Reconstructing the suberin pathway in poplar by chemical and transcriptomic analysis of bark tissues.
Identifieur interne : 000D03 ( Main/Exploration ); précédent : 000D02; suivant : 000D04Reconstructing the suberin pathway in poplar by chemical and transcriptomic analysis of bark tissues.
Auteurs : Meghan K. Rains [Canada] ; Nayana Dilini Gardiyehewa De Silva [Canada] ; Isabel Molina [Canada]Source :
- Tree physiology [ 1758-4469 ] ; 2018.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Cires (composition chimique), Lignine (analyse), Lipides (composition chimique), Lipides (génétique), Populus (génétique), Populus (métabolisme), Régulation de l'expression des gènes végétaux (MeSH), Tiges de plante (métabolisme), Transcriptome (MeSH), Écorce (croissance et développement).
- MESH :
- analyse : Lignine.
- composition chimique : Cires, Lipides.
- croissance et développement : Écorce.
- génétique : Lipides, Populus.
- métabolisme : Populus, Tiges de plante.
- Analyse de profil d'expression de gènes, Régulation de l'expression des gènes végétaux, Transcriptome.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Lignin.
- chemical , chemistry : Lipids, Waxes.
- chemical , genetics : Lipids.
- genetics : Populus.
- growth & development : Plant Bark.
- metabolism : Plant Stems, Populus.
- Gene Expression Profiling, Gene Expression Regulation, Plant, Transcriptome.
Abstract
The tree bark periderm confers the first line of protection against pathogen invasion and abiotic stresses. The phellogen (cork cambium) externally produces cork (phellem) cells that are dead at maturity; while metabolically active, these tissues synthesize cell walls, as well as cell wall modifications, namely suberin and waxes. Suberin is a heteropolymer with aliphatic and aromatic domains, composed of acylglycerols, cross-linked polyphenolics and solvent-extractable waxes. Although suberin is essentially ubiquitous in vascular plants, the biochemical functions of many enzymes and the genetic regulation of its synthesis are poorly understood. We have studied suberin and wax composition in four developmental stages of hybrid poplar (Populus tremula x Populus alba) stem periderm. The amounts of extracellular ester-linked acyl lipids per unit area increased with tissue age, a trend not observed with waxes. We used RNA-Seq deep-sequencing technology to investigate the cork transcriptome at two developmental stages. The transcript analysis yielded 455 candidates for the biosynthesis and regulation of poplar suberin, including genes with proven functions in suberin metabolism, genes highlighted as candidates in other plant species and novel candidates. Among these, a gene encoding a putative lipase/acyltransferase of the GDSL-motif family emerged as a suberin polyester synthase candidate, and specific isoforms of peroxidase and laccase genes were preferentially expressed in cork, suggesting that their corresponding proteins may be involved in cross-linking aromatics to form lignin-like polyphenolics. Many transcriptional regulators with possible roles in meristem identity, cork differentiation and acyl-lipid metabolism were also identified. Our work provides the first large-scale transcriptomic dataset on the suberin-synthesizing tissue of poplar bark, contributing to our understanding of tree bark development at the molecular level. Based on these data, we have proposed a number of hypotheses that can be used in future research leading to novel biological insights into suberin biosynthesis and its physiological function.
DOI: 10.1093/treephys/tpx060
PubMed: 28575526
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Rains</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON, Canada K7L 3N6.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, Canada P6A 2G4.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author><author><name sortKey="Gardiyehewa De Silva, Nayana Dilini" sort="Gardiyehewa De Silva, Nayana Dilini" uniqKey="Gardiyehewa De Silva N" first="Nayana Dilini" last="Gardiyehewa De Silva">Nayana Dilini Gardiyehewa De Silva</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology and Institute of Biochemistry, Nesbitt Biology Building, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Biology and Institute of Biochemistry, Nesbitt Biology Building, Carleton University, 1125 Colonel By Drive, Ottawa, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author><author><name sortKey="Molina, Isabel" sort="Molina, Isabel" uniqKey="Molina I" first="Isabel" last="Molina">Isabel Molina</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON, Canada K7L 3N6.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, Canada P6A 2G4.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:28575526</idno><idno type="pmid">28575526</idno><idno type="doi">10.1093/treephys/tpx060</idno><idno type="wicri:Area/Main/Corpus">001300</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001300</idno><idno type="wicri:Area/Main/Curation">001300</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">001300</idno><idno type="wicri:Area/Main/Exploration">001300</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Reconstructing the suberin pathway in poplar by chemical and transcriptomic analysis of bark tissues.</title><author><name sortKey="Rains, Meghan K" sort="Rains, Meghan K" uniqKey="Rains M" first="Meghan K" last="Rains">Meghan K. Rains</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON, Canada K7L 3N6.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, Canada P6A 2G4.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author><author><name sortKey="Gardiyehewa De Silva, Nayana Dilini" sort="Gardiyehewa De Silva, Nayana Dilini" uniqKey="Gardiyehewa De Silva N" first="Nayana Dilini" last="Gardiyehewa De Silva">Nayana Dilini Gardiyehewa De Silva</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology and Institute of Biochemistry, Nesbitt Biology Building, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Biology and Institute of Biochemistry, Nesbitt Biology Building, Carleton University, 1125 Colonel By Drive, Ottawa, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author><author><name sortKey="Molina, Isabel" sort="Molina, Isabel" uniqKey="Molina I" first="Isabel" last="Molina">Isabel Molina</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON, Canada K7L 3N6.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, Canada P6A 2G4.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author></analytic><series><title level="j">Tree physiology</title><idno type="eISSN">1758-4469</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Lignin (analysis)</term><term>Lipids (chemistry)</term><term>Lipids (genetics)</term><term>Plant Bark (growth & development)</term><term>Plant Stems (metabolism)</term><term>Populus (genetics)</term><term>Populus (metabolism)</term><term>Transcriptome (MeSH)</term><term>Waxes (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Cires (composition chimique)</term><term>Lignine (analyse)</term><term>Lipides (composition chimique)</term><term>Lipides (génétique)</term><term>Populus (génétique)</term><term>Populus (métabolisme)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Tiges de plante (métabolisme)</term><term>Transcriptome (MeSH)</term><term>Écorce (croissance et développement)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Lignin</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Lipids</term><term>Waxes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Lipids</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Lignine</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Cires</term><term>Lipides</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Écorce</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Plant Bark</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Lipides</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Plant Stems</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Populus</term><term>Tiges de plante</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Régulation de l'expression des gènes végétaux</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The tree bark periderm confers the first line of protection against pathogen invasion and abiotic stresses. The phellogen (cork cambium) externally produces cork (phellem) cells that are dead at maturity; while metabolically active, these tissues synthesize cell walls, as well as cell wall modifications, namely suberin and waxes. Suberin is a heteropolymer with aliphatic and aromatic domains, composed of acylglycerols, cross-linked polyphenolics and solvent-extractable waxes. Although suberin is essentially ubiquitous in vascular plants, the biochemical functions of many enzymes and the genetic regulation of its synthesis are poorly understood. We have studied suberin and wax composition in four developmental stages of hybrid poplar (Populus tremula x Populus alba) stem periderm. The amounts of extracellular ester-linked acyl lipids per unit area increased with tissue age, a trend not observed with waxes. We used RNA-Seq deep-sequencing technology to investigate the cork transcriptome at two developmental stages. The transcript analysis yielded 455 candidates for the biosynthesis and regulation of poplar suberin, including genes with proven functions in suberin metabolism, genes highlighted as candidates in other plant species and novel candidates. Among these, a gene encoding a putative lipase/acyltransferase of the GDSL-motif family emerged as a suberin polyester synthase candidate, and specific isoforms of peroxidase and laccase genes were preferentially expressed in cork, suggesting that their corresponding proteins may be involved in cross-linking aromatics to form lignin-like polyphenolics. Many transcriptional regulators with possible roles in meristem identity, cork differentiation and acyl-lipid metabolism were also identified. Our work provides the first large-scale transcriptomic dataset on the suberin-synthesizing tissue of poplar bark, contributing to our understanding of tree bark development at the molecular level. Based on these data, we have proposed a number of hypotheses that can be used in future research leading to novel biological insights into suberin biosynthesis and its physiological function.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28575526</PMID><DateCompleted><Year>2018</Year><Month>10</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>10</Month><Day>24</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1758-4469</ISSN><JournalIssue CitedMedium="Internet"><Volume>38</Volume><Issue>3</Issue><PubDate><Year>2018</Year><Month>03</Month><Day>01</Day></PubDate></JournalIssue><Title>Tree physiology</Title><ISOAbbreviation>Tree Physiol</ISOAbbreviation></Journal><ArticleTitle>Reconstructing the suberin pathway in poplar by chemical and transcriptomic analysis of bark tissues.</ArticleTitle><Pagination><MedlinePgn>340-361</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/treephys/tpx060</ELocationID><Abstract><AbstractText>The tree bark periderm confers the first line of protection against pathogen invasion and abiotic stresses. The phellogen (cork cambium) externally produces cork (phellem) cells that are dead at maturity; while metabolically active, these tissues synthesize cell walls, as well as cell wall modifications, namely suberin and waxes. Suberin is a heteropolymer with aliphatic and aromatic domains, composed of acylglycerols, cross-linked polyphenolics and solvent-extractable waxes. Although suberin is essentially ubiquitous in vascular plants, the biochemical functions of many enzymes and the genetic regulation of its synthesis are poorly understood. We have studied suberin and wax composition in four developmental stages of hybrid poplar (Populus tremula x Populus alba) stem periderm. The amounts of extracellular ester-linked acyl lipids per unit area increased with tissue age, a trend not observed with waxes. We used RNA-Seq deep-sequencing technology to investigate the cork transcriptome at two developmental stages. The transcript analysis yielded 455 candidates for the biosynthesis and regulation of poplar suberin, including genes with proven functions in suberin metabolism, genes highlighted as candidates in other plant species and novel candidates. Among these, a gene encoding a putative lipase/acyltransferase of the GDSL-motif family emerged as a suberin polyester synthase candidate, and specific isoforms of peroxidase and laccase genes were preferentially expressed in cork, suggesting that their corresponding proteins may be involved in cross-linking aromatics to form lignin-like polyphenolics. Many transcriptional regulators with possible roles in meristem identity, cork differentiation and acyl-lipid metabolism were also identified. Our work provides the first large-scale transcriptomic dataset on the suberin-synthesizing tissue of poplar bark, contributing to our understanding of tree bark development at the molecular level. Based on these data, we have proposed a number of hypotheses that can be used in future research leading to novel biological insights into suberin biosynthesis and its physiological function.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Rains</LastName><ForeName>Meghan K</ForeName><Initials>MK</Initials><AffiliationInfo><Affiliation>Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON, Canada K7L 3N6.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, Canada P6A 2G4.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gardiyehewa de Silva</LastName><ForeName>Nayana Dilini</ForeName><Initials>ND</Initials><AffiliationInfo><Affiliation>Department of Biology and Institute of Biochemistry, Nesbitt Biology Building, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Molina</LastName><ForeName>Isabel</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON, Canada K7L 3N6.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, Canada P6A 2G4.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>Canada</Country><MedlineTA>Tree Physiol</MedlineTA><NlmUniqueID>100955338</NlmUniqueID><ISSNLinking>0829-318X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D008055">Lipids</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014885">Waxes</NameOfSubstance></Chemical><Chemical><RegistryNumber>8072-95-5</RegistryNumber><NameOfSubstance UI="C065875">suberin</NameOfSubstance></Chemical><Chemical><RegistryNumber>9005-53-2</RegistryNumber><NameOfSubstance UI="D008031">Lignin</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008055" MajorTopicYN="N">Lipids</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D024301" MajorTopicYN="N">Plant Bark</DescriptorName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018547" MajorTopicYN="N">Plant Stems</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="Y">Transcriptome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014885" MajorTopicYN="N">Waxes</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>11</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>05</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>6</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>10</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>6</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28575526</ArticleId><ArticleId IdType="pii">3859995</ArticleId><ArticleId IdType="doi">10.1093/treephys/tpx060</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Canada</li></country></list><tree><country name="Canada"><noRegion><name sortKey="Rains, Meghan K" sort="Rains, Meghan K" uniqKey="Rains M" first="Meghan K" last="Rains">Meghan K. Rains</name></noRegion><name sortKey="Gardiyehewa De Silva, Nayana Dilini" sort="Gardiyehewa De Silva, Nayana Dilini" uniqKey="Gardiyehewa De Silva N" first="Nayana Dilini" last="Gardiyehewa De Silva">Nayana Dilini Gardiyehewa De Silva</name><name sortKey="Molina, Isabel" sort="Molina, Isabel" uniqKey="Molina I" first="Isabel" last="Molina">Isabel Molina</name><name sortKey="Molina, Isabel" sort="Molina, Isabel" uniqKey="Molina I" first="Isabel" last="Molina">Isabel Molina</name><name sortKey="Rains, Meghan K" sort="Rains, Meghan K" uniqKey="Rains M" first="Meghan K" last="Rains">Meghan K. Rains</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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