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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    ABSTRACT: In recent years a major worldwide problem has arisen with regard to infectious diseases caused by resistant bacteria. Resistant pathogens are related to high mortality and also to enormous healthcare costs. In this field, cultured microorganisms have been commonly focused in attempts to isolate antibiotic resistance genes or to identify antimicrobial compounds. Although this strategy has been successful in many cases, most of the microbial diversity and related antimicrobial molecules have been completely lost. As an alternative, metagenomics has been used as a reliable approach to reveal the prospective reservoir of antimicrobial compounds and antibiotic resistance genes in the uncultured microbial community that inhabits a number of environments. In this context, this review will focus on resistance genes as well as on novel antibiotics revealed by a metagenomics approach from the soil environment. Biotechnology prospects are also discussed, opening new frontiers for antibiotic development.
    Frontiers in Microbiology; 09/2014
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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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    ABSTRACT: Mining of natural sources for new secondary metabolites has a successful history, which is reflected by the fact that over 50% of all drugs, currently on the market, are derived from natural products. Bacteria are one of the most important sources of bioactive natural products destined for drug discovery. However, less than 1% of the microorganisms observed in different habitats have been cultivated and characterized. To explore the genomic and functional diversity of the vast majority of the microbial world, novel methods were introduced, which are based on analysis of a DNA isolated from environmental communities. Metagenomics represents a strategy offering access to the genetic information present in uncultured bacteria by screening of libraries constructed from DNA isolated from different habitats. Functional- and sequence-driven screens are the major approaches employed to mine metagenomic libraries. This review aims to highlight discoveries in this area and discusses the possible future directions of the field.
    Biologia 12/2013; 68(6). DOI:10.2478/s11756-013-0246-7 · 0.83 Impact Factor
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    ABSTRACT: Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics.
    PLoS ONE 06/2015; 10(6):e0130659. DOI:10.1371/journal.pone.0130659 · 3.23 Impact Factor
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