- Mitochondrial DNA (mtDNA) is an independent DNA genome, usually circular, that is located in the mitochondrion.
- Chloroplast DNA (ctDNA) is an independent genome (usually circular) found in a plant chloroplast.
- Organelle genomes are usually (but not always) circular molecules of DNA.
- Organelle genomes code for some but not all of the proteins found in the organelle.
Most organelle genomes take the form of a single circular molecule of DNA of unique sequence (denoted mtDNA in the mitochondrion and ctDNA in the chloroplast). There are a few exceptions where mitochondrial DNA is a linear molecule, generally in lower eukaryotes.
Usually there are several copies of the genome in the individual organelle. Since there are multiple organelles per cell, there are many organelle genomes per cell. Although the organelle genome itself is unique, it constitutes a repetitive sequence relative to any nonrepetitive nuclear sequence.
Chloroplast genomes are relatively large, usually ~140 kb in higher plants, and <200 kb in lower eukaryotes. This is comparable to the size of a large bacteriophage, for example, T4 at ~165 kb. There are multiple copies of the genome per organelle, typically 20-40 in a higher plant, and multiple copies of the organelle per cell, typically 20-40.
Mitochondrial genomes vary in total size by more than an order of magnitude. Animal cells have small mitochondrial genomes, ~16.5 kb in mammals. There are several hundred mitochondria per cell. Each mitochondrion has multiple copies of the DNA. The total amount of mitochondrial DNA relative to nuclear DNA is small, <1%.
In yeast, the mitochondrial genome is much larger. In S. cerevisiae, the exact size varies among different strains, but is ~80 kb. There are ~22 mitochondria per cell, which corresponds to ~4 genomes per organelle. In growing cells, the proportion of mitochondrial DNA can be as high as 18%.
Plants show an extremely wide range of variation in mitochondrial DNA size, with a minimum of ~100 kb. The size of the genome makes it difficult to isolate intact, but restriction mapping in several plants suggests that the mitochondrial genome is usually a single sequence, organized as a circle. Within this circle, there are short homologous sequences. Recombination between these elements generates smaller, subgenomic circular molecules that coexist with the complete, "master" genome, explaining the apparent complexity of plant mitochondrial DNAs.
With mitochondrial genomes sequenced from many organisms, we can now see some general patterns in the representation of functions in mitochondrial DNA (for review seeLang, Gray, and Burger, 1999). Figure 3.38 summarizes the distribution of genes in mitochondrial genomes. The total number of protein-coding genes is rather small, but does not correlate with the size of the genome. Mammalian mitochondria use their 16 kb genomes to code for 13 proteins, whereas yeast mitochondria use their 60-80 kb genomes to code for as few as 8 proteins. Plants, with much larger mitochondrial genomes, code for more proteins. Introns are found in most mitochondrial genomes, although not in the very small mammalian genomes.
The two major rRNAs are always coded by the mitochondrial genome. The number of tRNAs coded by the mitochondrial genome varies from none to the full complement (25-26 in mitochondria). This accounts for the variation in Figure 3.38.
The major part of the protein-coding activity is devoted to the components of the multisubunit assemblies of respiration complexes I-IV. Many ribosomal proteins are coded in protist and plant mitochondrial genomes, but there are few or none in fungi and animal genomes. There are genes coding for proteins involved in import in many protist mitochondrial genomes.