Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding

Dingwei He; Linlin You; Xiaoxian Wu; Jing Shi; Aijia Wen; Zhi Yan; Wenhui Mu; Chengli Fang; Yu Feng; Yu Zhang

doi:10.1038/s41467-022-31871-7

Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding

Nat Commun. 2022 Jul 20;13(1):4204. doi: 10.1038/s41467-022-31871-7.

Authors

Dingwei He^#^{1

2}, Linlin You^#^{1

2}, Xiaoxian Wu¹, Jing Shi³, Aijia Wen⁴, Zhi Yan¹, Wenhui Mu^{1

5}, Chengli Fang^{1

2}, Yu Feng⁶, Yu Zhang⁷

Affiliations

¹ Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
² University of Chinese Academy of Sciences, Beijing, China.
³ Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
⁴ Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
⁵ Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China.
⁶ Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China. yufengjay@zju.e.du.cn.
⁷ Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. yzhang@sippe.ac.cn.

^# Contributed equally.

Abstract

Pseudomonas aeruginosa (Pae) SutA adapts bacteria to hypoxia and nutrition-limited environment during chronic infection by increasing transcription activity of an RNA polymerase (RNAP) holoenzyme comprising the stress-responsive σ factor σ^S (RNAP-σ^S). SutA shows no homology to previously characterized RNAP-binding proteins. The structure and mode of action of SutA remain unclear. Here we determined cryo-EM structures of Pae RNAP-σ^S holoenzyme, Pae RNAP-σ^S holoenzyme complexed with SutA, and Pae RNAP-σ^S transcription initiation complex comprising SutA. The structures show SutA pinches RNAP-β protrusion and facilitates promoter unwinding by wedging RNAP-β lobe open. Our results demonstrate that SutA clears an energetic barrier to facilitate promoter unwinding of RNAP-σ^S holoenzyme.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacterial Proteins / metabolism
DNA / metabolism
DNA-Directed RNA Polymerases* / metabolism
Holoenzymes / metabolism
Pseudomonas aeruginosa* / metabolism
Sigma Factor / metabolism
Transcription, Genetic

Substances

Bacterial Proteins
Holoenzymes
Sigma Factor
DNA
DNA-Directed RNA Polymerases