An important feature of eukaryotes when discussing their evolution is that they are believed to have originally lacked cell walls or a rigid membrane as found in most prokar-yotes. These early eukaryotes would have needed some kind of cytoskeleton to maintain integrity and shape. Cytoskeletal elements are also involved in eukaryotic reproduction, mobility, and the ability to endocytoze. Curiously, no solid evidence exists for the evolution of the cytoskeleton from some prokaryotic precursor (though actin and tubulin have weak similarity to archeon proteins). Thus, it seems likely that the cytoskeleton evolved largely de novo within the early eukaryote and also that many of the structural and functional characteristics of modern eukar-yotes were possibly present in some of the earliest eukaryotes. Reasons for the loss of a cell wall are unclear though it may have been in response to bacteria-secreted antibiotics that often target cell walls.
Probably the simplest theory for the origin of eukaryotes is that the proto-eukaryote diverged from an archeon and that it later derived its bacterial characteristics from its proto-mitochondrial symbiote; however, another popular theory holds that a bacteria and archea genomes fused prior to the acquisition of the mitochondrion ancestor. In these scenarios it is unclear whether the early eukaryote possessed a nucleus before the mitochon-drial event or whether it developed afterwards. Some hypothesize that the nucleus must have been in place prior to prevent harmful genetic interactions with the proto-mitochondria genome, others that the nucleus evolved in response to the acquisition.
Other theories hold that the nucleus is the result of a host bacteria fusing with an archeon or virus (something resembling mimiviruses which have rather large genomes and are less dependent on their hosts cellular machinery; referred to as viral eukaryogenesis). In some versions the bacterial host is RNA-based and the genes controlling the manipulation of genetic code were replaced by those of the DNA-based archeon or virus, leaving the other cellular machinery bacterial.
Figure 1 shows the four major competing theories for the origin of early eukaryotes resulting from ambiguity of two major events. First, have they diverged from an archeon or are they the result of a fusion between an archeon and a bacterium, and second, did eukaryotes exist in an amitochondriate phase during their evolution?
The 'hydrogen hypothesis' proposed by Martin and Muller holds that a methanogen archeon (which metabolizes hydrogen and carbon dioxide and releases methane) endocytozed the future mitochondria and that it provided the host cell with hydrogen and carbon dioxide as by-products of anaerobic respiration. This idea was inspired by hydrogenosomes which are simplified mitochondria often found in anaerobic eukaryotes and are believed to have evolved independently multiple times.
Lynn Margulis has proposed that eukaryotes originated when an archeon developed an ectosymbiotic relationship with a spirochete (a types of bacteria) and eventually their genomes fused; this places an exogenous origin for the flagellum and occurs before acquiring a bacterial endo-symbiont. This idea was inspired when observing that some eukaryotes rely on symbiotic spirochetes for their motility (parabasalids within the termite gut). This theory has many of bacteria-like genes originating from the spirochete and not the later mitochondria. However given that there is little similarity between spirochetes and eukaryo-tic flagella, this theory is currently rather unpopular.
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