Biomedical Engineering Reference
In-Depth Information
1.3.3
Structure of the Entry and Exit Sites of mRNA:
Implication to Initiation
Analysis of our 80S crystal structure at the entry and exit sites of the mRNA
(Yusupova et al.
2001
) on the small subunit reveals features that are unique to
eukaryotes and may pertain to the ribosome interactions with mRNA and initiation
factors. At the entry site in prokaryotes, h16 assumes a closed conformation where
its tip is in proximity of S3p, a protein that forms the mRNA entry tunnel in collabo-
ration with proteins S4p and S5p (Fig.
1.10a
) (Jenner et al.
2010b
; Yusupova et al.
2001
). In contrast, this helix bends in eukaryotes to adopt a very different, open,
orientation that extends away from the body (Fig.
1.10b
). In prokaryotes a domain
that belongs to S4p composed of two a-helices forms strong interactions with h16,
virtually covering a large part of this RNA helix. In the eukaryotic homologue of
S4p, protein S9, this domain does not exist, while a helix that could potentially
interact with h16 tilts away. Thus, in yeast h16 is bare, with no rRNA-protein inter-
actions, free to rotate around its base. These observations must be viewed in the
context of the eukaryotic initiation step. Current models suggest that binding of fac-
tors eIF1 and eIF1A to 40S stimulates scanning by inducing h16 to adopt a closed
orientation that stabilizes an opening of the mRNA entry tunnel latch (Fig.
1.10c
,
d). It was shown that binding of IRES to 80S ribosome also induces such changes
(Spahn et al.
2001b,
2004c
). The latch is formed by interactions between the beak
of 40S and h18 at the body of the small subunit. Interestingly, the beak in eukaryotes
has a considerably different structure and harbors an additional protein moiety, par-
tially modeled here as the eukaryote-specific protein S17.
The exit site of the mRNA is more intricate in eukaryotes than in prokaryote and
contains several additional components (Fig.
1.10e
). In association with protein
S5 (S7p), just above the mRNA path, a eukaryote-specific protein is poised to
bind mRNA. This protein was modeled as S28e in accordance with biochemical
data (Pisarev et al.
2008
). We also located several protein secondary structure ele-
ments situated just below the proposed mRNA path, in a position similar to that
occupied in prokaryotes by protein S18p that binds the Shine-Dalgarno sequence
Fig. 1.10
(continued) at the mRNA entry tunnel. (
c
) The latch is formed by interactions between
h34 of the beak and h18 at the body of the small subunit. The superposition of the prokaryotic
ribosome (16S rRNA colored
grey
) on the eukaryotic ratcheted ribosome (18S rRNA colored
blue
)
shows that the beak in eukaryotes has a considerably different structure and harbors an additional
protein moiety, partially modeled here as the eukaryote-specific protein S17 (colored in
magenta
).
(
d
) Part of the secondary structure diagram of 18S rRNA from
S. cerevisiae
with expansion seg-
ment 9 (colored in
red
) (
upper panel
) and of 16S rRNA from
T. thermophilus
. The beak is formed
by h33 and h34. (
e
) View of the back of the 40S showing the connection between the mRNA exit
and entry sites in the yeast ribosome (prokaryotic mRNA shown in
red
). The eukaryote-speci fi c
additions to the N- and C-terminal of S2 (S5p) are shown in
magenta
. (
f
) The eukaryotic mRNA
exit site (mRNA from the prokaryotic model in
red
). The eukaryote-specific bridge eB8 is marked
with an
asterisk
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