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

In the course of investigating mitochondrial genome organization in Crypthe codinium cohnii, a non-photosynthetic dinoflagellate, we identified four Ec oRI fragments that hybridize to a probe specific for cox1, the gene that en codes subunit 1 of cytochrome oxidase. Cloning and sequence characterizatio n of the four fragments (5.7, 5.1, 4.1, 3.5 kilobase pairs) revealed that c ox1 exists in four distinct but related contexts in C. cohnii mtDNA, with a central repeat unit flanked by one of two possible upstream (flanking doma in 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-termina l 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 struct ure, which potentially could act to stabilize the mature mRNA against nucle olytic degradation. In addition, a high density of small inverted repeats ( 15-22 base pairs) has been identified at the 5'-end of cox1, further sugges ting that hairpin structures could be important for gene regulation. The or ganization of cox1 in C. cohnii mtDNA appears to reflect homologous recombi nation events within the central repeat between different cox1 sequence con texts. Such recombining repeats are a characteristic feature of plant (angi osperm) mtDNA, but they have not previously been described in the mitochond rial genomes of protists.