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+---Topic: Evolution of eukaryotic cilia/flagella started by niiicholas

Posted by: niiicholas on Nov. 28 2002,23:11

Similar to the < prokaryotic flagella thread >.

Introductory material:

< >
(don't confuse eukaryotic cilia/flagella with prokaryotic flagella)

< >

Here we have the interesting sideshow of Margulis' and fans' hypothesis that the cilium is derived from a spirochete.  For many critical comments on this see:

Cavalier-Smith T. Int J Syst Evol Microbiol 2002 Mar;52(Pt 2):297-354
< The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. >
Posted by: niiicholas on Dec. 03 2002,23:13

Another Miller article, presents his argument on cilia missing parts:

"Answering the Biochemical Argument from Design"

The ID movement pretends that its biochemical arguments against evolution are new, novel, and scientific. In fact, they are nothing of the sort.

< >
Posted by: niiicholas on Dec. 30 2002,08:49

In the "cytoskeletal protein homologs found in prokaryotes" category:


< II thread >

< Science News Article >

Week of March 31, 2001; Vol. 159, No. 13

Bacterial cells reveal skeletal structures
Jessa Netting

Bacteria are different from you and me. Always the minimalists, they lack features that plant and animal cells usually can't do without: a nucleus, special organelles, and an internal skeleton made of protein, to name a few. But research reported in the March 23 Cell knocks out one plank of this standard profile—bacteria, too, have a protein skeleton, or cytoskeleton.

A fluorescent tag for a specific bacterial protein reveals a helical skeleton.

"This is akin to finding the platypus, a mammal that lays eggs," says Laura J.F. Jones, who revealed the skeleton in Bacillus subtilis with her colleagues Rut Carballido-López and Jeffery Errington, all of Oxford University in England.

The researchers say their finding helps illuminate the origins of our own cell structure and eliminates a fundamental difference between two of the most basic groups of organisms, prokaryotes (bacteria and blue-green algae) and eukaryotes (plants, animals, and protozoans).

"Spectacular" is the how cell-mechanics researcher Piet De Boer of Case Western Reserve University in Cleveland rates the Oxford team's unmasking of a bacterial cytoskeleton. "Bacteria have really been thought of as bags of enzymes without much of an internal structure at all," says De Boer.

Bacteria were believed to have only a tough cell wall for support. Even powerful electron microscopes have failed to turn up any distinct internal structure. In contrast, eukaryotic cells, which evolved after bacteria, have a network of filaments for support and movement. A protein known as actin forms much of this cytoskeleton, which can look like a bushy spray of fibers.

In the past decade, bacteriologists have searched for complex structures in bacteria by using techniques for tagging proteins with fluorescent markers. These studies, which can illuminate otherwise hidden structures, have yielded evidence of a higher level of organization than previously believed, says De Boer.

Using fluorescent tags made with antibodies that can bind to specific proteins, the Oxford investigators looked for a bacterial cytoskeleton in the rod-shaped B. subtilis. "It seemed likely to me that something as important as the cytoskeleton must have evolved quite early, so I almost expected to find actin in bacteria even though the textbooks say it is absent," says Errington.

He and his colleagues focused on two bacterial proteins, MreB and Mbl, because of evidence that the genes coding for them have roles in determining cellular shape. Disabling the gene for MreB resulted in rounded cells, while disabling the gene for Mbl yielded elongated, twisted bacteria. Using a different fluorescent antibody to light up the intact protein in each altered cell, the researchers revealed complex internal structures made of either MreB or Mbl.

"We were ecstatic when we saw the first MreB and Mbl images, because they immediately told us that the proteins probably made filaments like actin," says Errington. Coiling within the cell as they did, the filaments clearly could determine cell shape in normal bacteria, he says.

Errington likens the filamentous structure to a scaffold: It doesn't have great strength itself, but instead provides the internal framework for a sturdier exterior shell, in this case the bacterium's tough cell wall.

The finding suggests that the cytoskeleton evolved before bacteria and our own cellular ancestors split into two groups, says Errington. Having a cytoskeleton isn't a defining feature of eukaryotic cells after all, he asserts.


Jones, L.J.F., R. Carballido-Lopez, and J. Errington. 2001. Control of cell shape in bacteria: Helical, actin-like filaments in Bacillus subtilis. Cell 104(March 23):913.


Posted by: niiicholas on Jan. 27 2003,19:39

Reposting from:

Topic: List of IC systems
< >

First off,

< An awful lot of entries in the NCBI protein database listing MotA, ExbB, and TolQ as being a "family", in opposition to what Mike Gene has been suggesting >


Originally posted by Mike Gene:
Nic: Hey, I'm just following the peer-reviewed lit., man. Take it up in the pages of Biochemistry if you like...

The authors never claim MTH1022 is a homolog of motA. And even if they did, the claim would be unsupported.  


People can read the quote I posted and decide for themselves exactly what the authors meant.  Mentioning significant sequence similarity in the middle of a discussion of homologs seems like a strong indication to me that they meant homolog or at least "likely homolog".  And see below for what some of those proteins are labeled as in the NCBI database.



Actually, running a PSI-BLAST of ExbB gets me four hits on archaeabacteria, but whatever.

With e values of 0.005 and higher.  That's not very impressive.  Furthermore, even if there is a non-convergent and real relationship here, note that it is not widely distributed and would thus seem to have evolved long after archaea appeared.  

A much stronger point is that the ExbB homologs are very widely distributed in eubacteria, in very basal lineages.

Think so?  What groups did you have in mind?[/qb]

Hmm, well a standard protein BLAST  on E coli ExbB gives me this taxonomy report:

< An E. coli "biopolymer transport exbB protein" >

< Here is the link >

Here are some of the results *outside* the proteobacteria:

---------------------CODE SAMPLE-------------------
 Chlamydophila pneumoniae CWL029 [chlamydias] taxid 115713
gi|15618694|ref|NP_224980.1| Macromolecule transporter [Ch...      61  1e-08

 Cytophaga hutchinsonii [CFB group bacteria] taxid 985
gi|23136461|gb|ZP_00118181.1| hypothetical protein [Cytoph...      60  1e-08
gi|23136843|gb|ZP_00118557.1| hypothetical protein [Cytoph...      36  0.35

 Chlamydia trachomatis [chlamydias] taxid 813
gi|15605326|ref|NP_220112.1| polysaccharide transporter [C...      59  4e-08

 Chlamydia muridarum (agent of mouse pneumonitis) [chlamydias] taxid 83560
gi|15835499|ref|NP_297258.1| MotA/TolQ/ExbB proton channel...      58  8e-08

 Aquifex aeolicus [aquificales] taxid 63363
gi|15606982|ref|NP_214364.1| TolQ homolog [Aquifex aeolicu...      55  5e-07
gi|15606823|ref|NP_214203.1| biopolymer transport exbB [Aq...      42  0.005


 Deinococcus radiodurans [eubacteria] taxid 1299
gi|15805483|ref|NP_294179.1| biopolymer transport protein,...      47  1e-04

 Methanothermobacter thermautotrophicus str. Delta H [euryarchaeotes] taxid 187420
gi|15679040|ref|NP_276157.1| biopolymer transport protein ...      43  0.002

 Synechocystis sp. PCC 6803 [cyanobacteria] taxid 1148
gi|16329196|ref|NP_439924.1| biopolymer transport ExbB pro...      41  0.013
gi|16329550|ref|NP_440278.1| biopolymer transport ExbB pro...      40  0.018

---------------------CODE SAMPLE-------------------

Note below that *even* some proteobacteria ExbB proteins have "unimpressive" similarity scores and yet are still called ExbB proteins (as are some **archaeabacteria** ExbB-family proteins):

---------------------CODE SAMPLE-------------------
Photobacterium damselae subsp. piscicida [g-proteobacteria] taxid 38294
gi|19577341|emb|CAD27898.1| ExbB protein [Photobacterium d...      33  1.9

 Plesiomonas shigelloides [enterobacteria] taxid 703
gi|13774064|gb|AAG23397.1| ExbB [Plesiomonas shigelloides]         33  2.0

 Sulfolobus solfataricus [crenarchaeotes] taxid 2287
gi|15899059|ref|NP_343664.1| Amino acid transporter, putat...      33  2.6


 Methanosarcina acetivorans C2A [euryarchaeotes] taxid 188937
gi|20089242|ref|NP_615317.1| MotA/TolQ/ExbB proton channel...      33  3.4
gi|20093212|ref|NP_619287.1| MotA/TolQ/ExbB proton channel...      33  3.8
gi|20093420|ref|NP_619495.1| MotA/TolQ/ExbB proton channel...      32  6.7
---------------------CODE SAMPLE-------------------

MotA and ExbB appear to have equally wide distributions

The distribution taxonomy report for ExbB is, in fact, rather like the taxonomy report for standard protein blast of < E. coli's MotA protein >: lots and lots of enterobacteria and proteobacteria, and a few hits out in spirochetes and other various deeply divergent bacteria.

< Here is said taxonomy report >

Are we to conclude that MotA is just as likely to be of late origin and derived as ExbB?

...methinks the database may be a wee bit biased towards certain intensively-studied gram-negative bacteria groups and that therefore seeing many hits in those groups and few outside means very little in terms of relative significance.  As I showed, you have to put MotA and ExbB in the same distribution bucket regardless.

Regarding low e-values:

Based on your blanket skepticism of marginal e-values, you may want to argue that some MotA proteins are of independent origins and convergent on standard MotA's.  Many of these scores are non too impressive, yet some are MotAs (or PomA, a related motor) despite this:

---------------------CODE SAMPLE-------------------
 Treponema denticola [spirochetes] taxid 158
gi|4426945|gb|AAD20619.1| flagellar motor protein MotA [Tr...      53  3e-06

 Pseudomonas putida [g-proteobacteria] taxid 303
gi|2853602|gb|AAC08066.1| MotA [Pseudomonas putida]                53  5e-06

 Leptospira interrogans serovar lai str. 56601 [spirochetes] taxid 189518
gi|24213362|ref|NP_710843.1| Chemotaxis motA protein [Lept...      52  6e-06
gi|24216276|ref|NP_713757.1| motility protein A [Leptospir...      39  0.056

 Bacillus anthracis str. A2012 [eubacteria] taxid 191218
gi|21402555|ref|NP_658540.1| MotA_ExbB, MotA/TolQ/ExbB pro...      52  8e-06
gi|21399546|ref|NP_655531.1| MotA_ExbB, MotA/TolQ/ExbB pro...      51  1e-05

 Shewanella oneidensis MR-1 [g-proteobacteria] taxid 211586
gi|24375769|ref|NP_719812.1| chemotaxis motA protein [Shew...      51  1e-05
gi|24373102|ref|NP_717145.1| chemotaxis motA protein [Shew...      38  0.13

 Thermotoga maritima [thermotogales] taxid 2336
gi|15643440|ref|NP_228484.1| motility protein A [Thermotog...      50  3e-05

 Campylobacter jejuni [e-proteobacteria] taxid 197
gi|15791705|ref|NP_281528.1| putative flagellar motor prot...      48  9e-05

 Rhodopseudomonas palustris [a-proteobacteria] taxid 1076
gi|22963976|gb|ZP_00011582.1| hypothetical protein [Rhodop...      42  0.006

 Magnetococcus sp. MC-1 [proteobacteria] taxid 156889
gi|22999422|gb|ZP_00043404.1| hypothetical protein [Magnet...      41  0.011
gi|23000123|gb|ZP_00044067.1| hypothetical protein [Magnet...      33  3.5

 Vibrio alginolyticus [g-proteobacteria] taxid 663
gi|3024412|sp|O06873|POMA_VIBAL Chemotaxis pomA protein >g...      40  0.038

 Bacillus halodurans [eubacteria] taxid 86665
gi|15615802|ref|NP_244106.1| flagellar motor apparatus [Ba...      39  0.058

 Vibrio vulnificus CMCP6 [g-proteobacteria] taxid 216895
gi|27363787|ref|NP_759315.1| Flagellar motor component Mot...      37  0.18

 Clostridium thermocellum ATCC 27405 [eubacteria] taxid 203119
gi|23021959|gb|ZP_00061601.1| hypothetical protein [Clostr...      35  0.87

 Vibrio cholerae [g-proteobacteria] taxid 666
gi|15640908|ref|NP_230539.1| chemotaxis protein PomA [Vibr...      32  5.6
---------------------CODE SAMPLE-------------------

Regarding the e-values of archaeal ExbB homologs, PSI-BLAST on E. coli ExbB gives an archaeabacterial homolog with e-value of 2e-17, which ought to be good enough for Mike Gene:

< PSI-BLAST search >


 Methanothermobacter thermautotrophicus str. Delta H [euryarchaeotes] taxid 187420
gi|15679040|ref|NP_276157.1| biopolymer transport protein ...      90  2e-17
gi|15678698|ref|NP_275813.1| unknown [Methanothermobacter ...      43  0.003
gi|15678311|ref|NP_275426.1| protein kinase [Methanothermo...      33  3.4


My point

These kinds of things ought to at least be mentioned and discussed before reckless statements are made about absolutely no evidence for precursors to flagellar proteins, that's my only point.  For some reason you guys prefer to sweep it under the rug by unsupported arguments about ExbB's narrow distribution.  Just acknowledge that this little bit of the biological world is a bit disharmonious with the flagellum-was-specially-created thesis.  All I've been saying, and now documenting, is that ExbB homologs are at least as widely distributed as MotA, and possibly more widely distributed.

Posted by: niiicholas on Feb. 15 2003,00:57

Stop the presses!  Tubulin (not just the tubulin homolog FtsZ) found in prokaryotes.


Proc Natl Acad Sci U S A 2002 Dec 24;99(26):17049-54
< Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter. >

< >

Jenkins C, Samudrala R, Anderson I, Hedlund BP, Petroni G, Michailova N, Pinel N, Overbeek R, Rosati G, Staley JT.

Department of Microbiology, University of Washington, Seattle, WA 98195, USA.

Tubulins, the protein constituents of the microtubule cytoskeleton, are present in all known eukaryotes but have never been found in the Bacteria or Archaea. Here we report the presence of two tubulin-like genes [bacterial tubulin a (btuba) and bacterial tubulin b (btubb)] in bacteria of the genus Prosthecobacter (Division Verrucomicrobia). In this study, we investigated the organization and expression of these genes and conducted a comparative analysis of the bacterial and eukaryotic protein sequences, focusing on their phylogeny and 3D structures. The btuba and btubb genes are arranged as adjacent loci within the genome along with a kinesin light chain gene homolog. RT-PCR experiments indicate that these three genes are cotranscribed, and a probable promoter was identified upstream of btuba. On the basis of comparative modeling data, we predict that the Prosthecobacter tubulins are monomeric, unlike eukaryotic alpha and beta tubulins, which form dimers and are therefore unlikely to form microtubule-like structures. Phylogenetic analyses indicate that the Prosthecobacter tubulins are quite divergent and do not support recent horizontal transfer of the genes from a eukaryote. The discovery of genes for tubulin in a bacterial genus may offer new insights into the evolution of the cytoskeleton.


It is evident that at some point in their evolution, the Eucarya acquired a structural complexity unrivaled by members of the other two domains of life. One of the major structural features that separates the Eucarya from the Bacteria and the Archaea is the presence of an internal cytoskeleton composed of actin and tubulin. Notably, these cytoskeletal elements are present in all known eukaryotes, even the a-mitochondriate protozoa (1, 2). Furthermore, their acquisition represented an important step in the evolution of eukaryotic cells by facilitating the engulfment of bacterial endosymbionts, which later became chloroplasts and mitochondria (3).

In contrast, there have been no conclusive reports of these cytoskeletal elements in the bacterial or archaeal domains. Over the years, there have been numerous reports of "microtubule-like" structures or "rhapidosomes" in members of both the Bacteria and the Archaea (summarized in ref. 4); however, thus far these observations lack any genetic basis. At present, the leading candidate for an evolutionary precursor of tubulin in the bacterial/archaeal domains is the cell division protein, FtsZ. Although there is strong evidence from their 3D structures that tubulin and FtsZ are homologous proteins (5, 6), they share only very low sequence identity, most of which is confined to the GTP-binding region (7). The strikingly low sequence identity is difficult to reconcile with the fact that tubulins and FtsZs are among the slowest-evolving proteins known and raises the question of whether any more closely related homologs of tubulin exist in members of the Bacteria or Archaea (8, 9).

Reports of microtubule-like structures in bacterial ectosymbionts ("epixenosomes") of ciliates in the genus Euplotidium present the most compelling structural evidence yet for the existence of tubulin-containing elements in bacteria. These organisms, which belong to the little-studied division, Verrucomicrobia, have been shown to possess tubular structures with diameters of 22 ± 3 nm, the size range of eukaryotic microtubules. These structures crossreact with anti-Paramecium tubulin antibodies and display sensitivity to microtubule-depolymerizing agents (10, 11). On the basis of these observations, we searched the partially sequenced genome of a free-living member of the Verrucomicrobia, Prosthecobacter dejongeii, for genes homologous to those for tubulin. To our knowledge, P. dejongeii is the first member of the division Verrucomicrobia to be subjected to genome-sequencing studies.


Evolutionary Origin of Prosthecobacter Tubulin Genes.

A significant question raised by this study relates to the evolutionary origin of the Prosthecobacter tubulin genes and may be summarized as two main hypotheses. First, the genes arose via a horizontal gene transfer from a eukaryote, and second, that the bacterial tubulins are ancestral to eukaryotic tubulins.

Relationships between the Prosthecobacter tubulins and a specific eukaryotic lineage, which would implicate a recent gene transfer, were never observed regardless of the sequence representatives, alignment subset, or mode of analysis used. Furthermore, btuba and btubb genes are present in all four species of the Prosthecobacter genus, suggesting that the genes were acquired before the divergence of this lineage. Thus, if the Prosthecobacter tubulin genes arose via horizontal transfer from a eukaryote, it was not during the recent history of the lineage.

The second hypothesis, that the bacterial tubulin genes are ancestral to eukaryotic tubulin genes, could be explained in terms of a shared ancestry between the two groups or a gene transfer from an ancestor of the Verrucomicrobia to a protoeukaryotic organism, before the radiation of extant eukaryotes. A gene transfer between the groups could also encompass a fusion event between an ancestor of the Verrucomicrobia and another organism, such as an archaeon (25). The phylogenetic analyses superficially support this hypothesis, in that the bacterial tubulin sequences were always seen to branch more deeply than eukaryotic  and  tubulin; however, this relies on the assumption that  and  tubulins were the first members of the tubulin family to arise. Even if this assumption is correct, caution is required in the interpretation of the analyses, given that the level of sequence divergence in the bacterial sequences may cause them to migrate to the base of the tree artifactually (24). The various evolutionary models for the origin of tubulins that are implied by these hypotheses are to be discussed in detail elsewhere.

Although the current evidence does not allow an effective distinction between the two hypotheses presented here, further indications as to the origin of the Prosthecobacter tubulin genes may be facilitated by determining the distribution of the genes within the division Verrucomicrobia. If the genes were present in members of several subdivisions of the Verrucomicrobia, this would suggest that the genes have been in these organisms for a long time. Furthermore, closer examination of the P. dejongeii genome, such as searching for other genes unique to eukaryotes, may aid in determining whether a large transfer event or a fusion occurred between members of the Verrucomicrobia and eukaryotes.

If it were true that the bacterial tubulins are ancestral to eukaryotic tubulins, it would have a significant impact on our understanding of eukaryote cell evolution. Although FtsZ is a homolog of tubulin, the evolutionary distance between the two proteins is substantial. Indeed, it has been suggested several times that a more immediate evolutionary precursor of tubulin may reside in some as-yet-undiscovered bacterial or archaeal lineage (26) or was acquired from an extinct lineage (25, 27) or "chronocyte" (2). Whether the Prosthecobacter tubulins satisfy this role as evolutionary intermediate between FtsZ and eukaryotic tubulin remains to be seen.


Obviously, research is just beginning on this bacterium and proteins.  However, it is interesting in light of one of Mike Gene's essays on his webpage:


< Tubulin and ftsZ: More than One Way to View Something >

For some unknown reason, many critics of ID think that design = uniqueness. That is, if a biological feature X is similar to biological feature Y, we are supposed to rule out design and instead infer common ancestry. But are things really this simple?

Consider tubulin and ftsZ. The former is a very important eukaryotic cytoskeletal protein involved in maintaining the cell structure, coordinating intracellular movement, separating chromosomes during mitosis, and forming the backbone of the eukaryotic flagellum. The latter gene product is a bacterial protein that plays an essential role in splitting the two cells during cell division and may also have cytoskeletal roles.

Although the two proteins have a similar role, most scientists did not originally consider them homologous (related by a common ancestral sequence). In a paper published in Cell by David Edgell and W. Ford Doolittle back in 1997, they noted that sequence identity less than 20% is attributed to chance. They also argued a "common function alone is not sufficient evidence of homology because two proteins can convergently arrive at the same mechanistic, structural, or biochemical solution to a particular biological problem." In fact, speaking directly about tubulin and ftsZ, they wrote, "amino acid alignments between these two proteins are not very convincing."

But today, the situation has changed as most scientists now think the two proteins are homologous. Why? The 3-D structure of both proteins has been solved and have been found to be very similar. One scientist has recently explained the picture:


There is now overwhelming evidence in favor of the idea that FtsZ is a homolog of tubulin, the ubiquitous eukaryotic cytoskeletal protein involved in many essential cellular processes including mitosis. Despite only limited primary sequence homology centered around a GTP binding motif termed the `tubulin signature sequence', the recently solved crystal structures of FtsZ and tubulin show extensive structural homology throughout the proteins. In addition, FtsZ, like tubulin, binds and hydrolyzes GTP and assembles into protofilaments that have structures similar to those within microtubules. This assembly is GTP-dependent and disassembly occurs when the GTP is exhausted, suggesting that FtsZ polymers, like microtubules, are dynamically unstable. FtsZ and tubulin also share similar responses to hydrophobic dyes: while bis-anilino-naphthalenesulfonate (bis-ANS) inhibits polymerization of both proteins, the related dye ANS has no effect on either. Another link between FtsZ and tubulin in vivo is that they can be made to coalign as polymers in mammalian cells in the presence of vinblastine, a microtubule-destabilizing drug. - Margolin, W. Themes and variations in prokaryotic cell division. Fems Microbiology Reviews, 2000 Oct, 24(4):531-48.


While this view is quite reasonable in science, we must remember that science is looking for the best non-teleological explanation. Thus, although no calculations have been made, it seems intuitively implausible that such similarities could be due to chance. And in science, chance is the only other viable alternative explanation to common descent.

But if we step out of this box and entertain teleological causes, structural similarity, and the similar properties that follow, are insufficient reason to infer common descent in place of design. In other words, while I would agree that both sequence and structural similarity are good evidence for common descent, this only holds true as long as we have no reason to suspect ID may be lurking in the background.

Now, my working hypothesis entails that life appeared on this planet as a consequence of seeding and the life forms that were seeded represented a consortium of sophisticated cell types. Since tubulin is basic to eukarya and ftsZ is basic to bacteria, and since both eukarya and bacteria may have been among that consortium (or separated by two distinct seeding events), ID may be lurking in the background. So let's see how we can think about the two proteins from an ID perspective.


Thirdly, we might expect these differences to be very important, explaining why a designer would employ the different variations on the GPD theme. And one of the facts not mention thus far in this thread is that although both ftsZ and tubulin have very different amino acid sequences when compared to each other, the sequences of both ftsZ and tubulin are highly conserved in bacteria and eukarya, respectively. In other words, when we compare ftsZ sequence within bacteria and tubulin sequence with eukarya, we find strong sequence conservation. FtsZ, for example, shows 40-50% identity when very different forms of bacteria are compared and I believe the tubulin conservation is even higher. In fact, one paper on my desk states "tubulins are among the most conserved proteins known."

This pattern is consistent with independent origins by design. That is, the first bacteria were endowed with a GPD variant known as ftsZ that has been conserved for billions of years due to its important design objective. Similarly, the first eukaryotes were endowed with a GPD variant known as tubulin that has been conserved for billions of years due to its important design objectives.

On the other hand, if we try to force common descent on the two distinct, highly conserved proteins, we face a strange situation. For prior to the evolution of ftsZ and tubulin from this hypothetical ftsZ/tubulin-like precursor, there was no apparent functional constraint. If there was, it is difficult to explain how the two sequences so radically drifted from each other only to be locked into place (of all places) in the last common ancestors of eukaryotes and bacteria. But wait a minute. The 3-D structure was being conserved. That's the basis for inferring the common descent. Yet what was it doing prior to the two sequences getting locked into place? Nothing bacterial. Nothing eukaryotic.


But here we have tubulin evidently doing something prokaryotic.

Never heard of these Prosthecobacter guys before?


Int J Syst Bacteriol 1996 Oct;46(4):960-6

Phylogeny of Prosthecobacter, the fusiform caulobacters: members of a recently discovered division of the bacteria.

Hedlund BP, Gosink JJ, Staley JT.

Department of Microbiology, University of Washington, Seattle 98195-7242,

Prosthecobacter fusiformis is morphologically similar to caulobacters; however, it lacks a dimorphic life cycle. To determine the relatedness of the genus Prosthecobacter to dimorphic caulobacters and other prosthecate members of the alpha subgroup of the Proteobacteria (alpha-Proteobacteria), we isolated and sequenced 16S rRNA genes from four Prosthecobacter strains. Surprisingly, the results of phylogenetic analyses placed the fusiform caulobacters in a deeply rooted division of the Bacteria that was most closely affiliated with the Planctomyces-Chlamydia group and only distantly related to the alpha-Proteobacteria. The genus Prosthecobacter shares a common lineage in this division with Verrucomicrobium spinosum, a polyprosthecate, heterotrophic bacterium. Consistent with this phylogenetic placement, menaquinones were isolated from Prosthecobacter strains and menaquinones have been isolated from Verrucomicrobium strains and planctomycetes but not from members of the alpha-Proteobacteria. Thus, the genus Prosthecobacter is a second genus in the recently described order Verrucomicrobiales. Members of the genus Prosthecobacter are susceptible to beta-lactam antibiotics and contain mesodiaminopimelic acid, indicating that they, unlike members of the Planctomycetales or Chlamydiales, have peptidoglycan cell walls. This major phenotypic difference, together with the phylogenetic independence of the verrucomicrobia, indicates that these bacteria and the sources of related 16S ribosomal DNAs obtained from soils, freshwater, and the marine pelagic environment represent an unrecognized division of the Bacteria.


Posted by: niiicholas on Mar. 31 2003,22:14

New TCS article gives us the short version of current euk. phylogeny & who may and may not be primitively non-ciliated:


J Mol Evol 2003 Apr;56(4):387-96
< Molecular phylogeny of centrohelid heliozoa, a novel lineage of bikont eukaryotes that arose by ciliary loss. >

Cavalier-Smith T, Chao EE.

Recent molecular and cellular evidence indicates that eukaryotes comprise three major lineages: the probably ancestrally uniciliate protozoan phylum Amoebozoa; the ancestrally posteriorly uniciliate opisthokont clade (animals, Choanozoa, and fungi); and a very diverse ancestrally biciliate clade, the bikonts-plants, chromalveolates, and excavate and rhizarian Protozoa. As Heliozoa are the only eukaryote phylum not yet placed on molecular sequence trees, we have sequenced the 18S rRNA genes of three centrohelid heliozoa, Raphidiophrys ambigua, Heterophrys marina, and Chlamydaster sterni, to investigate their phylogenetic position. Phylogenetic analysis by distance and maximum likelihood methods allowing for intersite rate variation and invariable sites confirms that centrohelid heliozoa are a robust clade that does not fall within any other phyla. In particular, they are decisively very distant from the heterokont pedinellid chromists, at one time thought to be related to heliozoa, and lack the unique heterokont signature sequence. They also appear not to be specifically related to either Amoebozoa or Radiolaria, with which they have sometimes been classified, so it is desirable to retain Heliozoa as a separate protozoan phylum. Even though centrohelids have no cilia or centrioles, the centrohelid clade branches among the bikont eukaryotes, but there is no strong bootstrap support for any particular position. Distance trees usually place centrohelids as sisters to haptophytes, whereas parsimony puts them as sisters to red algae, but there is no reason to think that either position is correct; both have very low bootstrap support. Quartet puzzling places them with fairly low support as sisters to the apusozoan zooflagellate Ancyromonas. As Ancyromonas is the only other eukaryote that shares the character combination of flat plate-like mitochondrial cristae and kinetocyst-type extrusomes with centrohelids, this position is biologically plausible, but because of weak support and conflict between trees it might not be correct. Irrespective of their precise position, our trees (together with previous evidence that Chlamydaster sterni has the derived dihydrofolate reductase/thymidylate synthetase gene fusion unique to bikonts) indicate that centrohelid heliozoa are ancestrally derived from a bikont flagellate by the loss of cilia. The centroplast that nucleates their axonemal microtubules is therefore almost certainly homologous with the centrosome of ciliated eukaryotes and should simply be called a centrosome.


Recent reappraisal of the basal radiation of eukaryotes argues that all eukaryotes belong to one of three major lineages: Amoebozoa, opisthokonts, and bikonts (Cavalier-Smith 2002a). Opisthokonts comprise the kingdoms Animalia and Fungi and the protozoan phylum Choanozoa (Cavalier-Smith 1987) and are the best-established multikingdom clade on the eukaryotic tree (Baldauf 1999; Baldauf et al. 2000; Cavalier-Smith 1998b, 2002a; Cavalier-Smith and Chao 2003; Patterson 1999; Stechmann and Cavalier-Smith 2002). Opisthokonts are characterized by a single posterior cilium with two centrioles, radiating singlet centrosomal microtubules, flat mitochondrial cristae, an insertion in EF-1, characteristic indels in enolase, and a very rare base-pair change in 18S rRNA (Cavalier-Smith and Chao 2003). Bikonts have only recently been recognized as a clade ancestrally with two divergent centrioles and cilia, at least two dissimilar microtubular centriolar roots, and often ciliary and centriolar root transformation spread over two cell cycles (Cavalier-Smith 2002a). The probable holophyly of the bikonts has been strikingly supported by the discovery that they share a derived gene fusion between dihydrofolate reductase and thymidylate synthetase (Stechmann and Cavalier-Smith 2002). The demonstration that the centrohelid heliozoan Chlamydaster sterni also has this fusion (Stechmann and Cavalier-Smith 2002) strongly indicates that it must have had a biciliate ancestry also and lost both cilia and centrioles. In agreement with this, we find no evidence for a grouping of Heliozoa with Amoebozoa, the only protozoan phylum for which a nonciliated ancestry remains open, given our present understanding of the position of the eukaryote root (Stechmann and Cavalier-Smith 2002).


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