Mycobacterial HelD connects RNA polymerase recycling with transcription initiation

Tomáš Kovaľ, Nabajyoti Borah, Petra Sudzinová, Barbora Brezovská, Hana Šanderová, Viola Vaňková Hausnerová, Alena Křenková, Martin Hubálek, Mária Trundová, Kristýna Adámková, Jarmila Dušková, Marek Schwarz, Jana Wiedermannová, Jan Dohnálek (), Libor Krásný () and Tomáš Kouba ()
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Tomáš Kovaľ: Institute of Biotechnology of the Czech Academy of Sciences
Nabajyoti Borah: Institute of Microbiology of the Czech Academy of Sciences
Petra Sudzinová: Institute of Microbiology of the Czech Academy of Sciences
Barbora Brezovská: Institute of Microbiology of the Czech Academy of Sciences
Hana Šanderová: Institute of Microbiology of the Czech Academy of Sciences
Viola Vaňková Hausnerová: Institute of Microbiology of the Czech Academy of Sciences
Alena Křenková: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Martin Hubálek: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Mária Trundová: Institute of Biotechnology of the Czech Academy of Sciences
Kristýna Adámková: Institute of Biotechnology of the Czech Academy of Sciences
Jarmila Dušková: Institute of Biotechnology of the Czech Academy of Sciences
Marek Schwarz: Institute of Microbiology of the Czech Academy of Sciences
Jana Wiedermannová: Institute of Microbiology of the Czech Academy of Sciences
Jan Dohnálek: Institute of Biotechnology of the Czech Academy of Sciences
Libor Krásný: Institute of Microbiology of the Czech Academy of Sciences
Tomáš Kouba: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-20

Abstract: Abstract Mycobacterial HelD is a transcription factor that recycles stalled RNAP by dissociating it from nucleic acids and, if present, from the antibiotic rifampicin. The rescued RNAP, however, must disengage from HelD to participate in subsequent rounds of transcription. The mechanism of release is unknown. We show that HelD from Mycobacterium smegmatis forms a complex with RNAP associated with the primary sigma factor σA and transcription factor RbpA but not CarD. We solve several structures of RNAP-σA-RbpA-HelD without and with promoter DNA. These snapshots capture HelD during transcription initiation, describing mechanistic aspects of HelD release from RNAP and its protective effect against rifampicin. Biochemical evidence supports these findings, defines the role of ATP binding and hydrolysis by HelD in the process, and confirms the rifampicin-protective effect of HelD. Collectively, these results show that when HelD is present during transcription initiation, the process is protected from rifampicin until the last possible moment.

Date: 2024
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DOI: 10.1038/s41467-024-52891-5

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