Surprisingly, the size of the mtDNA, the number and nature of the proteins it encodes, and even the mitochondrial genetic code itself vary greatly between different organisms. The mtDNAs of most multicellular animals are approximately 16-kb circular molecules that encode intron-less genes compactly arranged on both DNA strands. Vertebrate mtDNAs encode the two rRNAs found in mitochondrial ribosomes, the 22 tRNAs used to translate mitochondrial mRNAs, and 13 proteins involved in electron transport and ATP synthesis. The smallest mitochondrial genomes known are found in Plasmodium, a genus of single-celled obligate intracellular parasites that cause malaria in humans. Plasmodium mtDNAs are only about 6 kb, encoding three proteins and the mitochondrial rRNAs.

The mitochondrial genomes of a number of different metazoans have now been sequenced, revealing that mtDNAs from all these sources encode essential mitochondrial proteins that are synthesized on mitochondrial ribosomes (Figure 12-10). Most mitochondrially synthesized polypeptides identified thus far are subunits of multimeric complexes used in electron transport or ATP synthesis. However, most of the proteins localized in mitochondria, such as those involved in the processes listed at the top of Figure 12-10 and Table 12-1, are encoded by nuclear genes, synthesized on cytosolic ribosomes, and imported into the organelle by processes discussed in Chapter 13.

Plant mitochondrial genomes are many times larger than those of metazoans. For instance, Arabidopsis thaliana, a member of the mustard weed family, has 366 kb of mtDNA. The largest known mitochondrial genome, about 2 Mb, is found in cucurbit plants (e.g., melon and cucumber). Most plant mtDNA does not encode proteins, but rather consists of long introns, pseudogenes, mobile DNA elements restricted to the mitochondrial compartment, and pieces of foreign (chloroplast, nuclear, and viral) DNA that were probably inserted into plant mitochondrial genomes during their evolution. Duplicated sequences also contribute to the greater length of plant mtDNAs.

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Differences in the numbers of genes in the mtDNA from various organisms most likely reflect the movement of DNA between mitochondria and the nucleus during evolution. Direct evidence for this movement comes from the observation that several proteins encoded by mtDNA in some species are encoded by nuclear DNA in other, closely related species. A striking example of this phenomenon involves the coxII gene, which encodes subunit 2 of cytochrome c oxidase, which constitutes complex IV in the mitochondrial electron-transport chain (described in detail below). This gene is found in mtDNA in all multicellular plants studied except for certain related species of legumes, including the mung bean and the soybean, in which the coxII gene is nuclear. The coxII gene is completely missing from mung bean mtDNA, but a defective coxII pseudogene that has accumulated many mutations can still be recognized in soybean mtDNA.

Many RNA transcripts of plant mitochondrial genes are edited, mainly by the enzyme-catalyzed conversion of selected C residues to U, and occasionally of U to C. (RNA editing is discussed in Chapter 10.) Indeed, the nuclear coxII gene of the mung bean corresponds more closely to the edited coxII mtDNA-encoded mRNA transcripts in other legumes with functional coxII mtDNA than to their unedited mtDNA-encoded coxII genes. These observations are strong evidence that the coxII gene moved from the mitochondrion to the nucleus during mung bean evolution by a process that involved an edited, mRNA intermediate. Presumably this movement involved a reverse-transcription mechanism and insertion into a nuclear chromosome. This process would be similar to that by which processed pseudogenes are generated in the nuclear genome from nucleus-encoded mRNAs.

In addition to the large differences in the sizes of mitochondrial genomes among eukaryotes, the structure of the mtDNA also varies greatly. As mentioned above, mtDNA in most animals is a circular molecule of 6–16 kb. However, the mtDNA of many organisms, such as the protist Tetrahymena, exists as linear head-to-tail repeats. In the most extreme examples, the mtDNA of the protist Amoebidium parasiticum is composed of several hundred distinct short linear molecules. And the mtDNA of Trypanosoma is composed of multiple maxicircles concatenated (interlocked) to thousands of minicircles encoding guide RNAs involved in editing the sequence of the mitochondrial mRNAs encoded in the maxicircles.