title: A complex organization of the gene encoding cytochrome oxidase subunit 1 in the mitochondrial genome of the dinoflagellate, Crypthecodinium cohnii: homologous recombination generates two different cox1 open reading frames.
abstract: In the course of investigating mitochondrial genome organization in Crypthecodinium cohnii, a non-photosynthetic dinoflagellate, we identified four EcoRI fragments that hybridize to a probe specific for cox1, the gene that encodes subunit 1 of cytochrome oxidase. Cloning and sequence characterization of the four fragments (5.7, 5.1, 4.1, 3.5 kilobase pairs) revealed that cox1 exists in four distinct but related contexts in C. cohnii mtDNA, with a central repeat unit flanked by one of two possible upstream (flanking domain 1 or 2) and downstream (flanking domain 3 or 4) regions. The majority of the cox1 gene is located within the central repeat; however, the C-terminal portion of the open reading frame extends into flanking domains 3 and 4, thereby creating two distinct cox1 coding sequences. The 3'-terminal region of one of the cox1 reading frames can assume an elaborate secondary structure, which potentially could act to stabilize the mature mRNA against nucleolytic degradation. In addition, a high density of small inverted repeats (15-22 base pairs) has been identified at the 5'-end of cox1, further suggesting that hairpin structures could be important for gene regulation. The organization of cox1 in C. cohnii mtDNA appears to reflect homologous recombination events within the central repeat between different cox1 sequence contexts. Such recombining repeats are a characteristic feature of plant (angiosperm) mtDNA, but they have not previously been described in the mitochondrial genomes of protists.
authors.affiliation: Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Room 8F-2, Tupper Medical Building, 5859 University Avenue, Halifax, Nova Scotia B3H 4H7, Canada.
authors.forename: J E
authors.initials: JE
authors.lastname: Norman
authors.forename: M W
authors.initials: MW
authors.lastname: Gray
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D004272:DNA, Mitochondrial / Q000235:genetics; D016054:DNA, Protozoan / Q000235:genetics; D004141:Dinoflagellida / Q000201:enzymology* / Q000235:genetics*; D003576:Electron Transport Complex IV / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D015870:Gene Expression; D017125:Genes, Protozoan; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D021122:Protein Subunits; D016053:RNA, Protozoan / Q000737:chemistry / Q000235:genetics; D011995:Recombination, Genetic; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004272:DNA, Mitochondrial; D016054:DNA, Protozoan; D021122:Protein Subunits; D016053:RNA, Protozoan; D003576:Electron Transport Complex IV