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...
Published in: | PLOS ONE |
---|---|
Main Authors: | , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Public Library of Science
2015
|
Subjects: | |
Online Access: | https://nrl.northumbria.ac.uk/id/eprint/24767/ https://doi.org/10.1371/journal.pone.0138327 https://nrl.northumbria.ac.uk/id/eprint/24767/1/Pearce%20D_%20Plos%20One_European%20Antarctic%20and%20Cuban%20soils.pdf |
id |
ftunivnorthumb:oai:nrl.northumbria.ac.uk:24767 |
---|---|
record_format |
openpolar |
spelling |
ftunivnorthumb:oai:nrl.northumbria.ac.uk:24767 2023-05-15T13:35:33+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 Borsetto, Chiara Laskaris, Paris Krsek, Martin Berry, Andrew Newsham, Kevin Calvo-Bado, Leo Pearce, David Vallin, Carlos Wellington, Elizabeth 2015-09-23 text https://nrl.northumbria.ac.uk/id/eprint/24767/ https://doi.org/10.1371/journal.pone.0138327 https://nrl.northumbria.ac.uk/id/eprint/24767/1/Pearce%20D_%20Plos%20One_European%20Antarctic%20and%20Cuban%20soils.pdf en eng Public Library of Science https://nrl.northumbria.ac.uk/id/eprint/24767/1/Pearce%20D_%20Plos%20One_European%20Antarctic%20and%20Cuban%20soils.pdf Amos, Gregory, Borsetto, Chiara, Laskaris, Paris, Krsek, Martin, Berry, Andrew, Newsham, Kevin, Calvo-Bado, Leo, Pearce, David, Vallin, Carlos and Wellington, Elizabeth (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. ISSN 1932-6203 cc_by_4_0 CC-BY C500 Microbiology F700 Ocean Sciences F800 Physical and Terrestrial Geographical and Environmental Sciences Article PeerReviewed 2015 ftunivnorthumb https://doi.org/10.1371/journal.pone.0138327 2022-09-25T06:02:55Z 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 Northumbria University, Newcastle: Northumbria Research Link (NRL) Antarctic PLOS ONE 10 9 e0138327 |
institution |
Open Polar |
collection |
Northumbria University, Newcastle: Northumbria Research Link (NRL) |
op_collection_id |
ftunivnorthumb |
language |
English |
topic |
C500 Microbiology F700 Ocean Sciences F800 Physical and Terrestrial Geographical and Environmental Sciences |
spellingShingle |
C500 Microbiology F700 Ocean Sciences F800 Physical and Terrestrial Geographical and Environmental Sciences Amos, Gregory Borsetto, Chiara Laskaris, Paris Krsek, Martin Berry, Andrew Newsham, Kevin Calvo-Bado, Leo Pearce, David Vallin, Carlos Wellington, Elizabeth Designing and implementing an assay for the detection of rare and divergent NRPS and PKS clones in European, Antarctic and Cuban soils |
topic_facet |
C500 Microbiology F700 Ocean Sciences F800 Physical and Terrestrial Geographical and Environmental Sciences |
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 Borsetto, Chiara Laskaris, Paris Krsek, Martin Berry, Andrew Newsham, Kevin Calvo-Bado, Leo Pearce, David Vallin, Carlos Wellington, Elizabeth |
author_facet |
Amos, Gregory Borsetto, Chiara Laskaris, Paris Krsek, Martin Berry, Andrew Newsham, Kevin Calvo-Bado, Leo Pearce, David Vallin, Carlos Wellington, Elizabeth |
author_sort |
Amos, Gregory |
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 |
https://nrl.northumbria.ac.uk/id/eprint/24767/ https://doi.org/10.1371/journal.pone.0138327 https://nrl.northumbria.ac.uk/id/eprint/24767/1/Pearce%20D_%20Plos%20One_European%20Antarctic%20and%20Cuban%20soils.pdf |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
https://nrl.northumbria.ac.uk/id/eprint/24767/1/Pearce%20D_%20Plos%20One_European%20Antarctic%20and%20Cuban%20soils.pdf Amos, Gregory, Borsetto, Chiara, Laskaris, Paris, Krsek, Martin, Berry, Andrew, Newsham, Kevin, Calvo-Bado, Leo, Pearce, David, Vallin, Carlos and Wellington, Elizabeth (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. ISSN 1932-6203 |
op_rights |
cc_by_4_0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0138327 |
container_title |
PLOS ONE |
container_volume |
10 |
container_issue |
9 |
container_start_page |
e0138327 |
_version_ |
1766067102628708352 |