Molecular evolution of trehalose-6-phosphate synthase (TPS) gene family in Populus, Arabidopsis and rice.
Identifieur interne : 002986 ( Main/Exploration ); précédent : 002985; suivant : 002987Molecular evolution of trehalose-6-phosphate synthase (TPS) gene family in Populus, Arabidopsis and rice.
Auteurs : Hai-Ling Yang [République populaire de Chine] ; Yan-Jing Liu ; Cai-Ling Wang ; Qing-Yin ZengSource :
- PloS one [ 1932-6203 ] ; 2012.
Descripteurs français
- KwdFr :
- Arabidopsis (enzymologie), Biologie informatique (méthodes), Cristallographie aux rayons X (méthodes), Glucosyltransferases (génétique), Glucosyltransferases (physiologie), Introns (MeSH), Modèles génétiques (MeSH), Oryza (enzymologie), Phylogenèse (MeSH), Populus (enzymologie), RT-PCR (méthodes), Régulation de l'expression des gènes végétaux (MeSH), Spécificité d'espèce (MeSH), Structure tertiaire des protéines (MeSH), Uridine diphosphate glucose (métabolisme), Évolution moléculaire (MeSH).
- MESH :
- enzymologie : Arabidopsis, Oryza, Populus.
- génétique : Glucosyltransferases.
- métabolisme : Uridine diphosphate glucose.
- méthodes : Biologie informatique, Cristallographie aux rayons X, RT-PCR.
- physiologie : Glucosyltransferases.
- Introns, Modèles génétiques, Phylogenèse, Régulation de l'expression des gènes végétaux, Spécificité d'espèce, Structure tertiaire des protéines, Évolution moléculaire.
English descriptors
- KwdEn :
- Arabidopsis (enzymology), Computational Biology (methods), Crystallography, X-Ray (methods), Evolution, Molecular (MeSH), Gene Expression Regulation, Plant (MeSH), Glucosyltransferases (genetics), Glucosyltransferases (physiology), Introns (MeSH), Models, Genetic (MeSH), Oryza (enzymology), Phylogeny (MeSH), Populus (enzymology), Protein Structure, Tertiary (MeSH), Reverse Transcriptase Polymerase Chain Reaction (methods), Species Specificity (MeSH), Uridine Diphosphate Glucose (metabolism).
- MESH :
- chemical , genetics : Glucosyltransferases.
- enzymology : Arabidopsis, Oryza, Populus.
- chemical , metabolism : Uridine Diphosphate Glucose.
- methods : Computational Biology, Crystallography, X-Ray, Reverse Transcriptase Polymerase Chain Reaction.
- chemical , physiology : Glucosyltransferases.
- Evolution, Molecular, Gene Expression Regulation, Plant, Introns, Models, Genetic, Phylogeny, Protein Structure, Tertiary, Species Specificity.
Abstract
Trehalose-6-phosphate synthase (TPS) plays important roles in trehalose metabolism and signaling. Plant TPS proteins contain both a TPS and a trehalose-6-phosphate phosphatase (TPP) domain, which are coded by a multi-gene family. The plant TPS gene family has been divided into class I and class II. A previous study showed that the Populus, Arabidopsis, and rice genomes have seven class I and 27 class II TPS genes. In this study, we found that all class I TPS genes had 16 introns within the protein-coding region, whereas class II TPS genes had two introns. A significant sequence difference between the two classes of TPS proteins was observed by pairwise sequence comparisons of the 34 TPS proteins. A phylogenetic analysis revealed that at least seven TPS genes were present in the monocot-dicot common ancestor. Segmental duplications contributed significantly to the expansion of this gene family. At least five and three TPS genes were created by segmental duplication events in the Populus and rice genomes, respectively. Both the TPS and TPP domains of 34 TPS genes have evolved under purifying selection, but the selective constraint on the TPP domain was more relaxed than that on the TPS domain. Among 34 TPS genes from Populus, Arabidopsis, and rice, four class I TPS genes (AtTPS1, OsTPS1, PtTPS1, and PtTPS2) were under stronger purifying selection, whereas three Arabidopsis class I TPS genes (AtTPS2, 3, and 4) apparently evolved under relaxed selective constraint. Additionally, a reverse transcription polymerase chain reaction analysis showed the expression divergence of the TPS gene family in Populus, Arabidopsis, and rice under normal growth conditions and in response to stressors. Our findings provide new insights into the mechanisms of gene family expansion and functional evolution.
DOI: 10.1371/journal.pone.0042438
PubMed: 22905132
PubMed Central: PMC3414516
Affiliations:
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Plant TPS proteins contain both a TPS and a trehalose-6-phosphate phosphatase (TPP) domain, which are coded by a multi-gene family. The plant TPS gene family has been divided into class I and class II. A previous study showed that the Populus, Arabidopsis, and rice genomes have seven class I and 27 class II TPS genes. In this study, we found that all class I TPS genes had 16 introns within the protein-coding region, whereas class II TPS genes had two introns. A significant sequence difference between the two classes of TPS proteins was observed by pairwise sequence comparisons of the 34 TPS proteins. A phylogenetic analysis revealed that at least seven TPS genes were present in the monocot-dicot common ancestor. Segmental duplications contributed significantly to the expansion of this gene family. At least five and three TPS genes were created by segmental duplication events in the Populus and rice genomes, respectively. Both the TPS and TPP domains of 34 TPS genes have evolved under purifying selection, but the selective constraint on the TPP domain was more relaxed than that on the TPS domain. Among 34 TPS genes from Populus, Arabidopsis, and rice, four class I TPS genes (AtTPS1, OsTPS1, PtTPS1, and PtTPS2) were under stronger purifying selection, whereas three Arabidopsis class I TPS genes (AtTPS2, 3, and 4) apparently evolved under relaxed selective constraint. Additionally, a reverse transcription polymerase chain reaction analysis showed the expression divergence of the TPS gene family in Populus, Arabidopsis, and rice under normal growth conditions and in response to stressors. Our findings provide new insights into the mechanisms of gene family expansion and functional evolution.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22905132</PMID><DateCompleted><Year>2013</Year><Month>02</Month><Day>11</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><Issue>8</Issue><PubDate><Year>2012</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Molecular evolution of trehalose-6-phosphate synthase (TPS) gene family in Populus, Arabidopsis and rice.</ArticleTitle><Pagination><MedlinePgn>e42438</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0042438</ELocationID><Abstract><AbstractText>Trehalose-6-phosphate synthase (TPS) plays important roles in trehalose metabolism and signaling. Plant TPS proteins contain both a TPS and a trehalose-6-phosphate phosphatase (TPP) domain, which are coded by a multi-gene family. The plant TPS gene family has been divided into class I and class II. A previous study showed that the Populus, Arabidopsis, and rice genomes have seven class I and 27 class II TPS genes. In this study, we found that all class I TPS genes had 16 introns within the protein-coding region, whereas class II TPS genes had two introns. A significant sequence difference between the two classes of TPS proteins was observed by pairwise sequence comparisons of the 34 TPS proteins. A phylogenetic analysis revealed that at least seven TPS genes were present in the monocot-dicot common ancestor. Segmental duplications contributed significantly to the expansion of this gene family. At least five and three TPS genes were created by segmental duplication events in the Populus and rice genomes, respectively. Both the TPS and TPP domains of 34 TPS genes have evolved under purifying selection, but the selective constraint on the TPP domain was more relaxed than that on the TPS domain. Among 34 TPS genes from Populus, Arabidopsis, and rice, four class I TPS genes (AtTPS1, OsTPS1, PtTPS1, and PtTPS2) were under stronger purifying selection, whereas three Arabidopsis class I TPS genes (AtTPS2, 3, and 4) apparently evolved under relaxed selective constraint. Additionally, a reverse transcription polymerase chain reaction analysis showed the expression divergence of the TPS gene family in Populus, Arabidopsis, and rice under normal growth conditions and in response to stressors. 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