m4C DNA methylation regulates biosynthesis of daptomycin in Streptomyces roseosporus L30

Jiao-Le Fang; Wen-Li Gao; Wei-Feng Xu; Zhong-Yuan Lyu; Lie Ma; Shuai Luo; Xin-Ai Chen; Xu-Ming Mao; Yong-Quan Li

doi:10.1016/j.synbio.2022.06.001

m4C DNA methylation regulates biosynthesis of daptomycin in Streptomyces roseosporus L30

Synth Syst Biotechnol. 2022 Jun 17;7(4):1013-1023. doi: 10.1016/j.synbio.2022.06.001. eCollection 2022 Dec.

Authors

Jiao-Le Fang^{1

2}, Wen-Li Gao^{1

2}, Wei-Feng Xu^{1

2}, Zhong-Yuan Lyu^{1

2}, Lie Ma^{1

2}, Shuai Luo², Xin-Ai Chen^{1

2}, Xu-Ming Mao¹, Yong-Quan Li^{1

2}

Affiliations

¹ Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China.
² Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China.

Abstract

Despite numerous studies on transcriptional level regulation by single genes in drug producing Actinomyces, the global regulation based on epigenetic modification is not well explored. N4-methylcytosine (m4C), an abundant epigenetic marker in Actinomycetes' genome, but its regulatory mechanism remains unclear. In this study, we identify a m4C methyltransferase (SroLm3) in Streptomyces roseosporus L30 and multi-omics studies were performed and revealed SroLm3 as a global regulator of secondary metabolism. Notably, three BGCs in ΔsroLm3 strain exhibited decreased expression compared to wild type. In-frame deletion of sroLm3 in S.roseosporus L30 further revealed its role in enhancing daptomycin production. In summary, we characterized a m4C methyltransferase, revealed the function of m4C in secondary metabolism regulation and biosynthesis of red pigment, and mapped a series of novel regulators for daptomycin biosynthesis dominated by m4C methylation. Our research further indicated that m4C DNA methylation may contribute to a metabolic switch from primary to secondary metabolism in Actinomyces.

Keywords: DNA methyltransferase; Daptomycin; N4-methylcytosine; Secondary metabolism; Transcriptional regulator.