# Link between sea and land animals found

Discussion in 'Biology & Genetics' started by KennyJC, Apr 6, 2006.

1. ### valichRegistered Senior Member

Messages:
3,501
That Eukaryote "Tree of Life" page makes a lot of references to endosymbiosis with protists. Prokaryotes aren't even considered as a seperate branch anymore. Instead, Archae are now seen as a seperate branch with Eubacteria being the third. They really show an excellent photo of symbiotic bacteria attached to a flagellate. And then they come right out and state: "the formation of the eukaryotic cell was a consequence of genome fusions between a host cell and endosymbionts representing distinct evolutionary lineages...The origins of mitochondria from cyanobacteria.... Chloroplasts are also rooted in endosymbiosis when a cyanobacterium took up residence in an ancient eukaryote. These primary endosymbionts were destined to become the chloroplasts which are found in eukaryotic algae." You might want to browse through some of the links on the righthand side of the page and also the reference links at the bottom.

Dinoflagellates, genus Symbiodinium, commonlly called zooxanthellae, are endosymbionts that form coral reefs by providing their hosts with energy for the carbonate deposition.

I'm focussing in on endosymbiosis in flagella development with flagellates, dinoflagellates, bacteria and algae.

3. ### Walter L. WagnerCosmic Truth SeekerValued Senior Member

Messages:
2,551
Valich:

When I asserted that the single-celled organisms left no fossil records, I meant they left no fossil records of their cellular mechanisms. I am aware of the ancient cyanobactria, which apparently clumped in shallow seas, leaving fossilized formations of their entire mass. Whether each individual cell is identifiable as such I'm uncertain about, but certainly the development of the spindle apparatus, and the mechanistics of mitosis-meiosis left no fossil imprints -- instead we are left with extant descendants from which me must deduce origins.

So you agree I was correct that we cannot deduce the ages of ancient fossils from their DNA, but instead use the "biological clock" of the extant descendants. Mitochondrial DNA is sometimes used for this (such as estimating that "Eve" lived circa 120,000 years ago, as per a report I read, since the mitochondria are not present in the sperm, but only in the egg, leaving a trace of DNA for the females only), and I'm sure the much larger genome of the chromosomes allows for certain select genes, preserved in both lines, to serve as such a "clock". However, it has no where near the accuracy of radiometric and stratigraphic dating, and makes many assumptions regarding life habits.

Incidentally, the C-14 was previously accurate to only about 30,000 to 40,000 years ago, but mass-spectroscopy allows for detection of smaller amounts of C-14, pushing its accuracy back to about 60,000 to 80,000 years ago. (Due to the 'short' half-life of C-14 being 5,730 years.). Ancient fossils cannot use that technique, as the C-14 decays to nothing measureable after about 100,000 years (20- half-lifes)

However, the above being said, I have read some reports that some fossils from 60 mya did have some residual DNA still intact, and of course amber fossils likely have intact DNA, from which some direct biological clock detective work might be ascertainable.

On another note, today's MSNBC is reporting that Nature is publishing an article about interbreeding between a human ancestor (Toumai) and a chimpanzee ancestor some 5 mya, apparently about 4 million years after the initial split, and that the descendants of the hybrid product of that union is now the modern chimp.

It makes sense that such things occurred with a certain degree of frequency back then; after all, it is now postulated that the HIV virus was acquired in people when someone had sex with a chimpanzee, where apparently the HIV virus ancestor also exists. But then again, maybe someone gave it to the chimps?

5. ### valichRegistered Senior Member

Messages:
3,501
This website provides extreme detail about the composition, length, structure, and function of flagellum, and has numerous links to the evolution and the various diverse containing species in the three groups: Bacteria, Archaea, and Eukaryotes. You could spend days following all their weblinks so there's no use in me posting what they state: http://gouvieux.fr.infovx.com/en/flagellum

7. ### valichRegistered Senior Member

Messages:
3,501
Yes, as far as I know, any solid "absolute dating" beyond about 1 mya is from the rock that the fossils are found in. Evidence is left of cellular mechanisms, but not in the sense that you refer to such as of active metabolic changes: mitosis-meiosis.

As cited above, there are about five distinct computational methods in use to arrive at the organisms age without relying on the geological stratum. You can refer to these loosely as "biological clocks," but strictly speaking, the one method called the "molecular clock" is now considered innacurate. For example, we know that the "Cambrian Explosion" occurred in large part due to the rapid increase in atmospheric oxygen. So a number of factors alter a strict age determination based on a "biological clock."

Acritarchs are known from 1400 mya with considerable diversity by 1300 mya, but then crashed 800 mya. Apparently we don't really know what they are but they serve as a great out source marker for dating.

"The acritarchs show their greatest diversity during the Cambrian, Ordovician, Silurian and Devonian. The nature of some Acritarchs can be identified by their structure. A few can be tentatively identified by the presence of specific chemicals associated with the fossils....Acritarchs are small organic structures. In general, any small, non-acid soluble (i.e. non carbonate, non-silicate) organic structure that can not otherwise be accounted for is an acritarch. Most acritarchs are surely remains of single celled lifeforms. They are found in sedimentary rocks from the present back into the Precambrian. They are easily isolated from limestones with hydrochloric acid, and can also be isolated from silica rich rocks using hydrofluoric acid. They are excellent candidates for index fossils to be used for formation dating in the Palaeozoic and when other fossils are not available. They are also useful for palaeoenvironmental interpretation. Acritarchs include the remains of several quite different kinds of organisms including bacteria and dinoflagellates. The nature of the creatures associated with older acritarchs is generally not clear, though many are probably related to unicellular marine algae." http://gouvieux.fr.infovx.com/en/acritarch

Yeh, the MSNBC article is very interesting but I'll have to wait till it's printed in the journal Nature to read its entirety. Spurious started a new thread on that a few weeks ago on Sciforum: "New genus of monkey discovered." The original article that he posted shows a picture of its skull: http://news.bbc.co.uk/2/hi/science/nature/4759535.stm

8. ### Walter L. WagnerCosmic Truth SeekerValued Senior Member

Messages:
2,551
I thought the new genus of monkey thread was about a different discovery, namely an actual new extant genus of monkey; whereas the Nature article will be about mating between pre-humans and pre-chimpanzees, giving rise to a hybrid which is the ancestor of our extant chimpanzee, using an entirely DNA analysis.

The eukaryote web page is interesting, and does detail that the mitochondria arose as endosymbiosis of bacteria, which idea has been around at least since the early 1970s when I first heard about it, and likely quite a few years before that. It has also suggested that some of the eukaryotes that were previously thought to be ancestral due to their lack of mitochondria, are now believed to have lost their mitochondria (reduction), with some of the mitochondrial DNA now found in the chromosomes.

Likewise, it details several routes for the alga and land plants (as I previously noted) by various cyanobacterial endosymbiots.

Unfortunately, it does not detail how a simple eubacteria, with a simple circular DNA, could develop into an advanced eukaryote, even without the mitochondria and cholorploasts.

I suspect that the ingestion and endosybiosis of one type into a larger cell, allowed the now internally-situated bacteria to evolve into a cellular nucleus, but how that occurred, and how it developed larger ribosomes, etc. for DNA transcription compared to the bacterial/mitochondrial ribosomes, etc. is certainly not yet clear to me.

I'm hoping that more work will be done in this area to elucidate those remaining mysteries.

9. ### valichRegistered Senior Member

Messages:
3,501
Apparently these are two different monkey species. The one described in the MSNBC article is called "Toumai" or "Sahelanthropus tchadensis" and the one in the other Sciforum thread is called "Rungwecebus kipunji." The suggestion that we may have been interbreeding with monkeys for 4 million years till full speciation 5.4 mya is going to reek havoc with the creationists. http://www.livescience.com/humanbiology/ap_050406_chad_bones.html

"Evolution of Flagella" http://wiki.cotch.net/index.php/Evolution_of_flagella

"Evolution of Bacterial Flagellum" http://www.talkdesign.org/faqs/flagellum.html

"Evolving the Bacterial Flagellum Through Mutation and Cooption: Part VI....Homology, Design, Analogy, Beginnings....." http://www.idthink.net/biot/flag6/index.html

"Sequencing of Flagellin Genes from Natrialba magadii Provides New Insight into Evolutionary Aspects of Archaeal Flagellins" http://www.bionewsonline.com/o/q/inna_serganova_2002_318.htm

"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)....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....The homology of tubulin to the bacterial replication/cytoskeletal 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).
the archaeal flagellum appears to grow at the base rather than the tip, and is about 15 nanometers (nm) in diameter rather than 20.

Sequence comparison indicates that the archaeal flagellum is homologous to Type IV pili (pili are filamentous structures outside the cell). Interestingly, some type IV pili can retract. Pilus retraction provides the driving force for a different form of bacterial motility called "twitching" or "social gliding" which allows baterial cells to crawl along a surface. Thus type IV pili can, in different bacteria, promote either swimming or crawling.Type IV pili are asembled through the Type II transport system. So far, no species of bacteria is known to use its type IV pili for both swimming and crawling." http://www.aseannewsnetwork.de/articles/content/e/ev/evolution_of_flagella.html

Mol Biol Evol, 2003 Jul, 20(7), 1098 - 112 Epub 2003 May 30.
"The molecular evolution of catalatic hydroperoxidases: evidence for multiple lateral transfer of genes between prokaryota and from bacteria into eukaryota; Klotz MG et al.; The past decade has produced an increasing number of reports on horizontal gene transfer between prokaryotic organisms . Only recently, with the flood of available whole genome sequence data and a renewed intensity of the debate about the universal tree of life, a very few reports on lateral gene transfer (LGT) from prokaryotes into the Eukaryota have been published . We have investigated and report here on the molecular evolution of the gene families that encode catalatic hydroperoxidases . We have found that this process included not only frequent horizontal gene transfer among prokaryotes but also several lateral gene transfer events between bacteria and fungi and between bacteria and the protistan ancestor of the alga/plant lineage." http://www.bionewsonline.com/r/2/prokaryote_c.htm

"Flagellar determinants of bacterial sensitivity to c-phage. Bacteriophage c is known to infect motile strains of enteric bacteria by adsorbing randomly along the length of a flagellar filament and then injecting its DNA into the bacterial cell at the filament base. Here, we provide evidence for a “nut and bolt” model for translocation of phage along the filament: the tail fiber of c fits the grooves formed by helical rows of flagellin monomers, and active flagellar rotation forces the phage to follow the grooves as a nut follows the threads of a bolt." http://www.mansfield.ohio-state.edu/~sabedon/ab_all.htm

"Variations on the classical flagellum, such as different lateral and polar flagella on the same cell, and the periplasmic flagella of spirochaetes. Motility is also conferred by flagella in the domain Archaea, yet these structures bear little similarity to their bacterial counterparts. Rather, archaeal flagella demonstrate similarity to another bacterial motility apparatus, type IV pili. Additional structures involved in bacterial motility include the junctional pore complex and the ratchet structure involved in gliding motility, and the unique contractile cytoskeleton of Spiroplasma....Insight into how changes in the arrangement of the flagellin subunits assembled in the filament lead to a switch in bacterial motility, from swimming to tumbling, has been obtained from flagellin crystals....An intriguing aspect of the polar/lateral flagellation systems in various Vibrio species is that the polar flagellum is sheathed (possibly an extension of the cell membrane) and driven by a sodium ion gradient, while the lateral flagella are unsheathed and driven by a proton gradient.

Perhaps the most unusual case of bacterial flagellation is that of the spirochaetes. Here flagella are located in the periplasm between the outer membrane sheath and cell cylinder, subterminally attached to one end of the cell cylinder. The number of periplasmic flagella and whether the flagella overlap at the centre of the cell varies among species. The flagella function by rotating within the periplasmic space. Unlike some other bacteria in which flagellation depends on environmental changes, the spirochaete periplasmic flagella are expressed throughout the cell's life-cycle and are believed to have vital skeletal and motility functions. Due to their continuous presence, the complex regulatory controls observed for motility gene expression in many bacteria seem to be absent in at least certain spirochaetes.

Spirochaete periplasmic flagella are compositionally some of the most complex yet described. They are comprised of FlaA sheath proteins and usually multiple (two to four) FlaB core proteins. The FlaA proteins are made with a leader peptide and are likely secreted via a sec-dependent pathway into the periplasm before assembly onto the flagellar filament. FlaA proteins bear no sequence similarity to the FlaB proteins which make up the filament proper. The FlaB proteins have N- and C-terminal sequence similarity to other bacterial flagellins and are not processed at their N terminus. They are presumed to be secreted through the hollow basal body–hook structure via the type III mechanism found for other bacterial flagellins.
The spirochaete flagellar motion is driven by the proton-motive force (PMF) and the cellular movement depends on asymmetrical rotation of the two ends of the cell. In other words, when the periplasmic flagella located at either end of the spirochaete are rotating in the same direction the cells do not swim. One of the interesting aspects to be determined for spirochaete motility is how the cell controls the rotation of the flagella at the opposite ends of the cell so that both structures rotate in opposite directions. Since some unique motility genes are believed to exist in spirochaetes it has been speculated that some of these might be present to address this problem.

Fundamental differences between archaeal and bacterial flagella have become obvious from analysis of complete genome sequences of many flagellated archaea. Genes encoding bacterial proteins involved in structure or assembly of flagella have not been reported in archaeal genomes. If archaeal flagella have an anchoring structure it appears to be composed of proteins that are archaea-specific. Even the archaeal flagellins, which compose the major portion of the flagellar filament, lack sequence similarity to bacterial flagellins. In several ways they appear more similar to type IV pilins which themselves form a structure involved in other forms of motility, such as twitching motility (see below). There is sequence similarity between type IV pilins and archaeal flagellins over the first 50 aa, which are extremely hydrophobic. In addition, both type IV pilins and archaeal flagellins are made as preproteins with short positively charged leader peptides. These proteins are processed by specific leader peptidases, distinct from the leader peptidase I equivalent. Mutations in the leader peptidase in either system prevent the assembly of a detectable structure. In the case of the archaeal flagellum this strongly suggests that the assembly mechanism is distinct from the bacterial one involving a type III secretion mechanism with flagellins that lack leader peptides.

In archaea, only one major gene cluster involving up to 12 genes has been reported to be involved with flagellation. Mutations in a number of these genes result in nonflagellated cells. Recently the gene encoding a preflagellin peptidase has been reported. In Methanococcus jannaschii it is part of the large gene cluster involved in flagellation but in other Methanococcus species it is located quite removed from the flagellin gene cluster. All flagellated archaeal species have three conserved genes, termed flaHIJ, located near the genes for the flagellins. Interestingly, FlaI is a homologue of TadA, an ATPase involved in type IV pilus production in Actinobacillus, while FlaJ is similar to TadB, a multitopic membrane protein needed in the same system. In archaea, there are always multiple (2–6) flagellin genes present (Sulfolobus solfataricus appears to be an exception). Thus far the only components of the archaeal flagellum identified are the flagellins themselves, where it appears that the multiple flagellins are all present as structural components of the assembled flagellum. Recent work indicated that the hook protein might in fact be a minor flagellin, FlaB3 in the case of Methanococcus voltae. The flagellins are often, perhaps even universally, posttranslationally modified, usually by glycosylation although only in the case of halobacteria have the associated carbohydrate moieties been determined. Flagellin glycosylation may be necessary for proper flagellar assembly.

Ratchet Structure: Members of the Cytophaga–Flavobacterium group of bacteria appear to glide by a yet different mechanism. Here it seems motility at a rate of 2–10 µm s-1 is the result of the movement of cell surface components. This has been readily demonstrated through the use of latex beads which can be observed to move along the surface of cells in complex paths. One proposed model for gliding in Flavobacterium johnsoniae and related organisms is specific motility proteins anchored in the cytoplasmic and outer membrane. Movement of the cytoplasmic proteins may be driven by the PMF and their interaction with the outer-membrane proteins in a ratcheting mechanism may propel the cells forward. The outer-membrane proteins may be anchored to the peptidoglycan, forming tracks. Several genes have been implicated in gliding motility in F. johnsoniae including three (gldA, gldF and gldG) whose products may form an ATP transporter required for movement. The exact function of any of these proteins in gliding is unknown. Another possibility is that gliding in this organism is due to slime extrusion and subsequent uptake with the gld gene products forming the transporter for import or export.

From: "Prokaryotic Motility Structures," by Sonia L. Bardy, Sandy Y. M. Ng and Ken F. Jarrell, Department of Microbiology and Immunology, Queen's University, Kingston, ON, Canada K7L 3N6. Microbiology 149 (2003), 295-304; DOI 10.1099/mic.0.25948-0. http://mic.sgmjournals.org/cgi/content/full/149/2/295

10. ### valichRegistered Senior Member

Messages:
3,501
Walter: You're referring to where it says "there is now increasing evidence that genes normally found in alpha-proteo bacteria are also present in the nucleus of amitochondriate prostists and that mitochondria were present much earlier than previously thought, but have now been lost from some early eukaryotes (Roger, 1999)" "Reconstructing Early Events in Eukaryotic Evolution," by A. J. Roger, 1999: http://www.botany.ubc.ca/keeling/BIOL332/Papers/Roger99.pdf.
or html version at: http://72.14.203.104/search?q=cache...eukaryotic evolution&hl=en&gl=us&ct=clnk&cd=1

You also state: "I suspect that the ingestion and endosybiosis of one type into a larger cell, allowed the now internally-situated bacteria to evolve into a cellular nucleus, but how that occurred, and how it developed larger ribosomes, etc. for DNA transcription compared to the bacterial/mitochondrial ribosomes, etc. is certainly not yet clear to me."

What about the "RNA-World"? Basal to all eukaryotes, eubacteria, and archaea. You can start with any simple life-form of RNA and then it became engulfed in a simple enclosed membrane structure - a plasma membrane.

11. ### Walter L. WagnerCosmic Truth SeekerValued Senior Member

Messages:
2,551
Valich:

As to your last post - yes, I was referring to the a-mitochondriate protists referenced by the quoted author (Roger, 1999), though I reached it through my originally posted web-page, not the ones you've posted.

And yes, likely RNA preceded DNA for genetic coding. As I recall, though, the mitochondria and the eu-bacteria and the archaea all have ribosomes much smaller than those for the eukaryotes, and they are made of two major sub-units, and they are all comparably sized, compared to the much larger ribosomes utilized for gene transcription by the eukaryotic nucleus (as determined by centrifugal units of mass). However, we now see the RNA used as both the t-RNA, as well as I believe incorporated into the ribosomes, and how such a change from a presumptively more primitive cell utilizing RNA genetic coding to the DNA based genetic coding of extant archaea, eu-bacterial, eukaryotes, etc. is also not known to me.

Somewhere I read that the spindle apparatus were believed by some to be derived from endosymbiots, but I really know very little about that, too. Under the microscope, they suddenly seem to 'appear' whenever a cell begins to undergo mitosis or meiosis, though clearly they must be there all along, though what causes them to become conspicous under the light microscope is also not known to me.

What is interesting about all this, as I've indicated before, is that the more me learn and know, the more we learn how little we know. Anyway, any further enlightenment along those lines would likewise be appreciate.

By the by, I suspect that most casual readers of these posts are not following this thread, as they likely don't have the more in-depth background you seem to possess, or the more general background I happen to have, since this is not my major field of study.

12. ### valichRegistered Senior Member

Messages:
3,501
I think that the reference on the "Tree of Life - Eukaryote" page that states amitochondriate acquired then lost mitochondria is innacurate. I highly doubt that this sequence of evolutionary events (lost their mitochondria - reduction) ever occurred and it appears that this subject is currently hotly debated. The very prestiguous Woods Hole Oceanographic Institution states that:

"It is now widely accepted that the eukaryotes we call protists are far more diverse in cellular organization than the non-protist eukaryote groups—namely animals, plants and fungi. A variety of heterotrophic protists lack classical mitochondria, inhabiting low- oxygen environments such as the guts and tissues of animals, marine or freshwater sediments, and the lower reaches of stratified water bodies. Over the last two decades these 'amitochondriate' organisms have been of great interest to evolutionary biologists, as some may have diverged before the acquisition of the mitochondrion and consequently represent very early stages in the evolution of the eukaryotic cell. Some amitochondriate groups—particularly the largely parasitic trichomonads, diplomonads, and microsporidia— have indeed tended to form the most basal branches in evolutionary trees of eukaryotes, based on molecular sequence comparisons. However the validity of these deep branches has, of late, been vigorously challenged, as has the contention that these organisms lack any trace of having had mitochondria. To date, almost all of the research into amitchondriate protists has focused on those groups with parasitic members. However surveys of sediments and anoxic water bodies reveal a considerable and drastically understudied diversity of free-living, low-oxygen protists, frequently of unclear affinities. In several instances, electron-microscopical studies indicate the absence of classical mitochondria. Detailed morphological data in concert with molecular phylogenies, covering both free-living and parasitic taxa, are leading us towards a more authoritative state regarding the affinities of the amitochondriate protists and whether any groups remain candidates for being primitively amitochondriate relicts of early eukaryotic evolution.”

From: “The evolutionary importance and affinities of 'amitochondriate' protists,”by Virginia Edgcomb, Andrew Roger, and Alastair Simpson. Woods Hole Oceanographic Institution, University of Sydney, Australia, November 4, 1998. http://www.mbari.org/seminars/1998/nov4_simpson.html

"Phylogenetic evidence is presented that primitively amitochondriate eukaryotes containing the nucleus, cytoskeleton, and endomembrane system may have never existed. Instead, the primary host for the mitochondrial progenitor may have been a chimeric prokaryote, created by fusion between an archaebacterium and a eubacterium, in which eubacterial energy metabolism (glycolysis and fermentation) was retained. A Rickettsia-like intracellular symbiont, suggested to be the last common ancestor of the family Rickettsiaceae and mitochondria, may have penetrated such a host (pro-eukaryote), surrounded by a single membrane, due to tightly membrane-associated phospholipase activity, as do present-day rickettsiae. The relatively rapid evolutionary conversion of the invader into an organelle may have occurred in a safe milieu via numerous, often dramatic, changes involving both partners, which resulted in successful coupling of the host glycolysis and the symbiont respiration. Establishment of a potent energy-generating organelle made it possible, through rapid dramatic changes, to develop genuine eukaryotic elements. Such sequential, or converging, global events could fill the gap between prokaryotes and eukaryotes known as major evolutionary discontinuity."
From: http://content.febsjournal.org/cgi/content/full/270/8/1599

"“We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial consortium "Thiodendron latens." By eubacterial-archaebacterial genetic integration, the chimera, an amitochondriate heterotroph, evolved. This "earliest branching protist" that formed by permanent DNA recombination generated the nucleus as a component of the karyomastigont, an intracellular complex that assured genetic continuity of the former symbionts. The karyomastigont organellar system, common in extant amitochondriate protists as well as in presumed mitochondriate ancestors, minimally consists of a single nucleus, a single kinetosome and their protein connector. As predecessor of standard mitosis, the karyomastigont preceded free (unattached) nuclei. The nucleus evolved in karyomastigont ancestors by detachment at least five times (archamoebae, calonymphids, chlorophyte green algae, ciliates, foraminifera). This specific model of syntrophic chimeric fusion can be proved by sequence comparison of functional domains of motility proteins isolated from candidate taxa. Here we outline the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. The common ancestor of all eukaryotes by genome fusion of two or more different prokaryotes became "chimeras" via symbiogenesis. Long term physical association between metabolically dependent consortia bacteria led, by genetic fusion, to this chimera. The chimera originated when an archaebacterium (a thermoacidophil) and a motile eubacterium emerged under selective pressure: oxygen threat and scarcity both of carbon compounds and electron acceptors. The nucleus evolved in the chimera. The earliest descendant of this momentous merger, if alive today, would be recognized as an amitochondriate protist.

Study of conserved protein sequences [a far larger data set than that used by Woese et al.] led Gupta to conclude "all eukaryotic cells, including amitochondriate and aplastidic cells received major genetic contributions to the nuclear genome from both an archaebacterium (very probably of the eocyte, i.e., thermoacidophil group and a Gram-negative bacterium - the ancestral eukaryotic cell never directly descended from archaebacteria but instead was a chimera formed by fusion and integration of the genomes of an archaebacerium and a Gram-negative bacterium.” The eubacterium ancestor has yet to be identified. The archaebacterial sequences, we posit, comes from a Thermoplasma acidophilum-like thermoacidophilic (eocyte) prokaryote. This archaebacterial ancestor lived in warm, acidic, and sporadically sulfurous waters, where it used either elemental sulfur (generating H2S) or less than 5% oxygen (generating H2O) as terminal electron acceptor. As does its extant descendant, the ancient archaebacterium survived acid-hydrolysis environmental conditions by nucleosome-style histone-like protein coating of its DNA and actin-like stress-protein synthesis. The wall-less archaebacterium was remarkably pleiomorphic; it tended into tight physical association with globules of elemental sulfur by use of its rudimentary cytoskeletal system. The second member of the consortium, an obligate anaerobe, required for growth the highly reduced conditions provided by sulfur and sulfate reduction to hydrogen sulfide. Degradation of carbohydrate (e.g., starch, sugars such as cellobiose) and oxidation of the sulfide to elemental sulfur by the eubacterium generated carbon-rich fermentation products and electron acceptors for the archaebacterium. When swimming eubacteria attached to the archaebacterium, the likelihood that the consortium efficiently reached its carbon sources was enhanced. This hypothetical consortium, before the integration to form a chimera, differs little from the widespread and geochemically important "Thiodendron.” The "Thiodendron" stage refers to an extant bacterial consortium that models our idea of an archaebacteria-eubacteria sulfur syntrophic motility symbiosis. The partners in our view merged to become the chimeric predecessor to archaeprotists. The membrane-bounded nucleus, by hypothesis, is the morphological manifestation of the chimera genetic system that evolved from a Thiodendron-type consortium. Each phenomenon we suggest, from free-living bacteria to integrated association, enjoys extant natural analogues.”

Karyomastigonts Preceded Nuclei: The term "karyomastigont" refer to a organellar system observed in certain protists: the mastigont ("cell whip," eukaryotic flagellum, or undulipodium, the [9 (2) + (2)] microtubular axoneme underlain by its [9 (3) + 0)] kinetosome) attached by a "nuclear connector" or "rhizoplast" to a nucleus….The karyomastigont, an ancestral feature of eukaryotes, is present in "early branching protists.” Archaeprotists, are heterotrophic unicells that inhabit anoxic environments. All lack mitochondria. At least 28 families are placed in the phylum Archaeprotista, including archaemoebae (Pelomyxa and Mastigamoeba), metamonads (Retortamonas), diplomonads (Giardia), oxymonads (Pyrsonympha), and the two orders of Parabasalia: Trichomonadida [Devescovina, Mixotricha, Monocercomonas, Trichomonas, and calonymphids (Coronympha, Snyderella)] and Hypermastigida (Lophomonas, Staurojoenina, and Trichonympha). These cells either bear karyomastigonts or derive by differential organelle reproduction (simple morphological steps) from those that do. When, during evolution of these protists, nuclei were severed from their karyomastigonts, akaryomastigonts were generated. Nuclei, unattached, at least temporarily, to undulipodia were freed to proliferate and occupy central positions in cells. Undulipodia, also freed to proliferate, generated larger, faster-swimming cells in the same evolutionary step.

The karyomastigont is the conspicuous central cytoskeleton in basal members of virtually all archaeprotist lineages [three classes: Archamoeba, Metamonads, and Parabasalia. In trichomonads, the karyomastigont, which includes a parabasal body (Golgi complex), coordinates the placement of hydrogenosomes (membrane-bounded bacterial-sized cell inclusions that generate hydrogen). The karyomastigont reproduces as a unit structure. Typically, four attached kinetosomes with rolled sheets of microtubules (the axostyle and its extension the pelta) reproduce as their morphological relationships are retained. Kinetosomes reproduce first, the nucleus divides, and the two groups of kinetosomes separate at the poles of a thin microtubule spindle called the paradesmose. Kinetosomes and associated structures are partitioned to one of the two new karyomastigonts. The other produces components it lacks such as the Golgi complex and axostyle. Nuclear proteobacterial genes were interpreted to have originated from lost or degenerate mitochondria in at least two archaeprotist species Giardia lamblia; Trichomonas vaginalis and in a microsporidian. Hydrogenosomes, at least some types, share common origin with mitochondria. In the hydrogen hypothesis, hydrogenosomes are claimed to be the source of eubacterial genes in amitochondriates. That mitochondria were never acquired in the ancestors we consider more likely than that they were lost in every species of these anaerobic protists. Eubacterial genes in the nucleus that are not from the original spirochete probably were acquired in amitochondriate protists from proteobacterial symbionts other than those of the mitochondrial lineage. Gram-negative bacteria, some of which may be related to ancestors of hydrogenosomes, are rampant as epibionts, endobionts, and even endonuclear symbionts, for example, in Caduceia versatilis.

Karyomastigonts freed (detached from) nuclei independently in many lineages both before and after the acquisition of mitochondria. Calonymphid ancestors of Snyderella released free nuclei before the mitochondrial symbiosis, and Chlamydomonas-like ancestors of other chlorophytes such as Acetabularia released the nuclei after the lineage was fully aerobic. In trophic forms of protists that lack mastigote stages, the karyomastigont is generally absent. An exception is Histomonas, an amoeboid trichomonad cell that lacks an axoneme but bears enough of the remnant karyomastigont structure to permit its classification with parabasalids rather than with rhizopod amoebae. This organellar system appears in the zoospores, motile trophic forms, or sperm of many organisms, suggesting the relative ease of karyomastigont development. The karyomastigont, apparently in some cells, is easily lost, suppressed, and regained. In many taxa of multinucleate or multicellular protists (foraminifera, green algae) and even in plants, the karyomastigont persists only in the zoospores or gametes.

From: “The chimeric eukaryote: Origin of the nucleus from the karyomastigont in amitochondriate protists,” by Lynn Margulis, Michael F. Dolan , and Ricardo Guerrero. Department of Geosciences, Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003; and Department of Microbiology, and Special Research Center Complex Systems (Microbiology Group), University of Barcelona, 08028 Barcelona, Spain. Proceedings of the National Academy of Science, June 20, 2000, vol. 97, no. 13, 6954-6959. http://www.pnas.org/cgi/content/full/97/13/6954

13. ### valichRegistered Senior Member

Messages:
3,501
Walter: Yes, this thread has advanced to be esoteric, but this is a scientific forum (sciforums). CharonZ also has a very advanced background in this field and may contribute. You state "primitive cell utilizing RNA genetic coding to the DNA based genetic coding of extant archaea, eu-bacterial, eukaryotes, etc. is also not known to me."

It goes like this:
preRNA-World> RNA-World > preArchaea >archaebacterium/eubacterium (prokaryokes) > eukaryotes

Walter states: "Somewhere I read that the spindle apparatus were believed by some to be derived from endosymbiots, but I really know very little about that, too. Under the microscope, they suddenly seem to 'appear' whenever a cell begins to undergo mitosis or meiosis, though clearly they must be there all along, though what causes them to become conspicous under the light microscope is also not known to me."

Yes, I've read about this numerous times but never thought of it as a matter of speculation. I'll review it and post. Yes, it is derived by endosymbiosis but there is a unique facter involving the spindle fit. Now you're using the same terminology as stated in the research papers so I can compile a post on that. Getting too late right now, too tired, and still have to walk my dog tonight: Kodi say "roof, roof."

This is the best "tree of life" that I have ever come across:

Tree of life based on 16-18S rRNA sequences. Archaea may have more similarity to Bacteria or Eucarya than both of them have to each other, in good agreement with the finding that archaea exhibit a mixture of eucaryal and bacterial traits at the molecular level. This kind of tree often has been called "universal tree of life". http://www.icp.ucl.ac.be/~opperd/private/tree_o_l.html

14. ### Walter L. WagnerCosmic Truth SeekerValued Senior Member

Messages:
2,551
Valich:

This helps a lot. I make note of the statement "Eubacterial genes in the nucleus that are not from the original spirochete probably were acquired in amitochondriate protists from proteobacterial symbionts other than those of the mitochondrial lineage." In other words, these authors also believe, as you state at the outset, that those earliest eukaryotes never had mitochondria, and then lost them but keeping some of the genes by fusion into the nucleus; rather those amitochondriates acquried those genes by fusion from other prokaryotes that were endosybiotic, and not by fusion from the ones contained in the prokaryote that became mitochondria. While that may be true, I'm not certain how that conclusion is reached.

As for most people, to me a 'icture is worth a thousand words', and wouldn't it be fun to show a video of each of the stages of the change from the union of two primitive prokaryotes into a chimera of fused genomes, which eventually continued to evolve into the amitochondriate eukaryote.

Anyway, I look forward to your post on the origins of the spindle apparatus. While I can envision the formation of a chimera as a union of two different prokaryotes, it is difficult to see how such primitive circular strands of DNA in such early chimera became the highly complex chromosomes, which undergo a full mitosis with spindle apparatus in the primitive amitochondriate eukaryote.

And then, how did mitosis evolve in cells to become both mitosis and the even more complex meiosis? Clearly the benefit of sexual exchange of genes is undisputed, but how did that arise? I believe all extant eukaryotes are derived from ones that evolved meiosis, but clearly there must have first been pre-eukaryotes that only had mitosis, or am I mistaken? Also still unaswered is how/why did the eukaryote ribosomes become so much larger? That is not too difficult to envision; though worthy of further research.

Anyway, more food for thought. Hopefully, these posts might serve as a good lower-level course for a budding collegiate biology student.

15. ### valichRegistered Senior Member

Messages:
3,501
I find that statement of interest too and am searching through the literature on proteobacterial symbionts and protoarchaea. There's another theory that amitochondriates acquired mitochondria but that it was later converted to an "anaerobic hydrogenosome" as is the case in the trichomonads, belonging to the Parabasalia." This theory is supported by protein coding. Thus, strictly speaking, maybe they never lost it. It was an adaptation to an anaerobic environment. It's conflicting to me because other articles say that amitochondriate were first adapted to an anaerobic environment and then acquired mitochondria from an alpha-proteobacteria endosymbiont. All eukaryotes have mitochondria, so I want to trace the origin.

I was being extremely cautious yesterday on the subject of fossil dating because I recalled an article where they found an femur of Tyrannosaurus rex with intact soft tissue, blood vessels, and mineralized bone - that's 85 to 65 mya. Then I found it the article. They don't come out and say that they can extract DNA from it but: "shorter-chain protein molecules could be recovered from the soft tissues." Also, the same researchers have successfully "extracted a protein sequence from the bones of a 500,000-year-old musk ox." As I stated above, acritarch fossils left chemical signatures dating back 1400 mya. The skies the limit? Good photos of the tissues and femur: http://www.msnbc.msn.com/id/11385533/

16. ### valichRegistered Senior Member

Messages:
3,501
Let me correct myself. Some eukaryotes do not have mitochondria: microsporidians, metamonads, entamoebids, and pelobionts. "On rRNA trees these groups appeared as the most primitive eukaryotes, suggesting they appeared before the origin of mitochondrion, but this is now known to be an artifact of long branch attraction - they are apparently derived groups and retain genes or organelles derived from mitochondria. Thus it appears that there are no primitively amitochondriate eukaryotes, and so the origin of mitochondria may have played a critical part in the development of eukaryotic cells." http://en.wikipedia.org/wiki/Mitochondria

This seems to imply that the origin of eukaryotes could be found in the origin of mitochondria, and the proto-mitochondrion is the alphaproteobacteria: "an aerobic alpha-proteobacterium catabolyzing lipids, glycerol and other compounds provided by the host. At least 630 gene families derived from this organism can still be found in the 9 eukaryotic genomes analyzed in the study. http://en.wikipedia.org/wiki/Proto-mitochondrion

One hypothesis is "that all eukaryotes once possessed a proto-organelle that evolved into a hydrogen and ATP-generating organelle in anaerobic environments, while it evolved into a mitochondrion in aerobic niches.” http://www.uni-kl.de/FB-Biologie/AG-Neuhaus/Forschung/Tjaden et al 2004.pdf

What I find confusing is that amitochondriates, ciliates, trichomonads and fungi are said to have evolved a hydrogenosome from mitochondria to produce hydrogen and ATP, and that this transition occurred 2 bya. Cyanobacteria are 3.6 bya and eukaryotes evolved 2 bya. How can this event coincide with the origin of eukaryotes? This has to push the origin of eukaryotes beyond 2 bya.

Anaerobic protozoa and fungi evolved hydrogenosomes by the loss of the respiration and organellar genomes in mitochondria. This could only happen by endosymbiosis. "The matrix of N. ovalis hydrogenosomes contains ribosome-like particles of the same size as a numerous type of ribosome (70s) of the endosymbiotic methanogenic Archaea." http://en.wikipedia.org/wiki/Hydrogenosome

"The mitochondrial progenitor may have been a chimeric prokaryote, created by fusion between an archaebacterium and a eubacterium, in which eubacterial energy metabolism (glycolysis and fermentation) was retained . A Rickettsia-like intracellular symbiont, suggested to be the last common ancestor of the family Rickettsiaceae and mitochondria, may have penetrated such a host (pro-eukaryote), surrounded by a single membrane, due to tightly membrane-associated phospholipase activity, as do present-day rickettsiae . The relatively rapid evolutionary conversion of the invader into an organelle may have occurred in a safe milieu via numerous, often dramatic, changes involving both partners, which resulted in successful coupling of the host glycolysis and the symbiont respiration . Establishment of a potent energy-generating organelle made it possible, through rapid dramatic changes, to develop genuine eukaryotic elements . Such sequential, or converging, global events could fill the gap between prokaryotes and eukaryotes known as major evolutionary discontinuity." "Mitochondrial connection to the origin of the eukaryotic cell," by Emelyanov V.V., Eur J Biochem, 2003 Apr, 270(8),1599-618. http://www.bionewsonline.com/7/2/eubacteria_a.htm

This is what I've been looking for as the origin of eukaryotes. This pushes the timeline back to 2.7 bya: "Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis . However, details of the timing and number of symbiotic events are unclear. We used refined methods of sequence alignment, site selection, and time estimation to address these questions with protein sequences from complete genomes of prokaryotes and eukaryotes . RESULTS: Eukaryotes were found to evolve faster than prokaryotes, with those eukaryotes derived from eubacteria evolving faster than those derived from archaebacteria . We found an early time of divergence (approximately 4 bya) for archaebacteria and the archaebacterial genes in eukaryotes . Our analyses support at least two horizontal gene transfer events in the origin of eukaryotes, at 2.7 bya and 1.8 bya. Time estimates for the origin of cyanobacteria (2.6 bya) and the divergence of an early-branching eukaryote that lacks mitochondria (Giardia) (2.2 bya) fall between those two events . CONCLUSIONS: We find support for two symbiotic events in the origin of eukaryotes: one premitochondrial and a later mitochondrial event . The appearance of cyanobacteria immediately prior to the earliest undisputed evidence for the presence of oxygen (2.4-2.2 bya) suggests that the innovation of oxygenic photosynthesis had a relatively rapid impact on the environment as it set the stage for further evolution of the eukaryotic cell." "A genomic timescale for the origin of eukaryotes," by Hedges SB et al., BMC Evol Biol, 2001;1(1):4. Epub 2001 Sep 12. http://www.bionewsonline.com/8/1/eubacteria_b.htm

Evolution of Flagella: "Contrasting with the symbiotic model, cilia may have 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 dyneins 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." http://en.wikipedia.org/wiki/Evolution_of_flagella

17. ### valichRegistered Senior Member

Messages:
3,501

"The line of evolution from the universal ancestor evolved some early apomorphies during anagenesis: development of histone proteins, distinctive DNA promoters, and distinctive RNA polymerases. These features are conserved among all living organisms that evolved subsequently along this line....One branch after these developments specialized and produced descendants that are today known as kingdom Archaebacteria and domain Archaea. These organisms lack a nucleus and so are prokaryotic still, and they also lack chloroplasts and mitochondria. The main line of evolution then produced a nuclear envelope to enclose the DNA. This innovation (apomorphy) is shared by all descendents from that point and so is a synapomorphy but also, in a way, a plesiomorphy for the eukarytoic clade. Thus all subsequent new life forms in this line and its branches are eukaryotic (have a true nucleus) constituting domain Eukarya. Perhaps the most primitive eukaryotic group splitting out (cladogenesis) and evolving along its own branch is members of the kingdom Archezoa. An example archaezoan is Giardia...These organisms have a nucleus but lack any kind of mitochondrion or chloroplast. They are the "archetypal" eukaryote.

Sometime after the archaezoans split off from the main line of evolution, the ancient apomorphies, which are now plesiomorphies of all subsequent groups, include the endosymbiosis events. Ancient protobacteria were taken in by primitive eukaryote hosts as respiratory endosymbionts and evolved into mitochondria. Ancient cyanobacteria were taken in as photosynthetic endosymbionts and evolved into chloroplasts. Major organisms that evolved as a single branch early after these endosymbiosis events are now called kingdom Protista. Dinoflagellates (phylum Pyrrophyta) perhaps represent an early-departing twig on that branch. Ciliates and Zooflagellates lost the chloroplast and therefore have more animal-like characteristics. Euglenoids (phylum Euglenophyta), perhaps allied with Zooflagellates, departed along their own separate twig retaining the chloroplast.

Another eukaryotic branch developed when the original chloroplast was replaced by a secondary endosymbiosis. These organisms, now called kingdom Chromista, share the synapomorphy of having a derived red algal endosymbiosis that evolved to replace the standard chloroplast. This derived Chromista chloroplast thus has characteristics that are shared with derived chloroplasts of red algae. The Chromista include Brown algae (phylum Phaeophyta), the water molds (phylum Oomycota), the golden algae (phylum Xanthophyta), and the diatoms (phylum Chrysophyta).

Yet another eukaryotic branch, evolving with the original chloroplast, diversified into the organisms known today as members of kingdom Plantae. One twig on this branch specialized to become the red algae (phylum Rhodophyta), which participated in the later endosymbiosis event that gave rise to kingdom Chromista. Another twig of kingdom Plantae became what are now known as green algae (phylum Chlorophyta). From this came another twig that diversified into the "true plants." These include mosses (phylum Bryophyta), ferns (phylum Pteridophyta), conifers (phylum Coniferophyta), and the flowering plants (phylum Anthophyta). Yet another eukaryotic branch lost the chloroplast and evolved into sister groups now known as two separate kingdoms: Fungi and Animalia."

Messages:
3,501
19. ### Walter L. WagnerCosmic Truth SeekerValued Senior Member

Messages:
2,551
The last post (1994 "Plant Basics") has the eukaryote animals evolving from a choroplastic eukaryote ancestor which subsequently lost the chloroplast. This is contrary to the earlier posts, and I suspect is not correct. In particular the other posts are from a later time (e.g. 1998, 1999, 2001), and the Eukaryote web page I posted had several separate origins for different lines based on endosymbiosis of different cyanobacteria over time.

What I also found interesting from the above posts is the hint that the centriole of the spindle apparatus is possibly derived from/related to cilia, though exactly how that occurred, and how it subsequently became involved with mitosis is not clear.

What is clear is that far more work is left to be done in this area, to more clearly elucidate the complexities of those first two billion years of evolution from primitive prokaryotes to a chimeric form giving rise to a primitive amitochondriate and a-mitotic pre-eukaryote, ultimately forming the advanced eukaryote that we see today.

As you noted, the introduction of oxygen into the atmosphere sufficiently changed the environment over the course of 200 million years that eukaryote evolution was driven to accomodate cells living in such oxygen-rich environment.

Anyway, now when my kids ask me "Daddy, where do babies come from?" I'll be able to give them a more involved answer!

20. ### valichRegistered Senior Member

Messages:
3,501
That can't be correct. It's a good article, but it is outdated. Chloroplastic organelles evolved from an endosymbiont prokaryote. Specifically, everything points to an alpha-proteobacteria endosymbiont for both the origins of chloroplasts and mitochondria. As you stated above, some eukaryotes lost their mitochondria: anaerobic amitochondriates acquired mitochondria and it was later converted to a hydrogenosome. However, some recent articles dispute this and say that the origins of mitochondria and hydrogenosomes came from different symbionts and not evolved into. "Cavilier-Smith 1983" set the whole field of phylogenetic paleontology back ten years when they created the so-called Archezoa group and thought that it was the most basal eukaryotic group because they were the simplest organisms. These were all simple amitochondriates that originally had mitochondria but later the mitochondria evolved into hydrogenosomes - maybe? Their work has since been disproven.

This is getting intense. They're able to trace back mitochondria to a phylum that's called Chaperonin 60 (cpn60). Since they can trace this genetic sequence through all the lineages, it also provides support for a secondary absence of mitochondria in early-branching eukaryotes: http://mbe.oxfordjournals.org/cgi/content/full/18/10/1970

This is not a fossil dating technique. They're able to see the same gene sequences in all species and then trace these back using special algorithms that take into account a number of factors in mutation rates. Since this is all new to me, I'm having trouble understanding it, but it's new to a lot of other biologists too.

What puzzles me is the following (2001 article): "Eukaryotes were found to evolve faster than prokaryotes, with those eukaryotes derived from eubacteria evolving faster than those derived from archaebacteria. We found an early time of divergence (~4 billion years ago, Ga) for archaebacteria and the archaebacterial genes in eukaryotes. Our analyses support at least two horizontal gene transfer events in the origin of eukaryotes, at 2.7 Ga and 1.8 Ga. Time estimates for the origin of cyanobacteria (2.6 Ga) and the divergence of an early-branching eukaryote that lacks mitochondria (Giardia) (2.2 Ga) fall between those two events." http://www.biomedcentral.com/1471-2148/1/4

Basically their tracing the origin of life back to 4 bya through gene sequences found in eukaryotes. Then there were two major gene transfer events for eukaryotes: 2.7 and 1.8 bya. Therefore, the origin of eukaryotes is greater than 2.7 bya. Other articles that I'm reading also place the origin of cyanobacteria at about this same time (~2 bya) and not at 3.6 bya. So the fossils found in Australia of cyanobacteria dating back to 3.6 bya are not cyanobacteria. I assume that they are suggesting that they are the original alpha-proteobacteria symbiont.

We were talking about dating fossils. Apparently some ancient bacteria fossils (extremophiles) leave chemical signatures of a carbon isotope that can be accurately dated. Oxygen first appeared ~3.8 bya with the origin of life, then approached current levels with the Cambrian diversification period 550 mya. But what happened 1.8 bya to cause a similar eukaryote diversification (horizontal gene transfer)???

Certainly the origin of cilia and flagella are related, and also related to the spindle apparatus through the diversification of the usage of microtubules. I'll try to get on this later, but right now I'm downloading files faster than I can read them. See ya.

21. ### valichRegistered Senior Member

Messages:
3,501
“Cilium developed from pre-existing components of the eukaryotic cytoskeleton 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 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 (heliozoan, or sun animalcules, are roughly spherical amoeboids with many stiff, microtubule-supported projections called axopods radiating outward).

Regarding the origin of the individual protein components, 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.

An obvious approach to the evolution of the bacterial flagellum is suggested by the fact that a subset of flagellar components can serve a function as a Type III transport system.
Admittedly, all currently known nonflagellar Type III transport systems are for injecting toxins into eukaryotic cells, and are therefore presumably descended from the flagellum, which is likely older than eukaryotes. For example, the bubonic plague bacterium Yersinia pestis (a species of rod-shaped bacterium belonging to the family enterobactieriaceae) has an organelle assembly very similar to a complex flagellum except that it functions as a needle to inject toxins into host cells. However, the Type III transport system still undergirds the hypothesis that the flagellum did not have to come about all at once, as a subset of components has a selectable function. That all known nonflagellar Type III transport systems are disease mechanisms is not shocking as the Type III secretion system was only discovered in 1994 and as our scientific study of eubacteria is significantly biased towards disease-causing organisms for obvious good reasons. We have another rather spectacular case of co-option, where a motility organelle has evolved into a "complex weapon for close combat." http://www.absoluteastronomy.com/encyclopedia/e/ev/evolution_of_flagella.htm

“Many eukaryotes have slender motile projections, usually called flagella when long and cilia when short, that are variously involved in movement, feeding, and sensation. These are entirely distinct from prokaryotic flagella. They are supported by a bundle of microtubules arising from a basal body, also called a kinetosome or centriole, characteristically arranged as nine doublets surrounding two singlets. Flagella also may have hairs or mastigonemes, scales, connecting membranes and internal rods. Their interior is continuous with the cell's cytoplasm. Centrioles are often present even in cells and groups that do not have flagella. They generally occur in groups of one or two, called kinetids, that give rise to various microtubular roots. These form a primary component of the cytoskeletal structure, and are often assembled over the course of several cell divisions, with one flagellum retained from the parent and the other derived from it. Centrioles are also associated in the formation of a spindle during nuclear division. Some protists have various other microtubule-supported organelles. These include the radiolaria and heliozoa, which produce axopodia used in flotation or to capture prey, and the haptophytes, which have a peculiar flagellum-like organelle called the haptonema.” http://wikiax.biz/cs/endosymbiont

“From Green Algae to Land Plants: The results of approximately 25 years of electron-microscopic analyses of members of the green lineage have resulted in a number of hypotheses regarding the origin and diversification of these taxa. The most important of these is based on the observation that two fundamentally different types of microtubule organization are found within the green lineage during cytokinesis. The first, termed a phycoplast, is characterized by the collapse of the spindle apparatus after mitosis, with the microtubules oriented in the same direction as the plane of cell division. The second, termed a phragmoplast, is characterized by the development of a persistent telophase spindle and a cleavage furrow, with the microtubules oriented at right angles to the plane of cell division. That charophytes and land plants have a phragmoplast type of cell division, whereas chlorophytes, trebouxiophytes, and some members of the ulvophytes have a phycoplast type of cell division led to the division of the green algae and land plants into two distinct groups based on this cytokinetic character.”

Figure 4. Small subunit rDNA phylogeny of the green lineage. This tree has been constructed with a weighted maximum parsimony method, and the results of bootstap analyses (200 replications) are shown as branch nodes of differing thicknesses (see box on the right). The likely position of divergence of the prasinophyte M. viride is shown with a broken line. The phylogeny is rooted within the branch leading to the rDNA sequence of the glaucocystophyte C. paradoxa.

In summary, there is now some evidence for a prasinophyte ancestry for the charophytes, which themselves are the ancestors of the bryophytes, ferns, gymnosperms, and angiosperms. Fossil evidence shows that the land plants have existed for approximately 450 to 470 million years. This assemblage has therefore seen its members evolve from a single-celled alga similar to M. viride to the charophytes, the most complex green algae, with some members (Charales) reaching a size of 2 to 30 cm, to the bryophytes and then to the other land plants. To gain insights into the genetic developments that have led stepwise to the origin of land plants we are analyzing actin-coding regions to see whether duplications of this important cytoskeletal gene family may have accompanied the origin of multicellularity in the green lineage. Actin exists as a constitutively expressed single-copy gene in all green algae except the ulvophytes, which appear to have undergone independent gene duplications. The charophytes also contain single-copy actin genes. The present data show actin gene duplications to appear first within the ferns, which are positioned as the sister group to the complex flowering plant actin gene families…It is likely that the evolution of multicellularity within plants has followed another plan than that in animals and that phylogeny reconstruction can play an important role in creating a logical framework for understanding the basis for plant organismal evolution.”
From: “Algal Phylogeny and the Origin of Land Plants,” by Debashish Bhattacharya and Linda Medlin, Plant Physiol. (1998) 116: 9-15. http://www.plantphysiol.org/cgi/content/full/116/1/9

Spindle mutations lead to a tubulin cytoskeletal structure: “In addition to the absence of the contractile ring, the ana-telophases of all the chic mutants exhibit another obvious abnormality: a defect in central spindle morphology. In wild-type ana-telophases of both meiotic divisions, the two daughter nuclei are connected by a prominent bundle of interdigitating microtubules. In chic mutants, this central spindle structure is considerably less dense than in wild type, and microtubules show very little or no interdigitation. In wild type, the central spindle is already evident by mid-anaphase, before the actin ring constriction has caused substantial equatorial pinching. In the strongest chic mutants, these early stages of central spindle formation are never seen, indicating that the chic phenotype reflects a failure of central spindle assembly rather than a degradation of this structure in the absence of the actin ring. This result is surprising because the central spindle is a tubulin based cytoskeletal structure…. In all cases examined, the central spindle and the contractile ring in meiotic ana-telophases were simultaneously absent. Together, these results suggest a cooperative interaction between elements of the actin-based contractile ring and the central spindle microtubules: when one of these structures is disrupted, the proper assembly of the other is also affected.” From: “Genes involved in tissue and organ development: spermatogenesis,” 1996 Thomas B. Brody, Ph.D. http://cricket.bio.indiana.edu:7081/allied-data/lk/interactive-fly/aimorph/spermat.htm

Tons of Links to microtubule spindle formation: http://www.textpresso.org/davidc/results/clusters/CellBio/161.html

Tim Stearns’ Lab at Stanford University: “We study the organization and regulation of the microtubule cytoskeleton, and the relationship between the cell cycle and the cytoskeleton. How do cells organize microtubules into complex structures such as the mitotic spindle? One of the keys is the centrosome, which nucleates microtubule polymerization from free tubulin subunits, and organizes the array of microtubules. We're interested in understanding the centrosome, and its role in cell division and differentiation.” http://stearnslab.stanford.edu/WWD.html
contact: stearns@stanford.edu

22. ### valichRegistered Senior Member

Messages:
3,501
This is the most recent Tree of Life: 2005. I'm not sure how it will post, but you should be able to see that the Last Common Ancestor is most related to Neomuran Archaebacteria: "The origin from actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of quantum evolution since cells began....Negibacteria are the most ancient, radiating rapidly into six phyla. Evidence from molecular sequences, ultrastructure, evolution of photosynthesis, envelope structure and chemistry and motility mechanisms fits the view that the cenancestral cell was a photosynthetic negibacterium, specifically an anaerobic green non-sulphur bacterium, and that the universal tree is rooted at the divergence between sulphur and non-sulphur green bacteria. The negibacterial outer membrane was lost once only in the history of life, when Posibacteria arose about 2800 My ago after their ancestors diverged from Cyanobacteria."

LIFE
|--Eubacteria
| |--Actinobacteria
| --+--+--Thermotogae
| | --Firmicutes
| --Didermata
| |--Cyanobacteria
| | |--Gloeobacter
| | --Phycobacteria
| | |--Chroococcales
| | |--Pleurocapsales
| | |--Oscillatoriales
| | --Hormogoneae
| | |--Nostocales
| | --Stigonematales
| --+--+--Caldithrix
| | --+--Deferribacteres
| | --+--Nitrospina
| | --Thermodesulfobacterium
| --+--+--Sphingobacteria
| | | |--Chlorobi
| | | --Bacteroidetes
| | --+--Spirochaetes
| | --+--Fusobacteria
| | --Proteobacteria
| | |--Rhodobacteria
| | | |--Alphabacteria
| | | --Chromatibacteria
| | --Thiobacteria
| | |--Deltabacteria
| | --+--Aquificae
| | --Epsilobacteria
| --+--+--Acidobacteria
| | --+--Nitrospira
| | |--Magnetobacterium
| | |--Leptospirillum
| | --Thermodesulfovibrio
| --+--Eobacteria
| | |--Deinococci
| | --+--Thermodesulfobium
| | --Chloroflexi
| --Planctobacteria
| |--Planctomycetes
| --+--Chlamydiae
| --+--Victivallis
| --Verrucomicrobia
--Neomura
|--Eukaryota
--Archaea
|--Crenarchaeota
|--‘Nanoarchaeum’
--Euryarchaeota
|--Eurythermea
| |--Protoarchaea
| --Picrophilea
--Neobacteria
|--Archaeoglobales
--+--Halomebacteria
--Methanothermea

See: "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification," http://ijs.sgmjournals.org/cgi/reprint/52/1/7

23. ### valichRegistered Senior Member

Messages:
3,501
After a thorough research, the evidence points to an initial evolution of flagella in bacteria and other protists, and an endosymbiotic evolution of cilia and flagellum in other species. Lynn Margulis, in her book "Symbiosis in Cell Evolution" argues that endosymbiotic parasitic spirochetes (anaerobic helical bacteria with flagella) developed into eukaryotic flagella and cilia. Endosymiosis is a convincing hypothisis since there are parabasalids (smbiotic flagelette protozoa) inside the guts of termites and cockroaches that do use spirochetes as their motility organelles.

However, since the apparatus, mechanism, and purpose of mitotic spindles differs from that of the centioles that make up the underlying basal body of cilia and flagellum, the only relationship that I can see here is that they are both made up of microtubules: spindles have a 9 microtuble organization, while cilia and flagellum have a 9 + 2 microtubule organization. In all cases the origin starts with the central microtubule organizing center (MTOC) that seems to orchestrate the formation of the 9 microtubules into a spherical arrangement. In eukaryotes, most authors refer to the basal body as being similar (homologous) to the centriole in eubacteria and in the centriole of the mitotic spindle, but not the same.

The centrosome refers to the central microtubule organizing center (MTOC) that the nine double or triplet microtubules grow out of to make up the centriole. In cilia and flagellum there are then two more microtubules in the middle of the centriole that form the basal body that the cilia or flagellum grow out of. The centriole forms the spindle for mitosis or the basal body for cilia and flagellum, but not all basal bodies are the same and they undergo a flagellar modification in different species, e.g., the flagellar hook-basal body complex with the protein FliE. Also, dyneins become involved that then move down the centrosome microtubules to transport ATP toward the centrosome (MTOC).

For an excellent overview of all aspects of cilia and flagella, including the ATP activity in the dynein arms and centriole structure, function and replication, with lots of great pictures, go to: http://www.cytochemistry.net/Cell-biology/cilia.htm

Centrioles replicate autonomously like mitochondria and peroxisomes. They begin from centers which contain proteins needed for their formation (tubulin, etc.), Then the procentrioles form. Each grows out a single microtubule from which the triplet can form. Once a centriole is made, daughter centrioles can grow out from the tubules at right angles as shown in this cartoon. These then add to the daughter cell (in a dividing cell), or they move to the periphery and form the basal body for the cilium." Source: http://cellbio.utmb.edu/cellbio/cilia.htm

On the evolution of cilia into vertebrate photoreceptor cells and invertebrate chemoreceptor neurons, and the loss of cilia in certain species and lineages:

"The evolution of the ancestral eukaryotic flagellum is an example of a cellular organelle that became dispensable in some modern eukaryotes while remaining an essential motile and sensory apparatus in others…. In sperm and in unicellular eukaryotes, a motile form of cilia called flagellum propels cells to their destination, while in epithelial cells, multiple motile cilia beat synchronously to stir extracellular fluid. In vertebrate photoreceptor cells and invertebrate mechano- and chemoreceptor neurons, the entire sensory transduction machinery is housed in a specialized cellular compartment derived from the cilium. This domain, known as the outer segment, is a hallmark of these sensory neurons and an outstanding example of subcellular compartmentalization as a strategy to optimize function. The ancestral nature of the eukaryotic cilia is evident by its presence in organisms from both lineages: Drosophila melanogaster [fruit fly], Homo sapiens, Trypanosoma brucei [parasitic single-flagellated protozoan], and Chlamydomonas reinhardtii [green algae]. In three independent events, cilia were lost in lineages leading to Arabidopsis thaliana [Mouse-ear cress], Dictyostelium discoideum [slime mold], and Saccharomyces cerevisiae [budding yeast]. Similarly, compartmentalized cilia were lost in Plasmodium falciparum [protozoan parasite cause malaria], while motile cilia were lost in Caenorhabditis elegans [worm].

Cilia formation begins when the basal body, a centriole-related structure, serves as a template for the assembly of the axoneme. This process can proceed through two different mechanisms. In most motile and sensory cilia, the basal body docks to the plasma membrane, and a bud-like structure containing the axoneme and the ciliary membrane projects out from the cell body; since the ciliary membrane and the axoneme are assembled concurrently as a compartment separated from the cell body, this process is referred to as compartmentalized ciliogenesis. In a few cases, however, such as in the sperm cells of Drosophila and the flagella of the parasite Plasmodium, the entire axoneme is first assembled inside the cytosol and only later is either extruded or matures into a flagellum (i.e., cytosolic biogenesis)."
From: "Zygotically Transcribed Genes: Decoding cilia function: defining specialized genes required for compartmentalized cilia biogenesis":http://www.sdbonline.org/fly/aignfam/cytoskel.htm

"Basal bodies and centrioles originate in a ring of amorphous material. The triplet microtubules of the blade of a typical centriole or basal body are known as the A, B and C tubules. The C tubule, which is the outermost microtubule, is confined to centrioles and basal bodies, whereas the A and B tubules are continuous with the doublet microtubules of the ciliary or flagellar axoneme. Doublet microtubules are also observed at the distal ends of centrioles. Mature basal bodies and centrioles usually have triplet microtubules. However, there are some exceptions. Caenorhabditis elegans has centrioles with singlet microtubules at the meiotic spindle poles and Toxoplasma gondii has centrioles with singlet microtubules. Immature basal bodies or centrioles may consist of singlet or doublet microtubules. Mastigamoeba schizophrenia, an anaerobic protozoan, has basal bodies with doublet microtubules that lack the C tubule. In Drosophila melanogaster embryos, centrioles with doublet microtubules were observed in situ isolated centrioles had singlet microtubules and sperm centrioles have triplet microtubules. The sperm centrioles are longer than the embryonic centrioles in Drosophila. The biflagellate green alga Chlamydomonas reinhardtii is an excellent model system for the analysis of basal body and microtubule function." From: "Mutations in -tubulin promote basal body maturation and flagellar assembly in the absence of -tubulin," by Sylvia Fromherz, Thomas H. Giddings, Natalia Gomez-Ospina, and Susan K. Dutcher. Journal of Cell Science 117, 303-314 (2004). Published online at: http://jcs.biologists.org/cgi/content/full/117/2/303

"[During the G1 and S phase of mitosis in mammalian cells] An older centriole differs functionally from a younger centriole by being able to assemble a primary cilium. This suggests a role for one or more of these proteins and for maturation in promoting the assembly of the cilium. Of those, only -tubulin has been identified to date in Chlamydomonas. In addition to the presence of the above proteins, the level of polyglutamylation on - and ß-tubulin is increased on older centrioles and on older basal bodies. Unlike centrioles, daughter basal bodies must mature early in their first cell cycle in order to assemble flagella or cilia and so for example, all basal bodies in the ciliated epithelium of the trachea have the ODF2 epitope (McKean et al., 2003). Therefore, there is a need for an additional maturation event in basal bodies which we refer to as early maturation and which must occur at M/G1 phase of the cell cycle rather than in G2/M phase, as for centrioles." From: "Mutations in -tubulin promote basal body maturation and flagellar assembly in the absence of -tubulin," by Sylvia Fromherz, Thomas H. Giddings, Jr, Natalia Gomez-Ospina1, and Susan K. Dutcher. Journal of Cell Science 117, 303-314 (2004). Published online at http://jcs.biologists.org/cgi/content/full/117/2/303

"The Sliding-Filament Model of Bending: The bending of cilia (and flagella) has many parallels to the contraction of skeletal muscle fibers: