Shotgun proteome profile of Populus developing xylem.
Identifieur interne : 003486 ( Main/Exploration ); précédent : 003485; suivant : 003487Shotgun proteome profile of Populus developing xylem.
Auteurs : Udaya C. Kalluri [États-Unis] ; Gregory B. Hurst ; Patricia K. Lankford ; Priya Ranjan ; Dale A. PelletierSource :
- Proteomics [ 1615-9861 ] ; 2009.
Descripteurs français
- KwdFr :
- Paroi cellulaire (composition chimique), Populus (composition chimique), Populus (croissance et développement), Populus (génétique), Protéines nucléaires (analyse), Protéines végétales (analyse), Protéines végétales (génétique), Protéome (analyse), Protéome (génétique), Protéomique (méthodes), Spectrométrie de masse en tandem (MeSH), Transcription génétique (MeSH), Xylème (composition chimique), Xylème (croissance et développement), Xylème (génétique).
- MESH :
- analyse : Protéines nucléaires, Protéines végétales, Protéome.
- composition chimique : Paroi cellulaire, Populus, Xylème.
- croissance et développement : Populus, Xylème.
- génétique : Populus, Protéines végétales, Protéome, Xylème.
- méthodes : Protéomique.
- Spectrométrie de masse en tandem, Transcription génétique.
English descriptors
- KwdEn :
- Cell Wall (chemistry), Nuclear Proteins (analysis), Plant Proteins (analysis), Plant Proteins (genetics), Populus (chemistry), Populus (genetics), Populus (growth & development), Proteome (analysis), Proteome (genetics), Proteomics (methods), Tandem Mass Spectrometry (MeSH), Transcription, Genetic (MeSH), Xylem (chemistry), Xylem (genetics), Xylem (growth & development).
- MESH :
- chemical , analysis : Nuclear Proteins, Plant Proteins, Proteome.
- chemistry : Cell Wall, Populus, Xylem.
- chemical , genetics : Plant Proteins, Populus, Proteome, Xylem.
- growth & development : Populus, Xylem.
- methods : Proteomics.
- Tandem Mass Spectrometry, Transcription, Genetic.
Abstract
Understanding the molecular pathways of plant cell wall biosynthesis and remodeling is central to interpreting biological mechanisms underlying plant growth and adaptation as well as leveraging that knowledge towards development of improved bioenergy feedstocks. Here, we report the application of shotgun MS/MS profiling to the proteome of Populus developing xylem. Nearly 6000 different proteins were identified from the xylem proteome. To identify low-abundance DNA-regulatory proteins from the developing xylem, a selective nuclear proteome profiling method was developed. Several putative transcription factors and chromatin remodeling proteins were identified using this method, such as NAC domain, CtCP-like and CHB3-SWI/SNF-related proteins. Public databases were mined to obtain information in support of subcellular localization, transcript-level expression and functional categorization of identified proteins. In addition to finding protein-level evidence of candidate cell wall biosynthesis genes from xylem (wood) tissue such as cellulose synthase, sucrose synthase and polygalacturonase, several other potentially new candidate genes in the cell wall biosynthesis pathway were discovered. Further application of such proteomics methods will aid in plant systems biology modeling efforts by enhancing the understanding not only of cell wall biosynthesis but also of other plant developmental and physiological pathways.
DOI: 10.1002/pmic.200800854
PubMed: 19743414
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Shotgun proteome profile of Populus developing xylem.</title><author><name sortKey="Kalluri, Udaya C" sort="Kalluri, Udaya C" uniqKey="Kalluri U" first="Udaya C" last="Kalluri">Udaya C. Kalluri</name><affiliation wicri:level="2"><nlm:affiliation>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. kalluriudayc@ornl.gov</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Hurst, Gregory B" sort="Hurst, Gregory B" uniqKey="Hurst G" first="Gregory B" last="Hurst">Gregory B. Hurst</name></author><author><name sortKey="Lankford, Patricia K" sort="Lankford, Patricia K" uniqKey="Lankford P" first="Patricia K" last="Lankford">Patricia K. Lankford</name></author><author><name sortKey="Ranjan, Priya" sort="Ranjan, Priya" uniqKey="Ranjan P" first="Priya" last="Ranjan">Priya Ranjan</name></author><author><name sortKey="Pelletier, Dale A" sort="Pelletier, Dale A" uniqKey="Pelletier D" first="Dale A" last="Pelletier">Dale A. Pelletier</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:19743414</idno><idno type="pmid">19743414</idno><idno type="doi">10.1002/pmic.200800854</idno><idno type="wicri:Area/Main/Corpus">003462</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003462</idno><idno type="wicri:Area/Main/Curation">003462</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003462</idno><idno type="wicri:Area/Main/Exploration">003462</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Shotgun proteome profile of Populus developing xylem.</title><author><name sortKey="Kalluri, Udaya C" sort="Kalluri, Udaya C" uniqKey="Kalluri U" first="Udaya C" last="Kalluri">Udaya C. Kalluri</name><affiliation wicri:level="2"><nlm:affiliation>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. kalluriudayc@ornl.gov</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Hurst, Gregory B" sort="Hurst, Gregory B" uniqKey="Hurst G" first="Gregory B" last="Hurst">Gregory B. Hurst</name></author><author><name sortKey="Lankford, Patricia K" sort="Lankford, Patricia K" uniqKey="Lankford P" first="Patricia K" last="Lankford">Patricia K. Lankford</name></author><author><name sortKey="Ranjan, Priya" sort="Ranjan, Priya" uniqKey="Ranjan P" first="Priya" last="Ranjan">Priya Ranjan</name></author><author><name sortKey="Pelletier, Dale A" sort="Pelletier, Dale A" uniqKey="Pelletier D" first="Dale A" last="Pelletier">Dale A. Pelletier</name></author></analytic><series><title level="j">Proteomics</title><idno type="eISSN">1615-9861</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cell Wall (chemistry)</term><term>Nuclear Proteins (analysis)</term><term>Plant Proteins (analysis)</term><term>Plant Proteins (genetics)</term><term>Populus (chemistry)</term><term>Populus (genetics)</term><term>Populus (growth & development)</term><term>Proteome (analysis)</term><term>Proteome (genetics)</term><term>Proteomics (methods)</term><term>Tandem Mass Spectrometry (MeSH)</term><term>Transcription, Genetic (MeSH)</term><term>Xylem (chemistry)</term><term>Xylem (genetics)</term><term>Xylem (growth & development)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Paroi cellulaire (composition chimique)</term><term>Populus (composition chimique)</term><term>Populus (croissance et développement)</term><term>Populus (génétique)</term><term>Protéines nucléaires (analyse)</term><term>Protéines végétales (analyse)</term><term>Protéines végétales (génétique)</term><term>Protéome (analyse)</term><term>Protéome (génétique)</term><term>Protéomique (méthodes)</term><term>Spectrométrie de masse en tandem (MeSH)</term><term>Transcription génétique (MeSH)</term><term>Xylème (composition chimique)</term><term>Xylème (croissance et développement)</term><term>Xylème (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Nuclear Proteins</term><term>Plant Proteins</term><term>Proteome</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Protéines nucléaires</term><term>Protéines végétales</term><term>Protéome</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Cell Wall</term><term>Populus</term><term>Xylem</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Paroi cellulaire</term><term>Populus</term><term>Xylème</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Populus</term><term>Xylème</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term><term>Populus</term><term>Proteome</term><term>Xylem</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Populus</term><term>Xylem</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term><term>Protéines végétales</term><term>Protéome</term><term>Xylème</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Proteomics</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Protéomique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Tandem Mass Spectrometry</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Spectrométrie de masse en tandem</term><term>Transcription génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Understanding the molecular pathways of plant cell wall biosynthesis and remodeling is central to interpreting biological mechanisms underlying plant growth and adaptation as well as leveraging that knowledge towards development of improved bioenergy feedstocks. Here, we report the application of shotgun MS/MS profiling to the proteome of Populus developing xylem. Nearly 6000 different proteins were identified from the xylem proteome. To identify low-abundance DNA-regulatory proteins from the developing xylem, a selective nuclear proteome profiling method was developed. Several putative transcription factors and chromatin remodeling proteins were identified using this method, such as NAC domain, CtCP-like and CHB3-SWI/SNF-related proteins. Public databases were mined to obtain information in support of subcellular localization, transcript-level expression and functional categorization of identified proteins. In addition to finding protein-level evidence of candidate cell wall biosynthesis genes from xylem (wood) tissue such as cellulose synthase, sucrose synthase and polygalacturonase, several other potentially new candidate genes in the cell wall biosynthesis pathway were discovered. Further application of such proteomics methods will aid in plant systems biology modeling efforts by enhancing the understanding not only of cell wall biosynthesis but also of other plant developmental and physiological pathways.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19743414</PMID><DateCompleted><Year>2009</Year><Month>12</Month><Day>16</Day></DateCompleted><DateRevised><Year>2009</Year><Month>11</Month><Day>02</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1615-9861</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>21</Issue><PubDate><Year>2009</Year><Month>Nov</Month></PubDate></JournalIssue><Title>Proteomics</Title><ISOAbbreviation>Proteomics</ISOAbbreviation></Journal><ArticleTitle>Shotgun proteome profile of Populus developing xylem.</ArticleTitle><Pagination><MedlinePgn>4871-80</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/pmic.200800854</ELocationID><Abstract><AbstractText>Understanding the molecular pathways of plant cell wall biosynthesis and remodeling is central to interpreting biological mechanisms underlying plant growth and adaptation as well as leveraging that knowledge towards development of improved bioenergy feedstocks. Here, we report the application of shotgun MS/MS profiling to the proteome of Populus developing xylem. Nearly 6000 different proteins were identified from the xylem proteome. To identify low-abundance DNA-regulatory proteins from the developing xylem, a selective nuclear proteome profiling method was developed. Several putative transcription factors and chromatin remodeling proteins were identified using this method, such as NAC domain, CtCP-like and CHB3-SWI/SNF-related proteins. Public databases were mined to obtain information in support of subcellular localization, transcript-level expression and functional categorization of identified proteins. In addition to finding protein-level evidence of candidate cell wall biosynthesis genes from xylem (wood) tissue such as cellulose synthase, sucrose synthase and polygalacturonase, several other potentially new candidate genes in the cell wall biosynthesis pathway were discovered. Further application of such proteomics methods will aid in plant systems biology modeling efforts by enhancing the understanding not only of cell wall biosynthesis but also of other plant developmental and physiological pathways.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kalluri</LastName><ForeName>Udaya C</ForeName><Initials>UC</Initials><AffiliationInfo><Affiliation>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. kalluriudayc@ornl.gov</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hurst</LastName><ForeName>Gregory B</ForeName><Initials>GB</Initials></Author><Author ValidYN="Y"><LastName>Lankford</LastName><ForeName>Patricia K</ForeName><Initials>PK</Initials></Author><Author ValidYN="Y"><LastName>Ranjan</LastName><ForeName>Priya</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Pelletier</LastName><ForeName>Dale A</ForeName><Initials>DA</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Proteomics</MedlineTA><NlmUniqueID>101092707</NlmUniqueID><ISSNLinking>1615-9853</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009687">Nuclear Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020543">Proteome</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002473" MajorTopicYN="N">Cell Wall</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009687" MajorTopicYN="N">Nuclear Proteins</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020543" MajorTopicYN="N">Proteome</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D040901" MajorTopicYN="N">Proteomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D053719" MajorTopicYN="N">Tandem Mass Spectrometry</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014158" MajorTopicYN="N">Transcription, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D052584" MajorTopicYN="N">Xylem</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2009</Year><Month>9</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2009</Year><Month>9</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2009</Year><Month>12</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">19743414</ArticleId><ArticleId IdType="doi">10.1002/pmic.200800854</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Tennessee</li></region></list><tree><noCountry><name sortKey="Hurst, Gregory B" sort="Hurst, Gregory B" uniqKey="Hurst G" first="Gregory B" last="Hurst">Gregory B. Hurst</name><name sortKey="Lankford, Patricia K" sort="Lankford, Patricia K" uniqKey="Lankford P" first="Patricia K" last="Lankford">Patricia K. Lankford</name><name sortKey="Pelletier, Dale A" sort="Pelletier, Dale A" uniqKey="Pelletier D" first="Dale A" last="Pelletier">Dale A. Pelletier</name><name sortKey="Ranjan, Priya" sort="Ranjan, Priya" uniqKey="Ranjan P" first="Priya" last="Ranjan">Priya Ranjan</name></noCountry><country name="États-Unis"><region name="Tennessee"><name sortKey="Kalluri, Udaya C" sort="Kalluri, Udaya C" uniqKey="Kalluri U" first="Udaya C" last="Kalluri">Udaya C. Kalluri</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 003486 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 003486 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:19743414
|texte= Shotgun proteome profile of Populus developing xylem.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:19743414" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |