282 Chapter 7
Figure 7.33 Pairing arrangements between snoRNAs and rRNAs. (a) Pairing between a guide snoRNA (black) and
a region of rRNA (red) leads to 2-O methylation (2-OMe) at specific sites. (b) Pairing between a
different type of double hairpin guide snoRNA (black) and another region of rRNA (red) leads to
specific pseudouridylation events ()
(Reprinted from Ref. 48. © (1997), with permission from Elsevier)
“maturase” protein. A group II intron maturase protein usually contains defined segments that are
involved in RNA binding, DNA endonuclease activity, and reverse transcription (Figure 7.22). After it is
translated, the maturase protein binds its parent intron and stimulates the self-splicing reaction that
releases lariat intron. The intron lariat and the maturase then form a stable RNP that is catalytically active
for retrotransposition of the intron sequence into duplex DNA.^39
The transposition reaction initially involves recognition of the DNA target site through interactions with
both the maturase and the intron RNA. This is followed by two distinct cleavage events (Figure 7.22). The
DNA sense strand is invaded through a reverse-splicing reactionthat is catalyzed by intron RNA. The anti-
sense strand is cleaved by an endonuclease activity in the maturase protein. Following partial or complete
reverse splicing, the maturase RT makes a DNA copy of the intronic RNA, which becomes stably incor-
porated through DNA repair pathways. Group II integration into duplex DNA represents the first known
example of catalytic collaboration between a ribozyme and a protein enzyme, that is active-site function-
alities on both components are essential for the reaction. Furthermore, this reaction demonstrated that
DNA (and not just RNA) can be the natural substrate for a ribozyme.
7.5.2 SnoRNAs: Guides for Modification of Ribosomal RNA
rRNAs contain numerous post-transcriptional modifications (Section 7.2.4). Although nucleotide-
modifying enzymes have been known for some time, it was difficult to understand how they are targeted to
specific sites on rRNA. The answer has come from studies of the nucleolus, which is a cellular organelle
that has long been a curiosity because it is literally packed with RNA.
The nucleolus is the manufacturing site for ribosomal subunits, which are exported to the cytoplasm
as highly stable RNPs. The raw materials for ribosomes are long pre-rRNAs, which require trimming,
modification, and assembly with ribosomal proteins. Prior to assembly, the pre-rRNA is sequence-
specifically modified. For example ribose 2-OH groups are converted into 2-OCH 3 groups, uridines into
pseudouridines, and various other modifications are also introduced (Section 7.2.4). This is accomplished by
annealing between the rRNA and “guide RNAs,” which are abundant small nucleolar RNAs (snoRNAs).^48
Modifying enzymes recognize the target nucleotide by measuring the distance between specific base pair-
ings and conserved sequences on the snoRNA (Figure 7.33). Thus, rRNA modification represents a natural