RNase P and MRP are ribonucleoprotein complexes that are involved in tRNA and rRNA processing, respectively. RNase P is found in all kingdoms of life while RNase MRP is only found in Eukaryotes. The RNA moiety of these RNPs is structurally related and the complexes share a number of protein subunits.
In this work a computational approach was used to better understand phylogeny as well as structure and function of the nuclear RNases P and MRP. Profile-based searches including PSI-BLAST were used in searches for homologs of the protein subunits. A number of novel homologs were identified, giving rise to a comprehensive phylogenetic table for these proteins.
Unexpectedly, the profile-based searches identified novel relationships within some of the RNase P/MRP families. Thus, Pop5, Rpp14, and Pop8 seem to be evolutionarily related. Furthermore, there is evidence that the fungal Pop3 protein is homologous to vertebrate Rpp38 and the archaeal L7Ae protein. Finally, Pop7 and Rpp25 are shown to be part of the same family and a paralog to Rpp25 was identified that appeared early in the development of vertebrates or possibly at an earlier stage. The protein core structure of the RNPs was defined by examining the phylogenetic distribution of the protein subunits: Pop4, Pop5, Rpp1, Rpr2, and Rpp38. For the eukaryal RNPs, Pop1 and Rpp40 can be added to the protein core structure, where Rpp40 homologs were not previously identified in the fungal RNase P/MRP complex. |