PoplarV1, Main, Exploration, bibRecord, 001364

Genome-wide identification and expression profiling of EIL gene family in woody plant representative poplar (Populus trichocarpa).

Identifieur interne : 001364 ( Main/Exploration ); précédent : 001363; suivant : 001365

Genome-wide identification and expression profiling of EIL gene family in woody plant representative poplar (Populus trichocarpa).

Auteurs : Ertugrul Filiz [Turquie] ; Recep Vatansever [Turquie] ; Ibrahim Ilker Ozyigit [Turquie] ; Mehmet Emin Uras [Turquie] ; Ugur Sen [Turquie] ; Naser A. Anjum [Portugal] ; Eduarda Pereira [Portugal]

Source :

Archives of biochemistry and biophysics [ 1096-0384 ] ; 2017.

RBID : pubmed:28625764

Descripteurs français

English descriptors

KwdEn :
- Amino Acid Sequence (MeSH), Conserved Sequence (MeSH), Ethylenes (metabolism), Gene Duplication (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Regulatory Networks (MeSH), Multigene Family (MeSH), Phylogeny (MeSH), Plant Proteins (chemistry), Plant Proteins (genetics), Plant Proteins (metabolism), Populus (chemistry), Populus (genetics), Populus (metabolism), Sequence Alignment (MeSH), Signal Transduction (MeSH), Transcription Factors (chemistry), Transcription Factors (genetics), Transcription Factors (metabolism), Transcriptome (MeSH).
MESH :
- chemical , chemistry : Plant Proteins, Transcription Factors.
- chemical , genetics : Plant Proteins, Transcription Factors.
- chemical , metabolism : Ethylenes, Plant Proteins, Transcription Factors.
- chemistry : Populus.
- genetics : Populus.
- metabolism : Populus.
- Amino Acid Sequence, Conserved Sequence, Gene Duplication, Gene Expression Regulation, Plant, Gene Regulatory Networks, Multigene Family, Phylogeny, Sequence Alignment, Signal Transduction, Transcriptome.

Abstract

This study aimed to improve current understanding on ethylene-insensitive 3-like (EIL) members, least explored in woody plants such as poplar (Populus trichocarpa Torr. & Grey). Herein, seven putative EIL members were identified in P. trichocarpa genome and were roughly annotated either as EIN3-like sequence associated with ethylene pathway or EIL3-like sequences related with sulfur (S)-pathway. Motif-distribution pattern of proteins also corroborated this annotation. They were distributed on six chromosomes (chr1, 3, 4 and 8-10), and were revealed to encode a protein of 509-662 residues with nuclear localization. The presence of ethylene insensitive 3 (EIN3; PF04873) domain (covering first 80-280 residues from N-terminus) was confirmed by Hidden Markov Model-based search. The first half of EIL proteins (∼80-280 residues including EIN3 domain) was substantially conserved. The second half (∼300-600 residues) was considerably diverged. Additionally, first half of proteins harbored acidic, proline-rich and glutamine-rich sites, and supported the essentiality of these regions in the transcriptional-activation and protein-function. Moreover, identified six segmental and one-tandem duplications demonstrated the negative or purifying selective nature of mutations. Furthermore, expression profile analysis indicated the possibility of a crosstalk between EIN3- and EIL3-like genes, and co-expression networks implicated their interactions with very diverse panels of biological molecules.

DOI: 10.1016/j.abb.2017.06.012
PubMed: 28625764

Affiliations:

Portugal, Turquie

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

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Le document en format XML

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<term>Conserved Sequence (MeSH)</term>
<term>Ethylenes (metabolism)</term>
<term>Gene Duplication (MeSH)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Gene Regulatory Networks (MeSH)</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>Populus (chemistry)</term>
<term>Populus (genetics)</term>
<term>Populus (metabolism)</term>
<term>Sequence Alignment (MeSH)</term>
<term>Signal Transduction (MeSH)</term>
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<term>Duplication de gène (MeSH)</term>
<term>Facteurs de transcription (composition chimique)</term>
<term>Facteurs de transcription (génétique)</term>
<term>Facteurs de transcription (métabolisme)</term>
<term>Famille multigénique (MeSH)</term>
<term>Phylogenèse (MeSH)</term>
<term>Populus (composition chimique)</term>
<term>Populus (génétique)</term>
<term>Populus (métabolisme)</term>
<term>Protéines végétales (composition chimique)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (métabolisme)</term>
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<term>Réseaux de régulation génique (MeSH)</term>
<term>Séquence conservée (MeSH)</term>
<term>Séquence d'acides aminés (MeSH)</term>
<term>Transcriptome (MeSH)</term>
<term>Transduction du signal (MeSH)</term>
<term>Éthylènes (métabolisme)</term>
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<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Plant Proteins</term>
<term>Transcription Factors</term>
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<term>Protéines végétales</term>
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<term>Conserved Sequence</term>
<term>Gene Duplication</term>
<term>Gene Expression Regulation, Plant</term>
<term>Gene Regulatory Networks</term>
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<term>Phylogeny</term>
<term>Sequence Alignment</term>
<term>Signal Transduction</term>
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<term>Réseaux de régulation génique</term>
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<front><div type="abstract" xml:lang="en">This study aimed to improve current understanding on ethylene-insensitive 3-like (EIL) members, least explored in woody plants such as poplar (Populus trichocarpa Torr. & Grey). Herein, seven putative EIL members were identified in P. trichocarpa genome and were roughly annotated either as EIN3-like sequence associated with ethylene pathway or EIL3-like sequences related with sulfur (S)-pathway. Motif-distribution pattern of proteins also corroborated this annotation. They were distributed on six chromosomes (chr1, 3, 4 and 8-10), and were revealed to encode a protein of 509-662 residues with nuclear localization. The presence of ethylene insensitive 3 (EIN3; PF04873) domain (covering first 80-280 residues from N-terminus) was confirmed by Hidden Markov Model-based search. The first half of EIL proteins (∼80-280 residues including EIN3 domain) was substantially conserved. The second half (∼300-600 residues) was considerably diverged. Additionally, first half of proteins harbored acidic, proline-rich and glutamine-rich sites, and supported the essentiality of these regions in the transcriptional-activation and protein-function. Moreover, identified six segmental and one-tandem duplications demonstrated the negative or purifying selective nature of mutations. Furthermore, expression profile analysis indicated the possibility of a crosstalk between EIN3- and EIL3-like genes, and co-expression networks implicated their interactions with very diverse panels of biological molecules.</div>
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<Abstract><AbstractText>This study aimed to improve current understanding on ethylene-insensitive 3-like (EIL) members, least explored in woody plants such as poplar (Populus trichocarpa Torr. & Grey). Herein, seven putative EIL members were identified in P. trichocarpa genome and were roughly annotated either as EIN3-like sequence associated with ethylene pathway or EIL3-like sequences related with sulfur (S)-pathway. Motif-distribution pattern of proteins also corroborated this annotation. They were distributed on six chromosomes (chr1, 3, 4 and 8-10), and were revealed to encode a protein of 509-662 residues with nuclear localization. The presence of ethylene insensitive 3 (EIN3; PF04873) domain (covering first 80-280 residues from N-terminus) was confirmed by Hidden Markov Model-based search. The first half of EIL proteins (∼80-280 residues including EIN3 domain) was substantially conserved. The second half (∼300-600 residues) was considerably diverged. Additionally, first half of proteins harbored acidic, proline-rich and glutamine-rich sites, and supported the essentiality of these regions in the transcriptional-activation and protein-function. Moreover, identified six segmental and one-tandem duplications demonstrated the negative or purifying selective nature of mutations. Furthermore, expression profile analysis indicated the possibility of a crosstalk between EIN3- and EIL3-like genes, and co-expression networks implicated their interactions with very diverse panels of biological molecules.</AbstractText>
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<AffiliationInfo><Affiliation>Marmara University, Faculty of Science and Arts, Department of Biology, 34722, Goztepe, Istanbul, Turkey.</Affiliation>
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<ForeName>Ibrahim Ilker</ForeName>
<Initials>II</Initials>
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<ForeName>Ugur</ForeName>
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<ForeName>Naser A</ForeName>
<Initials>NA</Initials>
<AffiliationInfo><Affiliation>CESAM-Centre for Environmental & Marine Studies and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.</Affiliation>
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<ForeName>Eduarda</ForeName>
<Initials>E</Initials>
<AffiliationInfo><Affiliation>CESAM-Centre for Environmental & Marine Studies and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.</Affiliation>
</AffiliationInfo>
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<Month>06</Month>
<Day>15</Day>
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<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D005030">Ethylenes</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance>
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<NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance>
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<Chemical><RegistryNumber>91GW059KN7</RegistryNumber>
<NameOfSubstance UI="C036216">ethylene</NameOfSubstance>
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<MeshHeading><DescriptorName UI="D020440" MajorTopicYN="N">Gene Duplication</DescriptorName>
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<MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName>
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<MeshHeading><DescriptorName UI="D053263" MajorTopicYN="N">Gene Regulatory Networks</DescriptorName>
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<MeshHeading><DescriptorName UI="D005810" MajorTopicYN="N">Multigene Family</DescriptorName>
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<MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName>
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<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
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<MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
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<MeshHeading><DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName>
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<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Ethylene</Keyword>
<Keyword MajorTopicYN="Y">Phytohormone</Keyword>
<Keyword MajorTopicYN="Y">Poplar</Keyword>
<Keyword MajorTopicYN="Y">SLIM1</Keyword>
<Keyword MajorTopicYN="Y">Sulfur</Keyword>
<Keyword MajorTopicYN="Y">Transcription factor</Keyword>
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<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year>
<Month>04</Month>
<Day>22</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised"><Year>2017</Year>
<Month>06</Month>
<Day>12</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2017</Year>
<Month>06</Month>
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<ArticleId IdType="doi">10.1016/j.abb.2017.06.012</ArticleId>
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<affiliations><list><country><li>Portugal</li>
<li>Turquie</li>
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<tree><country name="Turquie"><noRegion><name sortKey="Filiz, Ertugrul" sort="Filiz, Ertugrul" uniqKey="Filiz E" first="Ertugrul" last="Filiz">Ertugrul Filiz</name>
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<country name="Portugal"><noRegion><name sortKey="Anjum, Naser A" sort="Anjum, Naser A" uniqKey="Anjum N" first="Naser A" last="Anjum">Naser A. Anjum</name>
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   |texte=   Genome-wide identification and expression profiling of EIL gene family in woody plant representative poplar (Populus trichocarpa).
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Genome-wide identification and expression profiling of EIL gene family in woody plant representative poplar (Populus trichocarpa).

Genome-wide identification and expression profiling of EIL gene family in woody plant representative poplar (Populus trichocarpa).

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