title: The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b.
abstract: ymf39 is a conserved hypothetical protein-coding gene found in mitochondrial genomes of land plants and certain protists. We speculated earlier, based on a weak sequence similarity between Ymf39 from a green alga and the atpF gene product from Bradyrhizobium, that ymf39 might code for subunit b of mitochondrial F(0)F(1)-ATP synthase. To test this hypothesis, we have sequenced ymf39 from five protists with minimally derived mitochondrial genomes, the jakobids. In addition, we isolated the mitochondrial ATP synthase complex of the jakobid Seculamonas ecuadoriensis and determined the partial protein sequence of the 19-kDa subunit, the size expected for Ymf39. The obtained peptide sequence matches perfectly with a 3'-proximal region of the ymf39 gene of this organism, confirming that Ymf39 is indeed an ATP synthase subunit. Finally, we employed statistical tests to assess the significance of sequence similarity of Ymf39 proteins with each other, their nucleus-encoded functional counterparts, ATP4/ATP5F, from fungi and animals and alpha-proteobacterial ATP synthase b-subunits. This analysis provides clear evidence that ymf39 is an atpF homolog, while ATP4/ATP5F appears to be a highly diverged form of ymf39 that has migrated to the nucleus. We propose to designate ymf39 from now on atp4.
authors.affiliation: Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, 2900 Boulevard Edouard Montpetit, Montréal, Québec H3T 1J4, Canada.
authors.forename: Gertraud
authors.initials: G
authors.lastname: Burger
authors.forename: B Franz
authors.initials: BF
authors.lastname: Lang
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Braun
authors.forename: Stefanie
authors.initials: S
authors.lastname: Marx
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel; D056890:Eukaryota / Q000201:enzymology / Q000235:genetics*; D025261:Mitochondrial Proton-Translocating ATPases / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D015800:Protozoan Proteins / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid
chemical_list: D016054:DNA, Protozoan; D015800:Protozoan Proteins; D025261:Mitochondrial Proton-Translocating ATPases