TR-DB: an open-access database of compounds affecting the ethylene-induced triple response in Arabidopsis.
Identifieur interne : 000041 ( PubMed/Corpus ); précédent : 000040; suivant : 000042TR-DB: an open-access database of compounds affecting the ethylene-induced triple response in Arabidopsis.
Auteurs : Yuming Hu ; Pieter Callebert ; Ilse Vandemoortel ; Long Nguyen ; Dominique Audenaert ; Luc Verschraegen ; Filip Vandenbussche ; Dominique Van Der StraetenSource :
- Plant physiology and biochemistry : PPB [ 1873-2690 ] ; 2014.
English descriptors
- KwdEn :
- Amino Acids, Cyclic (genetics), Amino Acids, Cyclic (metabolism), Arabidopsis (genetics), Arabidopsis (metabolism), Arabidopsis Proteins (metabolism), Databases, Factual, Ethylenes (metabolism), Gene Expression Regulation, Plant, Hypocotyl (metabolism), Phenotype, Plant Growth Regulators (metabolism), Plant Roots (metabolism), Seedlings (metabolism).
- MESH :
- chemical , genetics : Amino Acids, Cyclic.
- chemical , metabolism : Amino Acids, Cyclic, Arabidopsis Proteins, Ethylenes, Plant Growth Regulators.
- genetics : Arabidopsis.
- metabolism : Arabidopsis, Hypocotyl, Plant Roots, Seedlings.
- Databases, Factual, Gene Expression Regulation, Plant, Phenotype.
Abstract
Small molecules which act as hormone agonists or antagonists represent useful tools in fundamental research and are widely applied in agriculture to control hormone effects. High-throughput screening of large chemical compound libraries has yielded new findings in plant biology, with possible future applications in agriculture and horticulture. To further understand ethylene biosynthesis/signaling and its crosstalk with other hormones, we screened a 12,000 compound chemical library based on an ethylene-related bioassay of dark-grown Arabidopsis thaliana (L.) Heynh. seedlings. From the initial screening, 1313 (∼11%) biologically active small molecules altering the phenotype triggered by the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), were identified. Selection and sorting in classes were based on the angle of curvature of the apical hook, the length and width of the hypocotyl and the root. A MySQL-database was constructed (https://chaos.ugent.be/WE15/) including basic chemical information on the compounds, images illustrating the phenotypes, phenotype descriptions and classification. The research perspectives for different classes of hit compounds will be evaluated, and some general screening tips for customized high-throughput screening and pitfalls will be discussed.
DOI: 10.1016/j.plaphy.2013.12.008
PubMed: 24441765
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pubmed:24441765Le document en format XML
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Electronic address: pieter.callebert@ugent.be.</nlm:affiliation></affiliation></author><author><name sortKey="Vandemoortel, Ilse" sort="Vandemoortel, Ilse" uniqKey="Vandemoortel I" first="Ilse" last="Vandemoortel">Ilse Vandemoortel</name><affiliation><nlm:affiliation>Direction Information and Communication Technology, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium. Electronic address: ilse.vandemoortel@ugent.be.</nlm:affiliation></affiliation></author><author><name sortKey="Nguyen, Long" sort="Nguyen, Long" uniqKey="Nguyen L" first="Long" last="Nguyen">Long Nguyen</name><affiliation><nlm:affiliation>VIB, Compound Screening Facility, Technologiepark 927, B-9052 Zwijnaarde, Belgium. Electronic address: longu@psb.vib-ugent.be.</nlm:affiliation></affiliation></author><author><name sortKey="Audenaert, Dominique" sort="Audenaert, Dominique" uniqKey="Audenaert D" first="Dominique" last="Audenaert">Dominique Audenaert</name><affiliation><nlm:affiliation>VIB, Compound Screening Facility, Technologiepark 927, B-9052 Zwijnaarde, Belgium. Electronic address: doaud@psb.vib-ugent.be.</nlm:affiliation></affiliation></author><author><name sortKey="Verschraegen, Luc" sort="Verschraegen, Luc" uniqKey="Verschraegen L" first="Luc" last="Verschraegen">Luc Verschraegen</name><affiliation><nlm:affiliation>Direction Information and Communication Technology, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium. 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Electronic address: yuming.hu@ugent.be.</nlm:affiliation></affiliation></author><author><name sortKey="Callebert, Pieter" sort="Callebert, Pieter" uniqKey="Callebert P" first="Pieter" last="Callebert">Pieter Callebert</name><affiliation><nlm:affiliation>Laboratory of Functional Plant Biology, Department of Physiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium. Electronic address: pieter.callebert@ugent.be.</nlm:affiliation></affiliation></author><author><name sortKey="Vandemoortel, Ilse" sort="Vandemoortel, Ilse" uniqKey="Vandemoortel I" first="Ilse" last="Vandemoortel">Ilse Vandemoortel</name><affiliation><nlm:affiliation>Direction Information and Communication Technology, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium. Electronic address: ilse.vandemoortel@ugent.be.</nlm:affiliation></affiliation></author><author><name sortKey="Nguyen, Long" sort="Nguyen, Long" uniqKey="Nguyen L" first="Long" last="Nguyen">Long Nguyen</name><affiliation><nlm:affiliation>VIB, Compound Screening Facility, Technologiepark 927, B-9052 Zwijnaarde, Belgium. Electronic address: longu@psb.vib-ugent.be.</nlm:affiliation></affiliation></author><author><name sortKey="Audenaert, Dominique" sort="Audenaert, Dominique" uniqKey="Audenaert D" first="Dominique" last="Audenaert">Dominique Audenaert</name><affiliation><nlm:affiliation>VIB, Compound Screening Facility, Technologiepark 927, B-9052 Zwijnaarde, Belgium. Electronic address: doaud@psb.vib-ugent.be.</nlm:affiliation></affiliation></author><author><name sortKey="Verschraegen, Luc" sort="Verschraegen, Luc" uniqKey="Verschraegen L" first="Luc" last="Verschraegen">Luc Verschraegen</name><affiliation><nlm:affiliation>Direction Information and Communication Technology, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium. Electronic address: luc.verschraegen@ugent.be.</nlm:affiliation></affiliation></author><author><name sortKey="Vandenbussche, Filip" sort="Vandenbussche, Filip" uniqKey="Vandenbussche F" first="Filip" last="Vandenbussche">Filip Vandenbussche</name><affiliation><nlm:affiliation>Laboratory of Functional Plant Biology, Department of Physiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium. Electronic address: filip.vandenbussche@ugent.be.</nlm:affiliation></affiliation></author><author><name sortKey="Van Der Straeten, Dominique" sort="Van Der Straeten, Dominique" uniqKey="Van Der Straeten D" first="Dominique" last="Van Der Straeten">Dominique Van Der Straeten</name><affiliation><nlm:affiliation>Laboratory of Functional Plant Biology, Department of Physiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium. Electronic address: dominique.vanderstraeten@ugent.be.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Plant physiology and biochemistry : PPB</title><idno type="eISSN">1873-2690</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acids, Cyclic (genetics)</term><term>Amino Acids, Cyclic (metabolism)</term><term>Arabidopsis (genetics)</term><term>Arabidopsis (metabolism)</term><term>Arabidopsis Proteins (metabolism)</term><term>Databases, Factual</term><term>Ethylenes (metabolism)</term><term>Gene Expression Regulation, Plant</term><term>Hypocotyl (metabolism)</term><term>Phenotype</term><term>Plant Growth Regulators (metabolism)</term><term>Plant Roots (metabolism)</term><term>Seedlings (metabolism)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Amino Acids, Cyclic</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Amino Acids, Cyclic</term><term>Arabidopsis Proteins</term><term>Ethylenes</term><term>Plant Growth Regulators</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Arabidopsis</term><term>Hypocotyl</term><term>Plant Roots</term><term>Seedlings</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Factual</term><term>Gene Expression Regulation, Plant</term><term>Phenotype</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Small molecules which act as hormone agonists or antagonists represent useful tools in fundamental research and are widely applied in agriculture to control hormone effects. High-throughput screening of large chemical compound libraries has yielded new findings in plant biology, with possible future applications in agriculture and horticulture. To further understand ethylene biosynthesis/signaling and its crosstalk with other hormones, we screened a 12,000 compound chemical library based on an ethylene-related bioassay of dark-grown Arabidopsis thaliana (L.) Heynh. seedlings. From the initial screening, 1313 (∼11%) biologically active small molecules altering the phenotype triggered by the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), were identified. Selection and sorting in classes were based on the angle of curvature of the apical hook, the length and width of the hypocotyl and the root. A MySQL-database was constructed (https://chaos.ugent.be/WE15/) including basic chemical information on the compounds, images illustrating the phenotypes, phenotype descriptions and classification. The research perspectives for different classes of hit compounds will be evaluated, and some general screening tips for customized high-throughput screening and pitfalls will be discussed.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24441765</PMID><DateCreated><Year>2014</Year><Month>1</Month><Day>31</Day></DateCreated><DateCompleted><Year>2014</Year><Month>09</Month><Day>29</Day></DateCompleted><DateRevised><Year>2016</Year><Month>10</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1873-2690</ISSN><JournalIssue CitedMedium="Internet"><Volume>75</Volume><PubDate><Year>2014</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Plant physiology and biochemistry : PPB</Title><ISOAbbreviation>Plant Physiol. Biochem.</ISOAbbreviation></Journal><ArticleTitle>TR-DB: an open-access database of compounds affecting the ethylene-induced triple response in Arabidopsis.</ArticleTitle><Pagination><MedlinePgn>128-37</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.plaphy.2013.12.008</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S0981-9428(13)00432-4</ELocationID><Abstract><AbstractText>Small molecules which act as hormone agonists or antagonists represent useful tools in fundamental research and are widely applied in agriculture to control hormone effects. High-throughput screening of large chemical compound libraries has yielded new findings in plant biology, with possible future applications in agriculture and horticulture. To further understand ethylene biosynthesis/signaling and its crosstalk with other hormones, we screened a 12,000 compound chemical library based on an ethylene-related bioassay of dark-grown Arabidopsis thaliana (L.) Heynh. seedlings. From the initial screening, 1313 (∼11%) biologically active small molecules altering the phenotype triggered by the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), were identified. Selection and sorting in classes were based on the angle of curvature of the apical hook, the length and width of the hypocotyl and the root. A MySQL-database was constructed (https://chaos.ugent.be/WE15/) including basic chemical information on the compounds, images illustrating the phenotypes, phenotype descriptions and classification. The research perspectives for different classes of hit compounds will be evaluated, and some general screening tips for customized high-throughput screening and pitfalls will be discussed.</AbstractText><CopyrightInformation>Copyright © 2013 Elsevier Masson SAS. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Yuming</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Laboratory of Functional Plant Biology, Department of Physiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium. Electronic address: yuming.hu@ugent.be.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Callebert</LastName><ForeName>Pieter</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Laboratory of Functional Plant Biology, Department of Physiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium. Electronic address: pieter.callebert@ugent.be.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vandemoortel</LastName><ForeName>Ilse</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Direction Information and Communication Technology, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium. Electronic address: ilse.vandemoortel@ugent.be.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nguyen</LastName><ForeName>Long</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>VIB, Compound Screening Facility, Technologiepark 927, B-9052 Zwijnaarde, Belgium. Electronic address: longu@psb.vib-ugent.be.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Audenaert</LastName><ForeName>Dominique</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>VIB, Compound Screening Facility, Technologiepark 927, B-9052 Zwijnaarde, Belgium. Electronic address: doaud@psb.vib-ugent.be.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Verschraegen</LastName><ForeName>Luc</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Direction Information and Communication Technology, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium. Electronic address: luc.verschraegen@ugent.be.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vandenbussche</LastName><ForeName>Filip</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Laboratory of Functional Plant Biology, Department of Physiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium. Electronic address: filip.vandenbussche@ugent.be.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Van Der Straeten</LastName><ForeName>Dominique</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Laboratory of Functional Plant Biology, Department of Physiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium. Electronic address: dominique.vanderstraeten@ugent.be.</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><ArticleDate DateType="Electronic"><Year>2014</Year><Month>Jan</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>France</Country><MedlineTA>Plant Physiol Biochem</MedlineTA><NlmUniqueID>9882449</NlmUniqueID><ISSNLinking>0981-9428</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000598">Amino Acids, Cyclic</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D029681">Arabidopsis Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005030">Ethylenes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010937">Plant Growth Regulators</NameOfSubstance></Chemical><Chemical><RegistryNumber>3K9EJ633GL</RegistryNumber><NameOfSubstance UI="C023863">1-aminocyclopropane-1-carboxylic acid</NameOfSubstance></Chemical><Chemical><RegistryNumber>91GW059KN7</RegistryNumber><NameOfSubstance UI="C036216">ethylene</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000598" MajorTopicYN="N">Amino Acids, Cyclic</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D029681" MajorTopicYN="N">Arabidopsis Proteins</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016208" MajorTopicYN="Y">Databases, Factual</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005030" MajorTopicYN="N">Ethylenes</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018546" MajorTopicYN="N">Hypocotyl</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010641" MajorTopicYN="Y">Phenotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010937" MajorTopicYN="N">Plant Growth Regulators</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D036226" MajorTopicYN="N">Seedlings</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">1-aminocyclopropane-1-carboxylic acid (ACC)</Keyword><Keyword MajorTopicYN="N">Arabidopsis</Keyword><Keyword MajorTopicYN="N">Chemical genetics</Keyword><Keyword MajorTopicYN="N">Database</Keyword><Keyword MajorTopicYN="N">Ethylene</Keyword><Keyword MajorTopicYN="N">High throughput phenotypic screen</Keyword><Keyword MajorTopicYN="N">Triple response</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>8</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>12</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>1</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>1</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>9</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24441765</ArticleId><ArticleId IdType="pii">S0981-9428(13)00432-4</ArticleId><ArticleId IdType="doi">10.1016/j.plaphy.2013.12.008</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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