Genes VII

Processing and modification of rRNA requires a class of small RNAs called snoRNAs (small nucleolar RNAs). They are associated with the protein fibrillarin, which is an abundant component of the nucleolus (the region of the nucleus where the rRNA genes are transcribed). Some snoRNAs are required for cleavage of the precursor to rRNA; one example is U3 snoRNA, which is required for the first cleavage event in both yeast and Xenopus. We do not know what role the snoRNA plays in cleavage. It could be required to pair with the rRNA sequence to form a secondary structure that is recognized by an endonuclease.

Other snoRNAs are required for the modifications that are made to bases in the rRNA (Kass et al., 1990). Vertebrate rRNAs contain >100 2′-O-methyl groups, which are found at conserved locations. These methylations require the C/D group of snoRNAs, so-called because they possess two short conserved sequences motifs called boxes C and D. Most of these snoRNAs contain sequences that are complementary to regions of the 18S or 28S rRNAs that are methylated. Loss of a particular snoRNA prevents methylation in the rRNA region to which it is complementary. Figure 22.35 suggests that the snoRNA base pairs with the rRNA to create the duplex region that is recognized as a substrate for methylation. Methylation occurs within the region of complementarity, at a position close to the D box. It is possible that each methylation event is specified by a different snoRNA; ~40 snoRNAs have been characterized so far. The methylase(s) have not been characterized; one possibility is that the snoRNA itself provides part of the methylase activity (Kiss-László et al., 1996).

Another group of snoRNAs is involved in the synthesis of pseudouridine. There are 43 Ψ residues in yeast rRNAs. The ACA group of snoRNAs has >20 members and is named for the presence of an ACA triplet 3 nucleotides from the 3′ end. Some of the ACA snoRNAs can be implicated in individual pseudouridine processing events: when the snoRNA is deleted or mutated, the pseudouridine is not generated. Their properties suggest the model shown in Figure 22.36. The snoRNA folds into a secondary structure in which the ACA triplet is at one end of a hairpin that has some unpaired regions. The unpaired regions (A and B) pair with complementary sequences in the rRNA. The Ψ is synthesized at a position 15 bases away from the ACA triplet (Ni et al., 1997).

Pseudouridine is synthesized by conversion of uridine; the reaction involves breaking the bond that connects ribose to the N1 of uridine, and reconnecting the ribose to position C5 of the uridine. The known uridine synthases are proteins that function without an RNA cofactor. Synthases that could be involved in snoRNA-mediated pseudouridine synthesis have not been identified.

The involvement of the U7 snRNA in 3′ end generation, and the role of snoRNAs in rRNA processing and modification, is consistent with the view we develop in 23 Catalytic RNA that many Xperhaps all XRNA processing events depend on RNA-RNA interactions. As with splicing reactions, the snRNA probably functions in the form of a ribonucleoprotein particle containing proteins as well as the RNA. It is common (although not the only mechanism of action) for the RNA of the particle to base pair with a short sequence in the substrate RNA.