Structural Insights into Transcription Activation of the Antibiotic Regulatory Protein, AfsR

Overview

Journal iScience

Publisher Cell Press

Date 2024 Aug 7

PMID 39108719

Authors

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

Affiliations

Soon will be listed here.

Abstract

The antibiotic regulatory proteins (SARPs) are ubiquitously distributed transcription activators in 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 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 σR4 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, σR4, and αCTD). Thus, these macromolecular snapshots support a general model and provide valuable clues for SARP-dependent transcription activation in .

References

Martin J, Sola-Landa A, Santos-Beneit F, Fernandez-Martinez L, Prieto C, Rodriguez-Garcia A . Cross-talk of global nutritional regulators in the control of primary and secondary metabolism in Streptomyces. Microb Biotechnol. 2011; 4(2):165-74. PMC: 3818857. DOI: 10.1111/j.1751-7915.2010.00235.x. View

Bibb M . Regulation of secondary metabolism in streptomycetes. Curr Opin Microbiol. 2005; 8(2):208-15. DOI: 10.1016/j.mib.2005.02.016. View

Shi W, Jiang Y, Deng Y, Dong Z, Liu B . Visualization of two architectures in class-II CAP-dependent transcription activation. PLoS Biol. 2020; 18(4):e3000706. PMC: 7192510. DOI: 10.1371/journal.pbio.3000706. View

Shi J, Wang L, Wen A, Wang F, Zhang Y, Yu L . Structural basis of three different transcription activation strategies adopted by a single regulator SoxS. Nucleic Acids Res. 2022; 50(19):11359-11373. PMC: 9638938. DOI: 10.1093/nar/gkac898. View

Yang X, Wang Y, Liu G, Deng Z, Lin S, Zheng J . Structural basis of Streptomyces transcription activation by zinc uptake regulator. Nucleic Acids Res. 2022; 50(14):8363-8376. PMC: 9371925. DOI: 10.1093/nar/gkac627. View

Boyaci H, Chen J, Jansen R, Darst S, Campbell E . Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding. Nature. 2019; 565(7739):382-385. PMC: 6399747. DOI: 10.1038/s41586-018-0840-5. View

Lee P, Umeyama T, Horinouchi S . afsS is a target of AfsR, a transcriptional factor with ATPase activity that globally controls secondary metabolism in Streptomyces coelicolor A3(2). Mol Microbiol. 2002; 43(6):1413-30. DOI: 10.1046/j.1365-2958.2002.02840.x. View

Martin J, Liras P . The Balance Metabolism Safety Net: Integration of Stress Signals by Interacting Transcriptional Factors in and Related Actinobacteria. Front Microbiol. 2020; 10:3120. PMC: 6988585. DOI: 10.3389/fmicb.2019.03120. View

Jose P, Maharshi A, Jha B . Actinobacteria in natural products research: Progress and prospects. Microbiol Res. 2021; 246:126708. DOI: 10.1016/j.micres.2021.126708. View

10.

Chen J, Chiu C, Gopalkrishnan S, Chen A, Olinares P, Saecker R . Stepwise Promoter Melting by Bacterial RNA Polymerase. Mol Cell. 2020; 78(2):275-288.e6. PMC: 7166197. DOI: 10.1016/j.molcel.2020.02.017. View

11.

Marquenet E, Richet E . How integration of positive and negative regulatory signals by a STAND signaling protein depends on ATP hydrolysis. Mol Cell. 2007; 28(2):187-99. DOI: 10.1016/j.molcel.2007.08.014. View

12.

Saecker R, Record Jr M, deHaseth P . Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. J Mol Biol. 2011; 412(5):754-71. PMC: 3440003. DOI: 10.1016/j.jmb.2011.01.018. View

13.

Horinouchi S, Kito M, Nishiyama M, Furuya K, Hong S, Miyake K . Primary structure of AfsR, a global regulatory protein for secondary metabolite formation in Streptomyces coelicolor A3(2). Gene. 1990; 95(1):49-56. DOI: 10.1016/0378-1119(90)90412-k. View

14.

Clara L, David C, Laila S, Virginie R, Marie-Joelle V . Comparative Proteomic Analysis of Transcriptional and Regulatory Proteins Abundances in and Suggests a Link between Various Stresses and Antibiotic Production. Int J Mol Sci. 2022; 23(23). PMC: 9739823. DOI: 10.3390/ijms232314792. View

15.

Santos-Beneit F, Rodriguez-Garcia A, Martin J . Complex transcriptional control of the antibiotic regulator afsS in Streptomyces: PhoP and AfsR are overlapping, competitive activators. J Bacteriol. 2011; 193(9):2242-51. PMC: 3133061. DOI: 10.1128/JB.01462-10. View

16.

Lilic M, Darst S, Campbell E . Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7. Mol Cell. 2021; 81(14):2875-2886.e5. PMC: 8311663. DOI: 10.1016/j.molcel.2021.05.017. View

17.

Smidova K, Zikova A, Pospisil J, Schwarz M, Bobek J, Vohradsky J . DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor. Nucleic Acids Res. 2018; 47(2):621-633. PMC: 6344877. DOI: 10.1093/nar/gky1018. View

18.

Busby S, Ebright R . Transcription activation by catabolite activator protein (CAP). J Mol Biol. 1999; 293(2):199-213. DOI: 10.1006/jmbi.1999.3161. View

19.

Decker K, Hinton D . Transcription regulation at the core: similarities among bacterial, archaeal, and eukaryotic RNA polymerases. Annu Rev Microbiol. 2013; 67:113-39. DOI: 10.1146/annurev-micro-092412-155756. View

20.

Wu Y, Sun Y, Richet E, Han Z, Chai J . Structural basis for negative regulation of the Escherichia coli maltose system. Nat Commun. 2023; 14(1):4925. PMC: 10427625. DOI: 10.1038/s41467-023-40447-y. View