Posttranscriptional ribosomal RNA modification is common in all branches of the tree of life. There are three basic types of modification found in rRNA: base methylation, ribose methylation, and pseudouridylation. Base methylation is the best conserved in total number and position among all species, with bacteria containing slightly more than the 10 commonly found in eukaryotes (see Table 1.1). Base methylation occurs late in ribosome maturation, and occurs only in highly conserved rRNA sequences. Base methylation within small subunit (SSU) rRNA in prokaryotes is not essential [Krzyzosiak et al., 1987], but it is thought to improve protein translation efficiency [Raue et al., 1988].
Pseudouridine rRNA modifications () are numerous in eukaryotes and few in bacteria and archaea (Table 1.1). Studies of eukaryotic residues show they are found in the most evolutionarily conserved regions of rRNA. are spread throughout SSU rRNA with no clear association with particular functional regions. In contrast, to LSU rRNA residues are clustered in three main regions, all within or structurally associated with the peptidyl transfer center (PTC) of the ribosome. Individual loss of residues is not lethal [Ni et al., 1997,Gannot et al., 1997], although global loss of pseudouridylation due to mutations in the putative pseudouridine synthase, Cbf5p, causes temperature-sensitive growth impairment. It is thought residues play a variety of roles in the ribosome, some improving translational efficiency, others with undetermined function.
Ribose methylation, always occurring at the 2' hydroxyl position on the sugar backbone (see Figure 1.2), is frequent in eukaryotes and very limited in bacteria (Table 1.1). Interestingly, ribose methylation in Sulfolobus solfataricus, an archaea, is on the order found in eukaryotes [Noon et al., 1998]. This contrasts with S. solfataricus' bacterial-like paucity of residues. Ribose methyls occur in highly evolutionary conserved regions of rRNA, in many cases co-clustering near residues [Maden, 1990]. Specific positions of methylation among eukaryotes is well conserved; of the 55 ribose methyls in yeast rRNA, roughly 75% overlap precisely with mammalian ribose methyls at homologous positions [Maden, 1990]. Because most ribose methylation takes place early in rRNA processing, it is hypothesized to be important for rRNA folding or association with chaperone proteins that may aid in folding. No single site of ribose methylation has been found to be essential [Weinstein & Steitz, 1999], although global rRNA demethylation caused by mutation in the NOP1 protein severely impairs growth [Tollervey et al., 1993]. In hyperthermophiles, ribose methylation may also be important in thermostability of rRNA and other structural RNA molecules [Noon et al., 1998]. One of the goals of this thesis was to learn more about the function(s) of rRNA methylation through study and genetic manipulation of the corresponding guide snoRNAs.