Title page for ETD etd-08112008-190113


Type of Document Dissertation
Author Tuli, Leepika
URN etd-08112008-190113
Title Proteome Profiling of Saccharomyces cerevisae stress response to Cumene Hydroperoxide (CHP)
Degree PhD
Department Genetics, Bioinformatics, and Computational Biology
Advisory Committee
Advisor Name Title
Shulaev, Vladimir Committee Chair
Bevan, David R. Committee Member
Hoeschele, Ina Committee Member
Laubenbacher, Reinhard C. Committee Member
Mendes, Pedro J. P. Committee Member
Keywords
  • Saccharomyces cerevisae
  • bioinformatics
  • oxidative stress
  • proteomics
  • systems biology
  • mass spectrometry
Date of Defense 2008-07-25
Availability unrestricted
Abstract
Oxidative stress, described as the state of disturbed intracellular redox balance, has been associated with several human conditions including ageing, apoptosis, cancer, autoimmune and neuro-degenerative diseases. Stress studies have shown that reactive oxygen species (ROS) and reactive nitrogen species (RNS) along with its intermediates can attack essential cell targets such as: DNA, proteins, lipids and carbohydrates, leaving behind dysfunctional biologic molecules. In effect, a cell’s primary response is to involve several defense mechanisms that are under a complex and intricate regulatory control to repair any damages that may have occurred. Although several stress studies have been conducted in the past that have approached this biologically complex process step by step, application of a Systems Biology towards a comprehensive understanding is still emerging.

The current objective of this project is to identify proteins that change in response to cumene hydroperxoide (CHP) treatment and in parallel make an attempt to uncover events and processes that are a part of CHP-induced oxidative stress response. From a systems biology viewpoint, the Yeast Oxidative Stress project will monitor response at three different levels: transcriptomics, proteomics and metabolomics, with dynamic changes being measured from 3 to 120 min after CHP addition. Data collected from the different levels will be integrated to accomplish a holistic viewpoint of stress response in the given system and to develop mathematical tools for modeling biochemical networks.

Saccharomyces cerevisiae was chosen as a model, based on its availability of a completely mapped genome sequence with a collection of null mutants that was relevant to our fundamental research of stress response mechanism. Yeast, a simple unicellular eukaryote has been extensively used for applied studies and has proven to be indispensable for stress research. Information derived from this project can reveal response mechanisms used by higher eukaryotes, especially if via analogous signaling cascades that are comparable between organisms.

Current research investigates an optimal workflow for generating 2D gel based protein expression data and identifying proteins that are induced by cumene hydroperoxide treatment. A non-targeted protein profiling followed by a 2-way ANOVA analysis provided a list of proteins that differ significantly between treatments. Protein identification provided relevant information on which proteins are affected by CHP induced stress response, including posttranslational modifications of peroxiredoxins. Redox active protein, Ahp1, was regulated post-translationally with sulfonic acid modification observed for its active Cys(62) residue.

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