Creative Science Thinking Education

Excellent article about Teaching creative science thinking in Science. This article is not only about how to prepare the next generation of scientists, but also about ourselves and how to improve our creative thinking in our daily scientific job.

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.

Welcome

This site is dedicated to the community of scientists working on the Planctomycetes, Verrucomicrobiae and Chlamydiae (PVC) bacterial superphylum. The foundation of this blog can be found in the Reynaud and Devos publications in Science Perspective (2010) and Proc. Royal Soc. B (2011). 
Bacteria are usually defined by a set of common characteristics. In the last couple of years, exceptions to the bacterial definition have been described in the bacterial Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum. These bacterial rarities have the potential to profoundly change our view and understanding of early evolution and relationship between the three kingdoms of life. Their phylogenetic importance have been highlighted in various recent publications. However, a controversy emerged (see the reply here). See also the reply to the perspective and its answer.

Here, I will try to keep you updated on the novelty of research and events related to this fascinating group of bacteria. I intend this blog to be the first stop reference for the PVC community.