PoplarV1, Main, Exploration, bibRecord, 002A61

Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon.

Identifieur interne : 002A61 ( Main/Exploration ); précédent : 002A60; suivant : 002A62

Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon.

Auteurs : Lihong Chen [République populaire de Chine] ; Wei Hu ; Shenglong Tan ; Min Wang ; Zhanbing Ma ; Shiyi Zhou ; Xiaomin Deng ; Yang Zhang ; Chao Huang ; Guangxiao Yang ; Guangyuan He

Source :

PloS one [ 1932-6203 ] ; 2012.

RBID : pubmed:23082129

Descripteurs français

English descriptors

Abstract

MAPK cascades are universal signal transduction modules and play important roles in plant growth, development and in response to a variety of biotic and abiotic stresses. Although MAPKs and MAPKKs have been systematically investigated in several plant species including Arabidopsis, rice and poplar, no systematic analysis has been conducted in the emerging monocot model plant Brachypodium distachyon. In the present study, a total of 16 MAPK genes and 12 MAPKK genes were identified from B. distachyon. An analysis of the genomic evolution showed that both tandem and segment duplications contributed significantly to the expansion of MAPK and MAPKK families. Evolutionary relationships within subfamilies were supported by exon-intron organizations and the architectures of conserved protein motifs. Synteny analysis between B. distachyon and the other two plant species of rice and Arabidopsis showed that only one homolog of B. distachyon MAPKs was found in the corresponding syntenic blocks of Arabidopsis, while 13 homologs of B. distachyon MAPKs and MAPKKs were found in that of rice, which was consistent with the speciation process of the three species. In addition, several interactive protein pairs between the two families in B. distachyon were found through yeast two hybrid assay, whereas their orthologs of a pair in Arabidopsis and other plant species were not found to interact with each other. Finally, expression studies of closely related family members among B. distachyon, Arabidopsis and rice showed that even recently duplicated representatives may fulfill different functions and be involved in different signal pathways. Taken together, our data would provide a foundation for evolutionary and functional characterization of MAPK and MAPKK gene families in B. distachyon and other plant species to unravel their biological roles.

DOI: 10.1371/journal.pone.0046744
PubMed: 23082129
PubMed Central: PMC3474763

Affiliations:

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<author><name sortKey="Ma, Zhanbing" sort="Ma, Zhanbing" uniqKey="Ma Z" first="Zhanbing" last="Ma">Zhanbing Ma</name>
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<author><name sortKey="Zhang, Yang" sort="Zhang, Yang" uniqKey="Zhang Y" first="Yang" last="Zhang">Yang Zhang</name>
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<author><name sortKey="Huang, Chao" sort="Huang, Chao" uniqKey="Huang C" first="Chao" last="Huang">Chao Huang</name>
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<term>Arabidopsis (enzymology)</term>
<term>Arabidopsis (genetics)</term>
<term>Arabidopsis (growth & development)</term>
<term>Arabidopsis (radiation effects)</term>
<term>Brachypodium (enzymology)</term>
<term>Brachypodium (genetics)</term>
<term>Brachypodium (growth & development)</term>
<term>Brachypodium (radiation effects)</term>
<term>Chromosomes, Plant (genetics)</term>
<term>Gene Duplication (genetics)</term>
<term>Gene Expression Profiling (MeSH)</term>
<term>Gene Expression Regulation, Plant (radiation effects)</term>
<term>Genes, Plant (genetics)</term>
<term>Genome, Plant (genetics)</term>
<term>Light (MeSH)</term>
<term>Mitogen-Activated Protein Kinase Kinases (chemistry)</term>
<term>Mitogen-Activated Protein Kinase Kinases (genetics)</term>
<term>Mitogen-Activated Protein Kinase Kinases (metabolism)</term>
<term>Mitogen-Activated Protein Kinases (chemistry)</term>
<term>Mitogen-Activated Protein Kinases (genetics)</term>
<term>Mitogen-Activated Protein Kinases (metabolism)</term>
<term>Molecular Sequence Annotation (MeSH)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Multigene Family (MeSH)</term>
<term>Oryza (enzymology)</term>
<term>Oryza (genetics)</term>
<term>Oryza (growth & development)</term>
<term>Oryza (radiation effects)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Proteins (chemistry)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Promoter Regions, Genetic (genetics)</term>
<term>Protein Binding (genetics)</term>
<term>Protein Binding (radiation effects)</term>
<term>Protein Structure, Tertiary (MeSH)</term>
<term>Sequence Alignment (MeSH)</term>
<term>Stress, Physiological (genetics)</term>
<term>Synteny (genetics)</term>
<term>Temperature (MeSH)</term>
<term>Terminology as Topic (MeSH)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences (MeSH)</term>
<term>Analyse de profil d'expression de gènes (MeSH)</term>
<term>Annotation de séquence moléculaire (MeSH)</term>
<term>Arabidopsis (croissance et développement)</term>
<term>Arabidopsis (effets des radiations)</term>
<term>Arabidopsis (enzymologie)</term>
<term>Arabidopsis (génétique)</term>
<term>Brachypodium (croissance et développement)</term>
<term>Brachypodium (effets des radiations)</term>
<term>Brachypodium (enzymologie)</term>
<term>Brachypodium (génétique)</term>
<term>Chromosomes de plante (génétique)</term>
<term>Données de séquences moléculaires (MeSH)</term>
<term>Duplication de gène (génétique)</term>
<term>Famille multigénique (MeSH)</term>
<term>Gènes de plante (génétique)</term>
<term>Génome végétal (génétique)</term>
<term>Liaison aux protéines (effets des radiations)</term>
<term>Liaison aux protéines (génétique)</term>
<term>Lumière (MeSH)</term>
<term>Mitogen-Activated Protein Kinase Kinases (composition chimique)</term>
<term>Mitogen-Activated Protein Kinase Kinases (génétique)</term>
<term>Mitogen-Activated Protein Kinase Kinases (métabolisme)</term>
<term>Mitogen-Activated Protein Kinases (composition chimique)</term>
<term>Mitogen-Activated Protein Kinases (génétique)</term>
<term>Mitogen-Activated Protein Kinases (métabolisme)</term>
<term>Oryza (croissance et développement)</term>
<term>Oryza (effets des radiations)</term>
<term>Oryza (enzymologie)</term>
<term>Oryza (génétique)</term>
<term>Phylogenèse (MeSH)</term>
<term>Protéines végétales (composition chimique)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Régions promotrices (génétique) (génétique)</term>
<term>Régulation de l'expression des gènes végétaux (effets des radiations)</term>
<term>Stress physiologique (génétique)</term>
<term>Structure tertiaire des protéines (MeSH)</term>
<term>Synténie (génétique)</term>
<term>Séquence d'acides aminés (MeSH)</term>
<term>Température (MeSH)</term>
<term>Terminologie comme sujet (MeSH)</term>
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<term>Mitogen-Activated Protein Kinases</term>
<term>Plant Proteins</term>
</keywords>
<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Mitogen-Activated Protein Kinase Kinases</term>
<term>Mitogen-Activated Protein Kinases</term>
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Arabidopsis</term>
<term>Brachypodium</term>
<term>Oryza</term>
</keywords>
<keywords scheme="MESH" qualifier="effets des radiations" xml:lang="fr"><term>Arabidopsis</term>
<term>Brachypodium</term>
<term>Liaison aux protéines</term>
<term>Oryza</term>
<term>Régulation de l'expression des gènes végétaux</term>
</keywords>
<keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Arabidopsis</term>
<term>Brachypodium</term>
<term>Oryza</term>
</keywords>
<keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Arabidopsis</term>
<term>Brachypodium</term>
<term>Oryza</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term>
<term>Brachypodium</term>
<term>Chromosomes, Plant</term>
<term>Gene Duplication</term>
<term>Genes, Plant</term>
<term>Genome, Plant</term>
<term>Mitogen-Activated Protein Kinase Kinases</term>
<term>Mitogen-Activated Protein Kinases</term>
<term>Oryza</term>
<term>Plant Proteins</term>
<term>Promoter Regions, Genetic</term>
<term>Protein Binding</term>
<term>Stress, Physiological</term>
<term>Synteny</term>
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<keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Arabidopsis</term>
<term>Brachypodium</term>
<term>Oryza</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term>
<term>Brachypodium</term>
<term>Chromosomes de plante</term>
<term>Duplication de gène</term>
<term>Gènes de plante</term>
<term>Génome végétal</term>
<term>Liaison aux protéines</term>
<term>Mitogen-Activated Protein Kinase Kinases</term>
<term>Mitogen-Activated Protein Kinases</term>
<term>Oryza</term>
<term>Protéines végétales</term>
<term>Régions promotrices (génétique)</term>
<term>Stress physiologique</term>
<term>Synténie</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Mitogen-Activated Protein Kinase Kinases</term>
<term>Mitogen-Activated Protein Kinases</term>
<term>Plant Proteins</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Mitogen-Activated Protein Kinase Kinases</term>
<term>Mitogen-Activated Protein Kinases</term>
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" qualifier="radiation effects" xml:lang="en"><term>Arabidopsis</term>
<term>Brachypodium</term>
<term>Gene Expression Regulation, Plant</term>
<term>Oryza</term>
<term>Protein Binding</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term>
<term>Gene Expression Profiling</term>
<term>Light</term>
<term>Molecular Sequence Annotation</term>
<term>Molecular Sequence Data</term>
<term>Multigene Family</term>
<term>Phylogeny</term>
<term>Protein Structure, Tertiary</term>
<term>Sequence Alignment</term>
<term>Temperature</term>
<term>Terminology as Topic</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term>
<term>Analyse de profil d'expression de gènes</term>
<term>Annotation de séquence moléculaire</term>
<term>Données de séquences moléculaires</term>
<term>Famille multigénique</term>
<term>Lumière</term>
<term>Phylogenèse</term>
<term>Structure tertiaire des protéines</term>
<term>Séquence d'acides aminés</term>
<term>Température</term>
<term>Terminologie comme sujet</term>
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<front><div type="abstract" xml:lang="en">MAPK cascades are universal signal transduction modules and play important roles in plant growth, development and in response to a variety of biotic and abiotic stresses. Although MAPKs and MAPKKs have been systematically investigated in several plant species including Arabidopsis, rice and poplar, no systematic analysis has been conducted in the emerging monocot model plant Brachypodium distachyon. In the present study, a total of 16 MAPK genes and 12 MAPKK genes were identified from B. distachyon. An analysis of the genomic evolution showed that both tandem and segment duplications contributed significantly to the expansion of MAPK and MAPKK families. Evolutionary relationships within subfamilies were supported by exon-intron organizations and the architectures of conserved protein motifs. Synteny analysis between B. distachyon and the other two plant species of rice and Arabidopsis showed that only one homolog of B. distachyon MAPKs was found in the corresponding syntenic blocks of Arabidopsis, while 13 homologs of B. distachyon MAPKs and MAPKKs were found in that of rice, which was consistent with the speciation process of the three species. In addition, several interactive protein pairs between the two families in B. distachyon were found through yeast two hybrid assay, whereas their orthologs of a pair in Arabidopsis and other plant species were not found to interact with each other. Finally, expression studies of closely related family members among B. distachyon, Arabidopsis and rice showed that even recently duplicated representatives may fulfill different functions and be involved in different signal pathways. Taken together, our data would provide a foundation for evolutionary and functional characterization of MAPK and MAPKK gene families in B. distachyon and other plant species to unravel their biological roles.</div>
</front>
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<Month>04</Month>
<Day>09</Day>
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<Abstract><AbstractText>MAPK cascades are universal signal transduction modules and play important roles in plant growth, development and in response to a variety of biotic and abiotic stresses. Although MAPKs and MAPKKs have been systematically investigated in several plant species including Arabidopsis, rice and poplar, no systematic analysis has been conducted in the emerging monocot model plant Brachypodium distachyon. In the present study, a total of 16 MAPK genes and 12 MAPKK genes were identified from B. distachyon. An analysis of the genomic evolution showed that both tandem and segment duplications contributed significantly to the expansion of MAPK and MAPKK families. Evolutionary relationships within subfamilies were supported by exon-intron organizations and the architectures of conserved protein motifs. Synteny analysis between B. distachyon and the other two plant species of rice and Arabidopsis showed that only one homolog of B. distachyon MAPKs was found in the corresponding syntenic blocks of Arabidopsis, while 13 homologs of B. distachyon MAPKs and MAPKKs were found in that of rice, which was consistent with the speciation process of the three species. In addition, several interactive protein pairs between the two families in B. distachyon were found through yeast two hybrid assay, whereas their orthologs of a pair in Arabidopsis and other plant species were not found to interact with each other. Finally, expression studies of closely related family members among B. distachyon, Arabidopsis and rice showed that even recently duplicated representatives may fulfill different functions and be involved in different signal pathways. Taken together, our data would provide a foundation for evolutionary and functional characterization of MAPK and MAPKK gene families in B. distachyon and other plant species to unravel their biological roles.</AbstractText>
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<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chen</LastName>
<ForeName>Lihong</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China.</Affiliation>
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<ForeName>Wei</ForeName>
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<ForeName>Shenglong</ForeName>
<Initials>S</Initials>
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<Author ValidYN="Y"><LastName>Wang</LastName>
<ForeName>Min</ForeName>
<Initials>M</Initials>
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<Author ValidYN="Y"><LastName>Ma</LastName>
<ForeName>Zhanbing</ForeName>
<Initials>Z</Initials>
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<Author ValidYN="Y"><LastName>Zhou</LastName>
<ForeName>Shiyi</ForeName>
<Initials>S</Initials>
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<Author ValidYN="Y"><LastName>Deng</LastName>
<ForeName>Xiaomin</ForeName>
<Initials>X</Initials>
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<Author ValidYN="Y"><LastName>Zhang</LastName>
<ForeName>Yang</ForeName>
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<Author ValidYN="Y"><LastName>Huang</LastName>
<ForeName>Chao</ForeName>
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<Author ValidYN="Y"><LastName>Yang</LastName>
<ForeName>Guangxiao</ForeName>
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<Author ValidYN="Y"><LastName>He</LastName>
<ForeName>Guangyuan</ForeName>
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<MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName>
<QualifierName UI="Q000201" MajorTopicYN="N">enzymology</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName>
<QualifierName UI="Q000528" MajorTopicYN="N">radiation effects</QualifierName>
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<MeshHeading><DescriptorName UI="D058431" MajorTopicYN="N">Brachypodium</DescriptorName>
<QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
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<QualifierName UI="Q000528" MajorTopicYN="N">radiation effects</QualifierName>
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<MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName>
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<MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName>
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Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon.

Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon.

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