Archaeal ribonuclease P has multiple protein subunits homologous to eukaryotic nuclear ribonuclease P subunits (Methanothermobacter thermoautotrophicus)

RNase P removes the 5′ leader from all transfer RNA. RNase P consists of a catalytic RNA molecule and a variable protein content. The 120 kDa RNA component from Bacteria is catalytic in vitro in the absence of its single 14 kDa protein. RNase P from the eukaryotic nucleus has more protein (nine proteins in yeast) and an RNA that displays no activity without its protein. The Archaea have RNase P RNAs similar in structure to those of Bacteria. However, many of these RNAs display no catalytic activity in vitro without their proteins, and those that are catalytic require extraordinarily high ionic concentrations.; Methanothermobacter thermoautotrophicus RNase P has an RNA strikingly similar in structure to bacterial RNase P RNA, but requires ∼3M monovalent cations and 300 mM Mg2+ for activity in vitro without its protein. The protein subunit of RNase P from Bacillus subtilis can reconstitute with the RNase P RNA from M. thermoautotrophicus at low ionic strengths. However, there is no open reading frame in the M. thermoautotrophicus genome with similarity to a bacterial RNase P subunit, and M. thermoautotrophicus RNase P has a buoyant density in Cs₂SO₄ of 1.42 g/ml, suggesting more protein than bacterial RNase P. There are four open reading frames (ORFs) in M. thermoautotrophicus, MTH11, MTH687, MTH688 and MTH1618, with similarity to the yeast RNase P subunits Pop4p, Pop5p, Rpp1p and Rpr2p, respectively, and these have homologs in other Archaea. Antibodies against these proteins detect them in western blots of purified M. thermoautotrophicus RNase P, and can immunoprecipitate RNase P activity. Yeast two-hybrid analyses have demonstrated in vivo interactions between MTH688 and MTH687, corresponding to findings with human and yeast nuclear RNase P proteins, and between MTH1618 and MTH11, corresponding to similar findings with yeast nuclear RNase P subunits. These results demonstrate that the archaeal RNase P holoenzyme has protein subunits homologous to eukaryotic nuclear RNase P, and also suggest that the overall architecture of the enzymes are similar.