WallProtDB
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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; Tenhaken et al. 2015, 5: 771; Le Gall et al. (2015) Plants 4: 712]. 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 many articles 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 half (nearly 1000 proteins) of the expected A. thaliana CWPs have been identified so far in different organs or in response to environmental constraints. More recently, systematic analyses have been performed on additional plant species like Brachypodium distachyon, or Marchantia polymorpha.

The WallProtDB-2 database aims at collecting cell wall proteomic experimental data. For each experiment, a scheme summarizing the strategy used for protein isolation and identification is provided. These data are organized and annotated as follows:

- 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 as cell wall proteins. They are listed in black. Indeed, cell wall proteins are secreted, going through the endoplasmic reticulum and the Golgi apparatus before reaching the extracellular space. 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; Regente et al. (2017) J Exp Bot 20: 5485]. Experimental data showing the presence of non canonical proteins in cell walls are still scarce.

- Functional domains have been predicted de novo thanks to available bioinformatics programs (see below). Cell wall proteins are grouped in protein families and in functional classes [Jamet et al. 2008, Proteomics 8: 893], e.g.: (1) proteins acting on cell wall carbohydrates, (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 of yet unknown function.

- The proteins which are neither predicted to be secreted, nor known to be extracellular, are considered as presumed "contaminant proteins". They are indicated in red. Their predicted functional domains are indicated (Pfam and Interpro domains) (protein putative function column).

To facilitate the interpretation of proteomics data, the protein accession numbers have been linked to the ProtAnnDB (Protein Annotation DataBase) which collects predictions of sub-cellular localization and functional domains. Whenever possible, a link to the Phytozome nomenclature is provided and mass spectrometry data are provided.

Presently, WallProtDB-2 is devoted to the following published cell wall proteomics or xylem sap studies (*) (see Detailed search):

DicotsMonocotsBryophytes
Arabidopsis thaliana
Brassica oleracea
Camellia sinensis (tea)
Gossypium hirsutum (upland cotton)
Linum usitatissimum (flax)
Medicago sativa (alfalfa)
Populus deltoides (poplar)
P. deltoides x P. trichocarpa
Solanum lycopersicum (tomato)
Solanum tuberosum (potato)
Brachypodium distachyon (stiff brome)
Oryza sativa (rice)
Saccharum officinarum (sugarcane)
Marchantia polymorpha
Physcomitrella patens

Since all the proteins present in WallProtDB-2 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). Then a BLAST search is possible.

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-2 is regularly completed with newly published cell wall proteomic experimental data.

If you use WallProtDB-2, please cite:
San Clemente H, Jamet E (2015) WallProtDB, a database resource for plant cell wall proteomics. Plant Methods, 11: 2 (Full text)
San Clemente H, Kolkas H, Canut H, Jamet (2022) Plant cell wall proteomes: the core of conserved protein families and the case of non-canonical proteins. Int J Mol Sci, 22: 4273 (Full text)


Contact: Elisabeth JAMET (jamet@lrsv.ups-tlse.fr)
Webmaster: Hélène San Clemente (sancle@lrsv.ups-tlse.fr)

Last update: July 5th 2022



Dynamics and Evolution of Plant cell walls team