From DNA Sequences to Chemical Structures – Methods for Mining Microbial Genomic and Metagenomic Data Sets for New Natural Products
Rapid mining of large genomic and metagenomic data sets for modular polyketide synthases, non-ribosomal peptide synthetases and hybrid polyketide synthase/non-ribosomal peptide synthetase biosynthetic gene clusters has been achieved using the generic computer program packages ClustScan and CompGen....
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| Format: | Article |
| Language: | English |
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University of Zagreb Faculty of Food Technology and Biotechnology
2010-01-01
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| Series: | Food Technology and Biotechnology |
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| Online Access: | http://hrcak.srce.hr/file/81787 |
| _version_ | 1797428583127318528 |
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| author | Jurica Zucko Antonio Starcevic Janko Diminic Mouhsine Elbekali Mohamed Lisfi Paul F. Long John Cullum Daslav Hranueli |
| author_facet | Jurica Zucko Antonio Starcevic Janko Diminic Mouhsine Elbekali Mohamed Lisfi Paul F. Long John Cullum Daslav Hranueli |
| author_sort | Jurica Zucko |
| collection | DOAJ |
| description | Rapid mining of large genomic and metagenomic data sets for modular polyketide synthases, non-ribosomal peptide synthetases and hybrid polyketide synthase/non-ribosomal peptide synthetase biosynthetic gene clusters has been achieved using the generic computer program packages ClustScan and CompGen. These program packages perform the annotation with the hierarchical structuring into polypeptides, modules and domains, as well as storage and graphical presentations of the data. This aims to achieve the most accurate predictions of the activities and specificities of catalytically active domains that can be made with present knowledge, leading to a prediction of the most likely chemical structures produced by these enzymes. The program packages also allow generation of novel clusters by homologous recombination of the annotated genes in silico. ClustScan and CompGen were used to construct a custom database of known compounds (CSDB) and of predicted entirely novel recombinant products (r-CSDB) that can be used for in silico screening with computer aided drug design technology. The use of these programs has been exemplified by analysing genomic sequences from terrestrial prokaryotes and eukaryotic microorganisms, a marine metagenomic data set and a newly discovered example of a 'shared metabolic pathway' in marine-microbial endosymbiosis. |
| first_indexed | 2024-03-09T09:00:58Z |
| format | Article |
| id | doaj.art-2dc45e17450542a0a2f671c0fc1fc772 |
| institution | Directory Open Access Journal |
| issn | 1330-9862 1334-2606 |
| language | English |
| last_indexed | 2024-03-09T09:00:58Z |
| publishDate | 2010-01-01 |
| publisher | University of Zagreb Faculty of Food Technology and Biotechnology |
| record_format | Article |
| series | Food Technology and Biotechnology |
| spelling | doaj.art-2dc45e17450542a0a2f671c0fc1fc7722023-12-02T11:43:15ZengUniversity of Zagreb Faculty of Food Technology and BiotechnologyFood Technology and Biotechnology1330-98621334-26062010-01-01482234242From DNA Sequences to Chemical Structures – Methods for Mining Microbial Genomic and Metagenomic Data Sets for New Natural ProductsJurica Zucko0Antonio Starcevic1Janko Diminic2Mouhsine Elbekali3Mohamed Lisfi4Paul F. Long5John Cullum6Daslav Hranueli7Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, CroatiaFaculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, CroatiaFaculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, CroatiaDepartment of Genetics, University of Kaiserslautern, Postfach 3049, DE-67653 Kaiserslautern, GermanyDepartment of Genetics, University of Kaiserslautern, Postfach 3049, DE-67653 Kaiserslautern, GermanySchool of Pharmacy, University of London, 29/39 Brunswick Square, London WC1N 1AX, United KingdomDepartment of Genetics, University of Kaiserslautern, Postfach 3049, DE-67653 Kaiserslautern, GermanyFaculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, CroatiaRapid mining of large genomic and metagenomic data sets for modular polyketide synthases, non-ribosomal peptide synthetases and hybrid polyketide synthase/non-ribosomal peptide synthetase biosynthetic gene clusters has been achieved using the generic computer program packages ClustScan and CompGen. These program packages perform the annotation with the hierarchical structuring into polypeptides, modules and domains, as well as storage and graphical presentations of the data. This aims to achieve the most accurate predictions of the activities and specificities of catalytically active domains that can be made with present knowledge, leading to a prediction of the most likely chemical structures produced by these enzymes. The program packages also allow generation of novel clusters by homologous recombination of the annotated genes in silico. ClustScan and CompGen were used to construct a custom database of known compounds (CSDB) and of predicted entirely novel recombinant products (r-CSDB) that can be used for in silico screening with computer aided drug design technology. The use of these programs has been exemplified by analysing genomic sequences from terrestrial prokaryotes and eukaryotic microorganisms, a marine metagenomic data set and a newly discovered example of a 'shared metabolic pathway' in marine-microbial endosymbiosis.http://hrcak.srce.hr/file/81787polyketidesnon-ribosomal peptidesActinobacteriahomologous recombination |
| spellingShingle | Jurica Zucko Antonio Starcevic Janko Diminic Mouhsine Elbekali Mohamed Lisfi Paul F. Long John Cullum Daslav Hranueli From DNA Sequences to Chemical Structures – Methods for Mining Microbial Genomic and Metagenomic Data Sets for New Natural Products Food Technology and Biotechnology polyketides non-ribosomal peptides Actinobacteria homologous recombination |
| title | From DNA Sequences to Chemical Structures – Methods for Mining Microbial Genomic and Metagenomic Data Sets for New Natural Products |
| title_full | From DNA Sequences to Chemical Structures – Methods for Mining Microbial Genomic and Metagenomic Data Sets for New Natural Products |
| title_fullStr | From DNA Sequences to Chemical Structures – Methods for Mining Microbial Genomic and Metagenomic Data Sets for New Natural Products |
| title_full_unstemmed | From DNA Sequences to Chemical Structures – Methods for Mining Microbial Genomic and Metagenomic Data Sets for New Natural Products |
| title_short | From DNA Sequences to Chemical Structures – Methods for Mining Microbial Genomic and Metagenomic Data Sets for New Natural Products |
| title_sort | from dna sequences to chemical structures methods for mining microbial genomic and metagenomic data sets for new natural products |
| topic | polyketides non-ribosomal peptides Actinobacteria homologous recombination |
| url | http://hrcak.srce.hr/file/81787 |
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