title: Designing and Implementing an Assay for the Detection of Rare and Divergent NRPS and PKS Clones in European, Antarctic and Cuban Soils.
abstract: 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.
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom.
authors.forename: Gregory C A
authors.initials: GC
authors.lastname: Amos
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom.
authors.forename: Chiara
authors.initials: C
authors.lastname: Borsetto
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom.
authors.forename: Paris
authors.initials: P
authors.lastname: Laskaris
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom.
authors.forename: Martin
authors.initials: M
authors.lastname: Krsek
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Berry
authors.affiliation: Ecosystem Programme, British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, CB3 OET, United Kingdom.
authors.forename: Kevin K
authors.initials: KK
authors.lastname: Newsham
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom.
authors.forename: Leo
authors.initials: L
authors.lastname: Calvo-Bado
authors.affiliation: Ecosystem Programme, British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, CB3 OET, United Kingdom.
authors.forename: David A
authors.initials: DA
authors.lastname: Pearce
authors.affiliation: Department of Biomedical Research, Center of Pharmaceutical Chemistry, Atabey, Playa, Havana, Cuba.
authors.forename: Carlos
authors.initials: C
authors.lastname: Vallin
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom.
authors.forename: Elizabeth M H
authors.initials: EM
authors.lastname: Wellington
mesh_terms: D039903:Actinobacteria / Q000201:enzymology / Q000235:genetics; D000864:Antarctic Regions; D001483:Base Sequence; D001681:Biological Assay / Q000379:methods*; D002999:Clone Cells; D003462:Cuba; D017931:DNA Primers / Q000378:metabolism; D004269:DNA, Bacterial / Q000235:genetics; D005060:Europe; D015723:Gene Library; D005810:Multigene Family; D010453:Peptide Synthases / Q000378:metabolism*; D010802:Phylogeny; D048630:Polyketide Synthases / Q000378:metabolism*; D012987:Soil / Q000737:chemistry*
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D012987:Soil; D048630:Polyketide Synthases; D010453:Peptide Synthases; C104385:non-ribosomal peptide synthase