Endosymbiosis

In the field of evolutionary biology, endosymbiosis is the hypothesis that the larger, more complex organelles within the cell actually came to be by one cell ingesting another. Specifically, those organelles are the chloroplast and the mitochondria, which have their own genomes and transcription and translation apparatus. As these organelles are found in most eukaryotes (and mitochondria are found in all), the endosymbiotic events are very important steps in the evolutionary history of "higher" life. Other complex organelles (endoplasmic reticulum, Golgi Complex, lysosomes, peroxisomes, secretory vesicles, and vacuoles) may also be endosymbionts, but these do not have their own genomes, and would have lost them during evolution.

The organelles
Endosymbiotic theory accounts for the origin of two centrally important organelles: the mitochondria and the chloroplasts.

Mitochondria
It has long been known that mitochondria have their own particular genetic code (mitochondrial DNA) which is independent of the DNA within the nucleus of the cell. The general hypothesis is that the ancestral mitochondrion was simply a cell endowed with special proteins involved in the electron transport chain. This cell was consumed by another one, but instead of destroying it, the larger cell preserved the ATP-producing cell and gained a massive competitive advantage. At first, this would have been considered simply a symbiotic relationship, but the lives of the two cells became so intertwined that they now function as a single entity.

The precursor to the mitochondrion was likely an aerobic bacterium that lived inside a large anaerobic cell. Although the lives of the two were independent, they did share a common channel for reproduction (that's important… see "Endosymbiotic theory and symbiosis", below).

Chloroplasts
As with the mitochondria, would have given a large competitive advantage to any cell which consumed but did not destroy the photosynthetic cell. Also like mitochondria, chloroplasts have their own particular genetic code and structure. Comparisons of photosynthetic lineages also suggest that the variety of chloroplasts may have arisen from multiple endosymbiotic events.

The various precursors to modern chloroplasts were all likely some form of (blue-green algae) and, like the chloroplasts, they were originally responsible for their own replication.

Evidence for endosymbiosis
The primary evidence for endosymbiotic events are the genetic make-ups of the organelles in question. Not only do they have their own, separate DNA, but this DNA is also held in a circular loop, an arrangement characteristic of prokaryotes. Furthermore, the organelles have their own support structures, such as ribosomes, DNA/protein synthesis mechanisms, and even an independent plasma membrane.

Endosymbiotic theory and symbiosis
Endosymbiosis may be simply considered a special form of a mutualistic relationship. In the beginning, the two partners benefited each other, but they were not necessary for each other's survival. After all, prokaryotic organisms are able to survive without mitochondria or chloroplasts, using only glycolytic metabolism. Now, however, the relationship is so intimate that they cannot survive without each other (to the point of being one organism). Why is this the case?

As mentioned above, mitochondria and chloroplasts share a reproductive channel with their host cell. That is, when the host passes on its genes, the mitochondria/chloroplasts also get a chance to pass on their genes. Using selfish gene theory as his base, Richard Dawkins suggests that such a system would almost certainly promote increasingly mutualistic relationships, until the point of mutual necessity. In other words, because the actions of the chloroplasts benefit the host and in turn ensure the chloroplasts' successful reproduction, natural selection will shift the nature of the relationship toward the extreme mutualistic end of the symbiotic continuum.

Evidence for endosymbiotic theory

 * Mitochondria and chloroplasts have their own DNA, which is circular and about the size of bacterial chromosomes.
 * Mitochondria and chloroplasts are about the same size (1-10 microns) as modern free-living prokaryotic organisms (bacteria).
 * Mitochondria and chloroplasts have double membranes, the inner one being similar in molecular structure to modern prokaryotic membranes.
 * Mitochondria and chloroplasts divide independently from the cell, through a process akin to binary fission.
 * Mitochondria and chloroplasts have their own ribosomes, which are 70 Svedbergs, like those found in bacteria, rather than 80 Svedbergs, like those in the eukaryotic cytosol.
 * The gamma subunit of the eukaryotic enzyme DNA polymerase III, used in mitochondrial DNA synthesis, is very similar to the bacterial Replication Factor C.
 * Some genes of mitochondria and chloroplasts are clearly related to genes in the genome of the nucleus of the eukaryotic cell as well as to genes in prokaryotes. In these cases, the genes in the mitochondria are more closely related to the genes of prokaryotes than they are to the genes of eukaryotes.

Genetic and metabolic comparisons
An apparent difficulty with the endosymbiosis hypothesis is that several mitochondrial and chloroplast proteins are made using nuclear genes and then shipped to those respective organelles. At first sight, this would imply that these organelles could never have been free-living. However, there is a solution: the organelles have lost genes to the nuclei. Gene loss also explains the variable sizes of these organelles' genomes; it has gone further in some organisms than in others. For example, the jakobid flagellate protist Reclinomonas americana has 69,034 base pairs in its mitochondrial genome, while human mitochondrial genome has around 16,568 bp. Gene loss is also known to have happened in other endosymbiotic organisms, like Buchnera aphidicola, a symbiont of aphids that supplies "essential" amino acids and other nutrients to their hosts, and Rickettsia prowazekii, which causes the disease typhus.

Mitochondria and chloroplasts were apparently acquired only once each. Mitochondria are genetically most closely related to alpha-proteobacteria like Rickettsia; they even have similar respiratory chains. This part takes electrons from food molecules, extracts energy from them, and then combines them with oxygen atoms and hydrogen ions, making water. The energy is then used to string together phosphates to form the energy intermediate ATP.

Likewise, chloroplasts are genetically closest to cyanobacteria; they share with cyanobacteria their architecture of photosynthetic system. This system uses two light-collecting systems, Photosystems I and II, to remove electrons from water molecules, energize them, and add them to organic molecules, making them more hydrogenated. Along the way, the electrons' energy can be tapped to assemble ATP. There are many photosynthetic bacteria other than cyanobacteria, but they all use only one light collector, and they extract electrons from hydrogen sulfide, organic molecules, or similar sources. Overall morphology is also comparable. Chloroplasts and most cyanobacteria have internal membrane systems called thylakoids where the light-collecting systems are concentrated.

How it happened
A common ability of eukaryotic cells is "phagocytosis", the ability to eat things by pulling them in, engulfing them, and letting their cell membranes become bubbles around them ("food vacuoles"). The contents are then digested by having digestive-enzyme-containing lysosomes fuse with them. After the digestion is finished and desired molecules absorbed, this bubble can be pushed toward the cell membrane and its contents released ("exocytosis").

Many protozoans (animal-like protists) eat by phagocytosis, and various animal immune-system cells, called hemocytes in invertebrates and phagocytes in vertebrates, also do this.

But consider the fate of a victim of phagocytosis that escapes being digested. It can live inside its "eater" and even proliferate, as the likes of Buchnera and Rickettsia do. And it is only a small step from there to a closer relationship.

Origin by phagocytosis also explains the double membranes of mitochondria and many chloroplasts; the inner membrane is the organelle's original membrane, while the outer membrane is the original food-vacuole membrane.

More than once
Some chloroplasts do not have only two membranes surrounding them, but sometimes three or four. And among these extra membranes is sometimes found a vestigial cell nucleus, or nucleomorph. This suggests that protists can sometimes make photosynthetic protists act like chloroplasts. The symbionts' nuclei then shrink to nucleomorphs or disappear entirely, with the chloroplasts being left surrounded by extra membranes.

"Primary endosymbiosis" of a prokaryote has apparently happened only a few times, almost certainly only once for mitochondria and probably once for chloroplasts. But the above-described "secondary endosymbiosis" has happened several times, and has sometimes been sequentially repeated to produce a "tertiary endosymbiosis" -- a chloroplast inside of a protist inside of a protist inside of a protist, like some nested Russian doll.

Vestigiality
The genomic apparatus and multiple membranes of mitochondria and chloroplasts are reasonably interpreted as vestigial features. They have only limited function and a structure that suggests an origin from more-highly-developed features.

And these organelles themselves can become vestigial. An interesting example is hydrogenosomes, structures in certain mitochondrion-less ("amitochondriate") protists that release hydrogen. These organelles have no internal genomes, but they have proteins which are recognizably related to mitochondrial ones. This suggests that they are mitochondria that have lost their genomes, and thus have only a broken respiratory chain that combines electrons directly with hydrogen ions, instead of extracting energy from them and combining them with oxygen.

There is also some controversy over whether mitochondrion-less protists never had them (primary) or lost them (secondary); cases of the latter can be recognized by the continued presence of genes for proteins typical of mitochondria.

Not only mitochondria but also chloroplasts can become vestigial. Apicomplexan protists like Toxoplasma gondii and Plasmodium falciparum contain an organelle called the apicoplast, which makes fatty acids, and which has its own genome. Sequencing of this genome reveals it to be a vestigial chloroplast, one that no longer photosynthesizes.

The rest of the cell also?
Finally, endosymbiosis may even explain the origin of eukaryotic cells themselves. The "hydrogen hypothesis" states that a hydrogen-consuming archaebacterium took up residence inside of a hydrogen-producing eubacterium (eubacteria: most familiar prokaryotes like proteobacteria and cyanobacteria; archaebacteria: methanogens and some other oddballs). This hypothesis explains why eukaryote informational systems are archaebacterium-like, while their metabolism is usually eubacterium-like. It also explains why the nucleus is surrounded by its own membrane, and why the cell's outer membrane is eubacterium-like (straight-chain esters) rather than archebacterium-like (branched-chain ethers). It even explains why there are some eukaryotic proteins which are more distantly related to their eubacterial counterparts than mitochondrial ones are; such relationships may make it difficult to distinguish primary from secondary mitochondrion-lessness.

A further twist has been proposed by Hyman Hartman: the "chronocyte" hypothesis. He has identified several "Eukaryote Signature Proteins", which do not have close relatives in either eubacteria or archaebacteria; several of them are involved in various eukaryote-specific features, like the eukaryotic cytoskeleton and internal signaling (calmodulin, inositol, etc.). He also proposes that the chronocyte had had a RNA genome instead of a DNA one, thus making it a relic of the proposed RNA world.

Its first endosymbiont was an archaebacterium, which became the nucleus. It was likely from Euryarchaeota (methanogens, etc.) on account of similar structure of genome-binding proteins (eukaryotic histones, etc.). The chronocyte's RNA genome was eventually copied into the nucleus's DNA genome by reverse transcriptases, likely being more faithfully replicated there. Various eubacteria later became symbionts; only mitochondria and chloroplasts have kept an approximation of their original cell structure.