Specific changes in the Arabidopsis proteome in response to bacterial challenge: differentiating basal and R-gene mediated resistance

Stable Isotope Labeling of Arabidopsis thaliana Cells and Quantitative Proteomics by Mass Spectrometry

“…Quantitation of MS spectra confirmed that SILAC labeling was uniform for all tested proteins at all concentrations of [ 13 C 6 ]Arg, averaging around 71 Ϯ 6.5% for 80 g ml Ϫ1 , 80 Ϯ 5.2% for 160 g ml Ϫ1 , and 81 Ϯ 6.9% for 320 g ml Ϫ1 [ 13 C 6 ]Arg (Fig. 2B) are regulated by various stress responses (20,25,26,38,39). For example, SA induced the expression of at least four distinct GSTs at the protein level (26) and led to transcriptional up-regulation of a number of additional GST genes (38).…”

“…Thus, in plant biology, quantitative proteomic approaches so far mainly relied on chemical modification of proteins (e.g. ICAT) to study membrane lipid rafts (19) or used a two-dimensional gel approach with quantitation via spot intensity (20). Direct quantitation of intensities within the same mass spectrum, as it is done with SILAC, has the advantage of significantly reducing variation of chemical tagging and of giving better statistics on the quantitation due to the large set of uniformly labeled peptides.…”

Update on Proteomics in Arabidopsis. Where Do We Go From Here?

“…the ones most people observe without going to very high resolution proteomic experiments, there was actually a relatively good correlation between transcript and protein levels (Gygi et al, 1999;Tian et al, 2004). In two proteomic studies in Arabidopsis, one examining programmed cell death in cell cultures (Swidzinski et al, 2004) and one comparing basal and R gene-mediated defense in leaves (Jones et al, 2004), differentially accumulating proteins were represented by only a small number of relatively abundant proteins, many of which were also transcriptionally regulated during the responses. An approximation, from these as well as yeast and mammalian studies, is that changes in mRNA alone gener-ally account for 60% to 70% of the changes in protein abundance.…”

Considerations on Post-Translational Modification and Protein Targeting in the Arabidopsis Defense Proteome

“…Many redox related systems showed changes in response to AvrRpm1/RPM1 interaction, including well known defense related proteins such a GSTs. 10 Of the 52 proteins identified by Jones et al, 9 ten were observed in two or more spots. These proteins were three GSTs and several metabolic enzymes; glyceraldehyde-3-phosphate dehydrogenase, phosphoribulokinase, malate dehydrogenase, carbonic anhydrase 2 (CA2) and rubisco activase.…”

“…11 While such a theory remains contentious, different forms of these proteins can be readily observed. 10,12 A naïve expectation was that the suppression of basal defenses would be evident in both DC3000 and the DC3000(avrRpm1) treatments when compared to the hrp mutant, as DC3000(avrRpm1) differs from DC3000 only by the addition of one effector. One unexpected result of this study was how few proteins responded in a similar manner in both DC3000 and the DC3000(avrRpm1) inoculations; 22 spots were identified as T3E responsive but only three proteins (peroxiredoxin A, hydroxybillane synthase and rubisco activase) showed a similar response with DC3000(avrRpm1).…”