Application of Data-Independent Acquisition Approach to Study the Proteome Change from Early to Later Phases of Tomato Pathogenesis Responses

Plants and pathogens are entangled in a continual arms race. Plants have evolved dynamic defence and immune mechanisms to resist infection and enhance immunity for second wave attacks from the same or different types of pathogenic species. In addition to evolutionarily and physiological changes, plant-pathogen interaction is also highly dynamic at the molecular level. Recently, an emerging quantitative mass spectrometry-based proteomics approach named data-independent acquisition (DIA), has been developed for the analysis of the proteome in a high-throughput fashion. Unlike the conventional data-dependent (DDA) approach which select a limited number of precursor ions for MS/MS scan, the DIA approach is based on the acquisition of fragment-ion information for all precursor ions within a certain range of m/z values, as demonstrated by the sequential window acquisition of all theoretical mass spectra (SWATH) approach. In the DIA approach, selected reaction monitoring (SRM)-like extracted ion chromatography (XIC) on sequence specific ion transitions can be used for the identification and SRM-like quantification of the peptides after the data acquisition. In this study, the DIA approach was applied to quantitatively trace the change in the plant proteome from the early to the later stage of Pseudomonas syringae pv. tomato (Pst) DC3000 pathogenesis progression. This study revealed that at the early stage of the pathogenesis response (4 hpi), proteins directly related to the chaperon or heat-shock protein (HSP) families were up-regulated. At the later stage (8 and 24 hpi), not only the defence proteins but also a set of the pathogen-associated molecular pattern-triggered immunity (PTI) and effector triggered immunity (ETI)-related proteins, as well as proteins involved in reactive oxygen species and oxidation-reduction reaction-related mechanism were highly induced. Our findings show the dynamics of the plant regulation of pathogenesis at the protein level and demonstrate the potential of using the DIA approach for tracing the dynamics of the plant proteome during pathogenesis responses.
Yet-Ran Chen

Kai-Ting Fan, Kuo-Hsin Wang, Wei-Hung Chang, Jhih-Ci Yang, Ching-Fang Yeh, Kai-Tan Cheng, Sheng-Chi Hung and Yet-Ran Chen * (2019) Application of Data-Independent Acquisition Approach to Study the Proteome Change from Early to Later Phases of Tomato Pathogenesis Responses Int J Mol Sci., 20(4), 863