Targeted Metagenomics: Finding Rare Tryptophan Dimer Natural Products in the Environment

Natural
product discovery from environmental genomes (metagenomics)
has largely been limited to the screening of existing environmental
DNA (eDNA) libraries. Here, we have coupled a chemical-biogeographic
survey of chromopyrrolic acid synthase (CPAS) gene diversity with
targeted eDNA library production to more efficiently access rare tryptophan
dimer (TD) biosynthetic gene clusters. A combination of traditional
and synthetic biology-based heterologous expression efforts using
eDNA-derived gene clusters led to the production of hydroxysporine
(1) and reductasporine (2), two bioactive
TDs. As suggested by our phylogenetic analysis of CPAS genes, identified
in our survey of crude eDNA extracts, reductasporine (2) contains an unprecedented TD core structure: a pyrrolinium indolocarbazole
core that is likely key to its unusual bioactivity profile. This work
demonstrates the potential for the discovery of structurally rare
and biologically interesting natural products using targeted metagenomics,
where environmental samples are prescreened to identify the most phylogenetically
unique gene sequences and molecules associated with these genes are
accessed through targeted metagenomic library construction and heterologous
expression.