Supporting Document: Viral Eukaryogenesis
Hatena is a single celled organism recently discovered in Japan. It is a flagellate and can resemble a plant or animal, acting as predator in one stage of its life, then carrying a photosynthesizing alga inside itself in another, appearing much more like a plant. Researchers believe that this organism is in the process of endosymbiosis where one lifeform incorporates itself into another, resulting in a completely new lifeform, in the same way that plants and animals diverged.
The name is from a Japanese interjection meaning roughly "how odd".
The hydrogen hypothesis is a model proposed by William Martin and Miklos Muller in 1998 that describes a possible way in which the mitochondrion developed in the first eukaryotic cell within the endosymbiotic theory framework.
According to the hydrogen hypothesis the first eukaryotic cell did not appear as a consequence of a primitive host cell engulfing a primitive bacteria, which wasn't fully digested and eventually became the mitochondrion as the current endosymbiotic theory suggests. It claims instead that the host - a methanogen archaea which used hydrogen and carbon dioxide, producing methane - and a primitive eubacteria, the future mitochondrion, which produced hydrogen and carbon dioxide as byproducts of anaerobic respiration, started a symbiotic relationship based on their byproducts.
The idea originated when Martin assisted at a talk by Muller on hydrogenosomes. These occur in anaerobic eukaryotic cells replacing the mitochondrial ATP production role, and producing large amounts of hydrogen and carbon dioxide. One of Muller's slides presented a cluster of methanogens around a hydrogenosome inside a eukaryotic cell they had invaded.
If the hypothesis is correct it would imply that eukaryotes are very close to archaea and appeared relatively late. This contradicts the current view which states that archaea and eukarya split before the modern groups of archaea appeared.
The evolution of flagella is of great interest to biologists because the three known varieties of flagella (eukaryotic, bacterial, and archaebacterial) each represent an extremely sophisticated cellular structure that requires the interaction of many different and finely-tuned systems to function correctly.
There are two competing groups of models for the evolutionary origin of the eukaryotic flagellum (referred to as a cilium below to distinguish it from its bacterial counterpart).
These models argue some version of the idea that the cilium evolved from a symbiotic spirochete that attached to a primitive eukaryote or archaebacterium (archaea). The modern version of the hypothesis was first proposed by Lynn Margulis (as Sagan (1967): Margulis was the first wife of the late Carl Sagan). The hypothesis, though very well publicized, was never widely accepted by the experts, in contrast to Margulis' arguments for the symbiotic origin of mitochondria and chloroplasts.
The primary point in favor of the symbiotic hypothesis is that there are eukaryotes that use symbiotic spirochetes as their motility organelles (some parabasalids inside termite guts). While this is an example of co-option and the flexibility of biological systems, none of the proposed homologies that have been reported between cilia and spirochetes have stood up to further scrutiny. The homology of tubulin to the bacterial replication/cytoskeletal protein FtsZ is a major argument against Margulis, as FtsZ is apparently found native in archaea, providing an endogenous ancestor to tubulin (as opposed to Margulis' hypothesis, that an archaea acquired tubulin from a symbiotic spirochete).
At present the symbiotic hypothesis for the origin of cilia seems to be limited to Margulis and a few of her associates. Margulis is, though, still strongly promoting and publishing a revised version of her hypothesis (Margulis' 1998 book Symbiotic planet: a new look at evolution has some frank autobiographical comments about her support of the symbiotic hypothesis for the origin of the cilium).
Contrasting with the symbiotic models, these models argue that cilia developed from pre-existing components of the eukaryotic cytoskeleton (which has tubulin, dynein, and nexin—also used for other functions) as an extension of the mitotic spindle apparatus. The connection can still be seen, first in the various early-branching single-celled eukaryotes that have a microtubule basal body, where microtubules on one end form a spindle-like cone around the nucleus, while microtubules on the other end point away from the cell and form the cilium. A further connection is that the centriole, involved in the formation of the mitotic spindle in many (but not all) eukaryotes, is homologous to the cilium, and in many cases is the basal body from which the cilium grows.
An obvious intermediate stage between spindle and cilium would be a non-swimming appendage made of microtubules with a selectable function like increasing surface area, helping the protozoan to remain suspended in water, increasing the chances of bumping into bacteria to eat, or serving as a stalk attaching the cell to a solid substrate. One can't argue that such a non-swimming appendage is merely convenient or unlikely to be selectable, as modern protists with analogous non-swimming microtubular appendages do exist and find them perfectly useful, the axopodia of heliozoa being an example.
Regarding the origin of the individual protein components, an interesting paper on the evolution of dyneins12 shows that the more complex protein family of ciliay dynein has an obvious ancestor in a simpler cytoplasmic dynein (which itself has evolved from the AAA protein family that occurs widely in all archea, bacteria and eukaryotes). Long-standing suspicions that tubulin was homologous to FtsZ (based on very weak sequence similarity and some behavioral similarities) were confirmed in 1998 by the independent resolution of the 3-dimensional structures of the two proteins.
As a logical conclusion of the endosymbiotic theory, since modern-day mitochondrial and chloroplast genomes do not contain a full set of housekeeping genes, and lack many that other descendants of their speculative ancestors share, there must have been a loss of genes. However, some of these genes likely migrated to the nucleus, where analogues of these genes are now found.
It is not clear why only a subset of genes have been transferred, when such gene transfer is known to be rapid - on a similar timescale as mutation. Mitochondria and chloroplasts perform redox reactions, which are known to be considerably mutagenic. Such mutagenicity would encourage migration of genes away from the organelles to the nucleus.
The Modern Synthesis established that over time, natural selection acting on mutations could generate new adaptations and new species. But did that mean that new lineages and adaptations only form by branching off of old ones and inheriting the genes of the old lineage? Some researchers answered no. Evolutionist Lynn Margulis showed that a major organizational event in the history of life probably involved the merging of two or more lineages through symbiosis.
In the late 1960s Margulis (left) studied the structure of cells. Mitochondria, for example, are wriggly bodies that generate the energy required for metabolism. To Margulis, they looked remarkably like bacteria. She knew that scientists had been struck by the similarity ever since the discovery of mitochondria at the end of the 1800s. Some even suggested that mitochondria began from bacteria that lived in a permanent symbiosis within the cells of animals and plants. There were parallel examples in all plant cells. Algae and plant cells have a second set of bodies that they use to carry out photosynthesis. Known as chloroplasts, they capture incoming sunlight energy. The energy drives biochemical reactions including the combination of water and carbon dioxide to make organic matter. Chloroplasts, like mitochondria, bear a striking resemblance to bacteria. Scientists became convinced that chloroplasts (below right), like mitochondria, evolved from symbiotic bacteria—specifically, that they descended from cyanobacteria (above right), the light-harnessing small organisms that abound in oceans and fresh water.
When one of her professors saw DNA inside chloroplasts, Margulis was not surprised. After all, that’s just what you’d expect from a symbiotic partner. Margulis spent much of the rest of the 1960s honing her argument that symbiosis (see figure, right) was an unrecognized but major force in the evolution of cells. In 1970 she published her argument in The Origin of Eukaryotic Cells.