Plant cell walls were discovered by Robert Hooke in 1665 while observing the cell walls in cork tissue under the microscope. Primary walls are mainly composed of polysaccharide networks such as cellulose microfibrills, hemicelluloses wrapping and interlacing cellulose microfibrills and pectins [Carpita and Gibeaut 1993, Plant J, 3: 1]. After the end of cell growth, secondary walls which contain additional compounds such as lignins, wax or cutin, are synthesized. Cell wall proteins (CWPs) play critical roles in plant cell walls during development and adaptation to environmental cues [Fry 2004, New Phytol 161: 641; Passardi et al. 2004, Trends Plant Sci 9: 534]. Extensive studies leading to their identification and characterization have been undertaken. Cell wall proteomics started in the 2000s when the first plant genome sequences became available. Nowadays, there are about 50 papers covering this field [Albenne et al. 2013, Front Plant Sci, 4: 111; Albenne et al. 2014, Proteomes, 2: 224-242], half of them dealing with Arabidopsis thaliana. Around one fourth (nearly 500 proteins) of the expected A. thaliana cell wall proteins have been identified in different organs or in response to environmental constraints. More recently, systematic analyses have been performed on additional plant species.
The WallProtDB database aims at collecting cell wall proteomic experimental data. These data are selected and annotated according to several criteria:
- Genomics or transcriptomics data of the plant of interest should be available to ensure the precise identification of proteins by mass spectrometry analysis and bioinformatics.
- Only proteins having a bona fide N-terminal signal peptide as predicted by several bioinformatics programs have been retained. Indeed, cell wall proteins are secreted, going through the endoplasmic reticulum and the Golgi apparatus before reaching the extracellular space. At present, the question of the contamination of cell wall extracts by intracellular proteins is still a matter of debate [Rose and Lee 2010, Plant Physiol Biochem 153: 433; Albenne et al. 2013, Front Plant Sci 4: 111]. Experimental data showing the presence of non canonical proteins in cell walls are still missing.
- Functional domains have been predicted de novo thanks to available sofware (see below). Proteins are grouped in functional classes: (1) proteins acting on cell wall polysaccharides, (2) oxido-reductases, (3) proteases, (4) proteins having domains of interaction with proteins or polysaccharides, (5) structural proteins, (6) proteins possibly involved in signaling, (7) proteins related to lipid metabolism, (8) miscellaneous proteins, (9) proteins with yet unknown function [Jamet et al. 2008, Proteomics 8: 893].
To facilitate the interpretation of proteomics data, protein accession numbers have been linked to ProtAnnDB (Protein Annotation DataBase) which collects predictions of sub-cellular localization and functional domains (www.polebio.lrsv.ups-tlse.fr/ProtAnnDB/). When possible, mass spectrometry data are provided.
In this new version, WallProtDB is devoted to the following published cell wall proteomic or xylem sap studies* (Detailed search):
Arabidopsis thaliana (thale cress)
Brassica oleracea *
Gossypium hirsutum (upland cotton)
Linum usitatissimum (flax)
Medicago sativa (lucerne)
Populus deltoides (poplar)
P. deltoides x P. trichocarpa * (poplar)
Solanum lycopersicum (tomato)
Solanum tuberosum (potato)
Brachypodium distachyon (stiff brome)
Oryza sativa (rice)
Saccharum officinarum (sugarcane)
Since all the proteins present in WallProtDB have been annotated in the same way, it is possible to compare cell wall proteomes between different plants or organs using comparison tools (Summarized search).
A list of references related to cell wall proteomics is regularly updated (References). It includes cell wall and xylem proteomic studies, reviews and database references.
WallProtDB is regularly completed with newly published cell wall proteomic experimental data.
If you use WallProtDB, please cite:
San Clemente H, Jamet E (2015) WallProtDB, a database resource for plant cell wall proteomics. Plant Methods, 11: 2 (Full text)
Contact: Elisabeth JAMET (firstname.lastname@example.org)
Webmaster: Hélène San Clemente (email@example.com)
Last update: Nov 13th 2017