Abstract
BackgroundDuring 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.ResultsWallProtDB (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.ConclusionsWallProtDB 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13007-015-0045-y) contains supplementary material, which is available to authorized users.
Highlights
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
Utility and discussion At present, WallProtDB contains 2170 proteins and expressed sequence tags (ESTs) identified in 36 cell wall proteomics studies performed on 11 different plant species (8 dicots and 3 monocots) (Table 1, Additional file 1)
Since all the proteins included in WallProtDB are annotated in the same way, it allows fine comparisons between cell wall proteomes of different species and of various plant materials
Summary
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. 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]. Recent progresses in mass spectrometry (MS) technologies have led to the identification of cell wall proteins (CWPs) allowing the description of many cell wall proteomes. It is difficult (i) to extract proteins by non-destructive methods avoiding the leakage of plasma membranes and the release of
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