New Natural Product Families from an Environmental DNA (eDNA) Gene Cluster

Journal of the American Chemical Society
2002.0

Abstract

Over 50 years ago, cultured soil microbes became central to drug discovery, but existing culture techniques access less than 1% of soil microbes, leaving uncultured ones as a potential source of bioactive molecules. We explored a method using environmental DNA (eDNA) from soil to construct cosmid libraries in E. coli and screen for clones biosynthesizing natural products. Previously, we described this approach and long-chain N-acyltyrosine antibiotics from a single eDNA open reading frame (ORF). Here, we report a biosynthetic gene cluster from antibiotic-producing clone CSLC-2, which produces two additional families of long-chain N-acyltyrosine-derived natural products. Characterization via low-resolution FABMS, HRFABMS, NMR, and total synthesis identified the two families: oxidatively decarboxylated long-chain N-acyltyrosines (family 2, with saturated/monounsaturated C12–C16 fatty acids) and long-chain fatty acid enol esters (family 3, with saturated/monounsaturated C14–C16 fatty acids). Sequencing revealed a 13-ORF (feeA-M) gene cluster organized into two operons. Transposon mutagenesis showed feeM is essential for all three families, feeG for families 2 and 3, and feeH for family 3; FeeM, FeeG, and FeeH are inferred as a long-chain N-acyl amino acid synthase, decarboxylase, and N,O-acyltransferase, respectively. BLAST searches indicated FeeG shares similarity with flavoprotein oxidases (suggesting a novel quinone methide-mediated tyrosine decarboxylation mechanism) and FeeH with sugar-modifying enzymes (potential unrecognized biosynthetic enzyme family). Remaining ORFs are implicated in acyl carrier protein (ACP) metabolism, fatty acid activation, modification, and transport. The eDNA approach links metabolites to biosynthetic machinery, confirming culture-independent methods reveal new molecular families and biosynthetic activities.

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