268 Chapter 7
Figure 7.21 Schematic of the secondary structure for a group II intron. The EBS1-IBS1 and 2 pairings (thick grey
and black lines, respectively) and domain numberings are shown. The 5-exon is recognized by
pairings between EBS1 and IBS1 (grey pairs with grey), and EBS2 and IBS2 (black pairs with black).
Step 1 can proceed via attack of the bulged A residue in Domain 6 or through attack of water (hydrolytic
step 1). In the second step of splicing, the liberated 5-exon is ligated to the 3-exon, thus releasing a
lariat intron (see Figure 7.18)
as the nucleophile during the first step of splicing.36,38However, they do not require spliceosomal compon-
ents or protein enzymes to carry out the chemical steps of catalysis. Unlike the spliceosome, group II
introns can also splice through a second pathway in which water serves as the nucleophile during the first
step of splicing (hydrolysis), thereby releasing a linear intron (Figure 7.21). Excised group II introns can
behave as infectious mobile elements, which reverse-spliceinto DNA and thereby spread throughout a
genome (or between genomes) (Figure 7.22). Indeed, it has been proposed that all eukaryotic introns may
have derived from group II introns that proliferated, degenerated, and were then taken over by the evolu-
tion of a spliceosomal apparatus. Group II introns therefore represent a distinctive class of transposon, in
which ribozyme catalysis plays a role in the mechanism of genetic mobility.^39 Notably, group I introns are
also transposable elements, although their mechanism for mobility differs (cf.Section 6.8.3).
7.2.2.3 Excision of Terminal Sequences: RNase P and RNase III. In addition to removal of a
sequence from the middle of a transcript, there are also mechanisms for removal of terminal RNA
sequences. Many RNA molecules, such as pre-tRNA, have terminal leader sequences that must be excised.
The 5-terminal leader of pre-tRNA is removed by an enzyme called ribonuclease P (RNase P), which
catalyzes the SN2 attack of a water molecule on the scissile phosphate.^40 In bacteria, RNase P consists of
a RNP complex in which the RNA component is sufficient for catalysis. In eukaryotes, RNase P is more
complex and requires additional protein components for reactivity. In fact, RNase P is the only “ribozyme”
in nature that functions as a true enzyme with multiple turnover in the cell. Most other catalytic RNA mol-
ecules are designed to undergo one round of self-cleavage or transposition. There are other enzymes for
removal of terminal leader sequences, such as the ribonuclease III family (RNase III). Enzymes in this
family catalyze a broad spectrum of endonucleolytic reactions on RNA, including the “dicing” of RNA
into interfering RNAs (siRNAs) and miRNAs (Section 5.7.2).^41