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WallProtDB, a database resource for plant cell wall proteomics.

San Clemente H, Jamet E - Plant Methods (2015)

Bottom Line: 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).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.

View Article: PubMed Central - PubMed

Affiliation: Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326 Castanet-Tolosan, France ; CNRS; UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France.

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.

No MeSH data available.


An example of comparison between different proteomes within a plant species using the Summarized search. The same criteria as in Figure 3 were used to obtain a table of results. Then, the Venn diagram was obtained after selection of B. distachyon as a plant, oxido-reductases as a functional class, and the four following experiments: young leaves (green), mature leaves (blue), apical internodes (pink), basal internodes (yellow).
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Fig4: An example of comparison between different proteomes within a plant species using the Summarized search. The same criteria as in Figure 3 were used to obtain a table of results. Then, the Venn diagram was obtained after selection of B. distachyon as a plant, oxido-reductases as a functional class, and the four following experiments: young leaves (green), mature leaves (blue), apical internodes (pink), basal internodes (yellow).

Mentions: The “Summarized search” interface provides tools for overall proteome comparisons. The result of the query is a table in which the numbers of proteins in each (i) protein functional class, (ii) protein family or (iii) protein (putative) function are indicated (Figure 3). As mentioned above, different formats are available for export of query results. It is also possible to draw a Venn diagram to visualize proteome comparisons within a plant species (Figure 4). All the figures are clickable, thus enabling retrieval of lists of the corresponding proteins.


WallProtDB, a database resource for plant cell wall proteomics.

San Clemente H, Jamet E - Plant Methods (2015)

An example of comparison between different proteomes within a plant species using the Summarized search. The same criteria as in Figure 3 were used to obtain a table of results. Then, the Venn diagram was obtained after selection of B. distachyon as a plant, oxido-reductases as a functional class, and the four following experiments: young leaves (green), mature leaves (blue), apical internodes (pink), basal internodes (yellow).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4302427&req=5

Fig4: An example of comparison between different proteomes within a plant species using the Summarized search. The same criteria as in Figure 3 were used to obtain a table of results. Then, the Venn diagram was obtained after selection of B. distachyon as a plant, oxido-reductases as a functional class, and the four following experiments: young leaves (green), mature leaves (blue), apical internodes (pink), basal internodes (yellow).
Mentions: The “Summarized search” interface provides tools for overall proteome comparisons. The result of the query is a table in which the numbers of proteins in each (i) protein functional class, (ii) protein family or (iii) protein (putative) function are indicated (Figure 3). As mentioned above, different formats are available for export of query results. It is also possible to draw a Venn diagram to visualize proteome comparisons within a plant species (Figure 4). All the figures are clickable, thus enabling retrieval of lists of the corresponding proteins.

Bottom Line: 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).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.

View Article: PubMed Central - PubMed

Affiliation: Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326 Castanet-Tolosan, France ; CNRS; UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France.

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.

No MeSH data available.