DICER: STRUCTURE, FUNCTION AND ROLE 427
among oligonucleotide binding pockets (Carlson et al., 2003; Saunders, 2003). The
protein/RNA interface that results from contact between a dsRBD and a dsRNA,
spans two minor and one major groove of the RNA helix (Ryter and Schultz,
1998). It is likely that dsRBDs differentiate dsRNA from DNA by recognition of
the 2’ hydroxyl groups on RNA molecules. Specifically, the amino terminal helix
of the dsRBD binds the 2’ hydroxyl groups that line the minor groove of dsRNA
(Bevilacqua and Cech, 1996; Ryter and Schultz, 1998). In addition, recent studies
have revealed that some dsRBDs contain a carboxyl terminal helix that binds to
hairpin structures (Leulliot et al., 2004). In theory, the dsRBD represents a means
whereby Dicer binds indiscriminately to dsRNA substrates, however, dsRBDs are
not strictly required for the function of Dicer in vivo. For example, the Giardia
intestinalis Dicer homolog does not contain a dsRBD, but is capable of “dicing”
dsRNA substrates into 25 nt products (MacRae et al., 2006). Accordingly, the role,
if any, of this domain in selectively retaining the dsRNA substrates for Dicer
cleavage (i.e. dsRNA containing 2 nt 3’ overhangs, 5’ phosphate groups and 3’
hydroxyl groups) is unknown.
2.5. Mechanism of Dicer Cleavage
As stated above, the RNase III domains of Dicer and other RNase III superfamily
enzymes are only active when they are in dimeric form. Unlike bacterial RNase
III enzymes whose cleavage products are typically 11 nt in length, Dicer cleavage
products are 21–25 nt. Accordingly, models of Dicer cleavage must account for the
differences in product lengths. Two early models proposed that Dicer functions as a
homodimer that is organized in antiparallel or head to tail orientations (reviewed in
Carmell and Hannon, 2004). A major concern regarding these models is that they
both require tight packing of the two Dicer molecules along the dsRNA substrate.
Because of the potential for steric hindrance between the RNase III domains and the
large amino-terminal region that contains the helicase, DUF283 and PAZ domains,
it is uncertain as to whether the RNase III domains of two Dicer molecules can
fit into a small enough space to generate 22 nt products. In fact, if the steric
relationship between the active domains is similar to the E. coli RNase III active
dimer, the products of cleavage are expected to be approximately 30 nt long, rather
than 21–25 nt (Carmell and Hannon, 2004). Finally, and perhaps more importantly,
current evidence suggests that Dicer exists as a monomer (Zhang et al., 2004).
Although the structure of a mammalian or invertebrate Dicer molecule has yet to
be solved, MacRae et al. (2006) recently determined the 3.3 Å resolution structure
of a Dicer homolog from Giardia. Interestingly, this enzyme is considerably smaller
than most Dicer proteins and lacks helicase, DUF 283 and dsRBD domains.
However, it is highly active and is able to generate 25 nt products from long dsRNA
substrates. The results obtained from the functional analyses of the Giardia Dicer
protein, are consistent with data from the Filipowicz group that support the idea
of a single processing center model (Zhang et al., 2004). Central to this model
is the observation that Dicer cleavage occurs from the ends of dsRNA molecules