Mitochondrial DNA organization is variable

KEY CONCEPTS:

• Animal cell mitochondrial DNA is extremely compact and typically codes for 13 proteins, 2 rRNAs, and 22 tRNAs.
• Yeast mitochondrial DNA is 5× longer than animal cell mtDNA because of the presence of long introns. 

Animal mitochondrial DNA is extremely compact. There are extensive differences in the detailed gene organization found in different animal phyla, but the general principle is maintained of a small genome coding for a restricted number of functions. In mammalian mitochondrial genomes, the organization is extremely compact. There are no introns, some genes actually overlap, and almost every single base pair can be assigned to a gene. With the exception of the D loop, a region concerned with the initiation of DNA replication, no more than 87 of the 16,569 bp of the human mitochondrial genome can be regarded as lying in intercistronic regions.

The complete nucleotide sequences of mitochondrial genomes in animal cells show extensive homology in organization (Boore, 1999). The map of the human mitochondrial genome is summarized in Figure 3.39. There are 13 protein-coding regions. All of the proteins are components of the apparatus concerned with respiration. These include cytochrome b, 3 subunits of cytochrome oxidase, one of the subunits of ATPase, and 7 subunits (or associated proteins) of NADH dehydrogenase (Anderson et al., 1981; for review see Clayton, 1984; Attardi, 1985; Gray, 1989).

The five-fold discrepancy in size between the S. cerevisiae (84 kb) and mammalian (16 kb) mitochondrial genomes alone alerts us to the fact that there must be a great difference in their genetic organization in spite of their common function. The number of endogenously synthesized products concerned with mitochondrial enzymatic functions appears to be similar. Does the additional genetic material in yeast mitochondria represent other proteins, perhaps concerned with regulation, or is it unexpressed?

The map shown in Figure 3.40 accounts for the major RNA and protein products of the yeast mitochondrion. The most notable feature is the dispersion of loci on the map.

The two most prominent loci are the interrupted genes box (coding for cytochrome b) and oxi3 (coding for subunit 1 of cytochrome oxidase). Together these two genes are almost as long as the entire mitochondrial genome in mammals! Many of the long introns in these genes have open reading frames in register with the preceding exon (see 26.5 Some group I introns code for endonucleases that sponsor mobility). This adds several proteins, all synthesized in low amounts, to the complement of the yeast mitochondrion.

The remaining genes are uninterrupted. They correspond to the other two subunits of cytochrome oxidase coded by the mitochondrion, to the subunit(s) of the ATPase, and (in the case of var1) to a mitochondrial ribosomal protein. The total number of yeast mitochondrial genes is unlikely to exceed ~25.