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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ftuwarwick:oai:wrap.warwick.ac.uk:72726 2023-05-15T13:55:48+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 A. Pearce, David A. Vallin, Carlos Wellington, E. M. H. 2015-09-23 application/pdf http://wrap.warwick.ac.uk/72726/ http://wrap.warwick.ac.uk/72726/1/WRAP_journal.pone.0138327.pdf https://doi.org/10.1371/journal.pone.0138327 unknown Public Library of Science http://wrap.warwick.ac.uk/72726/1/WRAP_journal.pone.0138327.pdf Amos, Gregory C. A., Borsetto, Chiara, Laskaris, Paris, Krsek, Martin, Berry, Andrew E., Newsham, Kevin K., Calvo-Bado, Leo A., Pearce, David A., Vallin, Carlos and Wellington, E. 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). pp. 1-15. e0138327. doi:10.1371/journal.pone.0138327 <http://dx.doi.org/10.1371/journal.pone.0138327> QR Microbiology Journal Article NonPeerReviewed 2015 ftuwarwick https://doi.org/10.1371/journal.pone.0138327 2022-03-16T21:01:10Z 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 The University of Warwick: WRAP - Warwick Research Archive Portal Antarctic PLOS ONE 10 9 e0138327 |
institution |
Open Polar |
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The University of Warwick: WRAP - Warwick Research Archive Portal |
op_collection_id |
ftuwarwick |
language |
unknown |
topic |
QR Microbiology |
spellingShingle |
QR Microbiology Amos, Gregory C. A. Borsetto, Chiara Laskaris, Paris Krsek, Martin Berry, Andrew E. Newsham, Kevin K. Calvo-Bado, Leo A. Pearce, David A. Vallin, Carlos Wellington, E. 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 |
QR Microbiology |
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 A. Pearce, David A. Vallin, Carlos Wellington, E. M. H. |
author_facet |
Amos, Gregory C. A. Borsetto, Chiara Laskaris, Paris Krsek, Martin Berry, Andrew E. Newsham, Kevin K. Calvo-Bado, Leo A. Pearce, David A. Vallin, Carlos Wellington, E. 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://wrap.warwick.ac.uk/72726/ http://wrap.warwick.ac.uk/72726/1/WRAP_journal.pone.0138327.pdf https://doi.org/10.1371/journal.pone.0138327 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
http://wrap.warwick.ac.uk/72726/1/WRAP_journal.pone.0138327.pdf Amos, Gregory C. A., Borsetto, Chiara, Laskaris, Paris, Krsek, Martin, Berry, Andrew E., Newsham, Kevin K., Calvo-Bado, Leo A., Pearce, David A., Vallin, Carlos and Wellington, E. 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). pp. 1-15. e0138327. doi:10.1371/journal.pone.0138327 <http://dx.doi.org/10.1371/journal.pone.0138327> |
op_doi |
https://doi.org/10.1371/journal.pone.0138327 |
container_title |
PLOS ONE |
container_volume |
10 |
container_issue |
9 |
container_start_page |
e0138327 |
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1766262643920732160 |