HYPOXIA AND CONSEQUENCES Mitochondria and Hypoxic Signaling A New View Robert O. Poyton, Pablo R. Castello, Kerri A. Ball, Dong Kyun Woo, and Ning Pan Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA Eukaryotic cells respond to low oxygen concentrations by upregulating hypoxic and downregulating aerobic nuclear genes (hypoxic signaling). Most of the oxygen-regulated genes in yeast require the mitochondrial respiratory chain for their up- or downregu- lation when cells experience hypoxia. Although it was shown previously that the mito- chondrial respiratory chain is required for the upregulation of some hypoxic genes in both yeast and mammalian cells, its underlying role in this process has been unclear. Recently, we have reported that mitochondria produce nitric oxide (NO • ) when oxygen becomes limiting. This NO • production is nitrite (NO 2 − )-dependent, requires an elec- tron donor, and is carried out by cytochrome c oxidase in a pH-dependent fashion. We call this activity Cco/NO • and incorporate it into a new model for hypoxic signaling. In addition, we have found that some of the NO • produced by Cco/NO • is released from cells, raising the possibility that mitochondrially generated NO • also functions in extracellular hypoxic signaling pathways. Key words: mitochondria; hypoxia; free radicals The ability of cells, tissues, and organisms to sense, respond, and adapt to changes in oxygen concentration is often crucial to their survival. In many organisms, adaptation to changing oxygen tensions is achieved both by the short- term effects of oxygen on energy metabolism and the long-term effects of oxygen on gene expression. 1 It is now well-recognized that oxygen-regulated genes in eukaryotic cells can be placed into two general groups: aerobic genes that are optimally expressed in normoxic cells and hypoxic genes that are optimally expressed in hypoxic or anoxic cells. 2,3 Some aerobic and hypoxic genes are gene pairs, which encode protein isoforms that are functionally differ- ent and which facilitate the adaptive response. Genes for these isoforms are tightly regulated Address for correspondence: Robert O. Poyton, Department of Molec- ular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA. Voice: 303-492-3823; fax: 303-492-8783. Robert.Poyton@colorado.edu by oxygen, which allows only one protein iso- form at a time to be expressed in the cells. 4 The differential effects of oxygen level on the expression of aerobic and hypoxic genes are easily observed when cells experience hy- poxia. Aerobic genes are downregulated and hypoxic genes are upregulated, and the genes for hypoxic/aerobic isoforms pairs switch on and off at precise oxygen concentrations. 4 Col- lectively, these alterations in gene expression have been referred to as “hypoxic signaling.” It is clear that successful cell, tissue, and or- ganismal adaptation to hypoxia requires both the upregulation of hypoxic genes and the downregulation of aerobic genes. This is espe- cially relevant for hypoxic/aerobic gene pairs that encode interchangeable proteins with dif- ferent functional properties. The failure to switch off one gene while the other is switched on would result in the presence of two pro- teins with competing functions and would prevent essential metabolic changes essential Hypoxia and Consequences: Ann. N.Y. Acad. Sci. 1177: 48–56 (2009). doi: 10.1111/j.1749-6632.2009.05046.x c  2009 New York Academy of Sciences. 48