The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis

• Published in: Nature communications 2019-08, Vol.10 (1), p.3698-12, Article 3698
• Main Authors: Rice, Kyle, Batul, Kissa, Whiteside, Jacqueline, Kelso, Jayne, Papinski, Monica, Schmidt, Edward, Pratasouskaya, Alena, Wang, Dacheng, Sullivan, Rebecca, Bartlett, Christopher, Weadge, Joel T., Van der Kamp, Marc W., Moreno-Hagelsieb, Gabriel, Suits, Michael D., Horsman, Geoff P.
• Format: Article
• Language: English
• Subjects: 631/45/535/1266; 631/45/607/1172; 639/638/60; 82/16; 82/58; 82/80; 82/83; Actinobacteria; Aminoethylphosphonic Acid - metabolism; Bacteria - genetics; Bacteria - metabolism; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; BASIC BIOLOGICAL SCIENCES; Biosynthesis; Biosynthetic Pathways - physiology; Cell Wall - metabolism; Crystallization; Crystallography, X-Ray; Escherichia coli; Gene clusters; Humanities and Social Sciences; multidisciplinary; N-Acylneuraminate Cytidylyltransferase - genetics; N-Acylneuraminate Cytidylyltransferase - metabolism; Natural products; Nucleotidyltransferases - genetics; Nucleotidyltransferases - metabolism; Organic chemistry; Organophosphonates - metabolism; Phosphocholine; Phosphoenolpyruvate mutase; Phospholipids - metabolism; Phosphonates; Phosphorylcholine - metabolism; Phosphotransferases (Phosphomutases); Polysaccharides - metabolism; Science; Science (multidisciplinary); Streptococcus infections; Substrate Specificity; Substrates; transferases; Virulence; Virulence factors; x-ray crystallography
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-11627-6

Phosphonates are rare and unusually bioactive natural products. However, most bacterial phosphonate biosynthetic capacity is dedicated to tailoring cell surfaces with molecules like 2-aminoethylphosphonate (AEP). Although phosphoenolpyruvate mutase (Ppm)-catalyzed installation of C-P bonds is known, subsequent phosphonyl tailoring (Pnt) pathway steps remain enigmatic. Here we identify nucleotidyltransferases in over two-thirds of phosphonate biosynthetic gene clusters, including direct fusions to ~60% of Ppm enzymes. We characterize two putative phosphonyl tailoring cytidylyltransferases (PntCs) that prefer AEP over phosphocholine (P-Cho) – a similar substrate used by the related enzyme LicC, which is a virulence factor in Streptococcus pneumoniae . PntC structural analyses reveal steric discrimination against phosphocholine. These findings highlight nucleotidyl activation as a predominant chemical logic in phosphonate biosynthesis and set the stage for probing diverse phosphonyl tailoring pathways. Phosphonate modifications can be present on microbial cell surfaces. Here the authors perform bioinformatics analyses and observe a widespread occurrence of nucleotidyltransferase-encoding genes in bacterial phosphonate biosynthesis and functionally characterize two of the identified phosphonate specific cytidylyltransferases (PntCs) and determine the crystal structure of T. denticola PntC.