We have previously identified several positive cis-acting regulatory regions in the promoters of the bovine and human nuclear-encoded mitochondrial F 0 F 1 -ATP synthase ␣-subunit genes (ATPA). One of these cis-acting regions contains the sequence 5 -CACGTG-3 (an Ebox), to which a number of transcription factors containing a basic helix-loop-helix motif can bind. This E-box element is required for maximum activity of the ATPA promoter in HeLa cells. The present study identifies the human transcription factor, upstream stimulatory factor 2 (USF2), as a nuclear factor that binds to the ATPA E-box and demonstrates that USF2 plays a critical role in the activation of the ATPA gene in vivo. Evidence includes the following. Antiserum directed against USF2 recognized factors present in HeLa nuclear extracts that interact with the ATPA promoter in mobility shift assays. Wild-type USF2 proteins synthesized from expression vectors trans-activated the ATPA promoter through the E-box, whereas truncated USF2 proteins devoid of the amino-terminal activation domains did not. Importantly, expression of a dominant-negative mutant of USF2 lacking the basic DNA binding domain but able to dimerize with endogenous USF proteins significantly reduced the level of activation of the ATPA promoter caused by ectopically coexpressed USF2, demonstrating the importance of endogenous USF2 in activation of the ATPA gene.Most cellular ATP is synthesized in the mitochondria through the process of oxidative phosphorylation. The mammalian mitochondrial oxidative phosphorylation system requires the functional interaction of gene products encoded by both the nuclear and the mitochondrial genomes (for reviews, see Refs. 1 and 2). The activities of the enzymes of the mammalian oxidative phosphorylation system vary greatly in response to a number of physiological conditions, including cell proliferation, hormonal stimulation, development, and differentiation (for reviews, see Refs. 3 and 4). The levels of these enzymes are controlled, at least in part, at a transcriptional level, although regulation at a post-transcriptional level also plays an important role in mitochondrial biogenesis (1-4).During the past several years, analysis of mammalian nuclear encoded oxidative phosphorylation genes has resulted in the identification of a number of regulatory factors that contribute to the transcription of these genes. Characterization of these gene regulatory mechanisms should allow the delineation of signals involved in the control of cellular energy production and, possibly, in the coordinate expression of genes encoding proteins of the oxidative phosphorylation system. Our laboratory has been analyzing the regulation of the nuclear gene that encodes the ␣-subunit of the mammalian mitochondrial F 0 F 1 -ATP synthase complex (ATPA) and has identified several positive cis-acting regulatory regions that are important for expression of this gene (5). Furthermore, we have found that protein factor(s) present in HeLa nuclei bind to these cis-acting regions. For e...