WallProtDB , a database resource for plant cell wall proteomics
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PLANT METHODS
DATABASE
Open Access
WallProtDB, a database resource for plant cell wall proteomics Hélène San Clemente1,2 and Elisabeth Jamet1,2*
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. Keywords: Cell wall, Mass spectrometry, Plant, ProtAnnDB, Proteomics
Background The plant cell wall is an external matrix containing polysaccharides and proteins. The interest in plant cell wall proteomes has been increasing during the last years with the discovery that plant cell walls are dynamic compartments constantly modified during development and in response to environmental cues [1,2]. The physiology of plant cell walls is strongly linked to its enzyme and structural protein content. The full description of the proteins present in various cell walls at precise stages of development or in response to biotic and abiotic stresses * Correspondence: [email protected] 1 Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326 Castanet-Tolosan, France 2 CNRS; UMR 5546,
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