Bacterial; Gene regulation; Metabolism; Phosphates; Promoter Regions, Genetic - genetics; Protein interaction; Proteins; RNA polymerase; Structural analysis; Trans-Activators - metabolism; Transcription activation; Transcriptional Activation - genetics
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2300282120

In actinobacteria, an OmpR/PhoB subfamily protein called GlnR acts as an orphan response regulator and globally coordinates the expression of genes responsible for nitrogen, carbon, and phosphate metabolism in actinobacteria. Although many researchers have attempted to elucidate the mechanisms of GlnR-dependent transcription activation, progress is impeded by lacking of an overall structure of GlnR-dependent transcription activation complex (GlnR-TAC). Here, we report a co-crystal structure of the C-terminal DNA-binding domain of GlnR (GlnR_DBD) in complex with its regulatory -element DNA and a cryo-EM structure of GlnR-TAC which comprises RNA polymerase, GlnR, and a promoter containing four well-characterized conserved GlnR binding sites. These structures illustrate how four GlnR protomers coordinate to engage promoter DNA in a head-to-tail manner, with four N-terminal receiver domains of GlnR (GlnR-RECs) bridging GlnR_DBDs and the RNAP core enzyme. Structural analysis also unravels that GlnR-TAC is stabilized by complex protein-protein interactions between GlnR and the conserved β flap, σ R4, αCTD, and αNTD domains of RNAP, which are further confirmed by our biochemical assays. Taken together, these results reveal a global transcription activation mechanism for the master regulator GlnR and other OmpR/PhoB subfamily proteins and present a unique mode of bacterial transcription regulation.