Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD

• Published in: Nature communications Vol. 11; no. 1; pp. 6420 - 11
• Main Authors: Newing, Timothy P., Oakley, Aaron J., Miller, Michael, Dawson, Catherine J., Brown, Simon H. J., Bouwer, James C., Tolun, Gökhan, Lewis, Peter J.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18-12-2020; Nature Publishing Group; Nature Portfolio
• Subjects: 101/28; 631/337/572; 631/45/173; 631/535/1258/1259; 82/83; Bacillus subtilis; Bacillus subtilis - enzymology; Bacteria; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Bacterial Proteins - ultrastructure; Cryoelectron Microscopy; Deoxyribonucleic acid; DNA; DNA biosynthesis; DNA damage; DNA helicase; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - metabolism; DNA-Directed RNA Polymerases - ultrastructure; Electron microscopy; Elongated structure; Elongation; Gram-positive bacteria; Humanities and Social Sciences; Imaging, Three-Dimensional; Models, Molecular; Molecular motors; multidisciplinary; Nucleic acids; Protein Binding; Recycling; Ribonucleic acid; RNA; RNA polymerase; Science; Science (multidisciplinary); Transcription Elongation, Genetic; Transcription factors; Transcription, Genetic
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-20157-5

In bacteria, transcription complexes stalled on DNA represent a major source of roadblocks for the DNA replication machinery that must be removed in order to prevent damaging collisions. Gram-positive bacteria contain a transcription factor HelD that is able to remove and recycle stalled complexes, but it was not known how it performed this function. Here, using single particle cryo-electron microscopy, we have determined the structures of
Bacillus subtilis
RNA polymerase (RNAP) elongation and HelD complexes, enabling analysis of the conformational changes that occur in RNAP driven by HelD interaction. HelD has a 2-armed structure which penetrates deep into the primary and secondary channels of RNA polymerase. One arm removes nucleic acids from the active site, and the other induces a large conformational change in the primary channel leading to removal and recycling of the stalled polymerase, representing a novel mechanism for recycling transcription complexes in bacteria.
Gram-positive bacteria contain a transcription factor HelD that is able to remove and recycle stalled transcription complexes. Here the authors provide mechanistic insights into this process by determining the cryo-EM structures of the
Bacillus subtilis
RNA polymerase (RNAP) elongation complex and the RNAP-HelD transcription recycling complex and propose a model of HelD catalysed transcription recycling.