A computational screen for type I polyketide synthases in metagenomics shotgun data.
<h4>Background</h4>Polyketides are a diverse group of biotechnologically important secondary metabolites that are produced by multi domain enzymes called polyketide synthases (PKS).<h4>Methodology/principal findings</h4>We have estimated frequencies of type I PKS (PKS I) - a...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2008-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18953415/?tool=EBI |
| _version_ | 1819018584249073664 |
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| author | Konrad U Foerstner Tobias Doerks Christopher J Creevey Anja Doerks Peer Bork |
| author_facet | Konrad U Foerstner Tobias Doerks Christopher J Creevey Anja Doerks Peer Bork |
| author_sort | Konrad U Foerstner |
| collection | DOAJ |
| description | <h4>Background</h4>Polyketides are a diverse group of biotechnologically important secondary metabolites that are produced by multi domain enzymes called polyketide synthases (PKS).<h4>Methodology/principal findings</h4>We have estimated frequencies of type I PKS (PKS I) - a PKS subgroup - in natural environments by using Hidden-Markov-Models of eight domains to screen predicted proteins from six metagenomic shotgun data sets. As the complex PKS I have similarities to other multi-domain enzymes (like those for the fatty acid biosynthesis) we increased the reliability and resolution of the dataset by maximum-likelihood trees. The combined information of these trees was then used to discriminate true PKS I domains from evolutionary related but functionally different ones. We were able to identify numerous novel PKS I proteins, the highest density of which was found in Minnesota farm soil with 136 proteins out of 183,536 predicted genes. We also applied the protocol to UniRef database to improve the annotation of proteins with so far unknown function and identified some new instances of horizontal gene transfer.<h4>Conclusions/significance</h4>The screening approach proved powerful in identifying PKS I sequences in large sequence data sets and is applicable to many other protein families. |
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| format | Article |
| id | doaj.art-3261e1002fea43c08699fcb7176d82e9 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T03:21:44Z |
| publishDate | 2008-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-3261e1002fea43c08699fcb7176d82e92022-12-21T19:17:41ZengPublic Library of Science (PLoS)PLoS ONE1932-62032008-01-01310e351510.1371/journal.pone.0003515A computational screen for type I polyketide synthases in metagenomics shotgun data.Konrad U FoerstnerTobias DoerksChristopher J CreeveyAnja DoerksPeer Bork<h4>Background</h4>Polyketides are a diverse group of biotechnologically important secondary metabolites that are produced by multi domain enzymes called polyketide synthases (PKS).<h4>Methodology/principal findings</h4>We have estimated frequencies of type I PKS (PKS I) - a PKS subgroup - in natural environments by using Hidden-Markov-Models of eight domains to screen predicted proteins from six metagenomic shotgun data sets. As the complex PKS I have similarities to other multi-domain enzymes (like those for the fatty acid biosynthesis) we increased the reliability and resolution of the dataset by maximum-likelihood trees. The combined information of these trees was then used to discriminate true PKS I domains from evolutionary related but functionally different ones. We were able to identify numerous novel PKS I proteins, the highest density of which was found in Minnesota farm soil with 136 proteins out of 183,536 predicted genes. We also applied the protocol to UniRef database to improve the annotation of proteins with so far unknown function and identified some new instances of horizontal gene transfer.<h4>Conclusions/significance</h4>The screening approach proved powerful in identifying PKS I sequences in large sequence data sets and is applicable to many other protein families.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18953415/?tool=EBI |
| spellingShingle | Konrad U Foerstner Tobias Doerks Christopher J Creevey Anja Doerks Peer Bork A computational screen for type I polyketide synthases in metagenomics shotgun data. PLoS ONE |
| title | A computational screen for type I polyketide synthases in metagenomics shotgun data. |
| title_full | A computational screen for type I polyketide synthases in metagenomics shotgun data. |
| title_fullStr | A computational screen for type I polyketide synthases in metagenomics shotgun data. |
| title_full_unstemmed | A computational screen for type I polyketide synthases in metagenomics shotgun data. |
| title_short | A computational screen for type I polyketide synthases in metagenomics shotgun data. |
| title_sort | computational screen for type i polyketide synthases in metagenomics shotgun data |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18953415/?tool=EBI |
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