Proteomic analysis of the Arabidopsis thaliana-Botrytis cinerea interaction using two-dimensional liquid chromatography

A two-dimensional liquid chromatography (2D LC) system, ProteomeLab PF 2D, was employed to study the defence proteome of Arabidopsis following infection with the necrotrophic fungal pathogen, Botrytis cinerea. This system demonstrated differential protein expression in control and treated samples in some fractions. However, the amount of proteins in the fractions and the level to which they were changing could not be established. Among the proteins identified in the fractions that displayed an increase in absorbance was catalase 3 and glutathione S-transferases, demonstrating the importance of an antioxidant system in defence against B. cinerea. Most of the proteins were identified in fractions that displayed reduction in absorbance. Functional categorisation of the identified proteins demonstrated the overrepresentation of photosynthetic pathway, a phenomenon also observed in other host and nonhost pathogen interactions. Proteomelab PF 2D did not identify as many proteins as expected possibly due to the masking effect of ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO) as this protein was identified in almost all fractions including those having an increase in absorbance. Depletion of this protein from crude plant protein extracts is likely to improve protein identification by mass spectrometry, especially for the low abundant proteins. A number of proteins were identified in each fraction and it was difficult to discern which of the proteins was responsible for the differential increase or reduction in absorbance