First book on PVC published

The first book entirely dedicated to Planctomycetes bacteria is eventually out. It is published by Springer and is entitled Planctomycetes: Cell Structure, Origins and Biology, Editor: Fuerst JA. It is the first book on planctomycetes focused on their cell biology. It provides details on the significant ecology and enviromental significance of planctomycetes. And it is valuable for those in the field of planctomycetology and those entering it for the first time. Here is the introduction:

"Planctomycetes, and their relatives within the PVC superphylum of domain Bacteria, including verrucomicrobia and chlamydia, challenge our classical concept of the bacterium and its modes of life and provide new experimental models for exploring evolutionary cell biology and the full diversity of how living cells can be organized internally. Unique among Bacteria they include species possessing cells with intracellular membrane-bounded compartments and a peptidoglycan-less cell wall, and bacteria such as the anammox organisms performing unique anaerobic ammonium oxidation significant for global nitrogen cycle. The book introduces these fascinating and important bacteria and deals in detail with their unusual structure, physiology, genomics and evolutionary significance. It is a definitive summary of our recent knowledge of this important distinctive group of bacteria, microorganisms which challenge our very concept of the bacterium."

The book is limited to Planctomycetes, but there is also some considerations of the other PVC members, mainly the Verrucomicrobia and Chlamydiae.

ISBN 978-1-62703-502-6

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

1st PVC metting (I)

What a great conference.

Excellent, amazing. Great talks by all speakers, great science. We have seen a very broad coverage of the best science that is done right now on those fascinating bacteria. Due to the amazing intracellular organization, lots of electron microscopy, tomography, and the likes, that gave us an impressive view of the diversity in this bacterial super group. Diversity that we are only glimpsing at so far, with many analysing aiming at broadening our coverage of this diversity, at the DNA level, selection and cultivation level, and at the cellular biology, microscopy level. Great coverage of this diversity has been presented.

Due to the small scale of the community, the conference was attended by a small number of participants, 40-45, which allowed for lots of interactions. The social part of the meeting also greatly helped, with an amazing visit to the botanical garden (including a Gregorian singer guide), and a dinner at the beautiful Heidelberg castle (that holds the big wine barrel). Interesting presentation of the artist Eveline Kolijn that presented her work based on science images, bringing a refreshing and colorful side to the conference.

A special issue of the Antonie van Leeuwenhoek publication will be dedicated to this conference, with articles by most of the keynote speakers and some participants. And hopefully a meeting report. If you have missed the conference that would be the best way to catch up. Coming up soon.

Thanks you very much to the EMBO for a generous grant that allowed us to organize this great event and keep the prices low.
All in all, a very good first conference entirely dedicated to the PVC bacteria. The decision was taken to attempt to have another PVC conference in two years. See you then in 2015.

First PVC meeting coming up

The time of the first workshop entirely dedicated to PVC bacteria is coming up soon. The (almost) final program is available on the EMBO web site but also here.

The program looks really exciting, with key players in the field given keynote or small talks, but also most posters being presented as small talks. Lots of interaction being expected from this. There is also a whole section dedicated to Chlamydiae. We will provide here continuous coverage of this exciting meeting.

Stay tuned.

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.

First PVC meeting

Hip hip hourra!!

That is it, we obtained a grant from the EMBO workshop and course program to organize the first meeting entirely dedicated to the PVCs. This event will be entitled: "EMBO workshop on Planctomycetes, Verrucomicrobia, Chlamydiae superphylum: exceptions to the bacterial definition?"  It will be organized by DP Devos (COS, Heidelberg Uni., Germany) with the help of co-organizers C Jogler (Harvard, Massachusetts, USA) and JA Fuerst (Brisbane Uni., Australia) and will be held in Heidelberg, Germany from the 28th of Feb. to the 2nd of March 2013. It will be the first time that scientists working on so different organisms will assemble together in the same room. Fascinating keynote talks have been secured and both tenants of the controversy about PVC phylogenetic link to eukaryotes will be invited. This promise to be a very exciting meeting. More details will come soon, but I want to share this excellent news with you. So mark you calendar for the 28th of Feb. 2013.

Please send me an email if you are interested, intend to come or just are thinking about it at microplatypus@gmail.com. Thanks.

EvolCell2012, NCBS, India.

Next (and first in this blog) conference in February 2012 on the Evolutionary Origins of Compartmentalized Cells at the National Centre for Biological Sciences, Bangalore, India. Interesting speakers includes: John Fuerst, Mike Rout, Monica Bettencourt-Dias and William Martin amongst others. This promises to be a very exciting conference.

Here is the very beautiful Aborginal style poster: .

I will keep you updated by regular posts.