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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ftpubmed:oai:pubmedcentral.nih.gov:4580463 2023-05-15T14:01:30+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 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580463/ http://www.ncbi.nlm.nih.gov/pubmed/26398766 https://doi.org/10.1371/journal.pone.0138327 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580463/ http://www.ncbi.nlm.nih.gov/pubmed/26398766 http://dx.doi.org/10.1371/journal.pone.0138327 http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited CC-BY Research Article Text 2015 ftpubmed https://doi.org/10.1371/journal.pone.0138327 2015-10-04T00:25:56Z 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. Text Antarc* Antarctic PubMed Central (PMC) Antarctic PLOS ONE 10 9 e0138327 |
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Research Article 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 |
Research Article |
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 |
Text |
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://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580463/ http://www.ncbi.nlm.nih.gov/pubmed/26398766 https://doi.org/10.1371/journal.pone.0138327 |
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Antarctic |
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Antarctic |
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Antarc* Antarctic |
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Antarc* Antarctic |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580463/ http://www.ncbi.nlm.nih.gov/pubmed/26398766 http://dx.doi.org/10.1371/journal.pone.0138327 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0138327 |
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