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Open AccessCommunication
Int. J. Mol. Sci. 2015, 16(12), 28285-28295; doi:10.3390/ijms161226101

Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS

1
Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Rio de Janeiro CEP 21040-360, Brazil
2
Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, OT Neuglobsow, Stechlin 16775, Germany
3
Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, Berlin 14195, Germany
4
Molecular Microbiology Laboratory, Federal University of São João del-Rei, Sete Lagoas Campus Rua Sétimo Moreira Martins 188, Itapoã II, Sete Lagoas CEP 35702-031, Brazil
*
Author to whom correspondence should be addressed.
Academic Editor: Patrick C. Y. Woo
Received: 5 October 2015 / Revised: 16 November 2015 / Accepted: 18 November 2015 / Published: 27 November 2015
(This article belongs to the Special Issue Microbial Genomics and Metabolomics)
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Abstract

Marine environments harbor a wide range of microorganisms from the three domains of life. These microorganisms have great potential to enable discovery of new enzymes and bioactive compounds for industrial use. However, only ~1% of microorganisms from the environment can currently be identified through cultured isolates, limiting the discovery of new compounds. To overcome this limitation, a metagenomics approach has been widely adopted for biodiversity studies on samples from marine environments. In this study, we screened metagenomes in order to estimate the potential for new natural compound synthesis mediated by diversity in the Polyketide Synthase (PKS) and Nonribosomal Peptide Synthetase (NRPS) genes. The samples were collected from the Praia dos Anjos (Angel’s Beach) surface water—Arraial do Cabo (Rio de Janeiro state, Brazil), an environment affected by upwelling. In order to evaluate the potential for screening natural products in Arraial do Cabo samples, we used KS (keto-synthase) and C (condensation) domains (from PKS and NRPS, respectively) to build Hidden Markov Models (HMM) models. From both samples, a total of 84 KS and 46 C novel domain sequences were obtained, showing the potential of this environment for the discovery of new genes of biotechnological interest. These domains were classified by phylogenetic analysis and this was the first study conducted to screen PKS and NRPS genes in an upwelling affected sample View Full-Text
Keywords: PKS; NRPS; metagenomics; environmental genomics; upwelling; coastal environment PKS; NRPS; metagenomics; environmental genomics; upwelling; coastal environment
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Cuadrat, R.R.C.; Cury, J.C.; Dávila, A.M.R. Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS. Int. J. Mol. Sci. 2015, 16, 28285-28295.

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