Chemoproteomics profiling of surfactin-producing nonribosomal peptide synthetases in living bacterial cells

• Published in: Cell chemical biology Vol. 29; no. 1; pp. 145 - 156.e8
• Main Authors: Ishikawa, Fumihiro, Konno, Sho, Uchida, Chiharu, Suzuki, Takehiro, Takashima, Katsuki, Dohmae, Naoshi, Kakeya, Hideaki, Tanabe, Genzoh
• Format: Journal Article
• Language: English
• Published: United States Elsevier Ltd 20.01.2022
• Subjects: activity-based protein profiling; adenylation domain; Bacillus subtilis - cytology; Bacillus subtilis - enzymology; cellular imaging; in vitro labeling; in vivo labeling; Lipopeptides - biosynthesis; Lipopeptides - chemistry; natural product biosynthesis; nonribosomal peptide synthetase; Peptide Synthases - metabolism; photoaffinity labeling; Protein Conformation; protein degradation; Proteomics; natural product biosynthesis; nonribosomal peptide synthetase; activity-based protein profiling; cellular imaging; proteomics; adenylation domain; in vivo labeling; photoaffinity labeling; protein degradation; in vitro labeling
• ISSN: 2451-9456; 2451-9448; 2451-9456
• DOI: 10.1016/j.chembiol.2021.05.014

Much of our current knowledge on nonribosomal peptide synthetases (NRPSs) is based on studies in which the full NRPS system or each protein domain is expressed in heterologous hosts. Consequently, methods to detect the endogenous activity of NRPSs, under natural cellular conditions, are needed for the study of NRPS cell biology. Here, we describe the in vivo activity-based protein profiling (ABPP) for endogenous NRPSs and its applications to the study of their activities in bacteria. Remarkably, in vitro and in vivo ABPP in the context of the surfactin producer Bacillus subtilis enabled the visualization, tracking, and imaging of an endogenous SrfAB-NRPS with remarkable selectivity and sensitivity. Furthermore, in vivo, ABPP allowed the discovery of the degradation processes of the endogenous SrfAB-NRPS in the context of its native producer bacteria. Overall, this study deepens our understanding of the properties of NRPSs that cannot be addressed by conventional methods. [Display omitted] •We developed an in vivo ABPP of NRPSs in living bacterial cells•Our chemical probe serves as a valuable tool to probe NRPS cell biology•Study highlights the degradation processes of SrfAB-NRPS in living bacterial cells Ishikawa et al. describe the in vivo activity-based protein profiling (ABPP) for endogenous nonribosomal peptide synthetases (NRPSs) and its applications to the study of their activities in living bacteria.