Evolution of the vesicle fusion machinery
Final Report Abstract
Unlike a bacterium, which generally consists of a single intracellular compartment surrounded by a plasma membrane, a eukaryotic cell is elaborately subdivided into functionally distinct, membrane-enclosed compartments. Each compartment contains its own characteristic set of enzymes and other specialized molecules. In fact, it is essential for the survival of the cell that each compartment can maintain its own identity. Complex distribution systems transport specific products from one compartment to another. Transport between the different compartments is mostly mediated by vesicles, small, membrane-enclosed sacs filled with cargo. These vesicles bud from a donor organelle, are transported through the cytosol, and afterwards fuse with a target organelle. Currently, it is becoming clear that the molecular machineries involved in the principal aspects of vesicular trafficking - budding, transport, docking and fusion -are highly conserved among all eukaryotes and also between different vesicle trafficking steps with the cell. This suggests that the evolution of the transport system is closely intertwined with episodes of duplication and divergence of prototypic machineries involved in vesicle trafficking. Aim of the project was to establish the evolutionary history of the vesicle fusion machine using state-of-the-art bioinformatic approaches. We wanted to uncover how the interaction network has adapted in different eukaryotic lineages and how it was most probably organized in the proto-eukaryotic cell. Moreover, we carried out co-evolutionary analyses on the protein complexes to identify functionally important sites. Up-to-now, we have established large sequence data collections and analyzed the history of most of the key families involved in the vesicle docking and fusion step such as the SNARE and Rab protein family. The classified sequences have been made available publicly (http://bioinformatics.mpibpc.mpg.de/SNARE/ & http://bioinformatics.mpibpc.mpg.de/rab/). Similar investigations on SM proteins and the disassembly machinery (NSF and SNAP) are well advanced, but not published yet. For most of the vesicle fusion proteins we were unable to identify a prokaryotic homologue. This is different for the disassembly ATPase NSF, however. Intriguingly, our analysis of the NSF/Cdc48 family confirmed that the family arose by a duplication of its ATP-binding domain and revealed that the family is closely related to the ATPases forming the lid of the proteasome. These factors exist in some prokaryotes as well and thus probably the evolutionary history of this protein family will allow us to take a look at earlier stages in the evolution of the endomembrane system of eukaryotic cells. Furthermore, our co-evolutionary approach is already advanced and provides us with new details about functionally important sites in the key factors of the vesicle fusion machine. Nevertheless, as the transition from the Max-Planck-Institute for biophysical chemistry to the DNF at the University of Lausanne took much more time, for several unexpected reasons, this part of our research project is clearly less advanced as envisioned during the application, while the other went according to plan and part of the results have been published already. As our bioinformatic approach is closely meshed with our other investigations, the bioinformatic investigations indeed inspire (our) biochemical/ cell biological research. Conversely, biochemical/cell biological investigations (e.g. discovery of new factors, understanding the exact molecular interplay of proteins etc.) stimulated our bioinformatic research.
Publications
- (2010). A coiled-coil trigger site is essential for rapid binding of synaptobrevin to the SNARE acceptor complex. J Biol Chem. 285:21549-59
Wiederhold K., Kloepper T.H., Walter A.M., Stein A., Kienle N., Sorensen J.B., and Fasshauer D.
- (2011). Primordial neurosecretory apparatus identified in the choanoflagellate Monosiga brevicollis. PNAS. 108(37):15264-9
Burkhardt P., Stegmann C.M., Cooper B., Kloepper T.H., Imig C., Varoqueaux F., Wahl M.C., Fasshauer D.
- (2012). Untangling the evolution of Rab G proteins: implications of a comprehensive genomic analysis. BMC Biol. 10:71
Klopper T.H., Kienle N., Fasshauer D., Munro S.
