Structure and Function of the Archaeal Box C/D Ribonucleoprotein Complex

Abstract

Box C/D ribonucleoprotein complexes (RNPs) are evolutionarily ancient nucleotide modification machines found in both Eukarya and Archaea. The box C/D RNAs are essential for ribosome biogenesis and primarily function by guiding 2'-O-methylation of ribosomal RNA (rRNA). The site of modification is determined by base-pairing between the target RNA and the box C/D RNA through a region of complementarity. The box C/D RNAs possess terminal box C/D and internal C'/D' motifs that fold to form K-turn RNA elements. In eukaryotes, the box C/D RNAs associate with a common set of four core proteins to form an RNP. The core proteins, 15.5kD, Nop56p, Nop58p and Fibrillarin, are differentially distributed on eukaryotic box C/D RNAs to form an asymmetric RNPs.

We have characterized the structure and function of the archaeal box C/D RNP using Methanocaldococcus jannaschii sR8 RNP as a model box C/D complex. Archaeal genomes contain genes for a Fibrillarin homolog and a single homolog for both Nop56p and Nop58p termed Nop56/58p. Our initial investigations identified ribosomal protein L7 as the archaeal homolog of the eukaryotic 15.5kD protein. Strikingly, L7 has a dual role as a component of both the ribosome and the box C/D RNP. A methylation-competent sR8 RNP was assembled in vitro using the three recombinant M. jannaschii box C/D RNA core proteins. This reconstituted complex is symmetric with respect to core protein binding and guides nucleotide modification from both the box C/D and C'/D' RNPs. Additionally, efficient RNA 2'-O-methylation requires juxtaposed box C/D and C'/D' motifs on the same box C/D RNP complex. Finally, the identification of box C/D RNPs in both Archaea and Eukarya led us to question the evolutionary origins of these ancient modification complexes. Based on the demonstration of a common RNP element (L7: K-turn motif) in both the archaeal large ribosomal subunit and the box C/D RNP complex, we propose that the trans-acting nucleotide modification machines evolved elements in the primitive translational apparatus.