Designing and Implementing an Assay for the Detection of Rare
and Divergent NRPS and PKS Clones in European, Antarctic and
Cuban Soils

J 2015

Designing and Implementing an Assay for the Detection of Rare and Divergent NRPS and PKS Clones in European, Antarctic and Cuban Soils

AMOS, G.C.A., C. BORSETTO, P. LASKARIS, Martin KRSEK, A.E. BERRY et. al.

Basic information

Original name

Designing and Implementing an Assay for the Detection of Rare and Divergent NRPS and PKS Clones in European, Antarctic and Cuban Soils

Name in Czech

Návrh a využití metody detekce nezvyklých a odlišných NRPS a PKS klonů v evropských, antarktických a kubánských půdách

Authors

AMOS, G.C.A., C. BORSETTO, P. LASKARIS, Martin KRSEK, A.E. BERRY, K.K. NEWSHAM, L. CALVO-BADO, D.A. PEARCE, C. VALLIN and E.M.H. WELLINGTON

Edition

Plos one, San Francisco, Public Library of Science, 2015, 1932-6203

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.057

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1371/journal.pone.0138327

UT WoS

000361797500060

Keywords (in Czech)

antibiotika; metagenomika; NRPS; PKS; půda; aktinobakterie; proteobakterie

Keywords in English

antibiotics; metagenomics; NRPS; PKS; actinobacteria; proteobacteria

Abstract

V originále

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.

Citovat

AMOS, G.C.A., C. BORSETTO, P. LASKARIS, Martin KRSEK, A.E. BERRY, K.K. NEWSHAM, L. CALVO-BADO, D.A. PEARCE, C. VALLIN and E.M.H. WELLINGTON. Designing and Implementing an Assay for the Detection of Rare and Divergent NRPS and PKS Clones in European, Antarctic and Cuban Soils. Plos one. San Francisco: Public Library of Science, 2015, vol. 10, No 9, p. 1-15. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0138327.

@article{1323288,
   author = {Amos, G.C.A. and Borsetto, C. and Laskaris, P. and Krsek, Martin and Berry, A.E. and Newsham, K.K. and CalvoandBado, L. and Pearce, D.A. and Vallin, C. and Wellington, E.M.H.},
   article_location = {San Francisco},
   article_number = {9},
   doi = {http://dx.doi.org/10.1371/journal.pone.0138327},
   keywords = {antibiotics; metagenomics; NRPS; PKS; actinobacteria; proteobacteria},
   language = {eng},
   issn = {1932-6203},
   journal = {Plos one},
   note = {Žádný z autorů nemá afiliaci na MU.},
   title = {Designing and Implementing an Assay for the Detection of Rare and Divergent NRPS and PKS Clones in European, Antarctic and Cuban Soils},
   url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0138327},
   volume = {10},
   year = {2015}
}

TY  - JOUR
ID  - 1323288
AU  - Amos, G.C.A. - Borsetto, C. - Laskaris, P. - Krsek, Martin - Berry, A.E. - Newsham, K.K. - Calvo-Bado, L. - Pearce, D.A. - Vallin, C. - Wellington, E.M.H.
PY  - 2015
TI  - Designing and Implementing an Assay for the Detection of Rare and Divergent NRPS and PKS Clones in European, Antarctic and Cuban Soils
JF  - Plos one
VL  - 10
IS  - 9
SP  - 1-15
EP  - 1-15
PB  - Public Library of Science
SN  - 19326203
N1  - Žádný z autorů nemá afiliaci na MU.
KW  - antibiotics
KW  - metagenomics
KW  - NRPS
KW  - PKS
KW  - actinobacteria
KW  - proteobacteria
UR  - http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0138327
N2  - 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.
ER  -

AMOS, G.C.A., C. BORSETTO, P. LASKARIS, Martin KRSEK, A.E. BERRY, K.K. NEWSHAM, L. CALVO-BADO, D.A. PEARCE, C. VALLIN and E.M.H. WELLINGTON. Designing and Implementing an Assay for the Detection of Rare and Divergent NRPS and PKS Clones in European, Antarctic and Cuban Soils. \textit{Plos one}. San Francisco: Public Library of Science, 2015, vol.~10, No~9, p.~1-15. ISSN~1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0138327.

Detailed Information on Publication Record