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

J 2020

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

KOUBA, T., T. KOVAL, P. SUDZINOVA, J. POSPISIL, B. BREZOVSKA et. al.

Basic information

Original name

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

Authors

KOUBA, T., T. KOVAL, P. SUDZINOVA, J. POSPISIL, B. BREZOVSKA, J. HNILICOVA, H. SANDEROVA, M. JANOUSKOVA, M. SIKOVA, P. HALADA, M. SYKORA, I. BARVIK, Jiří NOVÁČEK (203 Czech Republic, guarantor, belonging to the institution), M. TRUNDOVA, J. DUSKOVA, T. SKALOVA, U. CHON, K.S. MURAKAMI, J. DOHNALEK and L. KRASNY

Edition

Nature Communications, London, Nature Publishing Group, 2020, 2041-1723

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 14.919

RIV identification code

RIV/00216224:14740/20:00118335

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1038/s41467-020-20158-4

UT WoS

000608512400003

Keywords in English

ESCHERICHIA-COLI; STRUCTURAL BASIS; CRYO-EM; BACTERIAL; DNA; SOFTWARE; REFINEMENT; ELONGATION; INITIATION; TOOLS

Abstract

V originále

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. The bacterial helicase-like transcription factor HelD associates with the RNA polymerase (RNAP) and recycles stalled transcription complexes. Here, the authors present the cryo-EM structures of three Mycobacterium smegmatis HelD bound RNAP complexes and further show that HelD can prevent the binding of the RNAP core to non-specific DNA and also actively removes RNAP from stalled elongation complexes.

Links

90043, large research infrastructures

Name: CIISB

Citovat

KOUBA, T., T. KOVAL, P. SUDZINOVA, J. POSPISIL, B. BREZOVSKA, J. HNILICOVA, H. SANDEROVA, M. JANOUSKOVA, M. SIKOVA, P. HALADA, M. SYKORA, I. BARVIK, Jiří NOVÁČEK, M. TRUNDOVA, J. DUSKOVA, T. SKALOVA, U. CHON, K.S. MURAKAMI, J. DOHNALEK and L. KRASNY. Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase. Nature Communications. London: Nature Publishing Group, 2020, vol. 11, No 1, p. 6419-6431. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-020-20158-4.

@article{1749818,
   author = {Kouba, T. and Koval, T. and Sudzinova, P. and Pospisil, J. and Brezovska, B. and Hnilicova, J. and Sanderova, H. and Janouskova, M. and Sikova, M. and Halada, P. and Sykora, M. and Barvik, I. and Nováček, Jiří and Trundova, M. and Duskova, J. and Skalova, T. and Chon, U. and Murakami, K.S. and Dohnalek, J. and Krasny, L.},
   article_location = {London},
   article_number = {1},
   doi = {http://dx.doi.org/10.1038/s41467-020-20158-4},
   keywords = {ESCHERICHIA-COLI; STRUCTURAL BASIS; CRYO-EM; BACTERIAL; DNA; SOFTWARE; REFINEMENT; ELONGATION; INITIATION; TOOLS},
   language = {eng},
   issn = {2041-1723},
   journal = {Nature Communications},
   title = {Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase},
   url = {https://www.nature.com/articles/s41467-020-20158-4},
   volume = {11},
   year = {2020}
}

TY  - JOUR
ID  - 1749818
AU  - Kouba, T. - Koval, T. - Sudzinova, P. - Pospisil, J. - Brezovska, B. - Hnilicova, J. - Sanderova, H. - Janouskova, M. - Sikova, M. - Halada, P. - Sykora, M. - Barvik, I. - Nováček, Jiří - Trundova, M. - Duskova, J. - Skalova, T. - Chon, U. - Murakami, K.S. - Dohnalek, J. - Krasny, L.
PY  - 2020
TI  - Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase
JF  - Nature Communications
VL  - 11
IS  - 1
SP  - 6419
EP  - 6419
PB  - Nature Publishing Group
SN  - 20411723
KW  - ESCHERICHIA-COLI
KW  - STRUCTURAL BASIS
KW  - CRYO-EM
KW  - BACTERIAL
KW  - DNA
KW  - SOFTWARE
KW  - REFINEMENT
KW  - ELONGATION
KW  - INITIATION
KW  - TOOLS
UR  - https://www.nature.com/articles/s41467-020-20158-4
N2  - 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. The bacterial helicase-like transcription factor HelD associates with the RNA polymerase (RNAP) and recycles stalled transcription complexes. Here, the authors present the cryo-EM structures of three Mycobacterium smegmatis HelD bound RNAP complexes and further show that HelD can prevent the binding of the RNAP core to non-specific DNA and also actively removes RNAP from stalled elongation complexes.
ER  -

KOUBA, T., T. KOVAL, P. SUDZINOVA, J. POSPISIL, B. BREZOVSKA, J. HNILICOVA, H. SANDEROVA, M. JANOUSKOVA, M. SIKOVA, P. HALADA, M. SYKORA, I. BARVIK, Jiří NOVÁČEK, M. TRUNDOVA, J. DUSKOVA, T. SKALOVA, U. CHON, K.S. MURAKAMI, J. DOHNALEK and L. KRASNY. Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase. \textit{Nature Communications}. London: Nature Publishing Group, 2020, vol.~11, No~1, p.~6419-6431. ISSN~2041-1723. Available from: https://dx.doi.org/10.1038/s41467-020-20158-4.

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