Unveiling an indole alkaloid diketopiperazine biosynthetic pathway that features a unique stereoisomerase and multifunctional methyltransferase

• Authors: Garrett Deletti, University of North Florida; Sajan D Green, University of North Florida; Caleb Weber, University of North Florida; Kristen N Patterson, University of North Florida; Swapnil S Joshi, Indian Institute of Science Education and Research (IISER), Tirupati; Tushar M Khopade, Indian Institute of Science Education and Research (IISER), Tirupati; Mathew Coban, Mayo Clinic in Jacksonville, Florida; James Veek-Wilson, University of North Florida; Thomas R Caulfield, Mayo Clinic in Jacksonville, Florida; Rajesh Viswanathan, University of North Florida; Amy L Lane, University of North Florida
• Journal Title: Nature Communications
• Volume: Volume 14, Number 1
• Publisher: Springer Nature Limited | 2023-12-01, Pages 2558-2558
• Type of Work: Article | Final Publisher PDF
• Publisher DOI: http://doi.org/10.1038/s41467-023-38168-3
• Subjects: Chemistry, General; Chemistry, Biochemistry
• Keywords: Methyltransferases; Biosynthetic Pathways; Substrate Specificity; Indole Alkaloids; Diketopiperazines

Abstract

The 2,5-diketopiperazines are a prominent class of bioactive molecules. The nocardioazines are actinomycete natural products that feature a pyrroloindoline diketopiperazine scaffold composed of two D-tryptophan residues functionalized by N- and C-methylation, prenylation, and diannulation. Here we identify and characterize the nocardioazine B biosynthetic pathway from marine Nocardiopsis sp. CMB-M0232 by using heterologous biotransformations, in vitro biochemical assays, and macromolecular modeling. Assembly of the cyclo-L-Trp-L-Trp diketopiperazine precursor is catalyzed by a cyclodipeptide synthase. A separate genomic locus encodes tailoring of this precursor and includes an aspartate/glutamate racemase homolog as an unusual D/L isomerase acting upon diketopiperazine substrates, a phytoene synthase-like prenyltransferase as the catalyst of indole alkaloid diketopiperazine prenylation, and a rare dual function methyltransferase as the catalyst of both N- and C-methylation as the final steps of nocardioazine B biosynthesis. The biosynthetic paradigms revealed herein showcase Nature’s molecular ingenuity and lay the foundation for diketopiperazine diversification via biocatalytic approaches.