Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase

• 成果类型: Article
• 署名作者: Qayyum, M. Zuhaib; Imashimizu, Masahiko; Leanca, Miron; Vishwakarma, Rishi K.; Riaz-Bradley, Amber; Yuzenkova, Yulia; Murakami, Katsuhiko S.
• 署名单位: Pennsylvania Commonwealth System of Higher Education (PCSHE); Pennsylvania State University; Pennsylvania State University - University Park; National Institute of Advanced Industrial Science & Technology (AIST); Newcastle University - UK; St Jude Children's Research Hospital
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-11406
• DOI: 10.1073/pnas.2311480121
• 发表日期: 2024-02-20
• 关键词: cryo-em; transcription; subunits; enzymes

摘要

Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish them from canonical bacterial RNAPs. The largest subunit of cyanobacterial RNAP (cyRNAP) is divided into two polypeptides, beta ' 1 and beta ' 2, and contains the largest known lineage- specific insertion domain, Si3, located in the middle of the trigger loop and spanning approximately half of the beta ' 2 subunit. In this study, we present the X- ray crystal structure of Si3 and the cryo- EM structures of the cyRNAP transcription elongation complex plus the NusG factor with and without incoming nucleoside triphosphate (iNTP) bound at the active site. Si3 has a well- ordered and elongated shape that exceeds the length of the main body of cyRNAP, fits into cavities of cyRNAP in the absence of iNTP bound at the active site and shields the binding site of secondary channel- binding proteins such as Gre and DksA. A small transition from the trigger loop to the trigger helix upon iNTP binding results in a large swing motion of Si3; however, this transition does not affect the catalytic activity of cyRNAP due to its minimal contact with cyRNAP, NusG, or DNA. This study provides a structural framework for understanding the evolutionary significance of these features unique to cyRNAP and chloroplast RNAP and may provide insights into the molecular mechanism of transcription in specific environment of photosynthetic organisms and organelle.