Extracellular proteomes of Arabidopsis thaliana and Brassica napus roots: analysis and comparison by MudPIT and LC-MS/MS

An important principle of the functional organization of plant cells is the targeting of proteins to specific subcellular locations. The physical location of proteins within the apoplasm/ rhizosphere at the root-soil interface positions them to play a strategic role in plant response to biotic and abiotic stress. We previously demonstrated that roots of Triticum aestivum and Brassica napus exude a large suite of proteins to the apoplasm/rhizosphere [Basu et al. (1994)Plant Physiol 106:151-158; Basu et al. (1999)Physiol Plant 106:53-61]. This study is a first step to identify low abundance extracytosolic proteins from Arabidopsis thaliana and Brassica napus roots using recent advances in the field of proteomics. A total of 16 extracytosolic proteins were identified from B. napus using two-dimensional gel electrophoresis, tandem mass spectrometry (LC-MS/MS)and de novo sequencing. Another high-throughput proteomics approach, Multidimensional Protein Identification Technology (Mud PIT)was used to identify 52 extracytosolic proteins from A. thaliana. Signal peptide cleavage sites, the presence/absence of transmembrane domains and GPI modification were determined for these proteins. Functional classification grouped the extracellular proteins into different families including glycoside hydrolases, trypsin/ protease inhibitors, plastocyanin-like domains, copper-zinc superoxide dismutases, gamma-thioinins, thaumatins, ubiquitins, protease inhibitor/ seed storage/lipid transfer proteins, transcription factors, class III peroxidase, and plant basic secretory proteins (BSP). We have also developed an on-line, Extracytosolic Plant Proteins Database (EPPdb, http://eppdb.biology.ualberta. ca)to provide information about these extracytosolic proteins.