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Gacesa R, Baranasic D, Starcevic A, Diminic J, Korlević M, Najdek M, Blažina M, Oršolić D, Kolesarić D, Long PF, Cullum J, Hranueli D, Orlic S, Zucko J. Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from
Northern Adriatic Sea Sediments. Food Technol Biotechnol 2018; 56:270-277. [PMID: 30228802 DOI: 10.17113/ftb.56.02.18.5393] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Three metagenomic libraries were constructed using surface sediment samples from the northern Adriatic Sea. Two of the samples were taken from a highly polluted and an unpolluted site respectively. The third sample from a polluted site had been enriched using crude oil. The results of the metagenome analyses were incorporated in the REDPET relational database (http://redpet.bioinfo.pbf.hr/REDPET), which was generated using the previously developed MEGGASENSE platform. The database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic n-alkane degradation. The use of this system for bioprospecting was exemplified using potential alkB and almA genes from this library.
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Affiliation(s)
- Ranko Gacesa
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia.,Institute of Pharmaceutical Science King's College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK.,Department of Chemistry, King's College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK
| | - Damir Baranasic
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia.,Department of Genetics, University of Kaiserslautern, Postfach 3049, DE-67653 Kaiserslautern, Germany
| | - Antonio Starcevic
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia.,Centre of Research Excellence for Marine Bioprospecting - BioProCro, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Janko Diminic
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia.,Centre of Research Excellence for Marine Bioprospecting - BioProCro, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Marino Korlević
- Centre for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, HR-52210 Rovinj, Croatia
| | - Mirjana Najdek
- Centre for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, HR-52210 Rovinj, Croatia
| | - Maria Blažina
- Centre for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, HR-52210 Rovinj, Croatia
| | - Davor Oršolić
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia
| | - Domagoj Kolesarić
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia
| | - Paul F Long
- Institute of Pharmaceutical Science King's College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK.,Department of Chemistry, King's College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK
| | - John Cullum
- Department of Genetics, University of Kaiserslautern, Postfach 3049, DE-67653 Kaiserslautern, Germany
| | - Daslav Hranueli
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia.,Centre of Research Excellence for Marine Bioprospecting - BioProCro, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Sandi Orlic
- Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.,Center of Excellence for Science and Technology Integrating Mediterranean Region, Microbial Ecology, HR-10000 Zagreb, Croatia
| | - Jurica Zucko
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia.,Centre of Research Excellence for Marine Bioprospecting - BioProCro, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
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