Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants.
Identifieur interne : 003168 ( Main/Corpus ); précédent : 003167; suivant : 003169Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants.
Auteurs : Peifen Zhang ; Kate Dreher ; A. Karthikeyan ; Anjo Chi ; Anuradha Pujar ; Ron Caspi ; Peter Karp ; Vanessa Kirkup ; Mario Latendresse ; Cynthia Lee ; Lukas A. Mueller ; Robert Muller ; Seung Yon RheeSource :
- Plant physiology [ 1532-2548 ] ; 2010.
English descriptors
- KwdEn :
- MESH :
- enzymology : Arabidopsis, Populus.
- genetics : Arabidopsis, Metabolic Networks and Pathways, Populus.
- Databases, Genetic, Genome, Plant.
Abstract
Metabolic networks reconstructed from sequenced genomes or transcriptomes can help visualize and analyze large-scale experimental data, predict metabolic phenotypes, discover enzymes, engineer metabolic pathways, and study metabolic pathway evolution. We developed a general approach for reconstructing metabolic pathway complements of plant genomes. Two new reference databases were created and added to the core of the infrastructure: a comprehensive, all-plant reference pathway database, PlantCyc, and a reference enzyme sequence database, RESD, for annotating metabolic functions of protein sequences. PlantCyc (version 3.0) includes 714 metabolic pathways and 2,619 reactions from over 300 species. RESD (version 1.0) contains 14,187 literature-supported enzyme sequences from across all kingdoms. We used RESD, PlantCyc, and MetaCyc (an all-species reference metabolic pathway database), in conjunction with the pathway prediction software Pathway Tools, to reconstruct a metabolic pathway database, PoplarCyc, from the recently sequenced genome of Populus trichocarpa. PoplarCyc (version 1.0) contains 321 pathways with 1,807 assigned enzymes. Comparing PoplarCyc (version 1.0) with AraCyc (version 6.0, Arabidopsis [Arabidopsis thaliana]) showed comparable numbers of pathways distributed across all domains of metabolism in both databases, except for a higher number of AraCyc pathways in secondary metabolism and a 1.5-fold increase in carbohydrate metabolic enzymes in PoplarCyc. Here, we introduce these new resources and demonstrate the feasibility of using them to identify candidate enzymes for specific pathways and to analyze metabolite profiling data through concrete examples. These resources can be searched by text or BLAST, browsed, and downloaded from our project Web site (http://plantcyc.org).
DOI: 10.1104/pp.110.157396
PubMed: 20522724
PubMed Central: PMC2923894
Links to Exploration step
pubmed:20522724Le document en format XML
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Karthikeyan</name></author><author><name sortKey="Chi, Anjo" sort="Chi, Anjo" uniqKey="Chi A" first="Anjo" last="Chi">Anjo Chi</name></author><author><name sortKey="Pujar, Anuradha" sort="Pujar, Anuradha" uniqKey="Pujar A" first="Anuradha" last="Pujar">Anuradha Pujar</name></author><author><name sortKey="Caspi, Ron" sort="Caspi, Ron" uniqKey="Caspi R" first="Ron" last="Caspi">Ron Caspi</name></author><author><name sortKey="Karp, Peter" sort="Karp, Peter" uniqKey="Karp P" first="Peter" last="Karp">Peter Karp</name></author><author><name sortKey="Kirkup, Vanessa" sort="Kirkup, Vanessa" uniqKey="Kirkup V" first="Vanessa" last="Kirkup">Vanessa Kirkup</name></author><author><name sortKey="Latendresse, Mario" sort="Latendresse, Mario" uniqKey="Latendresse M" first="Mario" last="Latendresse">Mario Latendresse</name></author><author><name sortKey="Lee, Cynthia" sort="Lee, Cynthia" uniqKey="Lee C" first="Cynthia" last="Lee">Cynthia Lee</name></author><author><name sortKey="Mueller, Lukas A" sort="Mueller, Lukas A" uniqKey="Mueller L" first="Lukas A" last="Mueller">Lukas A. 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Karthikeyan</name></author><author><name sortKey="Chi, Anjo" sort="Chi, Anjo" uniqKey="Chi A" first="Anjo" last="Chi">Anjo Chi</name></author><author><name sortKey="Pujar, Anuradha" sort="Pujar, Anuradha" uniqKey="Pujar A" first="Anuradha" last="Pujar">Anuradha Pujar</name></author><author><name sortKey="Caspi, Ron" sort="Caspi, Ron" uniqKey="Caspi R" first="Ron" last="Caspi">Ron Caspi</name></author><author><name sortKey="Karp, Peter" sort="Karp, Peter" uniqKey="Karp P" first="Peter" last="Karp">Peter Karp</name></author><author><name sortKey="Kirkup, Vanessa" sort="Kirkup, Vanessa" uniqKey="Kirkup V" first="Vanessa" last="Kirkup">Vanessa Kirkup</name></author><author><name sortKey="Latendresse, Mario" sort="Latendresse, Mario" uniqKey="Latendresse M" first="Mario" last="Latendresse">Mario Latendresse</name></author><author><name sortKey="Lee, Cynthia" sort="Lee, Cynthia" uniqKey="Lee C" first="Cynthia" last="Lee">Cynthia Lee</name></author><author><name sortKey="Mueller, Lukas A" sort="Mueller, Lukas A" uniqKey="Mueller L" first="Lukas A" last="Mueller">Lukas A. Mueller</name></author><author><name sortKey="Muller, Robert" sort="Muller, Robert" uniqKey="Muller R" first="Robert" last="Muller">Robert Muller</name></author><author><name sortKey="Rhee, Seung Yon" sort="Rhee, Seung Yon" uniqKey="Rhee S" first="Seung Yon" last="Rhee">Seung Yon Rhee</name></author></analytic><series><title level="j">Plant physiology</title><idno type="eISSN">1532-2548</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (enzymology)</term><term>Arabidopsis (genetics)</term><term>Databases, Genetic (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Metabolic Networks and Pathways (genetics)</term><term>Populus (enzymology)</term><term>Populus (genetics)</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Arabidopsis</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Metabolic Networks and Pathways</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Genome, Plant</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Metabolic networks reconstructed from sequenced genomes or transcriptomes can help visualize and analyze large-scale experimental data, predict metabolic phenotypes, discover enzymes, engineer metabolic pathways, and study metabolic pathway evolution. We developed a general approach for reconstructing metabolic pathway complements of plant genomes. Two new reference databases were created and added to the core of the infrastructure: a comprehensive, all-plant reference pathway database, PlantCyc, and a reference enzyme sequence database, RESD, for annotating metabolic functions of protein sequences. PlantCyc (version 3.0) includes 714 metabolic pathways and 2,619 reactions from over 300 species. RESD (version 1.0) contains 14,187 literature-supported enzyme sequences from across all kingdoms. We used RESD, PlantCyc, and MetaCyc (an all-species reference metabolic pathway database), in conjunction with the pathway prediction software Pathway Tools, to reconstruct a metabolic pathway database, PoplarCyc, from the recently sequenced genome of Populus trichocarpa. PoplarCyc (version 1.0) contains 321 pathways with 1,807 assigned enzymes. Comparing PoplarCyc (version 1.0) with AraCyc (version 6.0, Arabidopsis [Arabidopsis thaliana]) showed comparable numbers of pathways distributed across all domains of metabolism in both databases, except for a higher number of AraCyc pathways in secondary metabolism and a 1.5-fold increase in carbohydrate metabolic enzymes in PoplarCyc. Here, we introduce these new resources and demonstrate the feasibility of using them to identify candidate enzymes for specific pathways and to analyze metabolite profiling data through concrete examples. These resources can be searched by text or BLAST, browsed, and downloaded from our project Web site (http://plantcyc.org).</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20522724</PMID><DateCompleted><Year>2010</Year><Month>10</Month><Day>25</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1532-2548</ISSN><JournalIssue CitedMedium="Internet"><Volume>153</Volume><Issue>4</Issue><PubDate><Year>2010</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Plant physiology</Title><ISOAbbreviation>Plant Physiol</ISOAbbreviation></Journal><ArticleTitle>Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants.</ArticleTitle><Pagination><MedlinePgn>1479-91</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1104/pp.110.157396</ELocationID><Abstract><AbstractText>Metabolic networks reconstructed from sequenced genomes or transcriptomes can help visualize and analyze large-scale experimental data, predict metabolic phenotypes, discover enzymes, engineer metabolic pathways, and study metabolic pathway evolution. We developed a general approach for reconstructing metabolic pathway complements of plant genomes. Two new reference databases were created and added to the core of the infrastructure: a comprehensive, all-plant reference pathway database, PlantCyc, and a reference enzyme sequence database, RESD, for annotating metabolic functions of protein sequences. PlantCyc (version 3.0) includes 714 metabolic pathways and 2,619 reactions from over 300 species. RESD (version 1.0) contains 14,187 literature-supported enzyme sequences from across all kingdoms. We used RESD, PlantCyc, and MetaCyc (an all-species reference metabolic pathway database), in conjunction with the pathway prediction software Pathway Tools, to reconstruct a metabolic pathway database, PoplarCyc, from the recently sequenced genome of Populus trichocarpa. PoplarCyc (version 1.0) contains 321 pathways with 1,807 assigned enzymes. Comparing PoplarCyc (version 1.0) with AraCyc (version 6.0, Arabidopsis [Arabidopsis thaliana]) showed comparable numbers of pathways distributed across all domains of metabolism in both databases, except for a higher number of AraCyc pathways in secondary metabolism and a 1.5-fold increase in carbohydrate metabolic enzymes in PoplarCyc. Here, we introduce these new resources and demonstrate the feasibility of using them to identify candidate enzymes for specific pathways and to analyze metabolite profiling data through concrete examples. These resources can be searched by text or BLAST, browsed, and downloaded from our project Web site (http://plantcyc.org).</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Peifen</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Plant Biology, Carnegie Institution, Stanford, California 94305, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dreher</LastName><ForeName>Kate</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Karthikeyan</LastName><ForeName>A</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Chi</LastName><ForeName>Anjo</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Pujar</LastName><ForeName>Anuradha</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Caspi</LastName><ForeName>Ron</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Karp</LastName><ForeName>Peter</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Kirkup</LastName><ForeName>Vanessa</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Latendresse</LastName><ForeName>Mario</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Cynthia</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Mueller</LastName><ForeName>Lukas A</ForeName><Initials>LA</Initials></Author><Author ValidYN="Y"><LastName>Muller</LastName><ForeName>Robert</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Rhee</LastName><ForeName>Seung Yon</ForeName><Initials>SY</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 GM080746</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM080746-03</GrantID><Acronym>GM</Acronym><Agency>NIGMS 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