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.