Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis
Identifieur interne : 000733 ( Main/Exploration ); précédent : 000732; suivant : 000734Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis
Auteurs : Desre Pinard [Afrique du Sud] ; Eshchar Mizrachi [Afrique du Sud] ; Charles A. Hefer [Afrique du Sud] ; Anna R. Kersting ; Fourie Joubert [Afrique du Sud] ; Carl J. Douglas ; Shawn D. Mansfield ; Alexander A. Myburg [Afrique du Sud]Source :
- BMC Genomics [ 1471-2164 ] ; 2015.
Abstract
Carbohydrate metabolism is a key feature of vascular plant architecture, and is of particular importance in large woody species, where lignocellulosic biomass is responsible for bearing the bulk of the stem and crown. Since Carbohydrate Active enZymes (CAZymes) in plants are responsible for the synthesis, modification and degradation of carbohydrate biopolymers, the differences in gene copy number and regulation between woody and herbaceous species have been highlighted previously. There are still many unanswered questions about the role of CAZymes in land plant evolution and the formation of wood, a strong carbohydrate sink.
Here, twenty-two publically available plant genomes were used to characterize the frequency, diversity and complexity of CAZymes in plants. We find that a conserved suite of CAZymes is a feature of land plant evolution, with similar diversity and complexity regardless of growth habit and form. In addition, we compared the diversity and levels of CAZyme gene expression during wood formation in trees using mRNA-seq data from two distantly related angiosperm tree species
CAZyme domain ratio across embryophytes is maintained, and the diversity of CAZyme domains is similar in all land plants, regardless of woody habit. The stoichiometric conservation of gene expression in woody and non-woody tissues of
The online version of this article (doi:10.1186/s12864-015-1571-8) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-1571-8
PubMed: 25994181
PubMed Central: 4440533
Affiliations:
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Kersting</name><affiliation><nlm:aff id="Aff3">Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hufferstr. 1, Munster, D48149 Germany</nlm:aff><wicri:noCountry code="subfield">D48149 Germany</wicri:noCountry></affiliation></author><author><name sortKey="Joubert, Fourie" sort="Joubert, Fourie" uniqKey="Joubert F" first="Fourie" last="Joubert">Fourie Joubert</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Centre for Bioinformatics and Computational Biology, Genomics Research Institute (GRI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028 South Africa</nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Centre for Bioinformatics and Computational Biology, Genomics Research Institute (GRI), University of Pretoria, Private bag X20 Hatfield, Pretoria</wicri:regionArea><wicri:noRegion>Pretoria</wicri:noRegion></affiliation></author><author><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name><affiliation><nlm:aff id="Aff4">Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4 Canada</nlm:aff><wicri:noCountry code="subfield">BC V6T 1Z4 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Mansfield, Shawn D" sort="Mansfield, Shawn D" uniqKey="Mansfield S" first="Shawn D" last="Mansfield">Shawn D. Mansfield</name><affiliation><nlm:aff id="Aff5">Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4 Canada</nlm:aff><wicri:noCountry code="subfield">BC V6T 1Z4 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Myburg, Alexander A" sort="Myburg, Alexander A" uniqKey="Myburg A" first="Alexander A" last="Myburg">Alexander A. Myburg</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028 South Africa</nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria</wicri:regionArea><wicri:noRegion>Pretoria</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25994181</idno><idno type="pmc">4440533</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440533</idno><idno type="RBID">PMC:4440533</idno><idno type="doi">10.1186/s12864-015-1571-8</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000585</idno><idno type="wicri:Area/Pmc/Curation">000584</idno><idno type="wicri:Area/Pmc/Checkpoint">000567</idno><idno type="wicri:Area/Ncbi/Merge">001B43</idno><idno type="wicri:Area/Ncbi/Curation">001B43</idno><idno type="wicri:Area/Ncbi/Checkpoint">001B43</idno><idno type="wicri:Area/Main/Merge">000733</idno><idno type="wicri:Area/Main/Curation">000733</idno><idno type="wicri:Area/Main/Exploration">000733</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis</title><author><name sortKey="Pinard, Desre" sort="Pinard, Desre" uniqKey="Pinard D" first="Desre" last="Pinard">Desre Pinard</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028 South Africa</nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria</wicri:regionArea><wicri:noRegion>Pretoria</wicri:noRegion></affiliation></author><author><name sortKey="Mizrachi, Eshchar" sort="Mizrachi, Eshchar" uniqKey="Mizrachi E" first="Eshchar" last="Mizrachi">Eshchar Mizrachi</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028 South Africa</nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria</wicri:regionArea><wicri:noRegion>Pretoria</wicri:noRegion></affiliation></author><author><name sortKey="Hefer, Charles A" sort="Hefer, Charles A" uniqKey="Hefer C" first="Charles A" last="Hefer">Charles A. Hefer</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Centre for Bioinformatics and Computational Biology, Genomics Research Institute (GRI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028 South Africa</nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Centre for Bioinformatics and Computational Biology, Genomics Research Institute (GRI), University of Pretoria, Private bag X20 Hatfield, Pretoria</wicri:regionArea><wicri:noRegion>Pretoria</wicri:noRegion></affiliation></author><author><name sortKey="Kersting, Anna R" sort="Kersting, Anna R" uniqKey="Kersting A" first="Anna R" last="Kersting">Anna R. Kersting</name><affiliation><nlm:aff id="Aff3">Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hufferstr. 1, Munster, D48149 Germany</nlm:aff><wicri:noCountry code="subfield">D48149 Germany</wicri:noCountry></affiliation></author><author><name sortKey="Joubert, Fourie" sort="Joubert, Fourie" uniqKey="Joubert F" first="Fourie" last="Joubert">Fourie Joubert</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Centre for Bioinformatics and Computational Biology, Genomics Research Institute (GRI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028 South Africa</nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Centre for Bioinformatics and Computational Biology, Genomics Research Institute (GRI), University of Pretoria, Private bag X20 Hatfield, Pretoria</wicri:regionArea><wicri:noRegion>Pretoria</wicri:noRegion></affiliation></author><author><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name><affiliation><nlm:aff id="Aff4">Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4 Canada</nlm:aff><wicri:noCountry code="subfield">BC V6T 1Z4 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Mansfield, Shawn D" sort="Mansfield, Shawn D" uniqKey="Mansfield S" first="Shawn D" last="Mansfield">Shawn D. Mansfield</name><affiliation><nlm:aff id="Aff5">Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4 Canada</nlm:aff><wicri:noCountry code="subfield">BC V6T 1Z4 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Myburg, Alexander A" sort="Myburg, Alexander A" uniqKey="Myburg A" first="Alexander A" last="Myburg">Alexander A. Myburg</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028 South Africa</nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria</wicri:regionArea><wicri:noRegion>Pretoria</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Carbohydrate metabolism is a key feature of vascular plant architecture, and is of particular importance in large woody species, where lignocellulosic biomass is responsible for bearing the bulk of the stem and crown. Since Carbohydrate Active enZymes (CAZymes) in plants are responsible for the synthesis, modification and degradation of carbohydrate biopolymers, the differences in gene copy number and regulation between woody and herbaceous species have been highlighted previously. There are still many unanswered questions about the role of CAZymes in land plant evolution and the formation of wood, a strong carbohydrate sink.</p></sec><sec><title>Results</title><p>Here, twenty-two publically available plant genomes were used to characterize the frequency, diversity and complexity of CAZymes in plants. We find that a conserved suite of CAZymes is a feature of land plant evolution, with similar diversity and complexity regardless of growth habit and form. In addition, we compared the diversity and levels of CAZyme gene expression during wood formation in trees using mRNA-seq data from two distantly related angiosperm tree species <italic>Eucalyptus grandis</italic> and <italic>Populus trichocarpa</italic>, highlighting the major CAZyme classes involved in xylogenesis and lignocellulosic biomass production.</p></sec><sec><title>Conclusions</title><p>CAZyme domain ratio across embryophytes is maintained, and the diversity of CAZyme domains is similar in all land plants, regardless of woody habit. The stoichiometric conservation of gene expression in woody and non-woody tissues of <italic>Eucalyptus</italic> and <italic>Populus</italic> are indicative of gene balance preservation.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-1571-8) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Coutinho, Pm" uniqKey="Coutinho P">PM Coutinho</name></author><author><name sortKey="Stam, M" uniqKey="Stam M">M Stam</name></author><author><name sortKey="Blanc, E" uniqKey="Blanc E">E Blanc</name></author><author><name sortKey="Henrissat, B" uniqKey="Henrissat B">B Henrissat</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wilson, Ibh" uniqKey="Wilson I">IBH Wilson</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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Sud</li></country></list><tree><noCountry><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name><name sortKey="Kersting, Anna R" sort="Kersting, Anna R" uniqKey="Kersting A" first="Anna R" last="Kersting">Anna R. Kersting</name><name sortKey="Mansfield, Shawn D" sort="Mansfield, Shawn D" uniqKey="Mansfield S" first="Shawn D" last="Mansfield">Shawn D. Mansfield</name></noCountry><country name="Afrique du Sud"><noRegion><name sortKey="Pinard, Desre" sort="Pinard, Desre" uniqKey="Pinard D" first="Desre" last="Pinard">Desre Pinard</name></noRegion><name sortKey="Hefer, Charles A" sort="Hefer, Charles A" uniqKey="Hefer C" first="Charles A" last="Hefer">Charles A. Hefer</name><name sortKey="Joubert, Fourie" sort="Joubert, Fourie" uniqKey="Joubert F" first="Fourie" last="Joubert">Fourie Joubert</name><name sortKey="Mizrachi, Eshchar" sort="Mizrachi, Eshchar" uniqKey="Mizrachi E" first="Eshchar" last="Mizrachi">Eshchar Mizrachi</name><name sortKey="Myburg, Alexander A" sort="Myburg, Alexander A" uniqKey="Myburg A" first="Alexander A" last="Myburg">Alexander A. Myburg</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis
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