Structure of the mitochondrial URFA6L gene and tRNA(Lys) gene from CARP

The carp mitochondrial URFA6L gene consists of 165 base pairs. The overall structural organization of the gene is very similar to that of the Xenopus URFA6L gene. Their nucleotide sequences exhibit 68% homology. The carp URFA6L gene encodes a protein of 54 amino acids. The amino acid composition of the protein is unusual because almost half of the residues consist of 5 hydrophobic amino acids (proline, tryptophan, leucine, isoleucine and tyrosine). A comparison between the amino acid sequences of 5 vertebrate URFA6L proteins and the yeast ATPase 8 showed that they have weak but very important common structural features, suggesting that the vertebrate URFA6L proteins may function as ATPase8. The nucleotide sequence of the lysine tRNA gene from carp has been determined and represented in clover-leaf secondary structure. Similar to amphibian and mammalian mitochondrial tRNA(Lys) genes, the carp mitochondrial tRNA(Lys) gene also has some unusual structural features as compared with its cytoplasmic counterpart. A comparison between the nucleotide sequences of the tRNA(Lys) gene from 7 vertebrates showed that the most conservative portions are the anticodon loop, nucleotides 8 and 9, the variable loop, the anticodon stem and the aminoacyl stem. The least conservative portions are the D-loop and the T-loop. These structural features may show that the mitochondrial tRNA(Lys) has a different interaction with mitochondrial ribosome.