Elucidating the evolutionary history and expression patterns of nucleoside phosphorylase paralogs (vegetative storage proteins) in Populus and the plant kingdom.
Identifieur interne : 002706 ( Main/Exploration ); précédent : 002705; suivant : 002707Elucidating the evolutionary history and expression patterns of nucleoside phosphorylase paralogs (vegetative storage proteins) in Populus and the plant kingdom.
Auteurs : Emily A. Pettengill [États-Unis] ; James B. Pettengill ; Gary D. ColemanSource :
- BMC plant biology [ 1471-2229 ] ; 2013.
Descripteurs français
- KwdFr :
- Duplication de gène (MeSH), Famille multigénique (MeSH), Pentosyltransferases (génétique), Pentosyltransferases (métabolisme), Phylogenèse (MeSH), Plantes (classification), Plantes (composition chimique), Plantes (enzymologie), Plantes (génétique), Populus (classification), Populus (enzymologie), Populus (génétique), Protéines végétales (génétique), Protéines végétales (métabolisme), Régions promotrices (génétique) (MeSH), Régulation de l'expression des gènes codant pour des enzymes (MeSH), Régulation de l'expression des gènes végétaux (MeSH), Séquence d'acides aminés (MeSH), Évolution moléculaire (MeSH).
- MESH :
- composition chimique : Plantes, Populus.
- enzymologie : Plantes, Populus.
- génétique : Pentosyltransferases, Plantes, Populus, Protéines végétales.
- métabolisme : Pentosyltransferases, Protéines végétales.
- Duplication de gène, Famille multigénique, Phylogenèse, Régions promotrices (génétique), Régulation de l'expression des gènes codant pour des enzymes, Régulation de l'expression des gènes végétaux, Séquence d'acides aminés, Évolution moléculaire.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Evolution, Molecular (MeSH), Gene Duplication (MeSH), Gene Expression Regulation, Enzymologic (MeSH), Gene Expression Regulation, Plant (MeSH), Multigene Family (MeSH), Pentosyltransferases (genetics), Pentosyltransferases (metabolism), Phylogeny (MeSH), Plant Proteins (genetics), Plant Proteins (metabolism), Plants (chemistry), Plants (classification), Plants (enzymology), Plants (genetics), Populus (classification), Populus (enzymology), Populus (genetics), Promoter Regions, Genetic (MeSH).
- MESH :
- chemical , genetics : Pentosyltransferases, Plant Proteins.
- chemical , metabolism : Pentosyltransferases, Plant Proteins.
- chemistry : Plants.
- classification : Plants, Populus.
- enzymology : Plants, Populus.
- genetics : Plants, Populus.
- Amino Acid Sequence, Evolution, Molecular, Gene Duplication, Gene Expression Regulation, Enzymologic, Gene Expression Regulation, Plant, Multigene Family, Phylogeny, Promoter Regions, Genetic.
Abstract
BACKGROUND
Nucleoside phosphorylases (NPs) have been extensively investigated in human and bacterial systems for their role in metabolic nucleotide salvaging and links to oncogenesis. In plants, NP-like proteins have not been comprehensively studied, likely because there is no evidence of a metabolic function in nucleoside salvage. However, in the forest trees genus Populus a family of NP-like proteins function as an important ecophysiological adaptation for inter- and intra-seasonal nitrogen storage and cycling.
RESULTS
We conducted phylogenetic analyses to determine the distribution and evolution of NP-like proteins in plants. These analyses revealed two major clusters of NP-like proteins in plants. Group I proteins were encoded by genes across a wide range of plant taxa while proteins encoded by Group II genes were dominated by species belonging to the order Malpighiales and included the Populus Bark Storage Protein (BSP) and WIN4-like proteins. Additionally, we evaluated the NP-like genes in Populus by examining the transcript abundance of the 13 NP-like genes found in the Populus genome in various tissues of plants exposed to long-day (LD) and short-day (SD) photoperiods. We found that all 13 of the Populus NP-like genes belonging to either Group I or II are expressed in various tissues in both LD and SD conditions. Tests of natural selection and expression evolution analysis of the Populus genes suggests that divergence in gene expression may have occurred recently during the evolution of Populus, which supports the adaptive maintenance models. Lastly, in silico analysis of cis-regulatory elements in the promoters of the 13 NP-like genes in Populus revealed common regulatory elements known to be involved in light regulation, stress/pathogenesis and phytohormone responses.
CONCLUSION
In Populus, the evolution of the NP-like protein and gene family has been shaped by duplication events and natural selection. Expression data suggest that previously uncharacterized NP-like proteins may function in nutrient sensing and/or signaling. These proteins are members of Group I NP-like proteins, which are widely distributed in many plant taxa. We conclude that NP-like proteins may function in plants, although this function is undefined.
DOI: 10.1186/1471-2229-13-118
PubMed: 23957885
PubMed Central: PMC3751785
Affiliations:
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Pettengill</name><affiliation wicri:level="4"><nlm:affiliation>Department of Plant Science and Landscape Architecture, University of Maryland, Plant Science Building, College Park, Maryland 20742, USA. emilyannpettengill@gmail.com</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Science and Landscape Architecture, University of Maryland, Plant Science Building, College Park, Maryland 20742</wicri:regionArea><orgName type="university">Université du Maryland</orgName><placeName><settlement type="city">College Park (Maryland)</settlement><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Pettengill, James B" sort="Pettengill, James B" uniqKey="Pettengill J" first="James B" last="Pettengill">James B. Pettengill</name></author><author><name sortKey="Coleman, Gary D" sort="Coleman, Gary D" uniqKey="Coleman G" first="Gary D" last="Coleman">Gary D. 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In plants, NP-like proteins have not been comprehensively studied, likely because there is no evidence of a metabolic function in nucleoside salvage. However, in the forest trees genus Populus a family of NP-like proteins function as an important ecophysiological adaptation for inter- and intra-seasonal nitrogen storage and cycling.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We conducted phylogenetic analyses to determine the distribution and evolution of NP-like proteins in plants. These analyses revealed two major clusters of NP-like proteins in plants. Group I proteins were encoded by genes across a wide range of plant taxa while proteins encoded by Group II genes were dominated by species belonging to the order Malpighiales and included the Populus Bark Storage Protein (BSP) and WIN4-like proteins. Additionally, we evaluated the NP-like genes in Populus by examining the transcript abundance of the 13 NP-like genes found in the Populus genome in various tissues of plants exposed to long-day (LD) and short-day (SD) photoperiods. We found that all 13 of the Populus NP-like genes belonging to either Group I or II are expressed in various tissues in both LD and SD conditions. Tests of natural selection and expression evolution analysis of the Populus genes suggests that divergence in gene expression may have occurred recently during the evolution of Populus, which supports the adaptive maintenance models. Lastly, in silico analysis of cis-regulatory elements in the promoters of the 13 NP-like genes in Populus revealed common regulatory elements known to be involved in light regulation, stress/pathogenesis and phytohormone responses.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>In Populus, the evolution of the NP-like protein and gene family has been shaped by duplication events and natural selection. Expression data suggest that previously uncharacterized NP-like proteins may function in nutrient sensing and/or signaling. These proteins are members of Group I NP-like proteins, which are widely distributed in many plant taxa. We conclude that NP-like proteins may function in plants, although this function is undefined.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23957885</PMID><DateCompleted><Year>2013</Year><Month>10</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><PubDate><Year>2013</Year><Month>Aug</Month><Day>19</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>Elucidating the evolutionary history and expression patterns of nucleoside phosphorylase paralogs (vegetative storage proteins) in Populus and the plant kingdom.</ArticleTitle><Pagination><MedlinePgn>118</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2229-13-118</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Nucleoside phosphorylases (NPs) have been extensively investigated in human and bacterial systems for their role in metabolic nucleotide salvaging and links to oncogenesis. In plants, NP-like proteins have not been comprehensively studied, likely because there is no evidence of a metabolic function in nucleoside salvage. However, in the forest trees genus Populus a family of NP-like proteins function as an important ecophysiological adaptation for inter- and intra-seasonal nitrogen storage and cycling.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We conducted phylogenetic analyses to determine the distribution and evolution of NP-like proteins in plants. These analyses revealed two major clusters of NP-like proteins in plants. Group I proteins were encoded by genes across a wide range of plant taxa while proteins encoded by Group II genes were dominated by species belonging to the order Malpighiales and included the Populus Bark Storage Protein (BSP) and WIN4-like proteins. Additionally, we evaluated the NP-like genes in Populus by examining the transcript abundance of the 13 NP-like genes found in the Populus genome in various tissues of plants exposed to long-day (LD) and short-day (SD) photoperiods. We found that all 13 of the Populus NP-like genes belonging to either Group I or II are expressed in various tissues in both LD and SD conditions. Tests of natural selection and expression evolution analysis of the Populus genes suggests that divergence in gene expression may have occurred recently during the evolution of Populus, which supports the adaptive maintenance models. Lastly, in silico analysis of cis-regulatory elements in the promoters of the 13 NP-like genes in Populus revealed common regulatory elements known to be involved in light regulation, stress/pathogenesis and phytohormone responses.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">In Populus, the evolution of the NP-like protein and gene family has been shaped by duplication events and natural selection. Expression data suggest that previously uncharacterized NP-like proteins may function in nutrient sensing and/or signaling. These proteins are members of Group I NP-like proteins, which are widely distributed in many plant taxa. We conclude that NP-like proteins may function in plants, although this function is undefined.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pettengill</LastName><ForeName>Emily A</ForeName><Initials>EA</Initials><AffiliationInfo><Affiliation>Department of Plant Science and Landscape Architecture, University of Maryland, Plant Science Building, College Park, Maryland 20742, USA. emilyannpettengill@gmail.com</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pettengill</LastName><ForeName>James B</ForeName><Initials>JB</Initials></Author><Author ValidYN="Y"><LastName>Coleman</LastName><ForeName>Gary D</ForeName><Initials>GD</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>08</Month><Day>19</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 2.4.2.-</RegistryNumber><NameOfSubstance UI="D010430">Pentosyltransferases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.4.2.-</RegistryNumber><NameOfSubstance UI="C067995">nucleoside phosphorylase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020440" MajorTopicYN="N">Gene Duplication</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015971" MajorTopicYN="Y">Gene Expression Regulation, Enzymologic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005810" MajorTopicYN="N">Multigene Family</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010430" MajorTopicYN="N">Pentosyltransferases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></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="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011401" MajorTopicYN="N">Promoter Regions, Genetic</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate 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Coleman</name><name sortKey="Pettengill, James B" sort="Pettengill, James B" uniqKey="Pettengill J" first="James B" last="Pettengill">James B. Pettengill</name></noCountry><country name="États-Unis"><region name="Maryland"><name sortKey="Pettengill, Emily A" sort="Pettengill, Emily A" uniqKey="Pettengill E" first="Emily A" last="Pettengill">Emily A. Pettengill</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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