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Dave Engelke's group performed the same 2 (and 3) hybrid analyses with the yeast proteins (and RNA; in fact, they helped us with our analysis), and amazingly our interactions in M. thermoautotrophicus are an almost perfect match to what they found in yeast. We see that Mth688 and Mth687 interact, and their homologs Rpp1 and Pop5 interact. Mth11 interacts with Mth1618 and probably Mth687 and Mth688, and sure enough Pop4 (the C-terminal half of which is homolgous to Mth11) interacts with Rpr2, Rpp1, and Pop5. The only real difference we see is that Mth11 seems to interact with itself, whereas they see Rpr2 interacting with itself, not Pop4. In other words, not only are these 4 proteins conserved between Archaea and eukaryotes, but so are the interactions between them.

The roles of all of these proteins in eukaryotes are still unclear, but given their conservation in Archaea, work on the eukaryotic system has focused on these 4 proteins. A lot of work needs to be done to decipher what these proteins are doing for RNase P function, and how they do it. The keys to these experiments are the ability to reconstitute a functional RNase P holoenzyme in vitro, solution of the structures of the proteins and, ultimately, holoenzyme, and the ability to manipulate these proteins and the RNA genetically. Kimuras group has shown, in somewhat quick-and-dirty experiments, that they can reconstitute fully active Pyrococcus horikoshi RNase P holoenzyme from the RNA and these 4 proteins, and our collaborators in Mark Fosters lab at The Ohio State University have reproduced this reconstitution with the M. thermoautotrophicum RNA and proteins. And so these 4 proteins (and the RNA) are both necessary and sufficient for reconstituion of funtional enzyme.

All of these proteins have had their 3D structures determined either by crystallography or NMR, and each is related to their known eukaryotic homolog (where the structure of these is known) but none of them are topologically related or related in secondary structure to the bacterial protein.