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

• Published in: Nature communications Vol. 14; no. 1; p. 2558
• Main Authors: Deletti, Garrett, Green, Sajan D, Weber, Caleb, Patterson, Kristen N, Joshi, Swapnil S, Khopade, Tushar M, Coban, Mathew, Veek-Wilson, James, Caulfield, Thomas R, Viswanathan, Rajesh, Lane, Amy L
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 03.05.2023; Nature Publishing Group UK; Nature Portfolio
• Subjects: Alkaloids; Biosynthesis; Biosynthetic Pathways; Biotransformation; Catalysts; Diketopiperazines - metabolism; Glutamate racemase; Homology; Indole Alkaloids; Indoles; Macromolecules; Methylation; Methyltransferase; Methyltransferases - metabolism; Natural products; Phytoene synthase; Precursors; Substrate Specificity; Substrates; Tryptophan
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-38168-3

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.