Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase

Tomáš Kouba (), Tomáš Koval’, Petra Sudzinová, Jiří Pospíšil, Barbora Brezovská, Jarmila Hnilicová, Hana Šanderová, Martina Janoušková, Michaela Šiková, Petr Halada, Michal Sýkora, Ivan Barvík, Jiří Nováček, Mária Trundová, Jarmila Dušková, Tereza Skálová, URee Chon, Katsuhiko S. Murakami, Jan Dohnálek () and Libor Krásný ()
Additional contact information
Tomáš Kouba: EMBL Grenoble, 71 Avenue des Martyrs
Tomáš Koval’: Centre BIOCEV, Průmyslová 595
Petra Sudzinová: Institute of Microbiology of The Czech Academy of Sciences
Jiří Pospíšil: Institute of Microbiology of The Czech Academy of Sciences
Barbora Brezovská: Institute of Microbiology of The Czech Academy of Sciences
Jarmila Hnilicová: Institute of Microbiology of The Czech Academy of Sciences
Hana Šanderová: Institute of Microbiology of The Czech Academy of Sciences
Martina Janoušková: Institute of Microbiology of The Czech Academy of Sciences
Michaela Šiková: Institute of Microbiology of The Czech Academy of Sciences
Petr Halada: Institute of Microbiology of The Czech Academy of Sciences
Michal Sýkora: Institute of Molecular Genetics of the Czech Academy of Sciences
Ivan Barvík: Faculty of Mathematics and Physics, Institute of Physics, Charles University
Jiří Nováček: CEITEC, Masaryk University
Mária Trundová: Centre BIOCEV, Průmyslová 595
Jarmila Dušková: Centre BIOCEV, Průmyslová 595
Tereza Skálová: Centre BIOCEV, Průmyslová 595
URee Chon: Pennsylvania State University
Katsuhiko S. Murakami: Pennsylvania State University
Jan Dohnálek: Centre BIOCEV, Průmyslová 595
Libor Krásný: Institute of Microbiology of The Czech Academy of Sciences

Nature Communications, 2020, vol. 11, issue 1, 1-13

Abstract: Abstract RNA synthesis is central to life, and RNA polymerase (RNAP) depends on accessory factors for recovery from stalled states and adaptation to environmental changes. Here, we investigated the mechanism by which a helicase-like factor HelD recycles RNAP. We report a cryo-EM structure of a complex between the Mycobacterium smegmatis RNAP and HelD. The crescent-shaped HelD simultaneously penetrates deep into two RNAP channels that are responsible for nucleic acids binding and substrate delivery to the active site, thereby locking RNAP in an inactive state. We show that HelD prevents non-specific interactions between RNAP and DNA and dissociates stalled transcription elongation complexes. The liberated RNAP can either stay dormant, sequestered by HelD, or upon HelD release, restart transcription. Our results provide insights into the architecture and regulation of the highly medically-relevant mycobacterial transcription machinery and define HelD as a clearing factor that releases RNAP from nonfunctional complexes with nucleic acids.

Date: 2020
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DOI: 10.1038/s41467-020-20158-4

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