Bioinformatic interrogation of phosphonate tailoring pathways

Phosphonates represent an underexploited class of natural products despite their tremendous potential for use in medicine and agriculture. Even less characterized are phosphonate-containing macromolecules such as cell wall lipids and glycans, distinguished by a P-C bond known to provide stability towards hydrolysis. Despite some progress made in revealing cell wall phosphonate tailoring (Pnt) pathways, several barriers impede the discovery and characterization of novel phosphonate biosynthetic pathways. Specifically, a large diversity of gene composition and arrangement is evident surrounding key genes established to participate in phosphonate tailoring pathways, which are identified alongside the presence of the ppm gene encoding the P-C bond forming enzyme phosphoenolpyruvate mutase (Ppm). In this thesis, the presence of a putative cytidylyltransferase called pntC has been identified in close genomic proximity to ppm in 120 microbial phosphonyl tailoring (pnt) gene neighbourhoods collected from non-redundant genome sets. Further, bioinformatic analysis of gene neighbourhoods surrounding ppm and pntC homologs, based on functional associations with Pfam families, has been completed and will allow for prediction of new phosphonate modifications. Indeed, 6 pnt gene clusters have been preliminarily classified based on uniquely identified Pfams, highlighting functions involved in transport, redox reactions, dehydrogenation, and deamination with a variety of substrates. The new bioinformatics tool described herein will enable further classification of pnt gene clusters and result in the generation of testable hypotheses for enzyme targets crucial to phosphonate tailoring pathways.