There are some major evolutionary jumps that seem to have occurred only once. Eukaryotic cells contain membrane-enclosed structures to perform different functions, and they comprise all forms of multicellular life on Earth. They arose from prokaryotes only once in four billion years, and no prokaryotic cells have been found that show intermediate levels of complexity.

Why only once? A recent "Hypothesis" paper in Nature posits that the answer lies in bioenergetics. The mitochondria that produce much of a eukaryotic cell's energy, which were once free living prokaryotes, and still carry their own genomes, now contain only genes essential for energy production. In order to get an equal dose of energy-producing genes, a prokaryote now has to make extra copies of its entire genome, a hurdle that keeps it from evolving a complex genome.

Power to the cells!

Everyone learns in elementary school (fifth grade, usually) that mitochondria are “the powerhouses of the cell.” Mitochondria use aerobic respiration to generate ATP, the form of energy that drives chemical reactions inside the cell, using glucose as the raw material. Specialized enzymes made only in the mitochondria sequentially oxidize the main products derived from glucose, pyruvate and NADH.

In the electron transport chain, electrons are transferred from NADH and FADH2 to O 2 and the incremental release of energy is used to pump protons (H+) into the space between the mitochondria’s inner and outer membranes. The protons' potential energy is used to synthesize ATP from ADP and inorganic phosphate (Pi) in a pathway dubbed oxidative phosphorylation.

Mitochondria use the proton pumps to maintain a potential of 150-200mV across their membranes, for a field strength of almost 30 million volts per meter: the same amount as discharged by a lightning bolt. Since each individual mitochondrion expresses its own genes encoding proteins involved in this respiratory chain, each individual mitochondrion can respond to changes in membrane potential. This proximity of the genes regulating oxidative phophsorylation with bioenergetic membranes enhances respiratory rates and thereby ATP generation.

But mitochondria are derived from prokaryotes, which can also localize DNA to their bioenergetic membrane, and are also able to compartmentalize. So again, why haven't they evolved the complexity of eukaryotes? Nick Lane and William Martin suggest that mitochondria, and specifically mitochondrial DNA (mtDNA), enabled an increase in the number of proteins a cell can express by four to six orders of magnitude.

Running the numbers: genomes vs. power

Protein synthesis uses about 75 percent of a cell’s energy; since mitochondria grant a eukaryotic cell 200,000 times more energy than a prokaryotic cell, they allow a eukaryotic cell to express 200,000 more genes. Another way to look at this is that eukaryotes are thus not under the stringent selective pressure that prokaryotes face—that to remove "extra" DNA.

The prokaryotes that evolved into mitochondria introduced roughly 3,000 new protein families, permitting the development of such complex processes as multicellularity, endomembrane trafficking, and even sexual reproduction. By removing the selective pressure to get rid of these genes, mitochondria also afforded eukaryotes the luxury of DNA that does not encode proteins, including regulatory elements, introns, and microRNAs. These also foster complexity.

The key is that the mitochondrial genome is small but highly specialized, maintaining only those genes required for oxidative phosphorylation. The remainder of the genome was taken up by the chromosomes of the host cell. Because prokaryotes lack anything like mitochondrial DNA (mtDNA), they can't localize the production of the respiratory machinery to specific locations. (They do have small DNA plasmids, but none of these contain all the respiratory chain.) Instead, big bacteria have to copy their entire genome many times over.

The net result is that, even though eukaryotes have larger genomes, they carry far less DNA for a cell of their size than a prokaryote would. The giant bacterium Epulopiscium can have up to 200,000 copies of its 3.8 million-base (Mb) genome, saddling it with 760,000Mb of DNA; a similarly sized eukaryote with 10,000 copies of a mitochondrial genome must sustain only 6,000Mb of nuclear DNA; the mtDNA is practically a rounding error.

Eukaryotes thus have 104 times more power per Mb of DNA—more power per gene—than prokaryotes. This is what enabled them to develop complexity.

Room to grow a genome

By sequestering the essential metabolic genes into high copy number, ATP generating organelles and shunting the remaining genes into the nuclear chromosomes, mtDNA freed up room in eukaryotic genomes for new and larger genes and proteins. Eukaryotic proteins have more complex structures, with as many as five times as many protein folds as prokaryotic proteins. Although the opportunity for complexity evolved only once, it has veered in many directions since then, giving us animals, plants, fungi, and protists.

Like any conscientious scientists, Lane and Martin encourage us to try to disprove their hypothesis. The existence of a primitive eukaryote without mitochondria would disprove it (they note that all eukaryotes had mitochondria at some point, although some have lost them). Another problem for their model would be giant prokaryotes with either membrane associated plasmids devoted to generating bioenergy or with high respiratory rates but without lots of copies of their genome. A prokaryote with a haploid genome the size of a eukaryote’s would disprove it as well.

But until any of these are found, they maintain that the lack of prokaryote-to-eukaryote intermediates is due to a bioenergetic constraint on the size of the prokaryotic genome, and that endosymbiosis was the critical step that allowed complexity to develop in eukaryotes.

Nature, 2010. DOI: 10.1038/nature09486 (About DOIs).

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