Joined: May 2002
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, USA.firstname.lastname@example.org
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.