Ribosome biogenesis in eukarya occurs in the nucleolar compartment of the nucleus. Several proteins, including fibrillarin, Nop56 and Nop58, and dozens of snoRNAs are involved in this process [Maxwell & Fournier, 1995,Balakin et al., 1996,Tollervey et al., 1991,Gautier et al., 1997]. The snoRNAs can be divided into two major classes: C/D box and H/ACA box RNAs. The C/D box snoRNAs are efficiently precipitated with antibodies against fibrillarin. Most C/D box snoRNAs are involved in targeting ribose methylation within rRNA, whereas most H/ACA box RNAs are involved in targeting the conversion of uridine to pseudouridine within rRNA [Balakin et al., 1996,Cavaille et al., 1996,Kiss-Laszlo et al., 1996,Ni et al., 1997,Gannot et al., 1997]. The small number of snoRNAs not involved in nucleotide modification are required for proper endonucleolytic processing of the pre-rRNA (reviewed in [Maden & Hughes, 1997]).
The general mechanism whereby C/D box snoRNAs target ribose methylation is well established. Each snoRNA contains a unique 9 to 20 nucleotide (nt) sequence located 5' to the D or D' box motif that is complementary to a sequence within small subunit (SSU) or large subunit (LSU) rRNA (see Figure 1.1). During ribosome biogenesis, a snoRNA:rRNA helix is formed and methylation is directed to the rRNA nucleotide that participates in the base pair 5 nt upstream from the start of the D or D' box.
In eukaryotes, it is likely that most, if not all, rRNA ribose methyl modifications are guided by snoRNAs. In the yeast S. cerevisiae, methylation guide snoRNAs have been assigned to all but four of the 55 rRNA ribose methylation sites [Lowe & Eddy, 1999]. Although no single methylation site and no individual C/D box snoRNA involved only in methylation appear to be essential, global rRNA methylation in yeast is apparently essential. Inhibition of methylation is believed to severely compromise the ability of the rRNA to fold into or maintain the active higher order structure [Tollervey et al., 1993,Maden & Hughes, 1997].
SnoRNAs have only been found in eukaryotic species. Ribose methyl modification levels in bacterial rRNA are much lower. Escherichia coli rRNA contains only four ribose methyls and these are anticipated to be modified by individual protein enzymes [Lafontaine & Tollervey, 1998]. In contrast, the rRNA of the archaeon Sulfolobus solfataricus has been shown to contain 67 ribose methylation sites [Noon et al., 1998], a number similar to that found in eukaryotes. Even though Archaea are unicellular prokaryotic organisms that lack a nucleolus [Woese et al., 1990], their genomes encode homologs to the essential eukaryotic nucleolar proteins, fibrillarin and NOP56/58 [Amiri, 1994,Lafontaine & Tollervey, 1998]. Based on these observations, we decided to examine Archaea for the presence of sno-like RNAs using both experimental and computational methods.