Application of data-independent acquisition approach to study the proteome dynamics of plant pathogenesis responses

Plants and pathogens are entangled in a continual arms race. The plants are evolved to have a dynamic defense and immune mechanisms to resist the infection and enhance the immunity for the second wave attacks from the same or different type of pathogenic species. Not only in the evolutionally or physiologically, the plant-pathogen interaction is also highly dynamic in the molecular level. Recently, the emerging quantitative mass spectrometry-based proteomics approach, data-independent acquisition (DIA), was developed for the analysis of proteome in a high throughput fashion. In this study, the DIA approach was applied to quantitatively trace the change of the plant proteome from the early to late stage of pathogenesis progression. This study revealed that the early stage of the pathogenesis response, the proteins directly related to the chaperon for the defense proteins. In the later stage, not only the defense proteins but also a set of the pathogen associate molecular pattern triggered immunity (PTI), effector triggered immunity (ETI) related proteins were highly induced. Our finding showed the dynamics of the regulation in protein level and demonstrated that the potential of using DIA approach for tracing the dynamics of the plant proteome during pathogenesis responses.