Oxygen Sensing and Oxygen-Regulated Gene Expression
The intracellular levels and activities of a large number of proteins in all organisms are affected by oxygen tension. Many of these proteins are involved in metabolic pathways or processes that use oxygen or reactive oxygen species as substrates. They include: cytochromes of the respiratory chain; enzymes involved in the synthesis of heme, sterols, or unsaturated fatty acids; and enzymes that function in the oxidative stress response. The effect of oxygen on intracellular levels of many of these proteins is exerted at the transcription level. In the budding yeast, Saccharomyces cerevisiae, most oxygen-regulated genes can be placed into one of two groups: 'aerobic' genes, which are transcribed optimally in the presence of air; and 'hypoxic' genes, which are transcribed optimally under anoxic or microaerophilic conditions.

Currently, it is not clear how oxygen is sensed in yeast or other eucaryotes. Also unclear is how an “oxygen sensor” transmits its signal to a signal transduction pathway for the activation or repression of oxygen-regulated genes and whether there is more than one signal transduction pathway involved in oxygen-regulated transcription. These questions form the focus of this study. Our current goals are to:1) identify the intracellular oxygen sensors that translate oxygen concentration into an effect on transcription and understand how the "O₂ switch" works; 2) locate oxygen-responsive promoter elements; and 3) to identify the transcription factors and components of the signal transduction pathways that connect the oxygen sensor to the transcriptional machinery.

Intergenomic Signaling From Mitochondrial to Nuclear Genome
Recent studies have demonstrated that the mitochondrion can affect the expression of nuclear genes in two fundamentally different ways. In the first, mitochondrial respiratory function is essential for the anoxic induction of some hypoxic genes. In the second, the mitochondrial genome itself functions independently of its respiratory function in the optimal expression of some aerobic genes. The later has been called Intergenomic Signaling; it is operative in the regulation of several nuclear genes. Detailed studies with one of these genes, COX6, reveal that Intergenomic Signaling is mediated by a cis site in the COX6 promoter that binds ABF1p, a multifunctional phosphoprotein involved in both DNA synthesis and transcription, and that the phosphorylation state of ABF1p is affected by the mitochondrial genome. These findings indicate that ABF1p, a protein that has been proposed to coordinate gene expression with DNA synthesis and cell division, is also involved in coordinating nuclear and mitochondrial gene expression. Currently, we are interested in: 1) identifying which mitochondrial gene(s) is (are) involved in Intergenomic Signaling; 2) elucidating the components of the Intergenomic Signaling transduction pathway; and 3) understanding how the phosphorylation of ABF1p affects COX6 transcription.

Mitochondrial Dysfunction and Aging
An increase in defective mitochondrial DNA molecules accompanies aging in a number of organisms. These defects profoundly affect both mitochondrial respiratory function and on the cross talk that occurs between the mitochondrion and the nucleus. This cross talk involves signaling pathways that connect either mitochondrial respiration or the mitochondrial genome (independently of its respiratory function) to the expression of specific nuclear genes. During the past few years mitochondrial-nuclear cross talk has taken on increased importance in models of aging in many organisms. Our research objectives are based on our recent discovery of a new signaling pathway (Intergenomic Signaling) from the mitochondrial genome to the nucleus in yeast and on the finding that life span is influenced by the mitochondrial genome independently of respiration. We are: 1) determining which mitochondrial genes are involved in longevity, 2) identifying nuclear gene targets of Intergenomic Signaling and determine which of these affect longevity, and 3) identifying molecular components of the Intergenomic Signaling pathway itself and examine their role in aging.

Structure, Function, and Assembly of Cytochrome c Oxidase: Implications for Disease and Aging
Many OXPHOS diseases (i.e., fatal and benign infantile myopathies, Leigh's syndrome, ischemic heart disease, Alzheimer's disease, and Parkinson's disease) involve deficiency in cytochrome c oxidase . This is significant because cytochrome c oxidase plays a key role in the regulation of oxidative phosphorylation and in regulating the overall rate of cellular energy production. In order to understand how cytochrome c oxidase functions to regulate energy metabolism and is related to OXPHOS diseases it is essential to examine both the function and expression of its subunit polypeptides. Cytochrome c oxidase is a complex multimeric membrane protein composed of six metal centers (two hemes, three coppers, one zinc, and one magnesium atom) as well as polypeptide subunits encoded by both nuclear and mitochondrial genes. Hence, it is also important to understand the functional cross talk that takes place between those subunit polypeptides encoded by nuclear genes and those subunit polypeptides encoded by mitochondrial genes. Currently, we are investigating how the oxygen-regulated isoforms of subunit V, a nuclear-encoded subunit regulates the rate of electron transfer to the binuclear reaction center, and how Pet100p, a nuclear-coded molecular chaperone that is located in the inner mitochondrial membrane functions to assemble cytochrome c oxidase.