An SI3-σ arch stabilizes cyanobacteria transcription initiation complex

Author:

Shen Liqiang12ORCID,Lai Giorgio3ORCID,You Linlin12,Shi Jing45,Wu Xiaoxian1,Puiu Maria3,Gu Zhanxi12,Feng Yu45ORCID,Yuzenkova Yulia3,Zhang Yu1ORCID

Affiliation:

1. Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China

2. University of Chinese Academy of Sciences, Beijing 100049, China

3. Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK

4. Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China

5. Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China

Abstract

Multisubunit RNA polymerases (RNAPs) associate with initiation factors (σ in bacteria) to start transcription. The σ factors are responsible for recognizing and unwinding promoter DNA in all bacterial RNAPs. Here, we report two cryo-EM structures of cyanobacterial transcription initiation complexes at near-atomic resolutions. The structures show that cyanobacterial RNAP forms an “SI3-σ” arch interaction between domain 2 of σ A2 ) and sequence insertion 3 (SI3) in the mobile catalytic domain Trigger Loop (TL). The “SI3-σ” arch facilitates transcription initiation from promoters of different classes through sealing the main cleft and thereby stabilizing the RNAP-promoter DNA open complex. Disruption of the “SI3-σ” arch disturbs cyanobacteria growth and stress response. Our study reports the structure of cyanobacterial RNAP and a unique mechanism for its transcription initiation. Our data suggest functional plasticity of SI3 and provide the foundation for further research into cyanobacterial and chloroplast transcription.

Funder

MOST | National Key Research and Development Program of China

Science and Technology Commission of Shanghai Municipality

Leverhulme Trust

UKRI | Engineering and Physical Sciences Research Council

Publisher

Proceedings of the National Academy of Sciences

Subject

Multidisciplinary

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