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WallProtDB, a database resource for plant cell wall proteomics.

Hélène San Clemente1, Elisabeth Jamet1

  • 1Université 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.

Plant Methods
|January 24, 2015
PubMed
Summary
This summary is machine-generated.

WallProtDB is a new database for plant cell wall proteomics, cataloging 2170 proteins from 11 species. It aids researchers in interpreting and comparing cell wall proteome data.

Keywords:
Cell wallMass spectrometryPlantProtAnnDBProteomics

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Area of Science:

  • Plant Biology
  • Proteomics
  • Bioinformatics

Background:

  • Cell wall proteomics is a rapidly growing field with over 50 publications in the last 15 years.
  • Existing research highlights the challenges in isolating pure cell wall fractions and accurately identifying proteins.
  • A centralized resource is needed to manage and interpret the increasing volume of cell wall proteome data.

Purpose of the Study:

  • To establish WallProtDB, a comprehensive database for plant cell wall proteomic data.
  • To facilitate the inventory, interpretation, and comparison of cell wall proteomes.
  • To serve as a reference point for researchers in plant cell wall biology.

Main Methods:

  • Proteins were included if identified experimentally in plants with available genomic or EST data.
  • Strict criteria were applied to ensure protein identification accuracy, excluding known intracellular proteins.
  • Data integrated information on extraction strategies, mass spectrometry, and bioinformatics analysis.

Main Results:

  • WallProtDB currently houses 2170 proteins and ESTs from 36 studies across 11 plant species.
  • Proteins are curated based on signal peptide presence and absence of intracellular retention signals.
  • All entries are linked to ProtAnnDB for detailed structural and functional annotations and external database cross-references.

Conclusions:

  • WallProtDB is designed to be a leading reference database for plant cell wall proteomes.
  • The database supports data sharing and literature referencing for the research community.
  • It can be continuously updated to reflect new discoveries in the field.