wDBTF: an integrated database resource for studying wheat transcription factor families

<p>Abstract</p> <p>Background</p> <p>Transcription factors (TFs) regulate gene expression by interacting with promoters of their target genes and are classified into families based on their DNA-binding domains. Genes coding for TFs have been identified in the sequences of model plant genomes. The rice (<it>Oryza sativa </it>spp. <it>japonica</it>) genome contains 2,384 TF gene models, which represent the mRNA transcript of a locus, classed into 63 families.</p> <p>Results</p> <p>We have created an extensive list of wheat (<it>Triticum aestivum </it>L) TF sequences based on sequence homology with rice TFs identified and classified in the Database of Rice Transcription Factors (DRTF). We have identified 7,112 wheat sequences (contigs and singletons) from a dataset of 1,033,960 expressed sequence tag and mRNA (ET) sequences available. This number is about three times the number of TFs in rice so proportionally is very similar if allowance is made for the hexaploidy of wheat. Of these sequences 3,820 encode gene products with a DNA-binding domain and thus were confirmed as potential regulators. These 3,820 sequences were classified into 40 families and 84 subfamilies and some members defined orphan families. The results were compiled in the Database of Wheat Transcription Factor (wDBTF), an inventory available on the web <url>http://wwwappli.nantes.inra.fr:8180/wDBFT/</url>. For each accession, a link to its library source and its Affymetrix identification number is provided. The positions of Pfam (protein family database) motifs were given when known.</p> <p>Conclusions</p> <p>wDBTF collates 3,820 wheat TF sequences validated by the presence of a DNA-binding domain out of 7,112 potential TF sequences identified from publicly available gene expression data. We also incorporated <it>in silico </it>expression data on these TFs into the database. Thus this database provides a major resource for systematic studies of TF families and their expression in wheat as illustrated here in a study of DOF family members expressed during seed development.</p

Etude biochimique et génétique de la diversité des protéines de réserve du triticale hexaploïde, de leur influence sur les caractéristiques technologiques et recherche de facteurs impliqués dans la dureté du grain par une analyse protéomique des protéines amphiphiles du blé tendre

CLERMONT FD-BCIU Sci.et Tech. (630142101) / SudocSudocFranceF

Sur la diversité des blés tendres cultivés en France

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Proteomic analysis of endosperm and peripheral layers during kernel development of wheat (Triticum aestivum L.) and a preliminary approach of data integration with transcriptome

Le blé est la seconde céréale la plus produite dans le monde. Il constitue une importante source de denrées alimentaires et de beaucoup d autres usages industriels. La compréhension des mécanismes impliqués dans le développement du grain de blé est fondamentale pour développer des blés à valeur ajoutée. La physiologie du grain de blé et les mécanismes moléculaires impliqués dans son développement nécessitent d être mieux connus et ces connaissances pourront être très utiles pour l amélioration du blé mais aussi des autres céréales. L approche protéomique a été aussi utilisée dans ce contexte mais aucun travail n avait jusqu ici été réalisé sur la totalité des phases de développement des tissus et sur des intervalles de temps très courts. La caractérisation des changements d expressions protéiques dans les couches périphériques du grain et de l albumen est présentée dans cette étude. Nous avons utilisé les grains de Triticum aestivum de la variété Récital, cultivés à l INRA de Clermont-Ferrand. Les grains ont été prélevés tous les 50C jour (Cj) depuis la fécondation jusqu à la maturité sur 15 stades de développement pour les couches périphériques et sur 21 stades pour l albumen amylacé. Pour chaque échantillon, les couches périphériques des grains ont été disséquées et les protéines totales extraites. L analyse des protéines en électrophorèse bidimensionnelle puis par spectrométrie de masse MALDI-TOF a permis d identifier via l interrogation des bases de données, 207 protéines différentiellement exprimées sur 15 stades de développement (0Cj-700Cj). Ces protéines ont ensuite été classées en 16 classes fonctionnelles. L analyse en cluster a révélé 5 profils d expression au cours du temps. Parallèlement, l albumen amylacé a été isolé des grains et les protéines métaboliques de ce tissu extraites. Après électrophorèse bidimensionnelle des protéines, 487 protéines variant significativement dans l albumen sur l ensemble des stades de développement (0Cj-1006Cj) ont été identifiées par utilisation de la LC-MS. Les protéines ont été réparties sur neuf profils d expression et 17 fonctions biochimiques. Le protéome des couches périphériques a ensuite été comparé au protéome de l albumen dans le but de comprendre si l évolution des processus biochimiques diffère dans chacun de ces tissus. Au final, nous avons optimisé l intégration des données protéomiques avec celles du transcriptome (en se focalisant sur les protéines du métabolisme carboné). Seulement 32% des profils d expression protéome/transcriptome montrent une corrélation significative au cours du développement (152Cj-700Cj). Les profils d expression des enzymes ont été comparés sur les deux niveaux. Ils devraient permettre de distinguer les processus régulés au niveau du transcriptome de ceux régulés au niveau du protéome. L ensemble de ces données pourra être compilé dans une base de données propre de la variété Récital et utilisé comme référence dans l étude des maladies et des stress abiotiques des tissus du grain de blé en développement.Wheat is the second most produced cereal in the world, important for food, feed and many industrial uses. Understanding of the mechanisms involved in grain development is fundamental for developing high quality wheat. In particular, detailed knowledge of the wheat grain physiology and molecular mechanisms involved in its development would help in breeding not only of wheat but also many other cereals. A proteomic approach has been used in this context but, up to now, there had been no work on developing tissues at very short temporal distances. This thesis presents, firstly, a proteomic study to characterize protein expression changes in peripheral layers and in starchy endosperm of wheat, during kernel development. We used grains of Triticum aestivum cv Récital, cultivated at INRA, Clermont-Ferrand. Grains were harvested at each 50Cd from fertilization to maturity at fifteen stages for peripheral layers and at twenty-one stages for starchy endosperm. After grain dissection, protein extraction and 2DE- MALDI-TOF MS and data mining, we identified 207 differentially expressed proteins at fifteen stages (0Cd-700Cd) of peripheral layers during kernel development. These proteins were then classed in sixteen different functional classes. HCA revealed five different expression profiles during development. Similarly after obtaining starchy endosperm from dissected grains, we performed protein extraction specific to metabolic proteins. After 2DE, 487 proteins were identified from fertilization to grain maturity (0Cd-1006Cd), using LC-MS and data mining. Proteins were grouped in nine different expression profiles and were classed in seventeen biochemical functions. We have constructed proteome maps of these two important grain tissues during kernel development. Further, the comparison of peripheral layers and starchy endosperm proteomic data was made, with an objective to understand whether the changes in different biochemical processes differ between these tissues.Finally, we performed an integration of our proteomic data (focusing our approach on proteins involved in carbohydrate metabolism) with that of transcriptomics. Only 32% of proteome/transcriptome expression profiles showed a significant correlation during development (from 152Cd-700Cd). Comparison of enzyme expression profiles with those of proteome and transcriptome would help to distinguish the processes regulated at transcriptome level and those controlled at the proteome level. This comprehensive grain development data could further help in construction of a Récital databank, which may be used as reference for studies of diseased and stressed grain tissues during development.CLERMONT FD-Bib.électronique (631139902) / SudocSudocFranceF

Les sous-unités gluténines de haut poids moléculaire des blés tendres et des blés durs cultivés en France

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Molecular Weight Distribution of Polymeric Proteins in Wheat Grains: The Rheologically Active Polymers

International audienceWe characterized the molecular weight distribution of polymeric proteins (PP) of bread wheat grains using asymmetric flow field flow fractionation (A4F). The experiment, involving six environmental conditions and 130 cultivars, offered the opportunity to approach the phenotypic values of the polymer characteristics and their contribution of the rheological properties of flours and/or doughs. The contents of high-molecular-weight polymers (M W > 2 × 10 6 g•mol −1) that can be considered as "rheologically active polymers" (RAPP) for their major contribution to dough baking strength and mixing tolerance were mainly controlled by environmental factors. Under the influence of the growing conditions, at the cellular level, the redox status of non-protein free thiol, such as glutathione, is modified and leads to the formation of polymeric protein-bound glutathione conjugates (PPSSG). The accumulation of these conjugates reduces the formation of the RAPP by limiting the intermolecular interactions between PP in the grain during desiccation. This phenomenon is, therefore, potentially responsible for decreases in the technological properties of the wheat genotypes concerned. These first results invite us to continue our investigations to fully confirm this phenomenon, with emphasis on the behavior of wheat genotypes under various growing conditions

Proteomics analysis : an efficient approach for investigating the genetic and environmental bases of wheat quality

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Wheat proteomics in the healthgrain project

The project HEALTHGRAIN concerns "Exploiting Bioactivity of European Cereal Grains for Improved Nutrition and Health Benefits". The proteome analysis within HEALTHGRAIN includes establishing the seed proteome reference map of the wheat cultivar Chinese Spring as well as proteome profiling of cultivars selected on the basis of properties relevant for health, nutrition and agronomical performance. The purpose of the proteome mapping is to provide data for integration with genetic analysis and for correlation of protein profiles with specific grain quality properties. In addition individual identified seed proteins will be characterized with regard to spatio-temporal occurrence and post-translational modifications. An overview of the current status of the project focusing on albumins and globulins and tissue localization will be given in addition to an outline of future plans.0info:eu-repo/semantics/publishe