Functional analysis of environmental DNA-derived type II PKS reveals structurally diverse secondary metabolites

Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 08/2011; 108(31):12629-34. DOI: 10.1073/pnas.1103921108
Source: PubMed


A single gram of soil is predicted to contain thousands of unique bacterial species. The majority of these species remain recalcitrant to standard culture methods, prohibiting their use as sources of unique bioactive small molecules. The cloning and analysis of DNA extracted directly from environmental samples (environmental DNA, eDNA) provides a means of exploring the biosynthetic capacity of natural bacterial populations. Environmental DNA libraries contain large reservoirs of bacterial genetic diversity from which new secondary metabolite gene clusters can be systematically recovered and studied. The identification and heterologous expression of type II polyketide synthase-containing eDNA clones is reported here. Functional analysis of three soil DNA-derived polyketide synthase systems in Streptomyces albus revealed diverse metabolites belonging to well-known, rare, and previously uncharacterized structural families. The first of these systems is predicted to encode the production of the known antibiotic landomycin E. The second was found to encode the production of a metabolite with a previously uncharacterized pentacyclic ring system. The third was found to encode the production of unique KB-3346-5 derivatives, which show activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis. These results, together with those of other small-molecule-directed metagenomic studies, suggest that culture-independent approaches are capable of accessing biosynthetic diversity that has not yet been extensively explored using culture-based methods. The large-scale functional screening of eDNA clones should be a productive strategy for generating structurally previously uncharacterized chemical entities for use in future drug development efforts.

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    • "The potential of polyketides was immediately associated with metagenomic techniques in order to explore uncultivable soil microorganisms as a remarkable polyketide reservoir (Feng et al., 2011). In order to find novel compounds with biotechnological compounds, (Owen et al., 2013) focused their efforts on a soil sample from the Chihuahuan Desert in southwestern New Mexico . "
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    • "In the third example the PKS construct obtained by PCR screen from the multimillion soil DNA library was expressed in S. albus, which yielded in three novel antibiotics of the fluostatin group (Feng et al. 2010). Feng et al. (2011) reported another successful sequence-based identification and heterologous expression of type II PKS. Three soil-derived PKS e-DNA cosmids in S. albus produced well-known antibiotic landomycin E, previously uncharacterized pentacyclic ring system, and unique KB-3346-5 derivatives (AZ 154; Fig. 2) which show activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis. "
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