Designing and implementing an assay for the detection of rare and divergent NRPS and PKS clones in European, Antarctic and Cuban soils
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 metabol...
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ftnerc:oai:nora.nerc.ac.uk:510893 2023-05-15T13:49:32+02:00 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. Calvo-Bado, Leo Pearce, David A. Vallin, Carlos Wellington, Elizabeth M. H. 2015-09-23 text http://nora.nerc.ac.uk/id/eprint/510893/ https://nora.nerc.ac.uk/id/eprint/510893/1/Amos.pdf en eng Public Library of Science https://nora.nerc.ac.uk/id/eprint/510893/1/Amos.pdf Amos, Gregory C. A.; Borsetto, Chiara; Laskaris, Paris; Krsek, Martin; Berry, Andrew E.; Newsham, Kevin K. orcid: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 <https://doi.org/10.1371/journal.pone.0138327> cc_by CC-BY Medicine Publication - Article PeerReviewed 2015 ftnerc https://doi.org/10.1371/journal.pone.0138327 2023-02-04T19:41:38Z 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 Article in Journal/Newspaper Antarc* Antarctic Natural Environment Research Council: NERC Open Research Archive Antarctic PLOS ONE 10 9 e0138327 |
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Natural Environment Research Council: NERC Open Research Archive |
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ftnerc |
language |
English |
topic |
Medicine |
spellingShingle |
Medicine Amos, Gregory C. A. Borsetto, Chiara Laskaris, Paris Krsek, Martin Berry, Andrew E. Newsham, Kevin K. Calvo-Bado, Leo Pearce, David A. Vallin, Carlos Wellington, Elizabeth M. H. Designing and implementing an assay for the detection of rare and divergent NRPS and PKS clones in European, Antarctic and Cuban soils |
topic_facet |
Medicine |
description |
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 |
format |
Article in Journal/Newspaper |
author |
Amos, Gregory C. A. Borsetto, Chiara Laskaris, Paris Krsek, Martin Berry, Andrew E. Newsham, Kevin K. Calvo-Bado, Leo Pearce, David A. Vallin, Carlos Wellington, Elizabeth M. H. |
author_facet |
Amos, Gregory C. A. Borsetto, Chiara Laskaris, Paris Krsek, Martin Berry, Andrew E. Newsham, Kevin K. Calvo-Bado, Leo Pearce, David A. Vallin, Carlos Wellington, Elizabeth M. H. |
author_sort |
Amos, Gregory C. A. |
title |
Designing and implementing an assay for the detection of rare and divergent NRPS and PKS clones in European, Antarctic and Cuban soils |
title_short |
Designing and implementing an assay for the detection of rare and divergent NRPS and PKS clones in European, Antarctic and Cuban soils |
title_full |
Designing and implementing an assay for the detection of rare and divergent NRPS and PKS clones in European, Antarctic and Cuban soils |
title_fullStr |
Designing and implementing an assay for the detection of rare and divergent NRPS and PKS clones in European, Antarctic and Cuban soils |
title_full_unstemmed |
Designing and implementing an assay for the detection of rare and divergent NRPS and PKS clones in European, Antarctic and Cuban soils |
title_sort |
designing and implementing an assay for the detection of rare and divergent nrps and pks clones in european, antarctic and cuban soils |
publisher |
Public Library of Science |
publishDate |
2015 |
url |
http://nora.nerc.ac.uk/id/eprint/510893/ https://nora.nerc.ac.uk/id/eprint/510893/1/Amos.pdf |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
https://nora.nerc.ac.uk/id/eprint/510893/1/Amos.pdf Amos, Gregory C. A.; Borsetto, Chiara; Laskaris, Paris; Krsek, Martin; Berry, Andrew E.; Newsham, Kevin K. orcid: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 <https://doi.org/10.1371/journal.pone.0138327> |
op_rights |
cc_by |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0138327 |
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PLOS ONE |
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10 |
container_issue |
9 |
container_start_page |
e0138327 |
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1766251493219893248 |