RNA 2001 (The RNA Society), May 29 - June 3, 2001, Banff, Canada

RNase P in Archaea: An evolutionary chimera.

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

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 eukaryotes, 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. Instead, there are 4 ORFs in most archaeal genomes that encode proteins that are distantly but recognizably related to eukaryotic nuclear RNase P proteins. In Methanothermobacter thermoautotrophicus (previously Methanobacterium thermoautotrophicum strain DH), 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 each copurifies 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 primitive form of RNase P proteins. This is contrary to the generally-held belief that the bacterial RNase P protein is primitive - just a step above the "RNA World". Instead, it seems that the small, single bacterial protein is an evolutionary simplification from a primitive RNase P that contained a more substantial protein complement.