Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments
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...
Main Authors: | , , , , , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
University of Zagreb
2018-01-01
|
Series: | Food Technology and Biotechnology |
Subjects: | |
Online Access: | http://hrcak.srce.hr/file/299544 |
id |
doaj-93c2d484daef4803a44779c7f62ad195 |
---|---|
record_format |
Article |
spelling |
doaj-93c2d484daef4803a44779c7f62ad1952020-11-25T01:43:00ZengUniversity of ZagrebFood Technology and Biotechnology1330-98621334-26062018-01-01562270277Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea SedimentsRanko GacesaDamir BaranasicAntonio StarcevicJanko DiminicMarino KorlevićMirjana NajdekMaria BlažinaDavor OršolićDomagoj KolesarićPaul F. LongJohn CullumDaslav HranueliSandi OrlicJurica ZuckoThree 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.http://hrcak.srce.hr/file/299544oil pollutionn-alkane degradationdatabase |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ranko Gacesa Damir Baranasic Antonio Starcevic Janko Diminic Marino Korlević Mirjana Najdek Maria Blažina Davor Oršolić Domagoj Kolesarić Paul F. Long John Cullum Daslav Hranueli Sandi Orlic Jurica Zucko |
spellingShingle |
Ranko Gacesa Damir Baranasic Antonio Starcevic Janko Diminic Marino Korlević Mirjana Najdek Maria Blažina Davor Oršolić Domagoj Kolesarić Paul F. Long John Cullum Daslav Hranueli Sandi Orlic Jurica Zucko Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments Food Technology and Biotechnology oil pollution n-alkane degradation database |
author_facet |
Ranko Gacesa Damir Baranasic Antonio Starcevic Janko Diminic Marino Korlević Mirjana Najdek Maria Blažina Davor Oršolić Domagoj Kolesarić Paul F. Long John Cullum Daslav Hranueli Sandi Orlic Jurica Zucko |
author_sort |
Ranko Gacesa |
title |
Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments |
title_short |
Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments |
title_full |
Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments |
title_fullStr |
Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments |
title_full_unstemmed |
Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments |
title_sort |
bioprospecting for genes encoding hydrocarbon-degrading enzymes from metagenomic samples isolated from northern adriatic sea sediments |
publisher |
University of Zagreb |
series |
Food Technology and Biotechnology |
issn |
1330-9862 1334-2606 |
publishDate |
2018-01-01 |
description |
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. |
topic |
oil pollution n-alkane degradation database |
url |
http://hrcak.srce.hr/file/299544 |
work_keys_str_mv |
AT rankogacesa bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT damirbaranasic bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT antoniostarcevic bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT jankodiminic bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT marinokorlevic bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT mirjananajdek bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT mariablazina bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT davororsolic bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT domagojkolesaric bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT paulflong bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT johncullum bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT daslavhranueli bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT sandiorlic bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments AT juricazucko bioprospectingforgenesencodinghydrocarbondegradingenzymesfrommetagenomicsamplesisolatedfromnorthernadriaticseasediments |
_version_ |
1725033681828970496 |