Arabidopsis cell wall proteome defined using multidimensional protein identification technology

Abstract

With the completion of the sequencing of the Arabidopsis genome and the recent advances in proteomic technology, the identification of proteins from highly complex mixtures is now possible. Rather than using gel electrophoresis and peptide mass fingerprinting, we have used multidimensional protein identification technology (MudPIT) to analyse the "tightly-bound" proteome for purified cell walls from Arabidopsis cell suspension cultures. Using bioinformatics for the prediction of signal peptides for targeting to the secretory pathway and for the absence of ER retention signal, 89 proteins were selected as potential extracellular proteins. Only 33% of these were identified in previous proteomic analyses of Arabidopsis cell walls. A functional classification revealed that a large proportion of the proteins were enzymes, notably carbohydrate active enzymes, peroxidases and proteases. Comparison of all the published proteomic analyses for the Arabidopsis cell wall identified 268 non-redundant genes encoding wall proteins. Sixty of these (22%) were derived from our analysis of tightly-bound wall proteins.

AnArabidopsisGPI-Anchor Plasmodesmal Neck Protein with Callose Binding Activity and Potential to Regulate Cell-to-Cell Trafficking

“…These proteins, misassigned in Elortza et al (2003) as 1,3-bglucanases, were also assessed for their expression levels as EST abundance and as MPSS (massive parallel signature sequencing; http://mpss.udel.edu/grape/) outputs. Interestingly, the MPSS data record high expression levels for PDCB1 in Arabidopsis callus; Arabidopsis suspension culture was the source material for our original proteomic analysis (Bayer et al, 2006). The predicted and biochemically verified GPI nature of these proteins was supported by our indirect observations that their subcellular location was stabilized by an inhibitor of phospholipase C, an activity for which GPI-anchor proteins are very vulnerable (Svetek et al, 1999).…”

“…Previous work (Bayer et al, 2006) identified a series of membraneassociated proteins from cell wall preparations of Arabidopsis suspension cells. As part of a survey of the subcellular targeting of these proteins as fusions to fluorescent markers, we have identified At5g61130 as a gene encoding a novel Pd protein.…”

Comparative Analyses of Extracellular Matrix Proteome: An Under-Explored Area in Plant Research

“…Defining proteins that change in abundance, form, location or other activities may indicate the presence and functional significance of a protein. Whereas comparative ECM proteome research is quite advanced in animals (Zhu et al, 2007) and yeast (Kim et al, 2007) (Liepman et al, 2010;Basu et al, 2006;Bayer et al, 2006;Borderies et al, 2003;Chivasa et al, 2002;Feiz et al, 2006;Jamet et al 2008a), Medicago sativa (Soares et al, 2007;Watson et al, 2004), and crop plants for, e.g., Oryza sativa (Choudhary et al, 2010), Brassica napus (Basu et al, 2006) Zea mays (Zhu et al, 2006) and Cicer arietinum (Bhushan et al, 2006). Around 500 CWPs of Arabidopsis, representing about one third of its estimated cell wall proteome, have been described (Liepman et al, 2010) while 219, 143, 102, 58 CWPs were identified in rice, chickpea, maize and Brassica, respectively.…”

Proteomic technology for biomarker profiling in cancer: an update

“…However, this methods still suffers some of the disadvantages seen in 2D gel electrophoresis, in particular limited sensitivity and resolution to detect low molecular weight proteins (Chakravarti et al, 2004). In contrast, multidimensional protein identification technology (MudPIT) is more widely used as a sensitive method (Bayer et al, 2006;Chen et al, 2006;Guzzetta and Chien et al, 2005;Durr et al, 2004). In MudPIT a complex protein mixture is digested with a specific protease (most commonly trypsin).…”