Did mitochondria arrive late in eukaryogenesis?

Gabaldon just published an interesting phylogenetic analysis of eukaryotic signature proteins. The evolutionary signal that they could recover for those proteins does not support an early aquisition of mitochondria during eukaryogenesis, but to the opposite a late one, suggesting that most of the ancestral eukaryotic cell was already quite complex, when the mitochondria was aquired.

Special Issue of AvL on the first PVC meeting

And the Special issue of Antonie van Leeuwenhoek entirely dedicated to the 1st PVC conference is now online at the AvL web site. It includes, an introduction by the organisers, a review and historical perspective, contributions by some keynote speakers and original contributions from the talks. Very nice way to wrap up the first PVC conference and a great way to keep on track if you missed it.

Articles from the first PVC workshop

Most of the article from Special Issue of the publication Antonie van Leeuwenhoek dedicated to the first PVC workshop are now available on the pre-publication page of the AvL. Articles are available freely for a short time, so get them while you can. I have just been told that the SI will be freely available for the rest of the year. That is a very good news. Summary of the workshop and of the articles in the SI can be found in Introduction article by Devos, Jogler and Fuerst. The whole special issue is in production phase and should be available soon. Stay tuned.

Quick guide to Gemmata obscuriglobus

A beginner's guide to our favorite bacterium has just been released in Current Biology. This is the perfect starting point if you are interested in microbiology's platypus. Current Biology's Quick Guides aim to give readers 'everything you need to know about...' for topics they're likely to see fairly regularly in major journals but aren't up to speed with. This one starts like this "What is Gemmata obscuriglobus? Gemmata obscuriglobus is the standard bearer of a group of bacteria that has recently been the focus of interest in cellular, environmental, medical and evolutionary biology. G. obscuriglobus bacteria have been dubbed the ‘platypus of microbiology’ because of their peculiar characteristics usually not observed in bacteria, including some that are more commonly associated with eukaryotes and archaea."

Three-Dimensional Reconstruction of Bacteria with a Complex Endomembrane System

That is it, our last paper is out, Santarella-Mellwig et al., PLoS Biology 2013. In this paper, we investigated the three-dimensional organization of the complex endomembrane system in the planctomycete bacterium Gemmata obscuriglobus. We reveal that the G. obscuriglobus cells are neither compartmentalized nor nucleated, contrary to previous claims, as none of the spaces created by the membrane invaginations is topologically closed; instead, they are all interconnected. The organization of cellular space is similar to that of a classical Gram-negative bacterium modified by the presence of large invaginations of the inner membrane inside the cytoplasm. Thus, the membrane organization of G. obscuriglobus, and most likely all PVC members, is not fundamentally different from, but is rather an extension of, the “classical” Gram-negative bacterial membrane system.

See also the blog post cleaverly entitled Bacterium excluded from the Eukaryote Club

How do Planctomycetes divide?

One of the particular features of Planctomycetes, and some other PVCs, is that they have lost the otherwise ubiquitous FtsZ gene. FtsZ is the main building block of the constriction ring that all other bacterial cells use to divide by fission. It is so important that it is one of the few proteins that are found in all bacteria, with very few exceptions. One of them, of course, are some of the PVCs, and in particular almost all Planctomycetes. And we know they have lost it, because the dcw cluster is still present but showing different degrees of erosion in actual PVCs, demonstrating that it was present in the Last PVC Ancestor, and most likely functional (see fig. 2 in the Pilhofer 2008 publication). So the very important question of "how do Planctomycetes divide, and in particular achieve the last steps of cytokinesis?".

This is the question that Jogler et a., 2102 Jbact address in their latest publication. Initial Phylogenetic analysis (Fig. 1)

provided a phylogenetic criterion to leave anammox bacteria out of our analysis

This is already important since it clearly splits the Planctomycetes in two group, the anammox on one side and all other non-anammox planctomycetes on the other. Anammox have been claimed to be early branching Planctomycetes and have particular biochemical reactions, endomembrane organization and dividing mode (most likely). Thus, it make sense to separate them from the other planctomycetes. This first analysis clearly puts them apart from the others.
The authors then go on to define the (non-anammox) planctomycetal core genome, by identifying those genes that have homologues in all selected genomes and discarding the ones that are also found in 'classical' bacteria such as E. coli and B. subtilis. They identified 114 clusters of exclusively planctomycetal proteins. No doubt that some of them should be related to the particular mode of division of those organisms. By example, one such cluster contain 39 membrane-coat like proteins that are structurally related to eukaryotic ones and likely to be involved in the membrane organisation in Planctomycetes (see Santarella-Mellwig et al., 2010 PLoS Biology,). Interestingly, a new FtsZ-like protein was recently described and found in a few Planctomycetes. However, Jogler et al. failed to detect homoloues in all other sequenced planctomycetes despite the use of a very similar strategy. Thus this FtsZ-like family might not be involved in division, at least not in all Planctomycetes.

They then provide an interesting analysis of the proteins found in this core planctomycetal genome and their domain composition.
One of the most interesting result is the finding that Planctomycetes are very poor in DNA-binding one-component systems (classical receptor-operator single proteins in bacteria, direct link between signal and output), but very rich in Ser/Thr protein kinases, which are common among eukaryotes and usually rare in bacteria. Again another striking relationship between those bacteria and eukaryotes.
They also found more two-components systems that are orphan genes, pointing toward a more complex regulation in planctomycetes.
But even more interesting, is their finding related to ECFs. ECFs are extracytoplasmic function sigma factors. In contrast to other bacteria, all planctomycetes are particularly rich in ECFs. Most planctomycetes ECFs can NOT be classified in the previously defined classes, which is probably just a reflexion of the bias towards model bacteria. G. obscuriglobus in particular is the second most ECF-rich bacteria, with the deltaproteobacterium Plesiocystis pacifica. They also identified a new class of ECFs that is specific to G. obscuriglobus. This class also contain more than half of the ECFs in the G. obscuriglobus genomes pointing to a recent evolution of those genes. Importantly, these are also the first membrane-anchored ECFs in bacteria. Given the conspicuous endomembrane organisation in this organism, it make sense that those proteins will play an important role in its regulation.

In conclusion, very interesting paper, even if not resolving the mystery of PVC division. On the other side, I would have found it interesting to do the same analysis on all PVC members. No doubt though that PVCs remains fascinating organisms, as this article beautifully illustrates.

HGT, no HGT?

By now you should know that PVC bacteria are very interesting for their particular features. Some of those are usually NOT observed in bacteria and usually more associated with eukaryotes or archaea. This is the base of the controversy around the PVCs, of which the McInerney paper is a good example. This point will also be addressed at the EMBO PVC workshop 2013 (please come, listen and contribute!).

Addressing the origin of those features is a difficult issue. Mostly because for the majority of those, we don't even know the proteins that are behind them. In addition, evaluating the origin of genes or proteins requires the elaboration of a multiple sequence alignment with satisfying quality assessment. This is only possible for a couple of such PVC features.

In a recent article, just published in the Frontiers PVC research topic, Budd and Devos review the few cases in which such phylogenetic reconstruction have been achieved for the PVC features. They found out that contrarily to what has been published (eg the reply to the Devos and Reynaud 2010 Science paper), no agreement has been reached on the origins of those features (which once again are only a small portion of the peculiar PVC features). In fact, about half of those analysis actually conclude against lateral gene transfer. They conclude that the HGT origin of those PVC features is still not established. In addition, they highlight the importance of taking into account alternative models and scenarios, including alternatives to the 'classical' 16S rRNA based (ie Woese-type) tree of life and HGT/no-HGT models.

Whatever it is, there is certainly more interesting surprises to expect from this intriguing bacterial superphylum.

DGZ publication 2012

Nice summary of one of the main hypothesis and our work has just been published in the Newsletter of the German Society for Cell Biology. Basically a sum up of previous paper and a few to come. Enjoy.

Ciliary pore complex

The protocoatomer hypothesis suggest a common evolutionary origin for key eukaryotic complexes like nuclear pores complexes (NPC) and coated vesicles based on a typical domain architecture, the membrane coat (MC) architecture, found only in some of the proteins forming those complexes. Adding to a growing list of data, Kee et al. (2012) Nat. Cell Biol. 14, 431–7, see also the preview by Obado and Rout (2012) Developmental Cell 22, 693-4, suggest that this connection should be increased to include cilia, another key eukaryotic feature. The presence of karyopherins and of a Ran gradient in both systems (Dishinger et al., 2010) already provided some links between the NPC and the cilia. At least one karyopherin recognize a CLS (ciliary localization sequence) that is suspiciously similar to a NLS (nuclear localization sequence). In addition, MC proteins are also found inside the cilia in the transport complexes (Taschner et al., 2012) and components of the BBSome (a multi-protein complex involved in cilia transport) share related structural organization with the coat complexes (Jin et al., 2010). Because this protein architecture is also found in clathrin, COPI and COPII complexes, this suggests a common evolutionary origin to NPCs, coated vesicles and some ciliary components in, to cite the original protocoatomer hypothesis,

an early membrane-curving module that led to the formation of the internal membrane systems in modern eukaryotes,

which can now possibly be expanded to include the cilia or its ancestor.

The origin of the eukaryotic cell is becoming a more complex but also more fascinating issue.

Time for a new genetics curriculum

Biology is changing fast. In an excellent article in Plos Biology, 10(7): e1001356, Redfield RJ, consider that the way we use to teach genetics is updated and propose alternative to teach useful and interesting material. Although we might not agree on everything she propose, it is to be admitted that the historical perspective in genetic teaching is outdated and in need of a shaking.

However, I personally believe that the historical aspect is part of the beauty and attraction of biology. I remember very well that learning about the elegance and beauty of the classical experiments by eg Jacob and Monod, amongst many others was part of the fascination to become a biologist. By example, I recently very much enjoyed an historical perspective on the first tree of life by Woese written by Pace et al., PNAS 2012. I believe that the combination of historical context and realization of the implications that it had and still has, is fascinating.

It is true that with the pace of change in current biology, it should probably be forming a separate less central aspect of a modern curriculum. I would however favor to keep the historical perspective because of the intrinsic beauty of the experiments and the lessons it teaches about scientific thinking.

The before last sentence is highly stimulating:

As long as we remain comfortable with teaching largely irrelevant material, we don't have to worry about changing it.

It has now to be seen how this develop in a new course and how this modifies the potential interest of the student.

NCBS meeting wrap-up publications

An excellent summary of the NCBS meeting has just been published by the organizers in Nature Cell Biology 14, 651 (2012). And another one by the American Society for Biochemistry and Molecular Biology.
We are preparing something on those lines for the NSF EvolCellBio meeting. Coming soon. In addition, the slides of some of the talks are available here. I recommend particularly recommend to look at the one of W. Martin.

Planctomycetes review

Fuerst and Sagulenko (Nature Review Microbiology 2011) present a nice review of the current knowledge of the Planctomycetes. They focus particularly on the genus Gemmata because of its endomembrane system seemingly surrounding the DNA, the presence of eukaryotic-like membrane coat proteins in its proteome and its capacity to do endocytosis. They conclude that:

"The compartmentalization of planctomycetes challenges our hypotheses regarding the origins of eukaryotic organelles."

This article nicely highlight the importance of studying other non-classical model of bacterial cell biology, like E. coli. There is also lots of phylogenetic interesting facts, evolution stimulating hints and questions are spread throughout the article.
They conclude with some hypothesis concerning the possible link between those bacteria and the origin of the eukaryotes, including convergent evolution, bacteria invention followed by LGT to the ancestral eukaryote, or LGT from the eukaryotes to the Planctomycetes and a complex LUCA. However, may be the strongest deduction is the following:

"Nevertheless, it seems clear that the planctomycetes are now a strong challenge to the idea that some form of fusion between archaeal and bacterial cells was necessary to evolve the eukaryote and its nucleus."

Whatever the correct answer, it is clear that Planctomycetes are fascinating bacteria that will keep us busy for the next couple of years. Keep watching!

Bacterial origin to our cytoskeleton?

FtsZ is the (almost) ubiquitous protein forming rings or pseudo-rings involved in bacterial division, while tubulin is the main eukaryotic cytoskeleton. The nature of the relationship and order of evolution between FtsZ and tubulin is unclear. It is clear that all tubulins evolved from a common ancestor shared with the bacterial FtsZ. In a beautiful article, Pilhofer and Jense (PLoS Biology 2011) add new evidences suggesting an ancient relationship between bacterial tubulin homologues and the eukaryotic ones. The discovery of bacterial tubulin in several Prosthecobacter, members of the Verrucomicrobia phylum, came as a surprise. The two genes, btubA and B are present in most, but not all, Prosthecobacter species. This diffuse pattern is similar to other eukaryotic or archaeal features found in PVC members. However, the function of BtubA/B in Prosthecobacter is unclear since they coexist with FtsZ also present in the proteome of those species. Is FtsZ also involved in cell division in Prosthecobacter is another question that would be fascinating to answer, as it has been shown that FtsZ can have divergent roles, not all of them involved in division, discussed in a previous post, Non FtsZ based division in Thaumarchaea, although in this case in archaea. It had been previously suggested that the bacterial tubulin genes were the results of lateral gene transfer, mainly based on genomic organization. On the other side, shaperon-less folding, weak associations (all presumably ancient properties) and sequence features argued against LGT and in favor of an ancient ancestral relationship between the proteins. Pilhofer et al. first realised the most comprehensive phylogenetic analysis of the tubulin family and failed to detect any stable associations between the bacterial and any eukaryotic tubulin subfamilies. They then undertook electron microscopy to show that BtubA/B form microtubules in bateria. They beautifully show that the bacterial microtubules are composed of only five protofilaments, unlike the eukaryotic ones that contain 13.

Figure 4. Structural model of “bacterial microtubules.”
(A) 2-D schematic of the proposed architecture of bacterial microtubules built from BtubA (dark-blue) and BtubB (light-blue). Protofilaments are numbered 1–5. (B) 3-D comparison of the architectures of a bacterial microtubule (left; BtubA in dark-blue; BtubB in light-blue) and a 13-protofilament eukaryotic microtubule (right; β-tubulin in black; α-tubulin in white). Seams and start-helices are indicated as in (A). doi:10.1371/journal.pbio.1001213.g004

This is to me the most compelling evidence to date against the LGT hypothesis. They thus suggest that the following scenario:

It therefore appears that in tubulin evolution, heterodimer formation correlated with tube formation and the five-protofilament, one-start helix was the simplest and earliest microtubule architecture realized, which later evolved into the larger eukaryotic microtubule ... An alternative "vertical evolution" hypothesis is that btubAB was present in the last common ancestor of Verrucomicrobia, but the genes were simply lost by the other members of the phylum.

Illustrated in this picture:

Figure 7. Model for the evolution of BtubA/B.
Tubulins, FtsZ, FtsZ-like, and TubZ all evolved from a common ancestor with the likely properties listed [5],[9],[58]–[61]. In contrast to the bacterial FtsZ, FtsZ-like, and TubZ proteins, the last common tubulin ancestor appears to have evolved to form heterodimers (consisting of “A”- and “B”-tubulins) with properties that enabled tube formation. Modern α- and β-tubulin further localized the activating T7 and short S9, S10 loop into different subunits, developed a need for chaperones, and began to form larger, ~13-protofilament microtubules. In contrast, BtubA and BtubB retained ancient features shared by FtsZ such as chaperone independence, weak dimerization, and both an activating T7 loop and short S9, S10 loop in both subunits [17],[19],[21]. The smaller, five-protofilament, one-start-helical architecture of the bacterial microtubule is therefore likely a primordial form. The ancestry of the other supplemental tubulins γ through κ is unclear, except that θ- and κ-tubulins derived from β and α, respectively. doi:10.1371/journal.pbio.1001213.g007

This is not unlike the presence of many features inferred to have been present in the last PVC common ancestor, and then subsequently lost in various members, as suggested in the Devos & Reynaud publications Science Perspective (2010) and Proc. Royal Soc. B (2011). As stated by the authors,

It is presently debated whether an ancient Planctomycetes-Verrucomicrobia-Chlamydiae bacterium was involved in the evolution of eukaryotes, but if so, such a relationship would be consistent with bMTs preceding modern eukaryotic MTs.

All in all, this suggest a bacterial origin to our cytoskeleton.

OpenKnowledge Foundation

Historically, scientists have mainly been isolated entities generating and keeping for themselves their own data. The web has opened up new ways of sharing and collaborations. But also for exploring new forms of analysis and exploration of the data. The Open Knowledge Foundation (OKF) is a community-based organization that promotes open knowledge. They have just published some principles and recommendations for Open Data in Science open knowledge foundation. To be considered as 'open' the data must be available and modifiable with the only limitation of a requirement for citation and similar sharing. I see the lack of career rewards as the main obstacle towards a more 'open' science.

Mixed education

All of us involved in teaching know that a mix of research and education is a difficult balance to find. In addition, undergraduate education can be improved by a higher level of student participation in authentic research. Kloser et al., (2011) PLoS Biology describe possible way to do just so. More than the article in itself, there is lots of references therein. Integrating Teaching and Research in Undergraduate Biology Laboratory Education is an interesting concept that deserve more attention.

Radiation tolerance

The Medalia team analyzed chromatin organization and radio resistance in the Planctomycetes Gemmata obscuriglobus. They report that Gemmata tolerates high doses of UV and ionizing radiation. Using cryoelectron tomography they found a highly ordered condensed-chromatin organization and a complex network of double membranes engulfing the condensed DNA. The complex double-membrane system emanates from the internal cell membrane. There is some ambiguity in the paper since on one side, they report that their results imply that the bacterial nucleoid is not completely sealed by the double-membrane system but on the other side, they conclude that multiple nucleoid domains are enclosed by the double-membrane system. So is it enclosed or not completely sealed?

The analysis of radio resistance is interesting. They report that G. obscuriglobus is highly resistant to UVC radiations. They suggest that this is linked to the condensed stated of the nucleoid and conclude that their observations support the notion that packed chromatin organization enhances radiation tolerance. Their tomography is based on a 15-nm-thick slice, when a typical bacteria is around 3 to 5 microns. When E. coli dies around 300 J/m2 of UV dose, Gemmata can support around 3 times that, close to 900 J/m2. This high level of radio resistance could be linked to non-homologuous DNA end joining (NHEJ), a phenomenon linked to double strand break repair, meiosis recombination and to the VDJ locus rearrangement processes in eukaryotes. Bioinformatics investigation of the Gemmata proteome revealed genes with homology to those for RecA, RecB, and RecD (no RecC), as well as for NHEJ mechanism ATP-dependent DNA ligases. Wittingly, they highlight that the G. obscuriglobus DNA repair ligase protein is significantly smaller than its bacterial homologues (58.4 vs >80kDa in other bacteria), suggesting that this lighter mass enhances the accessibility to the DNA breaks within the condensed DNA environment. Of course, the connection between higher radiation tolerance and DNA condensation is still to be demonstrated but the arguments and data presented here makes it very likely in this organism. Thus, G. obscuriglobus has evolved versatile mechanisms to deal with stress conditions.

Non FtsZ based division in Thaumarchaea

The nature of the evolutionary relationship between bacteria, eukaryotes and archaea is not clear. An interesting feature of the PVC is that some members, like some archaea, lack the otherwise ubiquitous FtsZ division protein. The lack of the otherwise ubiquitous FtsZ opens the question of how is cell division achieved in those organisms. Pelve et al. Mol. Microbiol (2011) demonstrate that in the thaumarchaea N. maritimus, an organism with one of the smallest genomes amongst free living organisms, it is the Cdv proteins, and not FtsZ, that localize to division sites. The authors found that the FtsZ protein did not temporally neither spatially correlate with nucleoid segregation and no band or ring structures were observed. Instead, FtsZ was distributed in the cell in a mainly uniform intracellular distribution, regardless of cell cycle stage, as determined by cell size or DNA distribution. Thus, not only did the authors established that N. maritiums utilizes the Cdv machinery for cell division, they also demonstrated that it did not use FtsZ for this, a unique feature in FtsZ function. Thus division in Thaumarchaea is based on Cdv proteins and not on FtsZ machinery, and is likely to be similar to crenarchaea, an archaea with Cdv and not FtsZ encoded in its genome. What function FtsZ fulfills in thaumarchaea remains an open question. Since they couldn't detect a cytokinesis function for FtsZ, the authors propose that the protein has evolved a different function in thaumarchaea. In line with this proposal, thaumarchaeal FtsZ sequences are phylogenetically separated from bacterial and euryarchaeal FtsZ groups. The observed pattern could be a transition point from a FtsZ-based division mechanism to a non FtsZ-based one. The pattern of FtsZ and Cdv machinery homologues in other prokaryotes indicates that further division variants should be found out there. It seems to me that it would be important to characterize them to get a full coverage of cell division mechanisms.

Mitochondria's dividER.

A recent paper by Friedman et a., Science 2011 reinforces the tight connection between the ER and the mitochondria. It was previously known that ER and mitochondria exhibit important and dynamic contacts. Now Friedman et al. report that the ER is involved in the division process of the mitochondria, reinforcing the tight link between the ER and mitochondaria. This result demonstrates the decisive role of the eukaryotic endomembrane system in the regulation of the organelle's faith.

But what's that to do with the PVC bacteria? Well, the PVC endomembrane has been suggested to be linked to the birth of the eukaryotic one. Even more,Devos & Reynaud PRSB (2011) have suggested that the eukaryotic endomembrane system originated by the internalization of the bacterial periplasm. The concomitant internalization of the ancestor of the symbiont with the periplasm establishes the endomembrane system at the same time as the mitochondria. This hypothesis suggests a tight interaction between the endomembrane system and the mitochondria. And this is exactly what the Friedman paper demonstrates.

The connection between the ER and the mitochodria is tightened by a study showing that the ER tether mitochondria specifically at the tip of the growing bud in Saccharomyces cerevisiae.

Let's build cathedrals in the open.

A recent article in Nature Chemistry by Woelfle et al. describe a fascinating new way of doing science in the open. This paper describe an 'open science'  research project in organic chemistry, which would be just like having your daily notebook published openly on the web. A Faculty of 1000 evaluation compare the classical way of doing science with building cathedrals:

... scientific progress, just like the erection of a splendid cathedral, is often a slow meandering process, riddled with challenging problems requiring the technical skills of a few highly trained experts.

The Woelfle et al. paper offers a remarkable and unexpected alternative to the building of cathedrals. The work was performed in full view of the public eye, with progress, data, results, analyses and manuscript drafts being posted online as they were generated (the synaptic leap).

This is related to the polymath project where mathematicians collaborated massively to solve a previously intractable problem. This is related to doing science online which was enlightening for me and one of the motivation behind this blog. This is in the line of what I intend to do with this blog. So come on, let's go, let us build cathedrals in the open.

Chlamydiae pan-genome

Matthias Horn (from the Uni. of Vienna) has just published an interesting paper about the Chlamydiae pan-genome. They obtained the genome of various members of the phylum and compared them with the existing ones. The most striking discovery for me, is the last sentence of the abstract:

Phylogenomic analysis focusing on chlamydial proteins with homology to plant proteins provided evidence for the acquisition of 53 chlamydial genes by a plant progenitor, lending further support for the hypothesis of an early interaction between a chlamydial ancestor and the primary photosynthetic eukaryote.