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There are two competing groups of models for the 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. 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' successful arguments for the symbiotic origin of mitochondria and chloroplasts.
The only real point in favor of the symbiotic hypothesis is that there apparently actually are eukaryotes that use symbiotic spirochetes as their motility organelles (some parabasalids inside termiteMastotermitidae Kalotermitidae Termopsidae Hodotermitidae Rhinotermitidae Serritermitidae Termitidae Reference: as of 2002-07-26 A termite (also known as a white ant is any member of the order Isoptera a group of social insects that eat wood and other cel guts). While this is a flabbergasting example of co-option and the creativity and 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 tubulinTubulin is the protein which makes up microtubules. Microtubules are assembled from dimers of &alpha and β-tubulin. Each of these subunits has three domains. tubulin is important in the nucleation and polar orientation of microtubule. Tubulin binds G to the bacterial replication/ cytoskeletalThe cytoskeleton is a cellular " scaffolding" or " skeleton" contained, as all other organelles, within the cytoplasm. It is a dynamic structure that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays i protein FtsZ would seem to clinch the case against Margulis, as FtsZ is apparently found native in archaebacteria, providing an endogenous ancestor to tubulin (as opposed to Margulis' hypothesis, that an archaebacterium acquired tubulin from a symbiotic spirochete).
At present the symbiotic hypothesis for the origin of cilia seems to be basically a pet idea of 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 stubborn support of the symbiotic hypothesis for the origin of the cilium).
Contrasting from the symbiotic models, these models argue that cilium developed from pre-existing components of the eukaryotic cytoskeleton (which has tubulin, dyneinDynein is a class of protein found in biological cells and is involved in their reproduction. Dyneins can be divided into two groups: cytoplasmic dynein and axonemal dynein. The axonemal dynein acts to activate a sliding within flagellar microtubules, whe, and nexin , used for other functions of course) as an extension of the mitotic spindleThe mitotic spindle is a structure of the eukaryotic cytoskeleton involved in mitosis and meiosis. It consists of a bundle of microtubules joined at the ends but spread out in the middle, vaguely resembling a spindle in shape, and a wire eggbeater in stru apparatus. The connection can still be seen, first in the various early-branching single-celled eukaryotes that have a microtubuleMicrotubules are protein structures found within cells. They have diameter of ~ 24 nm and varying length from several micrometers to possible millimeters in axons of nerve cells. Organization Microtubules are polymers of tubulin. They are hollow cylinders basal bodyA basal body is a short cylindrical array of microtubules plus their associated proteins found at the base of a eukaryotic cell cilium or flagellum. Serves as a nucleation site for the growth of the axoneme. Closely similar in structure to a centriole., 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 somehow (scientists are unsure of the purpose of the centriole) 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 imagination 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 dyneins (Gibbons, 1995; see also Asai and Koonce, 2001) shows that the more complex protein family of cilial dynein has an obvious ancestor in a simpler cytoplasmic dynein (which itself appears to be a result of a four-fold duplication of a smaller motif). Recently, long-standing suspicions that tubulin was homologous to FtsZ (based on very weak sequence similarity and some behavioral similarities), were impressively confirmed in 1998 by the independent resolution of the 3-dimensional structures of the two proteins.
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