2 research outputs found
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
(<b>1</b>) and reductasporine (<b>2</b>), two bioactive
TDs. As suggested by our phylogenetic analysis of CPAS genes, identified
in our survey of crude eDNA extracts, reductasporine (<b>2</b>) 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
Discovery and Synthetic Refactoring of Tryptophan Dimer Gene Clusters from the Environment
Here we investigate bacterial tryptophan
dimer (TD) biosynthesis
by probing environmental DNA (eDNA) libraries for chromopyrrolic acid
(CPA) synthase genes. Functional and bioinformatics analyses of TD
clusters indicate that CPA synthase gene sequences diverge in concert
with the functional output of their respective clusters, making this
gene a powerful tool for guiding the discovery of novel TDs from the
environment. Twelve unprecedented TD biosynthetic gene clusters that
can be arranged into five groups (A–E) based on their ability
to generate distinct TD core substructures were recovered from eDNA
libraries. Four of these groups contain clusters from both cultured
and culture independent studies, while the remaining group consists
entirely of eDNA-derived clusters. The complete synthetic refactoring
of a representative gene cluster from the latter eDNA specific group
led to the characterization of the erdasporines, cytotoxins with a
novel carboxy-indolocarbazole TD substructure. Analysis of CPA synthase
genes in crude eDNA suggests the presence of additional TD gene clusters
in soil environments