Mitochondrial genotypes drive differential expression of nuclear genes under varied levels of hypoxia in Drosophila. David M. Rand, Yawei Ge, Nicholas Jourjine, Patrick Flight. Ecology & Evolution, Brown Univ, Providence, RI.

   When organisms encounter reduced oxygen tension, or hypoxia, they reduce cellular demand for oxygen by down-regulating mitochondrial functions through altered expression of nuclear genes, mediated by the HIF pathway. Despite the central role mitochondria play in oxygen consumption, the effect of mitochondrial genotypes on the hypoxic response has not been examined. Here we use mtDNA introgression strains of Drosophila to examine the effects of alternative mtDNA-encoded genes on the nuclear transcriptional response to varied hypoxia. Flies carrying mtDNA from either D. melanogaster OreR, D. melanogaster Zimbabwe, D. simulans siI, or D. simulans siII on a D. melanogaster OreR nuclear chromosomal background were constructed using balancer substitutions and maternal cytoplasm from these four genotypes. We studied the expression profiles of these genotypes under two general conditions: 1) a gradient of hypoxic stress for 2 hours (normoxia, 6%, 3%, and 1.5% oxygen), and 2) a time course of 1.5% oxygen for 1, 2, 3, and 4 hours. Expression profiles of whole males were determined using Affymetrix 2.0 arrays. The mtDNA genotype design allows for association of alternative mtDNAs within a species, or fixed differences between Dmel and Dsim mtDNAs as drivers of nuclear gene expression, in trans. MtDNAs have subtle effects on gene expression under normoxia (~30 genes altered), but have pronounced effects at 3% (>200 genes altered) and 6% oxygen (~500 genes altered). These results are confirmed in the time course study, with gene expression effects peaking at 3 hours and subsiding by 4 hours. In each case the species-level differences between mtDNAs (Dmel vs. Dsim) drive different sets of genes than the individual mtDNA haplotypes within either species (OreR vs. Zimbabwe or siI vs. siII). These results provide strong evidence for mitochondrial retrograde signaling in the nuclear transcriptional response to hypoxia and offer the first evidence that genes in mtDNA play a critical role in modulating the transcriptional response to hypoxia under different levels of hypoxic stress.