Piperazic acid is a cyclic hydrazine and a non-proteinogenic amino acid found in diverse non-ribosomal peptide (NRP) and hybrid NRP–polyketide (PK) structures.
Piperazic acid (Piz) is a nonproteinogenic amino acid
possessing
a rare nitrogen–nitrogen bond. However, little is known about
how Piz is incorporated into nonribosomal peptides, including whether
adenylation domains specific to Piz exist. In this study, we show
that free piperazic acid is directly adenylated and then incorporated
into the incarnatapeptin nonribosomal peptides through isotopic incorporation
studies. We also use in vitro reconstitution to demonstrate
adenylation of free piperazic acid with a three-domain nonribosomal
peptide synthetase from the incarnatapeptin gene cluster. We furthermore
use bioinformatics and site-directed mutagenesis to outline consensus
sequences for the adenylation of piperazic acid, which can now be
used for the prediction of gene clusters linked to piperazic-acid-containing
peptides. Finally, we discover a fusion protein of a piperazate synthase
and an adenylation domain, highlighting the close biosynthetic relationship
of piperazic acid formation and its adenylation. Altogether, our work
demonstrates the evolution of biosynthetic systems for the activation
of free piperazic acid through adenylation, a pathway we suggest is
likely to be employed in the majority of pathways to piperazic-acid-containing
peptides.
Methods for the focused isolation
of low-abundance natural products
with specific chemical substructures could expand known bioactive
chemical diversity for drug discovery. Here we report the combined
use of genome mining and an 15N NMR-based screening method
for the targeted isolation of the low-abundance piperazic-acid-containing
peptides incarnatapeptins A (1) and B (3). Incarnatapeptin B (3) shows in vitro cytotoxicity to LNCaP prostate cancer cells.
Laboratory cultures of two ‘biosynthetically talented’ bacterial strains harvested from tropical and temperate Pacific Ocean sediment habitats were examined for the production of new natural products. Cultures of the tropical Salinispora arenicola strain RJA3005, harvested from a PNG marine sediment, produced salinorcinol (3) and salinacetamide (4), which had previously been reported as products of engineered and mutated strains of Amycolatopsis mediterranei, but had not been found before as natural products. An S. arenicola strain RJA4486, harvested from marine sediment collected in the temperate ocean waters off British Columbia, produced the new aminoquinone polyketide salinisporamine (5). Natural products 3, 4, and 5 are putative shunt products of the widely distributed rifamycin biosynthetic pathway.
This mini-review covers the use of nitrogen-15 in bacterial and fungal natural product discovery and biosynthetic characterization from 1970 to 2022. Nitrogen is an important element in a number of bioactive and structurally intriguing natural products including alkaloids, non-ribosomal peptides, and hybrid natural products. Nitrogen-15 can be detected at natural abundance utilizing two-dimensional nuclear magnetic resonance and mass spectrometry. Additionally, it is a stable isotope that can be added to growth media for both filamentous fungi and bacteria. With stable isotope feeding, additional two-dimensional nuclear magnetic resonance and mass spectrometry strategies have become available, and there is a growing trend to use nitrogen-15 stable isotope feeding for the biosynthetic characterization of natural products. This mini-review will catalog the use of these strategies, analyze the strengths and weaknesses of the different approaches, and suggest future directions for the use of nitrogen-15 in natural product discovery and biosynthetic characterization.
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