Plant cell wall is mainly composed of lignins and polysaccharides, representing the richest source of biomass for future biofuel production. Currently many of cell wall synthesis related (CWSR) proteins are still unknown, even in model plant Arabidopsis thaliana. The current understanding is that the cell-wall synthesis process consists of six major components: (1) substrate generation, (2) polysaccharide synthesis and modification, (3) secretion and targeting pathways, (4) assembly, architecture and growth, (5) differentiation and secondary wall formation, and (6) signaling and response during the wall development and disassembly according to Purdue Cell Wall Database. We developped a computational framework for prediction of CWSR proteins, based on known protein-protein interaction (PPI) data and 572 known CWSR proteins (called as seed proteins) in A.thaliana. Using this PPI approach, we predicted 100 candidate CWSR proteins, of which 92 were found to be novel and 8 were confirmed by known Cell Wall Databases or the literature. Validations of our prediction were done based on analyses of publicly available microarray gene expression data, subcellular localization analyses and co-evolutionary analyses.
For facilitating access to the interaction information of seed CWSR proteins in our prediction and 92 candidate CWSR proteins, we deveop this webpage to display them. Besides, we link each seed/predicted CWSR protein to TAIR database.
Reference: Chan Zhou, Yanbin Yin, Phuongan Dam and Ying Xu, Identification of novel proteins involved in plant cell-wall synthesis based on protein-protein interaction data, Journal of Proteome Research, 9(2010): 5025-5037. PubMed
Contact: Chan ZHOU (zhouchan at uga.edu)
Computational & Systems Biology Laboratory
Department of Biochemistry and Molecular Biology & Institute of Bioinformatics
University of Georgia
Last updated: Aug 2010.