6.14: Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts undergo binary fission and equally separate their DNA into the daughter organelles as observed in prokaryotes. Furthermore, ribosomes in both mitochondria and chloroplasts are sensitive to antibacterial antibiotics.

Prokaryotic genomes have millions of base pairs and thousands of genes; mitochondrial and chloroplast genomes, except in a few plants, are much smaller with numbers of base pairs in the thousands with a few hundred genes. This difference in genome size occurred because, during evolution, significant parts of primitive mitochondrial and chloroplast genomes were exported to the nucleus. This export of genes made them dependent on the nuclear genome for the supply of some of the proteins required for their biogenesis.

The different evolutionary paths taken by animals and plants have resulted in significant differences between genomes of animal mitochondria and plant mitochondria and chloroplasts. Animal mitochondrial genomes are smaller than plant mitochondrial and chloroplast genomes. Also, similar to most prokaryotic genomes, animal mitochondrial genomes do not carry any introns. However, introns are present in the genomes of both plant mitochondria and chloroplasts. Compared to mitochondrial genomes, chloroplast genomes show less variation in size and structure and also contain more genes. For example, the number of genes present in the chloroplast genome of Arabidopsis thaliana is almost double of the genes present in its mitochondrial genome. Furthermore, chloroplast genomes are more similar to their prokaryotic counterparts than the mitochondrial genome as they are similar in their regulatory sequences and arrangement of many gene clusters.

Primitive predator cells internalized bacteria that later evolved into mitochondria, forming eukaryotic cells. Photosynthetic cyanobacteria also formed symbiotic relationships with some of these eukaryotic cells and eventually developed into the chloroplast.

The present-day mitochondrial and chloroplast genomes are the remnants of these ancestral prokaryotic genomes.

Compared to mitochondrial genomes, the genomes of current day prokaryotes are large such as in Escherichia coli which contain around 5 million bps and nearly 5000 genes.

The human mitochondrial genome is almost 17,000 bps long and contains 37 genes - whereas the mitochondrial genome of Arabidopsis thaliana, a flowering plant, has over 350,000 bps but contains only 57 genes.

Compared to current day cyanobacterial genomes, like the Synechocystis genome which has around 3.5 million bps and carries approximately 3200 genes, the chloroplast genome among terrestrial plants has up to 200,000 bps contains 120-135 genes. 

Even though they are much smaller, both mitochondrial and chloroplast genomes are similar to the prokaryotic genome in several ways. Their DNA does not associate with histone proteins and is usually circular and double-stranded, similar to that of bacterial plasmids. 

Compared to the mitochondrial genome, the chloroplast genome more closely resembles the prokaryotic genome. Both chloroplast and prokaryotic genomes have quite similar DNA sequences for transcription promoters and terminators.

Additionally, animal mitochondrial genomes are generally smaller than the mitochondrial genome in plants, as both chloroplast and plant mitochondrial genomes have introns that are absent in most animal mitochondrial genomes.