Structural insights into transcription activation of the Streptomyces antibiotic regulatory protein, AfsR

Jing Shi; Zonghang Ye; Zhenzhen Feng; Aijia Wen; Lu Wang; Zhipeng Zhang; Liqiao Xu; Qian Song; Fulin Wang; Tianyu Liu; Shuang Wang; Yu Feng; Wei Lin

doi:10.1016/j.isci.2024.110421

Structural insights into transcription activation of the Streptomyces antibiotic regulatory protein, AfsR

iScience. 2024 Jun 29;27(8):110421. doi: 10.1016/j.isci.2024.110421. eCollection 2024 Aug 16.

Authors

Jing Shi^{1

2}, Zonghang Ye¹, Zhenzhen Feng¹, Aijia Wen², Lu Wang¹, Zhipeng Zhang^{3

4

5}, Liqiao Xu², Qian Song¹, Fulin Wang¹, Tianyu Liu¹, Shuang Wang^{5

6}, Yu Feng², Wei Lin^{1

7

8}

Affiliations

¹ School of Medicine, Nanjing University of Chinese Medicine, Nanjing Drum Tower Hospital, Nanjing 210023, China.
² Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
³ MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, Guangdong, China.
⁴ Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, Guangdong, China.
⁵ Songshan Lake Materials Laboratory, Dongguan 523808, Guangdong, China.
⁶ Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
⁷ State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
⁸ Nanjing Drum Tower Hospital Clinical College, Nanjing University of Chinese Medicine, Nanjing 210023, China.

Abstract

The Streptomyces antibiotic regulatory proteins (SARPs) are ubiquitously distributed transcription activators in Streptomyces and control antibiotics biosynthesis and morphological differentiation. However, the molecular mechanism behind SARP-dependent transcription initiation remains elusive. We here solve the cryo-EM structure of an AfsR-loading RNA polymerase (RNAP)-promoter intermediate complex (AfsR-RPi) including the Streptomyces coelicolor RNAP, a large SARP member AfsR, and its target promoter DNA that retains the upstream portion straight. The structure reveals that one dimeric N-terminal AfsR-SARP domain (AfsR-SARP) specifically engages with the same face of the AfsR-binding sites by the conserved DNA-binding domains (DBDs), replacing σ^HrdBR4 to bind the suboptimal -35 element, and shortens the spacer between the -10 and -35 elements. Notably, the AfsR-SARPs also recruit RNAP through extensively interacting with its conserved domains (β flap, σ^HrdBR4, and αCTD). Thus, these macromolecular snapshots support a general model and provide valuable clues for SARP-dependent transcription activation in Streptomyces.

Keywords: Microbiology; Molecular biology; Molecular structure.