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Open AccessArticle

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

1
Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
2
Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
3
Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
4
Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(4), 863; https://doi.org/10.3390/ijms20040863
Received: 27 December 2018 / Revised: 11 February 2019 / Accepted: 12 February 2019 / Published: 17 February 2019
(This article belongs to the Special Issue Plant Proteomic Research 2.0)
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. 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 pathogenesis progression. This study revealed that at the early stage of the pathogenesis response, proteins directly related to the chaperon were regulated for the defence proteins. At the later stage, 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 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. View Full-Text
Keywords: plant pathogenesis responses; data-independent acquisition; quantitative proteomics; Pseudomonas syringae plant pathogenesis responses; data-independent acquisition; quantitative proteomics; Pseudomonas syringae
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Fan, K.-T.; Wang, K.-H.; Chang, W.-H.; Yang, J.-C.; Yeh, C.-F.; Cheng, K.-T.; Hung, S.-C.; Chen, Y.-R. Application of Data-Independent Acquisition Approach to Study the Proteome Change from Early to Later Phases of Tomato Pathogenesis Responses. Int. J. Mol. Sci. 2019, 20, 863.

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