One focus of our current work, however, is the enzyme from Methanocaldococcus jannaschii. The RNase P RNAs from the methanococci, and their relatives Archaeoglobus, are different than those of other Archaea. Whereas most Archaea have 'type A' RNase P RNAs quite similar to those of Bacteria, the methanococci and Archaeoglobus have type M RNase P RNAs. These RNAs are basically like the others, but specifically lack two critical elements of structure; in fact, these are the only elements of structure that, in Bacteria, are known to recognize substrate outside the region of the cleavage site. Absent in the archaeal type M RNAs is P8, which is involved in recogition of the T-loop of the substrate pre-tRNA. Also absent is L15, which is the binding site for the pre-tRNA 3'-NCCA tail.
Not surprizingly, type M RNase P RNAs are absolutely dependent on protein for function, and it is our hypothesis that protein sequences have replaced the roles of the missing elements of RNA in substrate recognition. We have purified the enzyme from M. jannaschii and Chris Ellis, a Ph.D. student in my group, is currently working with a series of additional candidate RNase P protein subunits. If we can show that one or more of these proteins are, in fact, RNase P subunits, and are involved in substrate recognition, allowing the enzyme to compensate for the absence of essential substrate-recognition domains in the abbreviated RNA, this would be the first demonstration of the evolutionary replacement of specific elements of RNA structure and function by protein. Such replacements are a requirement of any reasonable RNA World hypothesis, and so we hope to provide the first "proof of principle" for this process.