title: Proteomics of weakly bound cell wall proteins in rice calli.
abstract: In the present work, we present a proteomic analysis of weakly bound cell wall proteins (CWPs) in rice. CWPs from rice calli were extracted with mannitol/CaCl(2), followed by back extraction with water-saturated phenol. The isolated CWPs were evaluated for contamination by cytosolic proteins by measuring the enzymatic activity of an intracellular marker (glucose-6-phosphate dehydrogenase). This revealed the presence of low levels of intracellular proteins and a significant enrichment of CWPs, as compared to the total extract. Protein samples were digested in gels with trypsin and analyzed using the multidimensional protein identification technology (MudPIT). A total of 292 proteins were identified, which included numerous classical CWPs and antioxidant proteins. Bioinformatics analysis showed that 72.6% of these proteins possessed a signal peptide, and a total of 198 proteins were determined to be CWPs in rice. Functional classification divided the extracellular proteins into different groups, including glycosyl hydrolases (23%), antioxidant proteins (12%), cell wall structure-related proteins (6%), metabolic pathways (9%), protein modifications (4%), defense (4%), and protease inhibitors (3%). Furthermore, comparative analysis of our identified rice CWPs with known Arabidopsis CWPs revealed 25 novel rice-specific CWPs. The study described here is an unprecedented large-scale analysis of CWPs in rice.
authors.affiliation: Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju 660-701, Republic of Korea.
authors.forename: Xiong-Yan
authors.initials: XY
authors.lastname: Chen
authors.forename: Sun Tae
authors.initials: ST
authors.lastname: Kim
authors.forename: Won Kyong
authors.initials: WK
authors.lastname: Cho
authors.forename: Yeonggil
authors.initials: Y
authors.lastname: Rim
authors.forename: Suwha
authors.initials: S
authors.lastname: Kim
authors.forename: Seon-Won
authors.initials: SW
authors.lastname: Kim
authors.forename: Kyu Young
authors.initials: KY
authors.lastname: Kang
authors.forename: Zee Yong
authors.initials: ZY
authors.lastname: Park
authors.forename: Jae-Yean
authors.initials: JY
authors.lastname: Kim
mesh_terms: D017360:Arabidopsis / Q000378:metabolism; D002473:Cell Wall / Q000378:metabolism*; D019295:Computational Biology; D004591:Electrophoresis, Polyacrylamide Gel; D005954:Glucosephosphate Dehydrogenase / Q000378:metabolism; D008970:Molecular Weight; D012275:Oryza / Q000378:metabolism*; D010936:Plant Extracts; D010940:Plant Proteins / Q000145:classification / Q000302:isolation & purification / Q000378:metabolism*; D011485:Protein Binding; D021382:Protein Sorting Signals; D040901:Proteomics; D013045:Species Specificity; D046509:Tissue Culture Techniques
chemical_list: D010936:Plant Extracts; D010940:Plant Proteins; D021382:Protein Sorting Signals; D005954:Glucosephosphate Dehydrogenase