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NEW FUNCTIONAL LOOKS INTO THE PROTEOME USING CO-FRACTION MASS SPECTROMETRY (CF-MS)

thesis
posted on 04.08.2020 by Youngwoo Lee
The sensitivity, speed, and reproducibility of modern mass spectrometers enable in-depth new functional looks into the cellular proteome. Thousands of proteins can be detected in a single sample. In Co-Fractionation Mass Spectrometry (CF-MS) method, the input sample is fractionated by any biochemical method of choice. The reduced complexity of each fractionated sample leads to better proteome coverage. The separation profiles provide functional information on the proteins. This application has been used to predict organelle localization based on co-purification with marker proteins. More recently, CF-MS is being used to measure the apparent masses and determine the localization of soluble or membrane-associated protein complexes. This Ph.D. dissertation focuses on the extension of the boundary of CF-MS application to learn how protein complex evolution and protein complex composition have been accomplished. In the first part of this dissertation, the data will be presented on the degree to which variation in protein oligomerization across plant species is present, how proteomics in phylogenetic analysis (phyloproteomics/evolutionary proteomics) helps understand the evolutionary changes, and how oligomerization drives neofunctionalization during plant evolution. The latter part will describe that CF-MS coupled with multiple orthogonal chromatographic separations increases the resolving power of the profiling technique, enabling the composition of protein complexes to be predicted in the subaleurone layers of rice endosperm. Lots of novel protein complexes involved in RNA binding protein, translation, and the tissue-species metabolism will be discussed.

Funding

Deciphering the role of RNA binding proteins in RNA transport, localization and post-transcriptional processes in plants

Directorate for Biological Sciences

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Novel Quantitative Proteomic Methods to Discover and Localize Endogenous Protein Complexes

Directorate for Biological Sciences

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Bilsland Dissertation Fellowship

Center for Plant Biology Graduate Research Award

History

Degree Type

Doctor of Philosophy

Department

Botany and Plant Pathology

Campus location

West Lafayette

Advisor/Supervisor/Committee Chair

Dr. Daniel B. Szymanski

Additional Committee Member 2

Dr. Mark C. Hall

Additional Committee Member 3

Dr. Gyeong Mee Yoon

Additional Committee Member 4

Dr. Thomas W. Okita

Licence

Exports