Unravelling cryptic phosphonate biosynthesis in Chelatococcus asaccharovorans through genome mining

Phosphonates are chemically distinctive natural products characterized by a stable carbon-phosphorus (C-P) bond and are traditionally associated with a limited number of well-studied bacterial genera. We performed comparative genome mining of four publicly available Chelatococcus asaccharovorans genomes along with related Chelatococcus species to investigate their potential for phosphonate biosynthesis. Genome analysis using antiSMASH identified putative phosphonate biosynthetic gene clusters (BGCs) in two of the four C. asaccharovorans strains, whereas no phosphonate BGCs were detected in the remaining C. asaccharovorans strains and other analyzed Chelatococcus species. Both identified clusters contained phosphoenolpyruvate mutase (PepM), responsible for C-P bond formation in phosphonate biosynthesis. Functional annotation using BLASTp and conserved domain database analyses revealed a conserved set of phosphonate-associated genes, including aminotransferases, phosphocholine cytidylyltransferase family protein, regulatory proteins, and S-adenosyl-L-methionine-dependent methyltransferase. Although antiSMASH-predicted cluster architectures differed between the two strains, the core phosphonate biosynthetic gene content was largely conserved. Comparison with the MIBiG database revealed moderate similarity to previously characterized phosphonate pathways, including FR-900098, dehydrophos, fosfomycin, and dehydrofosmidomycin, indicating that the identified clusters share core phosphonate biosynthetic components but are not closely related to any currently characterized pathway. The restricted occurrence of PepM-containing phosphonate BGCs within the analyzed dataset indicates strain-specific phosphonate biosynthetic potential and suggests that phosphonate biosynthesis is not uniformly distributed across the genus Chelatococcus. Collectively, our findings expand the phylogenetic scope of phosphonate biosynthesis and identify C. asaccharovorans as a previously unrecognized reservoir of putative phosphonate biosynthetic diversity. This genome-guided investigation provides a foundation for future experimental validation and natural product discovery efforts targeting novel phosphonate compounds.