Evolution of flagella

These models argue that cilia developed from pre-existing components of the eukaryotic cytoskeleton (which has tubulin and dynein – 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 intermediate stage between spindle and cilium would be a non-swimming appendage made of microtubules with a function subject to natural selection, such as increasing surface area, helping the protozoan 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.

Regarding the origin of the individual protein components, a paper on the evolution of dyneins[2][3] shows that the more complex protein family of ciliary dynein has an apparent 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.

These models argue that the cilium evolved from a symbiotic Gracilicutes (ancestor of spirochete and Prosthecobacter) that attached to a primitive eukaryote or archaebacterium (archaea).

The modern version of the hypothesis was first proposed by Lynn Margulis.[4] 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. Margulis did strongly promote and publish versions of this hypothesis until the end of her life.[5]

One primary point in favor of the symbiotic hypothesis was that there are eukaryotes that use symbiotic spirochetes as their motility organelles (some parabasalids inside termite guts, such as Mixotricha and Trichonympha). This is an example of co-option and the flexibility of biological systems, and the proposed homologies that have been reported between cilia and spirochetes have stood up to further scrutiny.

Margulis' hypothesis suggests that an archaea acquired tubulin proteins from a eubacter ancestor of Prosthecobacter. However, the homology of tubulin to the bacterial replication and cytoskeletal protein FtsZ (see Prokaryotic cytoskeleton), which was apparently native in archaea, suggesting an endogenous origin of tubulin rather than a symbiotic transfer.

Eubacterial flagellum is a multifunctional organelle. It is also one of a range of motility systems in bacteria. The structure of the organelle appears like a motor, shaft and a propeller.[8] However, the structure of eubacterial flagellae varies based on whether their motor systems run on protons or sodium, and on the complexity of the flagellar whip.[9] The evolutionary origin of eubacterial flagellae is probably an example of indirect evolution. A hypothesis on the evolutionary pathway of the eubacterial flagellum argues that a secretory system evolved first, based around the SMC rod- and pore-forming complex. This is presumed to be the common ancestor of the type-III secretory system and the flagellar system. Then, an ion pump was introduced to this structure which improved secretion. The ion pump later became the motor protein. This was followed by the emergence of the proto-flagellar filament as part of the protein-secretion structure. Gliding-twitching motility arose at this stage or later and was then refined into swimming motility.[8]