Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow
Identifieur interne : 000297 ( Main/Exploration ); précédent : 000296; suivant : 000298Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow
Auteurs : Thomas J. Mueller [États-Unis] ; Bertram M. Berla [États-Unis] ; Himadri B. Pakrasi [États-Unis] ; Costas D. Maranas [États-Unis]Source :
- BMC Systems Biology [ 1752-0509 ] ; 2013.
Abstract
Cyanobacteria are photoautotrophic prokaryotes that exhibit robust growth under diverse environmental conditions with minimal nutritional requirements. They can use solar energy to convert CO2 and other reduced carbon sources into biofuels and chemical products. The genus
Here we reconstruct and subsequently analyze and compare the metabolism of five
Our development workflow provides a path for constructing models using information from curated models of related organisms and reviewed gene annotations. This effort lays the foundation for the expedient construction of curated metabolic models for organisms that, while not being the target of comprehensive research, have a sequenced genome and are related to an organism with a curated metabolic model. Organism-specific models, such as the five presented in this paper, can be used to identify optimal genetic manipulations for targeted metabolite overproduction as well as to investigate the biology of diverse organisms.
Url:
DOI: 10.1186/1752-0509-7-142
PubMed: 24369854
PubMed Central: 3880981
Affiliations:
- États-Unis
- Missouri (État), Pennsylvanie
- University Park (Pennsylvanie)
- Université d'État de Pennsylvanie
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Mueller</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">University Park (Pennsylvanie)</settlement></placeName><orgName type="university">Université d'État de Pennsylvanie</orgName></affiliation></author><author><name sortKey="Berla, Bertram M" sort="Berla, Bertram M" uniqKey="Berla B" first="Bertram M" last="Berla">Bertram M. 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Maranas</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">University Park (Pennsylvanie)</settlement></placeName><orgName type="university">Université d'État de Pennsylvanie</orgName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24369854</idno><idno type="pmc">3880981</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3880981</idno><idno type="RBID">PMC:3880981</idno><idno type="doi">10.1186/1752-0509-7-142</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000335</idno><idno type="wicri:Area/Pmc/Curation">000335</idno><idno type="wicri:Area/Pmc/Checkpoint">000276</idno><idno type="wicri:Area/Ncbi/Merge">000485</idno><idno type="wicri:Area/Ncbi/Curation">000485</idno><idno type="wicri:Area/Ncbi/Checkpoint">000485</idno><idno type="wicri:Area/Main/Merge">000297</idno><idno type="wicri:Area/Main/Curation">000297</idno><idno type="wicri:Area/Main/Exploration">000297</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow</title><author><name sortKey="Mueller, Thomas J" sort="Mueller, Thomas J" uniqKey="Mueller T" first="Thomas J" last="Mueller">Thomas J. Mueller</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">University Park (Pennsylvanie)</settlement></placeName><orgName type="university">Université d'État de Pennsylvanie</orgName></affiliation></author><author><name sortKey="Berla, Bertram M" sort="Berla, Bertram M" uniqKey="Berla B" first="Bertram M" last="Berla">Bertram M. Berla</name><affiliation wicri:level="2"><nlm:aff id="I2">Department of Energy, Environmental, and Chemical Engineering, Washington University, St. Louis, Missouri, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy, Environmental, and Chemical Engineering, Washington University, St. Louis, Missouri</wicri:regionArea><placeName><region type="state">Missouri (État)</region></placeName></affiliation></author><author><name sortKey="Pakrasi, Himadri B" sort="Pakrasi, Himadri B" uniqKey="Pakrasi H" first="Himadri B" last="Pakrasi">Himadri B. Pakrasi</name><affiliation wicri:level="2"><nlm:aff id="I2">Department of Energy, Environmental, and Chemical Engineering, Washington University, St. Louis, Missouri, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy, Environmental, and Chemical Engineering, Washington University, St. Louis, Missouri</wicri:regionArea><placeName><region type="state">Missouri (État)</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Department of Biology, Washington University, St. Louis, Missouri, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Washington University, St. Louis, Missouri</wicri:regionArea><placeName><region type="state">Missouri (État)</region></placeName></affiliation></author><author><name sortKey="Maranas, Costas D" sort="Maranas, Costas D" uniqKey="Maranas C" first="Costas D" last="Maranas">Costas D. Maranas</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">University Park (Pennsylvanie)</settlement></placeName><orgName type="university">Université d'État de Pennsylvanie</orgName></affiliation></author></analytic><series><title level="j">BMC Systems Biology</title><idno type="eISSN">1752-0509</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Cyanobacteria are photoautotrophic prokaryotes that exhibit robust growth under diverse environmental conditions with minimal nutritional requirements. They can use solar energy to convert CO<sub>2</sub> and other reduced carbon sources into biofuels and chemical products. The genus <italic>Cyanothece</italic> includes unicellular nitrogen-fixing cyanobacteria that have been shown to offer high levels of hydrogen production and nitrogen fixation. The reconstruction of quality genome-scale metabolic models for organisms with limited annotation resources remains a challenging task.</p></sec><sec><title>Results</title><p>Here we reconstruct and subsequently analyze and compare the metabolism of five <italic>Cyanothece</italic> strains, namely <italic>Cyanothece</italic> sp. PCC 7424, 7425, 7822, 8801 and 8802, as the genome-scale metabolic reconstructions <italic>i</italic>Cyc792, <italic>i</italic>Cyn731, <italic>i</italic>Cyj826, <italic>i</italic>Cyp752, and <italic>i</italic>Cyh755 respectively. We compare these phylogenetically related <italic>Cyanothece</italic> strains to assess their bio-production potential. A systematic workflow is introduced for integrating and prioritizing annotation information from the Universal Protein Resource (Uniprot), NCBI Protein Clusters, and the Rapid Annotations using Subsystems Technology (RAST) method. The genome-scale metabolic models include fully traced photosynthesis reactions and respiratory chains, as well as balanced reactions and GPR associations. Metabolic differences between the organisms are highlighted such as the non-fermentative pathway for alcohol production found in only <italic>Cyanothece</italic> 7424, 8801, and 8802.</p></sec><sec><title>Conclusions</title><p>Our development workflow provides a path for constructing models using information from curated models of related organisms and reviewed gene annotations. This effort lays the foundation for the expedient construction of curated metabolic models for organisms that, while not being the target of comprehensive research, have a sequenced genome and are related to an organism with a curated metabolic model. Organism-specific models, such as the five presented in this paper, can be used to identify optimal genetic manipulations for targeted metabolite overproduction as well as to investigate the biology of diverse organisms.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Thiele, I" uniqKey="Thiele I">I Thiele</name></author><author><name sortKey="Palsson, Bo" uniqKey="Palsson B">BO Palsson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Price, Nd" uniqKey="Price N">ND Price</name></author><author><name sortKey="Reed, Jl" uniqKey="Reed J">JL Reed</name></author><author><name sortKey="Palsson, Bo" uniqKey="Palsson B">BO Palsson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Feist, Am" uniqKey="Feist A">AM Feist</name></author><author><name sortKey="Herrg Rd, Mj" uniqKey="Herrg Rd M">MJ Herrgård</name></author><author><name sortKey="Thiele, I" uniqKey="Thiele 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Notebaart</name></author><author><name sortKey="Van Enckevort, Fh" uniqKey="Van Enckevort F">FH van Enckevort</name></author><author><name sortKey="Francke, C" uniqKey="Francke C">C Francke</name></author><author><name sortKey="Siezen, Rj" uniqKey="Siezen R">RJ Siezen</name></author><author><name sortKey="Teusink, B" uniqKey="Teusink B">B Teusink</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Orth, Jd" uniqKey="Orth J">JD Orth</name></author><author><name sortKey="Thiele, I" uniqKey="Thiele I">I Thiele</name></author><author><name sortKey="Palsson, Bo" uniqKey="Palsson B">BO Palsson</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Missouri (État)</li><li>Pennsylvanie</li></region><settlement><li>University Park (Pennsylvanie)</li></settlement><orgName><li>Université d'État de Pennsylvanie</li></orgName></list><tree><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Mueller, Thomas J" sort="Mueller, Thomas J" uniqKey="Mueller T" first="Thomas J" last="Mueller">Thomas J. Mueller</name></region><name sortKey="Berla, Bertram M" sort="Berla, Bertram M" uniqKey="Berla B" first="Bertram M" last="Berla">Bertram M. Berla</name><name sortKey="Maranas, Costas D" sort="Maranas, Costas D" uniqKey="Maranas C" first="Costas D" last="Maranas">Costas D. Maranas</name><name sortKey="Pakrasi, Himadri B" sort="Pakrasi, Himadri B" uniqKey="Pakrasi H" first="Himadri B" last="Pakrasi">Himadri B. Pakrasi</name><name sortKey="Pakrasi, Himadri B" sort="Pakrasi, Himadri B" uniqKey="Pakrasi H" first="Himadri B" last="Pakrasi">Himadri B. Pakrasi</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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