Quantitative Proteomic Analysis of Bean Plants Infected by a Virulent and Avirulent Obligate Rust Fungus

Abstract

Plants appear to have two types of active defenses, a broad-spectrum basal system and a system controlled by R-genes providing stronger resistance to some pathogens that break the basal defense. However, it is unknown if the systems are separate entities. Therefore, we analyzed proteins from leaves of the dry bean crop plant Phaseolus vulgaris using a high-throughput liquid chromatography tandem mass spectrometry method. By statistically comparing the amounts of proteins detected in a single plant variety that is susceptible or resistant to infection, depending on the strains of a rust fungus introduced, we defined basal and R-gene-mediated plant defenses at the proteomic level. The data reveal that some basal defense proteins are potential regulators of a strong defense weakened by the fungus and that the R-gene modulates proteins similar to those in the basal system. The results satisfy a new model whereby R-genes are part of the basal system and repair disabled defenses to reinstate strong resistance. Molecular & Cellular Proteomics 8:19 -31, 2009.

Relative, label-free protein quantitation: Spectral counting error statistics from nine replicate MudPIT samples

“…As a result of a cut-off for accepting proteins identified with probabilities of 95% or greater, the protein would remain in the first dataset but not the other. In the past, we have accepted lower protein identification probabilities as long as there was a higher probability for identification in another sample [4]. Here, however, we have limited our analysis of spectral count variability to proteins common between datasets and exceeding the 95% cut-off.…”

“…Instead, we invented a software platform, PANORAMICS, that allows us to analyze large amounts of MudPIT data, and we were able to configure the program to perform tandem mass spectral counting [21]. We now regularly use MudPIT to identify hundreds and thousands of proteins from pathogenic fungi and their host plants and have used PANORAMICS to perform spectral counting and show alterations in protein accumulation that may be associated with developmental cues and disease resistance [4,22].…”

“…Instrumentation improvements for mass precision, sensitivity, selectivity, and speed, along with advances in software and computational approaches, are changing the ways that amounts of proteins are measured relative to one another in a single sample or between samples [1]. These quantitative applications are enabling systems biology studies and have led to broader understandings of protein dynamics in cells [3][4][5][6].Relative protein quantitation in MudPIT takes two forms: labeled and label-free. Labels include isotopes or isobaric tags that shift the mass of a labeled protein or peptide.…”

Proteomics: A Successful Approach to Understand the Molecular Mechanism of Plant-Pathogen Interaction

“…Proteome analysis was performed for the 50h elicitor-treated opium poppy cell cultures by 2D-PAGE coupled with LC-MS. Out of 340 spots on gel, 219 proteins were identified [88]. Within these 219 protein spots, 129 were identified in the pre-existing plant proteome databases, 63 were identified by comparing with predicted translation products in opium poppy EST databases, and the remaining were common in both databases [88,89]. Of the several categories, 38.4% of identified proteins were involved in metabolic processes representing the core category of proteins including several glycolytic and secondary metabolic enzymes, nearly entire set of TCA cycle enzymes, and one alkaloid biosynthetic protein [88].…”

“…Lee et al, [89] studied the proteomics of P. vulgaris and U. appendiculatus interaction. Leaves were inoculated with liquid suspension of uredeospores of U. appendiculatus race 41 and 49.…”