MFRS 2001 (Mathematical Formalisms in RNA Structure) April 26-27, 2001, Montreal, Canada

RNase P in Archaea - an evolutionary chimera.

James W. Brown, Ginger M. Bates, Elizabeth S. Haas, Thomas A. Hall, and Daniel Williams.

Department of Microbiology, North Carolina State University, Raleigh, NC USA 27695

In Bacteria, RNase P is composed of a ca. 140kD RNA, which is the catalytic subunit, and a single 14kD accessory protein. In the eukaryotic nucleus, RNase P contains a similar sized RNA, recognizably homologous to that of Bacteria but clearly distinct in sequence and structure, and at least 9 proteins, none of which are recognizably homologous to the bacterial protein.

The RNA of RNase P in Archaea is remarkably similar to the type A RNase P RNAs of Bacteria, suggesting that this form of the RNA is the ancestral form not only in Bacteria but also in the last common ancestor of Eukarya, Archaea, and Bacteria. Many archaeal RNase P RNAs are, like those of Bacteria, catalytically active (in extreme buffer conditions) in the absence of protein. Functional chimeric holoenzymes can be reconstituted from archaeal RNase P RNAs and bacterial RNase P protein.

However, no protein recognizably similar to bacterial RNase P protein is encoded in archaeal genomes. Rather, there are 4 ORFs in archaeal genome sequences that encode proteins that are distantly related to eukaryotic nuclear RNase P proteins. In Methanothermobacter thermoautotrophicus (previously Methanobacterium thermoaautotrophicum strain delta H), these ORFs are MTH11 (similar to POP4), MTH687 (similar to POP5), MTH688 (similar to RPP1), and MTH1618 (similar to RPR2). Antisera against each of these proteins specifically immunodeplete and immunoprecipitate RNase P activity from partially-purified enzyme preparations, and western blots demonstrate that all four copurify with RNase P enzymatic activity during purification of the enzyme. These proteins are therefore bona fide RNase P subunits.

The observation that RNase P in Archaea contains proteins homologous to those of the eukaryotic nucleus, and not recognizably homologous to those of Bacteria, suggests that the archaeal/nuclear protein type is the primative form of RNase P proteins. This is contrary to the generally-held belief that the bacterial RNase P protein is primative - just a step above the "RNA World". Instead, it seems that the small, single bacterial protein is an evolutionary simplification from a primative RNase P that contained a more substantial protein complement.