Dataset Information

WallProtDB, a database resource for plant cell wall proteomics.

ABSTRACT: BACKGROUND:During the last fifteen years, cell wall proteomics has become a major research field with the publication of more than 50 articles describing plant cell wall proteomes. The WallProtDB database has been designed as a tool to facilitate the inventory, the interpretation of cell wall proteomics data and the comparisons between cell wall proteomes. RESULTS:WallProtDB (http://www.polebio.lrsv.ups-tlse.fr/WallProtDB/) presently contains 2170 proteins and ESTs identified experimentally in 36 cell wall proteomics studies performed on 11 different plant species. Two criteria have to be met for entering WallProtDB. First one is related to the identification of proteins. Only proteins identified in plant with available genomic or ESTs data are considered to ensure unambiguous identification. Second criterion is related to the difficulty to obtain clean cell wall fractions. Indeed, since cell walls constitute an open compartment difficult to isolate, numerous proteins predicted to be intracellular and/or having functions inside the cell have been identified in cell wall extracts. Then, except proteins predicted to be plasma membrane proteins, only proteins having a predicted signal peptide and no known intracellular retention signal are included in the database. In addition, WallProtDB contains information about the strategies used to obtain cell wall protein extracts and to identify proteins by mass spectrometry and bioinformatics. Mass spectrometry data are included when available. All the proteins of WallProtDB are linked to ProtAnnDB, another database, which contains structural and functional bioinformatics annotations of proteins as well as links to other databases (Aramemnon, CAZy, Planet, Phytozome). A list of references in the cell wall proteomics field is also provided. CONCLUSIONS:WallProtDB aims at becoming a cell wall proteome reference database. It can be updated at any time on request and provide a support for sharing cell wall proteomics data and literature references with researchers interested in plant cell wall biology.

SUBMITTER: San Clemente H

PROVIDER: S-EPMC4302427 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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WallProtDB, a database resource for plant cell wall proteomics.

San Clemente Hélène H Jamet Elisabeth E

Plant methods 20150116 1

<h4>Background</h4>During the last fifteen years, cell wall proteomics has become a major research field with the publication of more than 50 articles describing plant cell wall proteomes. The WallProtDB database has been designed as a tool to facilitate the inventory, the interpretation of cell wall proteomics data and the comparisons between cell wall proteomes.<h4>Results</h4>WallProtDB (http://www.polebio.lrsv.ups-tlse.fr/WallProtDB/) presently contains 2170 proteins and ESTs identified expe ...[more]

PMID: 25614757

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Project description:BackgroundThe primary plant cell wall is a complex mixture of polysaccharides and proteins encasing living plant cells. Among these polysaccharides, cellulose is the most abundant and useful biopolymer present on earth. These polysaccharides also represent a rich source of energy for organisms which have evolved the ability to degrade them. A growing body of evidence suggests that phytophagous beetles, mainly species from the superfamilies Chrysomeloidea and Curculionoidea, possess endogenous genes encoding complex and diverse families of so-called plant cell wall degrading enzymes (PCWDEs). The presence of these genes in phytophagous beetles may have been a key element in their success as herbivores. Here, we combined a proteomics approach and transcriptome sequencing to identify PCWDEs present in larval gut contents of the mustard leaf beetle, Phaedon cochleariae.ResultsUsing a two-dimensional proteomics approach, we recovered 11 protein bands, isolated using activity assays targeting cellulose-, pectin- and xylan-degrading enzymes. After mass spectrometry analyses, a total of 13 proteins putatively responsible for degrading plant cell wall polysaccharides were identified; these proteins belong to three glycoside hydrolase (GH) families: GH11 (xylanases), GH28 (polygalacturonases or pectinases), and GH45 (β-1,4-glucanases or cellulases). Additionally, highly stable and proteolysis-resistant host plant-derived proteins from various pathogenesis-related protein (PRs) families as well as polygalacturonase-inhibiting proteins (PGIPs) were also identified from the gut contents proteome. In parallel, transcriptome sequencing revealed the presence of at least 19 putative PCWDE transcripts encoded by the P. cochleariae genome. All of these were specifically expressed in the insect gut rather than the rest of the body, and in adults as well as larvae. The discrepancy observed in the number of putative PCWDEs between transcriptome and proteome analyses could be partially explained by differences in transcriptional level.ConclusionsCombining proteome and transcriptome sequencing analyses proved to be a powerful tool for the discovery of active PCWDEs in a non-model species. Our data represent the starting point of an in-depth functional and evolutionary characterization of PCWDE gene families in phytophagous beetles and their contribution to the adaptation of these highly successful herbivores to their host plants.

Project description:BackgroundThe use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current porcine gene databases, however, lack the robust annotation to study pig models that are relevant to human studies and for comparative evaluation with rodent models. Furthermore, they contain a significant number of errors due to their primary reliance on machine-based annotation. To address these deficiencies, a comprehensive literature-based survey was conducted to identify certain selected genes that have demonstrated function in humans, mice or pigs.ResultsThe process identified 13,054 candidate human, bovine, mouse or rat genes/proteins used to select potential porcine homologs by searching multiple online sources of porcine gene information. The data in the Porcine Translational Research Database (( http://www.ars.usda.gov/Services/docs.htm?docid=6065 ) is supported by >5800 references, and contains 65 data fields for each entry, including >9700 full length (5' and 3') unambiguous pig sequences, >2400 real time PCR assays and reactivity information on >1700 antibodies. It also contains gene and/or protein expression data for >2200 genes and identifies and corrects 8187 errors (gene duplications artifacts, mis-assemblies, mis-annotations, and incorrect species assignments) for 5337 porcine genes.ConclusionsThis database is the largest manually curated database for any single veterinary species and is unique among porcine gene databases in regard to linking gene expression to gene function, identifying related gene pathways, and connecting data with other porcine gene databases. This database provides the first comprehensive description of three major Super-families or functionally related groups of proteins (Cluster of Differentiation (CD) Marker genes, Solute Carrier Superfamily, ATP binding Cassette Superfamily), and a comparative description of porcine microRNAs.

Dataset Information

WallProtDB, a database resource for plant cell wall proteomics.

Publications

WallProtDB, a database resource for plant cell wall proteomics.

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