Saccharomyces cerevisiae cells lacking Mne1 are deficient in intron splicing in the gene encoding the Cox1 subunit of cytochrome oxidase but contain wild-type levels of the bc 1 complex. Thus, Mne1 has no role in splicing of COB introns or expression of the COB gene. Northern experiments suggest that splicing of the COX1 aI5 intron is dependent on Mne1 in addition to the previously known Mrs1, Mss116, Pet54, and Suv3 factors. Processing of the aI5 intron is similarly impaired in mne1⌬ and mrs1⌬ cells and overexpression of Mrs1 partially restores the respiratory function of mne1⌬ cells. Mrs1 is known to function in the initial transesterification reaction of splicing. Mne1 is a mitochondrial matrix protein loosely associated with the inner membrane and is found in a high mass ribonucleoprotein complex specifically associated with the COX1 mRNA even within an intronless strain. Mne1 does not appear to have a secondary function in COX1 processing or translation, because disruption of MNE1 in cells containing intronless mtDNA does not lead to a respiratory growth defect. Thus, the primary defect in mne1⌬ cells is splicing of the aI5 intron in COX1.Cytochrome c oxidase (CcO) 3 biogenesis requires the expression and interaction of subunits encoded by mitochondrial and nuclear genomes. A myriad of nuclear-encoded assembly factors mediate CcO biogenesis (1, 2). These factors function in the processing of mitochondrial CcO subunit mRNAs, their translation and insertion into the inner membrane, and formation of metal and heme cofactor centers. Assembly is initiated with the synthesis and maturation of the Cox1 subunit, one of the three catalytic core components (3, 4). COX1 is the one CcO gene that is universally present in the mitochondrial genome. The COX1 mRNA requires processing prior to translation on mitochondrial ribosomes. Cox1 contains three of the redox centers of the enzyme with heme a, a 3 , and Cu B cofactors (5). The last redox center, the binuclear Cu A center, exists within the Cox2 subunit.Mitochondrial genomes of non-metazoan species tend to be larger due to the presence of non-coding regions including introns and additional genes not present in animals (6 -8). In Saccharomyces cerevisiae, introns are commonly found in COX1 as well as COB (the cytochrome b subunit of the bc 1 complex) and the large ribosomal RNA gene (9). Two types of introns, groups I and II, exist in COX1. Some of these introns contain open reading frames encoding maturases, related to DNA endonucleases for group I introns and reverse transcriptases for group II introns (8). Group I intron-containing COX1 alleles have been generated numerous times during evolution due to the invasive nature of the introns containing a DNA homing endonuclease (10). Most commonly used laboratory yeast strains contain up to seven introns within COX1 and in such multiple-intron strains, exons may be as short as 24 -37 bases. No compelling rationale is known why introns are maintained in COX1 and COB.The generation of mature COX1 mRNA transcript requir...