PoplarV1, Main, Exploration, bibRecord, 001363

Genome-wide identification, characterization, and expression profile of aquaporin gene family in flax (Linum usitatissimum).

Identifieur interne : 001363 ( Main/Exploration ); précédent : 001362; suivant : 001364

Genome-wide identification, characterization, and expression profile of aquaporin gene family in flax (Linum usitatissimum).

Auteurs : S M Shivaraj [Inde] ; Rupesh K. Deshmukh [Canada] ; Rhitu Rai [Inde] ; Richard Bélanger [Canada] ; Pawan K. Agrawal [Inde] ; Prasanta K. Dash [Inde]

Source :

Scientific reports [ 2045-2322 ] ; 2017.

RBID : pubmed:28447607

Descripteurs français

KwdFr :
- Alignement de séquences (MeSH), Analyse de profil d'expression de gènes (MeSH), Aquaporines (composition chimique), Aquaporines (génétique), Aquaporines (métabolisme), Domaines protéiques (MeSH), Exons (génétique), Famille multigénique (MeSH), Fractions subcellulaires (métabolisme), Gènes de plante (MeSH), Génome végétal (MeSH), Introns (génétique), Lin (effets des médicaments et des substances chimiques), Lin (génétique), Phylogenèse (MeSH), Protéines végétales (composition chimique), Protéines végétales (génétique), Protéines végétales (métabolisme), Régulation de l'expression des gènes végétaux (effets des médicaments et des substances chimiques), Silicium (pharmacologie), Structure tertiaire des protéines (MeSH), Séquence conservée (MeSH), Séquence d'acides aminés (MeSH), Évolution moléculaire (MeSH).
MESH :
- composition chimique : Aquaporines, Protéines végétales.
- effets des médicaments et des substances chimiques : Lin, Régulation de l'expression des gènes végétaux.
- génétique : Aquaporines, Exons, Introns, Lin, Protéines végétales.
- métabolisme : Aquaporines, Fractions subcellulaires, Protéines végétales.
- pharmacologie : Silicium.
- Alignement de séquences, Analyse de profil d'expression de gènes, Domaines protéiques, Famille multigénique, Gènes de plante, Génome végétal, Phylogenèse, Structure tertiaire des protéines, Séquence conservée, Séquence d'acides aminés, Évolution moléculaire.

English descriptors

KwdEn :
- Amino Acid Sequence (MeSH), Aquaporins (chemistry), Aquaporins (genetics), Aquaporins (metabolism), Conserved Sequence (MeSH), Evolution, Molecular (MeSH), Exons (genetics), Flax (drug effects), Flax (genetics), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (drug effects), Genes, Plant (MeSH), Genome, Plant (MeSH), Introns (genetics), Multigene Family (MeSH), Phylogeny (MeSH), Plant Proteins (chemistry), Plant Proteins (genetics), Plant Proteins (metabolism), Protein Domains (MeSH), Protein Structure, Tertiary (MeSH), Sequence Alignment (MeSH), Silicon (pharmacology), Subcellular Fractions (metabolism).
MESH :
- chemical , chemistry : Aquaporins, Plant Proteins.
- chemical , genetics : Aquaporins, Plant Proteins.
- chemical , metabolism : Aquaporins, Plant Proteins.
- drug effects : Flax, Gene Expression Regulation, Plant.
- genetics : Exons, Flax, Introns.
- metabolism : Subcellular Fractions.
- chemical , pharmacology : Silicon.
- Amino Acid Sequence, Conserved Sequence, Evolution, Molecular, Gene Expression Profiling, Genes, Plant, Genome, Plant, Multigene Family, Phylogeny, Protein Domains, Protein Structure, Tertiary, Sequence Alignment.

Abstract

Membrane intrinsic proteins (MIPs) form transmembrane channels and facilitate transport of myriad substrates across the cell membrane in many organisms. Majority of plant MIPs have water transporting ability and are commonly referred as aquaporins (AQPs). In the present study, we identified aquaporin coding genes in flax by genome-wide analysis, their structure, function and expression pattern by pan-genome exploration. Cross-genera phylogenetic analysis with known aquaporins from rice, arabidopsis, and poplar showed five subgroups of flax aquaporins representing 16 plasma membrane intrinsic proteins (PIPs), 17 tonoplast intrinsic proteins (TIPs), 13 NOD26-like intrinsic proteins (NIPs), 2 small basic intrinsic proteins (SIPs), and 3 uncharacterized intrinsic proteins (XIPs). Amongst aquaporins, PIPs contained hydrophilic aromatic arginine (ar/R) selective filter but TIP, NIP, SIP and XIP subfamilies mostly contained hydrophobic ar/R selective filter. Analysis of RNA-seq and microarray data revealed high expression of PIPs in multiple tissues, low expression of NIPs, and seed specific expression of TIP3 in flax. Exploration of aquaporin homologs in three closely related Linum species bienne, grandiflorum and leonii revealed presence of 49, 39 and 19 AQPs, respectively. The genome-wide identification of aquaporins, first in flax, provides insight to elucidate their physiological and developmental roles in flax.

DOI: 10.1038/srep46137
PubMed: 28447607
PubMed Central: PMC5406838

Affiliations:

Canada, Inde

Links toward previous steps (curation, corpus...)

to stream Main, to step Corpus: 001342
to stream Main, to step Curation: 001342

Le document en format XML

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<term>Aquaporins (chemistry)</term>
<term>Aquaporins (genetics)</term>
<term>Aquaporins (metabolism)</term>
<term>Conserved Sequence (MeSH)</term>
<term>Evolution, Molecular (MeSH)</term>
<term>Exons (genetics)</term>
<term>Flax (drug effects)</term>
<term>Flax (genetics)</term>
<term>Gene Expression Profiling (MeSH)</term>
<term>Gene Expression Regulation, Plant (drug effects)</term>
<term>Genes, Plant (MeSH)</term>
<term>Genome, Plant (MeSH)</term>
<term>Introns (genetics)</term>
<term>Multigene Family (MeSH)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Proteins (chemistry)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Protein Domains (MeSH)</term>
<term>Protein Structure, Tertiary (MeSH)</term>
<term>Sequence Alignment (MeSH)</term>
<term>Silicon (pharmacology)</term>
<term>Subcellular Fractions (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences (MeSH)</term>
<term>Analyse de profil d'expression de gènes (MeSH)</term>
<term>Aquaporines (composition chimique)</term>
<term>Aquaporines (génétique)</term>
<term>Aquaporines (métabolisme)</term>
<term>Domaines protéiques (MeSH)</term>
<term>Exons (génétique)</term>
<term>Famille multigénique (MeSH)</term>
<term>Fractions subcellulaires (métabolisme)</term>
<term>Gènes de plante (MeSH)</term>
<term>Génome végétal (MeSH)</term>
<term>Introns (génétique)</term>
<term>Lin (effets des médicaments et des substances chimiques)</term>
<term>Lin (génétique)</term>
<term>Phylogenèse (MeSH)</term>
<term>Protéines végétales (composition chimique)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Régulation de l'expression des gènes végétaux (effets des médicaments et des substances chimiques)</term>
<term>Silicium (pharmacologie)</term>
<term>Structure tertiaire des protéines (MeSH)</term>
<term>Séquence conservée (MeSH)</term>
<term>Séquence d'acides aminés (MeSH)</term>
<term>Évolution moléculaire (MeSH)</term>
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<term>Plant Proteins</term>
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<term>Plant Proteins</term>
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<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Flax</term>
<term>Gene Expression Regulation, Plant</term>
</keywords>
<keywords scheme="MESH" qualifier="effets des médicaments et des substances chimiques" xml:lang="fr"><term>Lin</term>
<term>Régulation de l'expression des gènes végétaux</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Exons</term>
<term>Flax</term>
<term>Introns</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Aquaporines</term>
<term>Exons</term>
<term>Introns</term>
<term>Lin</term>
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Subcellular Fractions</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Aquaporines</term>
<term>Fractions subcellulaires</term>
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Silicium</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Silicon</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term>
<term>Conserved Sequence</term>
<term>Evolution, Molecular</term>
<term>Gene Expression Profiling</term>
<term>Genes, Plant</term>
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<term>Phylogeny</term>
<term>Protein Domains</term>
<term>Protein Structure, Tertiary</term>
<term>Sequence Alignment</term>
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<term>Analyse de profil d'expression de gènes</term>
<term>Domaines protéiques</term>
<term>Famille multigénique</term>
<term>Gènes de plante</term>
<term>Génome végétal</term>
<term>Phylogenèse</term>
<term>Structure tertiaire des protéines</term>
<term>Séquence conservée</term>
<term>Séquence d'acides aminés</term>
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<front><div type="abstract" xml:lang="en">Membrane intrinsic proteins (MIPs) form transmembrane channels and facilitate transport of myriad substrates across the cell membrane in many organisms. Majority of plant MIPs have water transporting ability and are commonly referred as aquaporins (AQPs). In the present study, we identified aquaporin coding genes in flax by genome-wide analysis, their structure, function and expression pattern by pan-genome exploration. Cross-genera phylogenetic analysis with known aquaporins from rice, arabidopsis, and poplar showed five subgroups of flax aquaporins representing 16 plasma membrane intrinsic proteins (PIPs), 17 tonoplast intrinsic proteins (TIPs), 13 NOD26-like intrinsic proteins (NIPs), 2 small basic intrinsic proteins (SIPs), and 3 uncharacterized intrinsic proteins (XIPs). Amongst aquaporins, PIPs contained hydrophilic aromatic arginine (ar/R) selective filter but TIP, NIP, SIP and XIP subfamilies mostly contained hydrophobic ar/R selective filter. Analysis of RNA-seq and microarray data revealed high expression of PIPs in multiple tissues, low expression of NIPs, and seed specific expression of TIP3 in flax. Exploration of aquaporin homologs in three closely related Linum species bienne, grandiflorum and leonii revealed presence of 49, 39 and 19 AQPs, respectively. The genome-wide identification of aquaporins, first in flax, provides insight to elucidate their physiological and developmental roles in flax.</div>
</front>
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<DateCompleted><Year>2018</Year>
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<Abstract><AbstractText>Membrane intrinsic proteins (MIPs) form transmembrane channels and facilitate transport of myriad substrates across the cell membrane in many organisms. Majority of plant MIPs have water transporting ability and are commonly referred as aquaporins (AQPs). In the present study, we identified aquaporin coding genes in flax by genome-wide analysis, their structure, function and expression pattern by pan-genome exploration. Cross-genera phylogenetic analysis with known aquaporins from rice, arabidopsis, and poplar showed five subgroups of flax aquaporins representing 16 plasma membrane intrinsic proteins (PIPs), 17 tonoplast intrinsic proteins (TIPs), 13 NOD26-like intrinsic proteins (NIPs), 2 small basic intrinsic proteins (SIPs), and 3 uncharacterized intrinsic proteins (XIPs). Amongst aquaporins, PIPs contained hydrophilic aromatic arginine (ar/R) selective filter but TIP, NIP, SIP and XIP subfamilies mostly contained hydrophobic ar/R selective filter. Analysis of RNA-seq and microarray data revealed high expression of PIPs in multiple tissues, low expression of NIPs, and seed specific expression of TIP3 in flax. Exploration of aquaporin homologs in three closely related Linum species bienne, grandiflorum and leonii revealed presence of 49, 39 and 19 AQPs, respectively. The genome-wide identification of aquaporins, first in flax, provides insight to elucidate their physiological and developmental roles in flax.</AbstractText>
</Abstract>
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<ForeName>Rupesh K</ForeName>
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<AffiliationInfo><Affiliation>Departement de Phytologie, University Laval, Quebec, QC, Canada.</Affiliation>
</AffiliationInfo>
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<ForeName>Rhitu</ForeName>
<Initials>R</Initials>
<AffiliationInfo><Affiliation>ICAR-NRC on Plant Biotechnology, PUSA, New Delhi, India.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Bélanger</LastName>
<ForeName>Richard</ForeName>
<Initials>R</Initials>
<AffiliationInfo><Affiliation>Departement de Phytologie, University Laval, Quebec, QC, Canada.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Agrawal</LastName>
<ForeName>Pawan K</ForeName>
<Initials>PK</Initials>
<AffiliationInfo><Affiliation>National Agricultural Science Fund (NASF), PUSA, ICAR, New Delhi, India.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Dash</LastName>
<ForeName>Prasanta K</ForeName>
<Initials>PK</Initials>
<AffiliationInfo><Affiliation>ICAR-NRC on Plant Biotechnology, PUSA, New Delhi, India.</Affiliation>
</AffiliationInfo>
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<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
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<MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005091" MajorTopicYN="N">Exons</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
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<MeshHeading><DescriptorName UI="D019597" MajorTopicYN="N">Flax</DescriptorName>
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<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
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Genome-wide identification, characterization, and expression profile of aquaporin gene family in flax (Linum usitatissimum).

Genome-wide identification, characterization, and expression profile of aquaporin gene family in flax (Linum usitatissimum).

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