Respiratory-competent nuclear mutants have been isolated which presented a cryosensitive phenotype on a non-fermentable carbon source, due to a dysfunction of the mitochondrial F1-Fo ATP synthase. This defect results from an alteration of the mtDNA-encoded protein synthesis level of subunits 6 and 8 of the Fo sector, due to the simultaneous presence of a mutation in two unlinked nuclear genes. These mutations promote a modification of the expression of the cotranscript ATP8-ATP6 (formerly denoted AAP1-OL12): this mRNA undergoes a maturation at a unique site reaching to two cotranscripts of 5.2 and 4.6 kb in length: in the mutant, the relative amount of 5.2 kb cotranscript was greatly lowered. NCA2 was isolated from a wild-type yeast genomic library by genetic complementation. The relative level of the 5.2 kb transcript, as the synthesis of subunits 6 and 8, was partly restored in the transformed strain. A 1848 nucleotide open reading frame was depicted that encoded an amphiphilic protein of 70,816 Da. Disruption of chromosomal DNA within the reading frame promoted a dramatic decrease of the 5.2 kb mRNA but did not abolish the respiratory competence of a wild-type strain. Hybridization analyses indicated that NCA2 is located on chromosome XVI and produces a single 2750 base transcript.