One of the challenges facing researchers working on oxygen-regulated biological phenomenon, as well as medical practitioners attempting to minimize hypoxia-induced tissue damage, is gaining a fundamental understanding of the molecular mechanisms for gauging oxygen availability. In spite of significant progress in our understanding of the physiological response to hypoxia, the molecular components involved in sensing oxygen and the pathways for transducing this information are poorly understood. The long-term objective of our research is to delineate oxygen-sensing mechanisms and the signaling pathways involved in eliciting adaptive responses at the level of gene expression. In this revised proposal, we focus on determining the role that cytochrome c oxidase, and possibly other components of the mitochondrial respiratory chain, plays in oxygen-sensing pathways. A yeast model will be used to address the following specific aims.
Aim 1 : Identify the cis site(s) in the promoters of oxygen-responsive genes that confer(s) sensitivity to inhibitors and mutations in the respiratory chain. To address this aim, the promoter regions of several oxygen-responsive genes will be fused to the reporter gene LacZ and used to define the minimal-sized DNA fragment and essential nucleotides that confer sensitivity to inhibitors and mutations in the respiratory chain.
Aim 2 : Identify trans-acting factors that interact with these cis sites and other proteins involved in transducing the low oxygen signal from the mitochondrion to the nucleus. Once the cis site is defined, one-hybrid and two-hybrid screens will be used to identify the trans-acting factor(s) and other proteins responsible for mediating sensitivity to inhibitors and mutations in the respiratory chain. In addition, genome-wide transcript profiling analyses will be used to identify additional sensory and signaling proteins. These studies can be expected to provide novel findings and new insight into the crosstalk between the mitochondrion and nucleus that is involved in modulating the expression of oxygen-responsive genes and provide a general model of oxygen sensing in eukaryotic cells.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM059826-05
Application #
6861826
Study Section
Physiological Chemistry Study Section (PC)
Program Officer
Ikeda, Richard A
Project Start
2001-04-01
Project End
2007-03-31
Budget Start
2005-04-01
Budget End
2007-03-31
Support Year
5
Fiscal Year
2005
Total Cost
$219,278
Indirect Cost
Name
University of Illinois Urbana-Champaign
Department
Physiology
Type
Schools of Arts and Sciences
DUNS #
041544081
City
Champaign
State
IL
Country
United States
Zip Code
61820
Lai, Liang-Chuan; Kissinger, Matthew T; Burke, Patricia V et al. (2008) Comparison of the transcriptomic ""stress response"" evoked by antimycin A and oxygen deprivation in Saccharomyces cerevisiae. BMC Genomics 9:627
Yeater, Kathleen M; Chandra, Jyotsna; Cheng, Georgina et al. (2007) Temporal analysis of Candida albicans gene expression during biofilm development. Microbiology 153:2373-85
Parks, Bryan A; Jiang, Lihua; Thomas, Paul M et al. (2007) Top-down proteomics on a chromatographic time scale using linear ion trap fourier transform hybrid mass spectrometers. Anal Chem 79:7984-91
Du, Yi; Parks, Bryan A; Sohn, Seyoung et al. (2006) Top-down approaches for measuring expression ratios of intact yeast proteins using Fourier transform mass spectrometry. Anal Chem 78:686-94
Lai, Liang-Chuan; Kosorukoff, Alexander L; Burke, Patricia V et al. (2006) Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae. Eukaryot Cell 5:1468-89
Lai, Liang-Chuan; Kosorukoff, Alexander L; Burke, Patricia V et al. (2005) Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: differential response and role of Msn2 and/or Msn4 and other factors in galactose and glucose media. Mol Cell Biol 25:4075-91
Burke, Patricia V; Lai, Liang-Chuan; Kwast, Kurt E (2004) A rapid filtration apparatus for harvesting cells under controlled conditions for use in genome-wide temporal profiling studies. Anal Biochem 328:29-34
Kwast, Kurt E; Lai, Liang-Chuan; Menda, Nina et al. (2002) Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: functional roles of Rox1 and other factors in mediating the anoxic response. J Bacteriol 184:250-65