Nonribosomal peptide synthetases and nonribosomal cyanopeptides synthesis in Microcystis: A comparative genomics study

Microcystis, the most prevalent bloom-forming cyanobacterial genus, can synthesize a variety of toxic cyanopeptides, such as hepatotoxic microcystins, protease and phosphatase-inhibitory aeruginosins, and cyanopeptolins. Most toxic cyanopeptides are nonribosomal peptides (NRPs) synthesized via nonribosomal peptide synthetase (NRPS) or hybrid NRPS/polyketide synthase pathways. In NRPS modules, adenylation domains (Adomains) can selectively recognize and activate specificity substrates. The various toxicity and enzyme-inhibiting activities of cyanopeptides are mainly decided by the molecules' structure and composition, which can be deduced according to the order and specificity of NRPS modules in NRPS gene clusters using bioinformatics approaches. Here, we performed comparative genomic analyses mainly focused on the distribution of NRPS gene clusters in association with phylogenomic relationships, and on substrate and structural predictions of A-domains in the NRPS modules for nonribosomal cyanopeptide synthesis in 36 Microcystis strains. Aeruginosin, cyanopeptolin, and microcystin biosynthesis gene clusters are the most frequently observed in the Microcystis genomes we analyzed. Phylogenomic affiliation analysis of NRPS gene cluster profiles indicates that Microcystis phylogenomic marker genes and nonribosomal cyanopeptide synthesis genes have coevolved during evolution. The NRPS A-domains for toxic cyanopeptide synthesis were characterized based on NRPS gene clusters analysis. Substrate and structure prediction indicates varied substrates of the A-domains. Selection analysis demonstrates that all A-domains encoded by aer, mcn, and mcy gene clusters are subjected to purifying selection, and positive selection has acted on some residues in core motifs and substrate binding pockets of the A-domains. In summary, our study reveals that the distribution of NRPS gene clusters in Microcystis and the diversity of the nonribosomal cyanopeptides produced relate to an evolutionary history of environmental adaptations.

Automated summary

Microcystis, a prevalent bloom-forming cyanobacterial genus, can synthesize a variety of toxic cyanopeptides via nonribosomal peptide synthetase (NRPS) pathways. The toxicity and enzyme-inhibiting activities of cyanopeptides are mainly determined by the molecules' structure and composition, which can be predicted based on the order and specificity of NRPS modules in NRPS gene clusters using bioinformatics approaches.