NSF Evolutionary Cell Biology workshop

Going to this NSF-sponsored workshop on the new field of Evolutionary Cell Biology at the end of the month. The stated goal is to identify and address the major gaps in knowledge about the evolution of cell biological systems. This also includes a focus on education and new infrastructures, fundings, ... needed for the new field. Sounds fascinating. The participant list is as fascinating, from well-established 'old dogs' to younger ones, including some well known faces, most of them we have already seen at the EvolCell2012 NCBS meeting, last year in India.

A few of the questions that will be debated includes the roles of physical constraints in convergent evolution, the issue of the mutational cost of increased complexity in the evolution of cellular features, the rise of cell biological structures novelty, amongst other. We will attempt to identify the needs to move the field forward, eg what would it take to create a hypothesis-driven evolutionary cell biology? But also what new toolds, technologies and infrastructures are needed to advance this new field. Education will also be addressed as we will attempt to identify what the changes that are needed at all levels of education to push evolutionary cell biology forward.

An impressive program has been sent to all participants. Interesting discussions to be expected but looking forward to be there. Will keep you posted!

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.

NCBS 2012 III: Divers

Two recurrent themes throughout the conference were 1) the limits of detection by sequence-only based methods, and 2) the apparent extreme complexity of the LECA, the Last Eukaryotic Common Ancestor. This was best illustrated by MC Field in his contribution entitled "Finding things that are not there - lessons at the nuclear envelope". He demonstrated that a combination of molecular biology experiments combined with bioinformatics, essentially structural predictions, were able to detect proteins that could not be detected by Blast searches. This was illustrated in the case of the nuclear pore complex of the trypanosome. Of course, in this case, extreme care has to be taken to discriminate the real signal from the noise. He extended his analysis from the nuclear pore complex to the transporter that ensure the transfer of the cargo through the nuclear envelope, the karyopherins. He showed that karyopherins are conserved and ancient, with at least 14 being most likely present in the LECA, again adding to the complexity of this elusive ancestor. Eventually concluding on the detection of things that are not there, he showed conclusive data about the presence of Lamin analogue in Trypanosome which was so far thought not to possess such an intranuclear protein (a work in press in PLoS Biology).

On a related theme, but different organism, Margaret 'Rossie' Robinson presented her last work on the detection of a new, the fifth, adaptor complex, AP5. The list of adaptor complex was thought to be complete, prompting some article title like 'Adaptins: the final recount' (MBoC 2001). It is genuine to wonder about how many such discovery are still awaiting out there.

MP Rout then presented his work on the structure of the nuclear pore complex by integrative modeling. I won't go back to the details of the work published in 2007, but they have pushed the limits of the method to achieve a model of a major building block of the complex, the so-called Nup84 complex, to a precision of ~1.5 nm. This amazing work has just been published in JCB (Fernandez-Martinez et al., 2012). The suggestions derived from the structure about a possible ancestral two fold symmetry at the core of the Nup84 complex was very inspiring and very much in line of the evolution of the nuclear pore complex and thus the protocoatomer hypothesis.
It is so beautiful that I can't resist to show you the inspiring figure taken from the publication

You can see the possible axis of duplication and the losses of the Nup85/Seh1 equivalent, as well as the reductive loss of Nup84 Nt-domain and Sec13 equivalent. Very inspiring.

NCBS 2012 IV and end: WF Martin

The meeting closed by a spectacular show by William Martin. Clearly deeply involved in what he was presenting, Bill started by a thorough recapitulation of all evolutionary scenarios that have been proposed for the origin of the eukaryotes, starting back in 1910, a century ago. The presentation was very comprehensive and Bill's own style ensured the audience of a great show.
Bill went on to present his latest work, including the Evolutionary network of gene in eukaryotes where they present a new method to solve the evolution of eukaryotic genes based on a network of lateral gene transfer. This is based on the fact the the origin of much eukaryotic genes shared with prokaryotes are found all over the tree of life. The conclusions stress the importance of archaea and of mitochondria in the origin of eukaryotic genes, and thus of the eukaryotes.
Bill ended up by discussing the Energetics of genome complexity according to which eukaryogenesis was only possible thanks to the release of the energetic constraints on the genome due to the internalization of the mitochondria. We were even treated by evolutionary movies during the questions. In conclusion, a very complete, entertaining and stimulating presentation by Bill Martin.

There were many other very interesting talks at the conference, including M Munson on the exocyst, Mara Duncan on the linear motifs interaction in the clathrin adaptors, M Bettencourt-Dias on the centrosome, and Frances Brodsky on clathrin, amongst many others. However, time and space constraints and the subject of this blog don't allow me to describe them here. Contributions from other attendees are welcome to present those talks not covered here or even to correct, comment or contribute to the discussion of those covered. The conference itself was actually preceded and followed by tutorials on Cell biology and immunology as well as on Evolutionary and informatic approaches.

All together, a very interesting conference. As I said, one of the most interesting and most interactive I have been to. Thanks a lot to Frances Brodsky, Satyajit Mayor and Mukund Thattai for the organization and ensuring its success. Words are circulating that there might be a follow up to this one, may be in Europe in two years. I will certainly be looking forward to it.

NCBS 2012 II: DP Devos

Damien Devos (EMBL, Heidelberg Germany, moving to the Center of Organismal Studies (COS) at the Heidelberg University) then presented his talk entitled "Microbiology's platypus". He first recapitulated the origin of the protocoatomer hypothesis, starting from a structural analysis of the nuclear pore complex; again highlighting the limits of sequences-only based methods. The first part of his talk ended with the importance of the membrane coat innovation as they form the core of the multi-protein complexes sustaining most divisions of the eukaryotic endomembrane system. As such, they must have been present in the LECA (him again) and probably in the ancestor of.
He then developed a method to use structure (since sequence search is limited, remember?) to search for this particular protein architecture and found it only in some of the PVC proteomes. Immunological characterization located such bacterial membrane coat-like proteins in the paryphoplasm of Gemmata cells. However, the differences of interpretation between him and the previous speaker, John Fuerst, became clear at that moment. Damien doesn't interpret the planctomycetes cell plan as different from the classical bacterial one, but just as an extension of it, when John interprets it as fundamentally different. An interesting discussion ensued and was followed over tee. Damien then presented his last work, where they reconstructed in three-dimensions various complete Gemmata cells. He showed a movie that first went through the tomogram of a cell, followed by the process of modeling the membranes and other features and ending with the final model. Unlike the previous speaker, no isolated compartments or even nucleoid envelope could be observed in this study. It would be interesting to pursue this analysis and resolve this issue. Damien then ended with his interpretation of the possible evolutionary connections between the PVC and the eukaryotic or archaeal features. He made the parallel between the special features found in PVC and the eukaryotes or archaea and the avian or reptilian ones found in the mammal platypus, hence the title of his talk.

NCBS 2012 I: JA Fuerst

What a conference! You should have been there.

It was very very nice. Sincerely, one of the best conference I have been to. The conference was entitled Evolutionary Origins of Compartmentalized Cells. It was thus not strictly concerned with PVCs, but we had some interesting talks and discussion, including some pretty hot ones, about them. The protocoatomer hypothesis was present throughout the conference. Similarly, the LECA (Last Eukaryotic Common Ancestor) was refereed to in many many talks. An agreement, as supported in many publications, is that the LECA must have been very very complex. After two talks on conservation and innovation in membrane traffic in a divergent eukaryote and on assembly of division ring, John Fuerst (Queensland Uni., Brisbane, Au) took the stage. He first gave a nice and quite complete review of the PVCs and their particular traits. He insisted quite rightly about the limits that classical searches based on sequence only seem to have reached. This was also a recurrent theme that we repeated throughout the conference. John then insisted on the difference between the planctomycete paryphoplasm and the classical bacterial periplasm. The data invoked to justify this difference were not so convincing and left most of the audience suspicious. He then presented a model of the gemmata nucleoid envelope that is supposed to completely surround the bacterial genetic material. Unfortunately, he didn't present the data from which this model was derived. He ended by presenting images and the reconstruction of a nuclear pore complex-like structure that is claimed to be found in the nucleoid envelope of the bacteria. The resolution was not great, but if confirmed this would represent an impressive achievement. However, some doubts about the identity and localization of this complex remains. The round of questions were dominated by a heated exchange with William Martin that strongly criticized the data presented and the claims about their relationships with the eukaryotes. Both sides stood on their claims and the discussion continued during the tea break.

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.