Characterization of the protein component of Methanococcus jannaschii RNase P

Abstract

RNase P is the ribonuclease responsible for the 5' maturation of precursor transfer RNA (pre-tRNA). In Bacteria RNase P is composed of a single 14kDa protein accompanied by a single catalytic RNA subunit that is capable of cleave pre-tRNA without the protein cofactor in vitro. The RNA subunit of archaeal RNase P resembles those found in Bacteria, however holoenzymes characterized from the Archaea indicate that the accompanying protein component is much larger than in the bacterial enzyme. Purified RNase P from the Euryarchaeon Methanococcus jannaschii possesses approximately eight protein subunits and has an RNA that is incapable of cleaving pre-tRNA alone in vitro. Four putative M. jannaschii RNase P proteins have been identified by their similarity to RNase P proteins of Methanothermobacter thermoautotrophicus. Here we confirm the presence of two of these proteins, MJ0464 and MJ1139, as well as the presence of several other hypothetical proteins (MJ0332.1, MJ0376, MJ1128, and MJ1625), two 30S ribosomal protein subunits (S6E and S8E), and a nicotinamide-nucleotide adenylyltransferase in M. jannaschii RNase P preparations. Eukaryotic RNase P holoenzymes also contain multiple protein subunits and it is thought that these "extra" proteins are required for function in the increased compartmentalization of the eukaryotic cell. Archaeal cells do not have the distinct compartmentalization seen in eukaryotic cells and it is unclear what purpose the protein subunits described here would have in vivo. One possibility is protein-substrate interactions to facilitate formation of the substrate-enzyme complex. M. jannaschii RNase P RNA lacks certain secondary structures present in E. coli RNase P RNA that have been shown in the bacterial model to interact with pre-tRNA substrate. Archaeal RNase P RNAs that possess these elements, such as that of M. thermoautotrophicus, are capable of cleaving substrate in vitro without protein, although only at very high salt concentration. M. jannaschii RNase P RNA does not have any extra secondary structural elements to compensate for the lack of substrate binding helices and it is possible that the protein component has evolved to assume these responsibilities. In order to test this hypothesis, circularly permuted transfer RNAs containing a photoagent positioned in the T loop were used in ultra-violet cross-linking reactions.