A novel strategy of gene screen based on multi-omics in Streptomyces roseosporus

• Published in: Applied microbiology and biotechnology 2022-04, Vol.106 (8), p.3103-3112
• Main Authors: Xu, Wei-Feng, Fang, Jiao-Le, Bu, Qing-Ting, Lyu, Zhong-Yuan, Zhu, Chen-Yang, Sun, Chen-Fan, Zhao, Qing-Wei, Li, Yong-Quan
• Format: Article
• Language: English
• Subjects: Anti-Bacterial Agents - pharmacology; Antibiotics; Biomedical and Life Sciences; Biosynthesis; Biotechnology; Daptomycin; Drug resistance; Fermentation; Genes; Genomics; Life Sciences; Lysine; Microbial Genetics and Genomics; Microbiology; Mutation; Production costs; Proteasome Endopeptidase Complex; Proteasomes; Proteome - metabolism; Proteomes; Proteomics; Streptomyces; Streptomyces - metabolism; Transcriptomes; Transcriptomics
• ISSN: 0175-7598; 1432-0614
• DOI: 10.1007/s00253-022-11904-3

Daptomycin is a new lipopeptide antibiotic for treatment of severe infection caused by multi-drug-resistant bacteria, but its production cost remains high currently. Thus, it is very important to improve the fermentation ability of the daptomycin producer Streptomyces roseosporus . Here, we found that the deletion of proteasome in S . roseosporus would result in the loss of ability to produce daptomycin. Therefore, transcriptome and 4D label-free proteome analyses of the proteasome mutant ( Δprc ) and wild type were carried out, showing 457 differential genes. Further, five genes were screened by integrated crotonylation omics analysis. Among them, two genes ( orf04750 / orf05959 ) could significantly promote the daptomycin synthesis by overexpression, and the fermentation yield in shake flask increased by 54% and 76.7%, respectively. By enhancing the crotonylation modification via lysine site mutation (K-Q), the daptomycin production in shake flask was finally increased by 98.8% and 206.3%, respectively. This result proved that the crotonylation modification of appropriate proteins could effectively modulate daptomycin biosynthesis. In summary, we established a novel strategy of gene screen for antibiotic biosynthesis process, which is more convenient than the previous screening method based on pathway-specific regulators. Key points • Δprc strain has lost the ability of daptomycin production • Five genes were screened by multi-omics analysis • Two genes (orf04750/orf05959) could promote the daptomycin synthesis by overexpression