Designing and implementing an assay for the detection of rare and divergent NRPS and PKS clones in European, Antarctic and Cuban soils

Amos, Gregory C. A.; Borsetto, Chiara; Laskaris, Paris; Krsek, Martin; Berry, Andrew E.; Newsham, Kevin K. ORCID: https://orcid.org/0000-0002-9108-0936; Calvo-Bado, Leo; Pearce, David A.; Vallin, Carlos; Wellington, Elizabeth M. H.. 2015 Designing and implementing an assay for the detection of rare and divergent NRPS and PKS clones in European, Antarctic and Cuban soils. PLoS One, 10 (9), e0138327. 15, pp. https://doi.org/10.1371/journal.pone.0138327

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Abstract/Summary

The ever increasing microbial resistome means there is an urgent need for new antibiotics. Metagenomics is an underexploited tool in the field of drug discovery. In this study we aimed to produce a new updated assay for the discovery of biosynthetic gene clusters encoding bioactive secondary metabolites. PCR assays targeting the polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) were developed. A range of European soils were tested for their biosynthetic potential using clone libraries developed from metagenomic DNA. Results revealed a surprising number of NRPS and PKS clones with similarity to rare Actinomycetes. Many of the clones tested were phylogenetically divergent suggesting they were fragments from novel NRPS and PKS gene clusters. Soils did not appear to cluster by location but did represent NRPS and PKS clones of diverse taxonomic origin. Fosmid libraries were constructed from Cuban and Antarctic soil samples; 17 fosmids were positive for NRPS domains suggesting a hit rate of less than 1 in 10 genomes. NRPS hits had low similarities to both rare Actinobacteria and Proteobacteria; they also clustered with known antibiotic producers suggesting they may encode for pathways producing novel bioactive compounds. In conclusion we designed an assay capable of detecting divergent NRPS and PKS gene clusters from the rare biosphere; when tested on soil samples results suggest the majority of NRPS and PKS pathways and hence bioactive metabolites are yet to be discovered

Item Type:	Publication - Article
Digital Object Identifier (DOI):	https://doi.org/10.1371/journal.pone.0138327
Programmes:	BAS Programmes > BAS Programmes 2015 > Biodiversity, Evolution and Adaptation
ISSN:	1932-6203
NORA Subject Terms:	Medicine
Date made live:	30 Sep 2015 09:26 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/510893

Item Type:

Publication - Article

Digital Object Identifier (DOI):

https://doi.org/10.1371/journal.pone.0138327

Programmes:

BAS Programmes > BAS Programmes 2015 > Biodiversity, Evolution and Adaptation

ISSN:

1932-6203

NORA Subject Terms:

Medicine

Date made live:

30 Sep 2015 09:26 +0 (UTC)