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RNase P in the eukaryotic nucleus (nucleolus, to be specific) is much less well understood. It, too, contains an RNA of about 400nt, but the structure of this RNA is less well understood. The basic secondary structure is known, but it is very different than the bacterial RNA, and is much more variable in both sequence and structure. The protein composition is very different than in Bacteria; in yeast and humans, where it is best understood, there are at least 9 proteins, all essential for RNase P activity in vivo. The enzyme is therefore predominated by the proteins, rather than the RNA as in Bacteria, and in fact the RNA by itself is devoid of activity; it absolutely requires the proteins for function, although it is the RNA that is the catalyst. The roles played by the proteins are still poorly understood, and none of them is similar to the single, small bacterial RNase P protein in sequence; if one of these proteins is homologous to the bacterial protein, only the three-dimensional structures will make this clear (none are so far).

Mitochondria and plastids have their own protein synthesis machinery, of course, and their own RNase P enzymes. These are very poorly understood. Fungi encode an RNase P RNA in their mitochondrial DNA, but these RNAs are often amazingly A+U rich and variable in size, and so even their secondary structures are unknown. Fungal mitochondrial RNase P has a single RNase P protein, encoded in the nucleus, that is essential for function but unrelated to either the bacterial or nuclear RNase P proteins. Some protists have mitochondrial RNase P RNAs that are generally of the bacterial type, but the nature of the associated protein(s) are unknown. Plant and animal mitochondrial RNase Ps remain to be characterized; the human mitochondrial RNase P may be identical to the nuclear version. Some "primative" photosynthetic protists contain RNase P enzymes with both RNAs and proteins that are cyanobacterial-like, but the nature of the RNase P of the chloroplasts of vascular plants are unclear; they may not contain an RNA component. The situation is even muddier in the nucleolus; there is another enzyme, RNase MRP, that is obviously a member of the RNase P family and shares all but one of the proteins of the nucleolar RNase P and a distinct but recognizably homologous RNA subunit. RNase MRP is also an RNA endonuclease, involved in a cleavage in the rRNA (rather than tRNA) biosynthetic pathway.