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Lookup NU author(s): Miron Leanca, Amber Riaz-Bradley, Dr Yulia Yuzenkova
This is the final published version of an article that has been published in its final definitive form by National Academy of Sciences, 2024.
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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, β'1 and β'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 β'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.
Author(s): Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS
Publication type: Article
Publication status: Published
Journal: Proceedings of the National Academy of Sciences of the United States of America
Year: 2024
Volume: 121
Issue: 8
Print publication date: 20/02/2024
Online publication date: 14/02/2024
Acceptance date: 17/01/2024
Date deposited: 05/03/2024
ISSN (print): 0027-8424
ISSN (electronic): 1091-6490
Publisher: National Academy of Sciences
URL: https://doi.org/10.1073/pnas.2311480121
DOI: 10.1073/pnas.2311480121
ePrints DOI: 10.57711/q79a-6g98
Data Access Statement: The X-ray crystallographic density map and the refined model have been deposited in Protein Data Bank (https://www.rcsb.org) under accession number 8EMB. The cryo-EM density map and the refined model have been deposited in Electron Microscopy Data Bank (https://www.ebi.ac.uk/emdb/) under accession numbers EMD-40874 (iNTP-free EC-NusG) and EMD-42502 (iNTP-bound EC-NusG) and in Protein Data Bank (https://www.rcsb.org) under accession numbers 8SYI (iNTP-free EC-NusG) and 8URW (iNTP-bound EC-NusG). All other data are included in the manuscript and/or supporting information.
PubMed id: 38354263
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