Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments

• Published in: Food technology and biotechnology Vol. 56; no. 2; pp. 270 - 277
• Main Authors: Gacesa, Ranko, Baranasic, Damir, Starcevic, Antonio, Diminic, Janko, Korlević, Marino, Najdek, Mirjana, Blažina, Marijana, Oršolić, Davor, Kolesarić, Domagoj, Long, Paul F., Cullum, John, Hranueli, Daslav, Orlić, Sandi, Zucko, Jurica
• Format: Journal Article
• Language: English
• Published: Croatia Sveuciliste U Zagrebu 01.06.2018; Sveuciliste u Zagrebu, Prehramheno-Biotehnoloski Fakultet; University of Zagreb Faculty of Food Technology and Biotechnology
• Subjects: Alkanes; Biodegradation; Biodiversity; Bioinformatics; Bioprospecting; Bioremediation; Crude oil; Degradation; Deoxyribonucleic acid; DNA; Enzymes; Functional analysis; Genes; Genetic code; Genomes; Genomics; Hydrocarbon-degrading enzymes; Hydrocarbons; Markov chains; Markov processes; n-alkane degradation; oil pollution; Oil spills; Petroleum; Proteins; Relational data bases; Scientific Notes; Sediment samplers; Sediments; Taxonomy; Adriatic Sea; Germany; Croatia; oil pollution; database; n-alkane degradation
• ISSN: 1330-9862; 1334-2606
• DOI: 10.17113/ftb.56.02.18.5393

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 -alkane degradation. The use of this system for bioprospecting was exemplified using potential and genes from this library.