PoplarV1, Main, Exploration, bibRecord, 000932

Genome-wide characterization of aspartic protease (AP) gene family in Populus trichocarpa and identification of the potential PtAPs involved in wood formation.

Identifieur interne : 000932 ( Main/Exploration ); précédent : 000931; suivant : 000933

Genome-wide characterization of aspartic protease (AP) gene family in Populus trichocarpa and identification of the potential PtAPs involved in wood formation.

Source :

BMC plant biology [ 1471-2229 ] ; 2019.

RBID : pubmed:31234799

Descripteurs français

KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Aspartic acid proteases (génétique), Bois (croissance et développement), Duplication de gène (MeSH), Famille multigénique (MeSH), Glycosylation (MeSH), Gènes de plante (MeSH), Paroi cellulaire (génétique), Phylogenèse (MeSH), Populus (croissance et développement), Populus (enzymologie), Populus (génétique), Protéines végétales (génétique), Protéines végétales (métabolisme), Régions promotrices (génétique) (MeSH), Séquence conservée (MeSH), Végétaux génétiquement modifiés (MeSH).
MESH :
- croissance et développement : Bois, Populus.
- enzymologie : Populus.
- génétique : Aspartic acid proteases, Paroi cellulaire, Populus, Protéines végétales.
- métabolisme : Protéines végétales.
- Analyse de profil d'expression de gènes, Duplication de gène, Famille multigénique, Glycosylation, Gènes de plante, Phylogenèse, Régions promotrices (génétique), Séquence conservée, Végétaux génétiquement modifiés.

English descriptors

KwdEn :
- Aspartic Acid Proteases (genetics), Cell Wall (genetics), Conserved Sequence (MeSH), Gene Duplication (MeSH), Gene Expression Profiling (MeSH), Genes, Plant (MeSH), Glycosylation (MeSH), Multigene Family (MeSH), Phylogeny (MeSH), Plant Proteins (genetics), Plant Proteins (metabolism), Plants, Genetically Modified (MeSH), Populus (enzymology), Populus (genetics), Populus (growth & development), Promoter Regions, Genetic (MeSH), Wood (growth & development).
MESH :
- chemical , genetics : Aspartic Acid Proteases, Plant Proteins.
- enzymology : Populus.
- genetics : Cell Wall, Populus.
- growth & development : Populus, Wood.
- chemical , metabolism : Plant Proteins.
- Conserved Sequence, Gene Duplication, Gene Expression Profiling, Genes, Plant, Glycosylation, Multigene Family, Phylogeny, Plants, Genetically Modified, Promoter Regions, Genetic.

Abstract

BACKGROUND

Aspartic protease (AP) is one of four large proteolytic enzyme families that are involved in plant growth and development. Little is known about the AP gene family in tree species, although it has been characterized in Arabidopsis, rice and grape. The AP genes that are involved in tree wood formation remain to be determined.

RESULTS

A total of 67 AP genes were identified in Populus trichocarpa (PtAP) and classified into three categories (A, B and C). Chromosome mapping analysis revealed that two-thirds of the PtAP genes were located in genome duplication blocks, indicating the expansion of the AP family by segmental duplications in Populus. The microarray data from the Populus eFP browser demonstrated that PtAP genes had diversified tissue expression patterns. Semi-qRT-PCR analysis further determined that more than 10 PtAPs were highly or preferentially expressed in the developing xylem. When the involvement of the PtAPs in wood formation became the focus, many SCW-related cis-elements were found in the promoters of these PtAPs. Based on PtAP

CONCLUSIONS

Comprehensive characterization of the PtAP genes suggests their functional diversity during Populus growth and development. Our findings provide an overall understanding of the AP gene family in trees and establish a better foundation to further describe the roles of PtAPs in wood formation.

DOI: 10.1186/s12870-019-1865-0
PubMed: 31234799
PubMed Central: PMC6591973

Affiliations:

République populaire de Chine, Égypte

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Le document en format XML

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<author><name sortKey="Yang, Chuanping" sort="Yang, Chuanping" uniqKey="Yang C" first="Chuanping" last="Yang">Chuanping Yang</name>
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<term>Cell Wall (genetics)</term>
<term>Conserved Sequence (MeSH)</term>
<term>Gene Duplication (MeSH)</term>
<term>Gene Expression Profiling (MeSH)</term>
<term>Genes, Plant (MeSH)</term>
<term>Glycosylation (MeSH)</term>
<term>Multigene Family (MeSH)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Plants, Genetically Modified (MeSH)</term>
<term>Populus (enzymology)</term>
<term>Populus (genetics)</term>
<term>Populus (growth & development)</term>
<term>Promoter Regions, Genetic (MeSH)</term>
<term>Wood (growth & development)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term>
<term>Aspartic acid proteases (génétique)</term>
<term>Bois (croissance et développement)</term>
<term>Duplication de gène (MeSH)</term>
<term>Famille multigénique (MeSH)</term>
<term>Glycosylation (MeSH)</term>
<term>Gènes de plante (MeSH)</term>
<term>Paroi cellulaire (génétique)</term>
<term>Phylogenèse (MeSH)</term>
<term>Populus (croissance et développement)</term>
<term>Populus (enzymologie)</term>
<term>Populus (génétique)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Régions promotrices (génétique) (MeSH)</term>
<term>Séquence conservée (MeSH)</term>
<term>Végétaux génétiquement modifiés (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Aspartic Acid Proteases</term>
<term>Plant Proteins</term>
</keywords>
<keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Bois</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cell Wall</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Populus</term>
<term>Wood</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Aspartic acid proteases</term>
<term>Paroi cellulaire</term>
<term>Populus</term>
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Conserved Sequence</term>
<term>Gene Duplication</term>
<term>Gene Expression Profiling</term>
<term>Genes, Plant</term>
<term>Glycosylation</term>
<term>Multigene Family</term>
<term>Phylogeny</term>
<term>Plants, Genetically Modified</term>
<term>Promoter Regions, Genetic</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term>
<term>Duplication de gène</term>
<term>Famille multigénique</term>
<term>Glycosylation</term>
<term>Gènes de plante</term>
<term>Phylogenèse</term>
<term>Régions promotrices (génétique)</term>
<term>Séquence conservée</term>
<term>Végétaux génétiquement modifiés</term>
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<front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b>
</p>
<p>Aspartic protease (AP) is one of four large proteolytic enzyme families that are involved in plant growth and development. Little is known about the AP gene family in tree species, although it has been characterized in Arabidopsis, rice and grape. The AP genes that are involved in tree wood formation remain to be determined.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>RESULTS</b>
</p>
<p>A total of 67 AP genes were identified in Populus trichocarpa (PtAP) and classified into three categories (A, B and C). Chromosome mapping analysis revealed that two-thirds of the PtAP genes were located in genome duplication blocks, indicating the expansion of the AP family by segmental duplications in Populus. The microarray data from the Populus eFP browser demonstrated that PtAP genes had diversified tissue expression patterns. Semi-qRT-PCR analysis further determined that more than 10 PtAPs were highly or preferentially expressed in the developing xylem. When the involvement of the PtAPs in wood formation became the focus, many SCW-related cis-elements were found in the promoters of these PtAPs. Based on PtAP</p>
</div>
<div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b>
</p>
<p>Comprehensive characterization of the PtAP genes suggests their functional diversity during Populus growth and development. Our findings provide an overall understanding of the AP gene family in trees and establish a better foundation to further describe the roles of PtAPs in wood formation.</p>
</div>
</front>
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<DateCompleted><Year>2019</Year>
<Month>07</Month>
<Day>30</Day>
</DateCompleted>
<DateRevised><Year>2020</Year>
<Month>02</Month>
<Day>25</Day>
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<JournalIssue CitedMedium="Internet"><Volume>19</Volume>
<Issue>1</Issue>
<PubDate><Year>2019</Year>
<Month>Jun</Month>
<Day>24</Day>
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<Title>BMC plant biology</Title>
<ISOAbbreviation>BMC Plant Biol</ISOAbbreviation>
</Journal>
<ArticleTitle>Genome-wide characterization of aspartic protease (AP) gene family in Populus trichocarpa and identification of the potential PtAPs involved in wood formation.</ArticleTitle>
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<ELocationID EIdType="doi" ValidYN="Y">10.1186/s12870-019-1865-0</ELocationID>
<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Aspartic protease (AP) is one of four large proteolytic enzyme families that are involved in plant growth and development. Little is known about the AP gene family in tree species, although it has been characterized in Arabidopsis, rice and grape. The AP genes that are involved in tree wood formation remain to be determined.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">A total of 67 AP genes were identified in Populus trichocarpa (PtAP) and classified into three categories (A, B and C). Chromosome mapping analysis revealed that two-thirds of the PtAP genes were located in genome duplication blocks, indicating the expansion of the AP family by segmental duplications in Populus. The microarray data from the Populus eFP browser demonstrated that PtAP genes had diversified tissue expression patterns. Semi-qRT-PCR analysis further determined that more than 10 PtAPs were highly or preferentially expressed in the developing xylem. When the involvement of the PtAPs in wood formation became the focus, many SCW-related cis-elements were found in the promoters of these PtAPs. Based on PtAP<sub>promoter</sub>
::GUS techniques, the activities of PtAP66 promoters were observed only in fiber cells, not in the vessels of stems as the xylem and leaf veins developed in the transgenic Populus tree, and strong GUS signals were detected in interfascicular fiber cells, roots, anthers and sepals of PtAP17<sub>promoter</sub>
::GUS transgenic plants. Intensive GUS activities in various secondary tissues implied that PtAP66 and PtAP17 could function in wood formation. In addition, most of the PtAP proteins were predicted to contain N- and (or) O-glycosylation sites, and the integration of PNGase F digestion and western blotting revealed that the PtAP17 and PtAP66 proteins were N-glycosylated in Populus.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Comprehensive characterization of the PtAP genes suggests their functional diversity during Populus growth and development. Our findings provide an overall understanding of the AP gene family in trees and establish a better foundation to further describe the roles of PtAPs in wood formation.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cao</LastName>
<ForeName>Shenquan</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Guo</LastName>
<ForeName>Mengjie</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Wang</LastName>
<ForeName>Chong</ForeName>
<Initials>C</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Xu</LastName>
<ForeName>Wenjing</ForeName>
<Initials>W</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Shi</LastName>
<ForeName>Tianyuan</ForeName>
<Initials>T</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Tong</LastName>
<ForeName>Guimin</ForeName>
<Initials>G</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Zhen</LastName>
<ForeName>Cheng</ForeName>
<Initials>C</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Cheng</LastName>
<ForeName>Hao</ForeName>
<Initials>H</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Yang</LastName>
<ForeName>Chuanping</ForeName>
<Initials>C</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China. yangcp@nefu.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Elsheery</LastName>
<ForeName>Nabil Ibrahim</ForeName>
<Initials>NI</Initials>
<AffiliationInfo><Affiliation>Agriculture botany Department, Faculty of Agriculture, Tanta University, Tanta, Egypt.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Cheng</LastName>
<ForeName>Yuxiang</ForeName>
<Initials>Y</Initials>
<Identifier Source="ORCID">http://orcid.org/0000-0002-8530-6687</Identifier>
<AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China. chengyuxiang@nefu.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><GrantID>2572016AA02</GrantID>
<Agency>The Fundamental Research Funds for the Central Universities</Agency>
<Country></Country>
</Grant>
<Grant><GrantID>JC2016003</GrantID>
<Agency>Project of the Natural Sciences Foundation of Heilongjiang Province</Agency>
<Country></Country>
</Grant>
</GrantList>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2019</Year>
<Month>06</Month>
<Day>24</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>BMC Plant Biol</MedlineTA>
<NlmUniqueID>100967807</NlmUniqueID>
<ISSNLinking>1471-2229</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>EC 3.4.-</RegistryNumber>
<NameOfSubstance UI="D057055">Aspartic Acid Proteases</NameOfSubstance>
</Chemical>
</ChemicalList>
<MeshHeadingList><MeshHeading><DescriptorName UI="D057055" MajorTopicYN="N">Aspartic Acid Proteases</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D002473" MajorTopicYN="N">Cell Wall</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017124" MajorTopicYN="N">Conserved Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020440" MajorTopicYN="N">Gene Duplication</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006031" MajorTopicYN="N">Glycosylation</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005810" MajorTopicYN="Y">Multigene Family</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D030821" MajorTopicYN="N">Plants, Genetically Modified</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000201" MajorTopicYN="N">enzymology</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D011401" MajorTopicYN="N">Promoter Regions, Genetic</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName>
<QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Aspartic protease</Keyword>
<Keyword MajorTopicYN="N">Gene family</Keyword>
<Keyword MajorTopicYN="N">Glycosylation</Keyword>
<Keyword MajorTopicYN="N">Populus trichocarpa</Keyword>
<Keyword MajorTopicYN="N">Promoter activity</Keyword>
<Keyword MajorTopicYN="N">Secondary cell wall</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year>
<Month>11</Month>
<Day>19</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2019</Year>
<Month>06</Month>
<Day>03</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2019</Year>
<Month>6</Month>
<Day>26</Day>
<Hour>6</Hour>
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<name sortKey="Wang, Chong" sort="Wang, Chong" uniqKey="Wang C" first="Chong" last="Wang">Chong Wang</name>
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   |texte=   Genome-wide characterization of aspartic protease (AP) gene family in Populus trichocarpa and identification of the potential PtAPs involved in wood formation.
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Genome-wide characterization of aspartic protease (AP) gene family in Populus trichocarpa and identification of the potential PtAPs involved in wood formation.

Genome-wide characterization of aspartic protease (AP) gene family in Populus trichocarpa and identification of the potential PtAPs involved in wood formation.

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