http://dx.doi.org/10.1016/j.jmb.2012.07.020
J. Mol. Biol. (2012) 423, 475–481
Contents lists available at www.sciencedirect.com
Journal of Molecular Biology
j o u r n a l h o m e p a g e : h t t p : / / e e s . e l s e v i e r. c o m . j m b
COMMUNICATION
AIMP3/p18 Controls Translational Initiation by
Mediating the Delivery of Charged Initiator tRNA to
Initiation Complex
Taehee Kang 1 †, Nam Hoon Kwon 1 †, Jin Young Lee 1 , Min Chul Park 1 ,
Eunji Kang 1 , Hyo Hyun Kim 1 , Taek Jin Kang 2 and Sunghoon Kim 1, 3 ⁎
1
Medicinal Bioconvergence Research Center, Seoul National University, Seoul 151–742, Korea
Department of Chemical and Biochemical Engineering, Dongguk University-Seoul, Seoul 100–715, Korea
3
WCU Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science
and Technology, Seoul National University, Suwon 443–270, Korea
2
Received 17 May 2012;
received in revised form
11 July 2012;
accepted 17 July 2012
Available online
4 August 2012
Edited by R. L. Gonzales
Keywords:
AIMP3;
translation initiation;
methionine;
initiator tRNA;
eukaryotic initiation factor 2
γ subunit (eIF2γ)
Aminoacyl-tRNA synthetase-interacting multifunctional proteins (AIMPs)
are nonenzymatic scaffolding proteins that comprise multisynthetase
complex (MSC) with nine aminoacyl-tRNA synthetases in higher eukaryotes. Among the three AIMPs, AIMP3/p18 is strongly anchored to
methionyl-tRNA synthetase (MRS) in the MSC. MRS attaches methionine
(Met) to initiator tRNA (tRNAiMet ) and plays an important role in
translation initiation. It is known that AIMP3 is dispatched to nucleus or
nuclear membrane to induce DNA damage response or senescence;
however, the role of AIMP3 in translation as a component of MSC and
the meaning of its interaction with MRS are still unclear. Herein, we
observed that AIMP3 specifically interacted with Met-tRNAiMet in vitro,
while it showed little or reduced interaction with unacylated or lysinecharged tRNAiMet . In addition, AIMP3 discriminates Met-tRNAiMet from
Met-charged elongator tRNA based on filter-binding assay. Pull‐down
assay revealed that AIMP3 and MRS had noncompetitive interaction with
eukaryotic initiation factor 2 (eIF2) γ subunit (eIF2γ), which is in charge of
binding with Met-tRNAiMet for the delivery of Met-tRNAiMet to ribosome.
AIMP3 recruited active eIF2γ to the MRS–AIMP3 complex, and the level of
Met-tRNAiMet bound to eIF2 complex was reduced by AIMP3 knockdown
resulting in reduced protein synthesis. All these results suggested the novel
function of AIMP3 as a critical mediator of Met-tRNAiMet transfer from MRS
to eIF2 complex for the accurate and efficient translation initiation.
© 2012 Elsevier Ltd. All rights reserved.
*Corresponding author. Medicinal Bioconvergence Research Center, Seoul National University, Seoul 151-742, Korea.
E-mail address: sungkim@snu.ac.kr.
† T.K. and N.H.K. contributed equally to this work.
Abbreviations used: MRS, methionyl-tRNA synthetase; eIF2γ, eIF2 γ subunit; ARS, aminoacyl-tRNA synthetase; MSC,
multisynthetase complex; AIMP, ARS-interacting multifunctional protein; eEF, eukaryotic elongation factor; eIF2,
eukaryotic initiation factor 2; TC, ternary complex; MEF, mouse embryonic fibroblast; WT, wild type; GST, glutathione
S-transferase.
0022-2836/$ - see front matter © 2012 Elsevier Ltd. All rights reserved.
476
Introduction
Aminoacyl-tRNA synthetases (ARSs), which
conjugate amino acids to their cognate tRNAs,
form a multisynthetase complex (MSC) in higher
eukaryotes. 1 This complex consists of nine ARSs
and three nonenzymatic cofactors called ARSinteracting multifunctional proteins (AIMPs),
namely, AIMP1/p43, AIMP2/p38, and AIMP3/
p18. 2 AIMPs are involved in scaffolding the MSC
structure and controlling the stability of neighboring ARSs. 3 In addition, AIMPs dissociate from
MSC in response to various stimuli and are
involved in diverse biological functions and
signaling pathways, such as immune responses,
angiogenesis, wound healing, glucose homeostasis,
cell proliferation, and apoptosis. 4–11 Among them,
AIMP3 is known to be a potent tumor suppressor
via activation of p53 under UV damage or
oncogenic stress, 12,13 and elevated levels of
AIMP3 lead to cellular senescence via degradation
of mature lamin A. 14
While our understanding of the functions of
AIMPs outside MSC has advanced considerably,
their roles in the MSC as translation components
remain unclear. Arc1p, a yeast orthologue of human
AIMP1/p43, is known to increase the aminoacylation activities of methionyl-tRNA synthetase (MRS)
and glutamyl-tRNA synthetase by recruiting
tRNAs. 15,16 AIMP1 also binds to tRNA and enhances the aminoacylation activity of arginyl-tRNA
synthetase. 17 AIMP3 has sequence similarity to
valyl-tRNA synthetase and is also known as
eukaryotic elongation factor (eEF) 1 epsilon 1
based on sequence similarity to eEFs. 18 These results
imply that AIMPs can play an active role in the
translation process as members of MSC, although
little is known about their functions in protein
synthesis.
AIMP3 shows strong interaction with MRS in the
MSC, and knockdown of AIMP3 affects the
stability of MRS protein. 3 Recently, the importance
of MRS in global translational regulation was
suggested. 19 Under UV irradiation, MRS was
phosphorylated by GCN2 (general control non‐
repressed 2), and this modification reduced the
catalytic activity of MRS, resulting in decreased
levels of methionine (Met)-charged initiator tRNA
(Met-tRNAiMet ). For translation initiation, MettRNAiMet should bind to eukaryotic initiation factor
2 (eIF2) in a GTP-dependent manner to form the
ternary complex (TC), eIF2–GTP–Met-tRNAiMet ,
which delivers Met-tRNAiMet to the 40S ribosomal
subunit. 20 That is why MRS phosphorylation and
insufficient TC formation can reduce global protein
synthesis.
Because AIMP3 specifically binds to MRS in the
MSC and AIMP3 has sequence similarity to eEFs,
we hypothesized that AIMP3 may have a function
Translational Initiation Controlled by AIMP3/p18
in translation regarding MRS activation or MettRNAiMet delivery to other translation factors. Here,
we report that AIMP3 interacts with Met-tRNAiMet
and the eIF2 complex and plays an important role
in connecting aminoacylation to translation. These
results suggest that AIMP3 may be a critical
mediator of the accurate and efficient delivery of
the Met-tRNAiMet to eIF2 and a regulator of global
translation initiation.
AIMP3 specifically binds to Met-tRNAiMet
In yeast, Arc1p, a cofactor of MRS and
glutamyl‐tRNA synthetase, enhances aminoacylation activity via tRNA recruitment. 15,16 To test
whether AIMP3 can function similarly, we examined the binding affinity of AIMP3 to free or
charged tRNAiMet using a filter-binding assay. The
MRS and eIF2 γ subunit (eIF2γ) were used as
controls for binding with tRNAiMet and MettRNAiMet , respectively. In this assay, purified
AIMP3 did not exhibit interaction with in vitro
transcribed radioactive tRNAiMet (Fig. 1a). In
contrast, AIMP3 exhibited explicit interaction
with Met-tRNAiMet in a dose-dependent manner
(Fig. 1b and c). Because AIMP3 only bound to
Met-tRNAiMet , we hypothesized that AIMP3 might
recognize Met attached to the acceptor stem of
tRNAiMet. To test this, we analyzed the interaction
between AIMP3 and radioactive Met, revealing
that AIMP3 has binding affinity to Met as expected
(Fig. 1d). Next, we prepared Met-tRNAiMet and
Met-tRNAeMet to investigate the difference between
tRNA Met isoforms with regard to recognition by
AIMP3, and we also charged these tRNAs with the
nonnatural amino acid acetylated lysine (acK) to
compare its binding affinity to AIMP3 with that of
Met. It is interesting that the association between
AIMP3 and Met-tRNAiMet was more obvious than
that of any other types of tRNAs tested (Fig. 1e). It
shows that AIMP3 has binding preference for
tRNAiMet over tRNAeMet only when the two are
charged with Met (Fig. 1f). We introduced mutations in tRNAiMet to examine whether AIMP3
recognizes discriminating base pair in the acceptor
stem of tRNAiMet . As expected, MT1 tRNAiMet ,
which had A1:U72 substitution for G1:C72 as in
tRNAeMet , showed reduced binding affinity to
AIMP3 unlike wild-type (WT) tRNAiMet (Fig. 1g).
There was little difference in the binding affinity
between MT1 and MT2 tRNAs. Considering that
the latter had additional base‐pair substitution, this
suggests that the discriminating base pair A1:U72
is the most important one for the recognition by
AIMP3. Collectively, these results imply that
AIMP3 recognizes both Met and tRNAiMet , but
Met is prerequisite for the interaction of AIMP3
with tRNA iMet . Although AIMP3 knockdown
affected the stability of MRS, resulting in reduced
477
Translational Initiation Controlled by AIMP3/p18
Fig. 1. Specific interaction between AIMP3 and Met-tRNAiMet. (a) Radioactively labeled free [ 32P]tRNAiMet was
incubated with His-tagged MRS, eIF2γ, and AIMP3. Signals from tRNA bound to proteins were detected. (b) Unacylated
tRNAiMet and charged Met-[ 32P]tRNAiMet were subjected to a filter-binding assay with AIMP3 and eIF2γ. (c) [ 35S]Met was
ligated to tRNAiMet by incubation with purified MRS and used for the binding assay after purification to investigate the
interaction between Met-tRNAiMet and AIMP3. (d) Interaction between AIMP3 and Met was determined by the filterbinding assay. MRS and AIMP1 were used as positive and negative controls, respectively. (e) Radioactively labeled
tRNAiMet and tRNAeMet were charged with Met and acK using MRS and dFx (dinitro-flexizyme; a ribozyme-based tRNAacylating catalyst), 21 respectively, and their interaction with AIMP3 was analyzed. acK, a nonnatural amino acid, was
used as a substitute for comparison with Met. (f) The secondary structure of human tRNAiMet and tRNAeMet. Red-boxed
nucleotides indicate discriminating base pairs of tRNAiMet, whose mutations make tRNAiMet work as tRNAeMet. 22 Met is
attached to 3′ OH group via an ester linkage by MRS. (g) Mutations are introduced in tRNAiMet for in vitro transcription of
MT1 and MT2, whose A1:U72 and A1:U72/G2:C71 base pairs were substituted for G1:C72 and G1:C72/C2:G71,
respectively. Charged WT, MT1, and MT2 [ 32P]tRNAiMet were subjected to a filter-binding assay with AIMP3. Protein
concentrations used throughout this figure were serially increased by 2-fold with the highest concentration of 0.5 μM,
4 μM, 25 μM, and 14 μM for MRS, eIF2γ, AIMP3, and AIMP1, respectively.
aminoacylation activity of MRS in AIMP3 +/−
mouse embryonic fibroblast (MEF) cells, AIMP3
does not seem to give direct effect on the catalytic
reaction in vitro (Fig. S1).
MRS and AIMP3 interact with eIF2γ
Because AIMP3 did not affect the catalytic
activity of MRS, AIMP3 was assumed to mediate
478
Translational Initiation Controlled by AIMP3/p18
Fig. 2. Interaction of AIMP3 and
MRS with eIF2γ. (a and b) Radioactively labeled eIF2 subunits
(eIF2α, eIF2β, and eIF2γ) were
incubated with GST-MRS or GSTAIMP3. The bound eIF2 subunits
were detected by autoradiography.
Each protein, stained with Coomassie Brilliant Blue (CBB), is indicated
by an arrow. (c) Radioactively
labeled eIF2α, eIF2γ, and MRS
were mixed with GST-AIMP3.
Bound proteins were detected by
autoradiography. eIF2α, a binding
partner of eIF2γ, was also included
to investigate the possibility of eIF2
complex association with the MRS–
AIMP3 complex. (d) Interactions
between MRS, AIMP3, and the
eIF2 subunits (α, β, and γ) are
schematically represented based
on domain mapping (Fig. S3). The
N-termini of these proteins are
indicated by dense coloration.
Met-tRNAiMet delivery to downstream proteins.
Met-tRNAiMet should be transferred to the eIF2
complex for the formation of the TC; therefore, we
analyzed the interaction between MRS, AIMP3,
eIF2α subunit, eIF2β subunit, and eIF2γ subunit.
The glutathione S‐transferase (GST) pull-down
assays revealed that MRS and AIMP3 commonly
interacted with eIF2γ among the eIF2 subunits
(Fig. 2a and b), which is in charge of binding with
Met-tRNAiMet and GTP. 23 Lysyl-tRNA synthetase
did not show apparent interaction with eIF2 subunits unlike MRS and AIMP3 (Fig. S2). MRS and
eIF2γ were pulled down together in association with
AIMP3 (Fig. 2c), suggesting that this tripartite
interaction is not mutually exclusive. We identified
the binding domains of MRS and AIMP3 that were
hypothesized to interact with eIF2γ, using deletion
mutants, and confirmed that MRS and AIMP3 used
different domains for each binding partner, resulting in noncompetitive association with eIF2γ
(Fig. 2d and Fig. S3). This domain mapping suggests
that the GST homology domains of MRS and AIMP3
are important for binding to eIF2γ and that the GTPbinding domain of eIF2γ is crucial for binding to
MRS and AIMP3.
AIMP3 recruits active eIF2γ to the MRS–AIMP3
complex
Because the binding domains of each protein were
not overlapping, the interactions between MRS,
AIMP3, and eIF2γ may be regulated by one protein
working as an adapter. To examine whether AIMP3
can mediate interaction between MRS and eIF2γ, we
knocked down AIMP3 in HeLa cells using RNA
interference and analyzed the change in interaction
using an IP (immunoprecipitation) assay. As
expected, decreased interaction of eIF2γ with MRS
was observed in AIMP3 knockdown cells (Fig. 3a).
This result suggests that the interaction between
MRS and eIF2γ is dependent on the existence of
AIMP3. To investigate the possibility that AIMP3
can recruit active eIF2γ, we substituted Asn190 for
Asp (N190D) in the NKXD consensus sequence of
eIF2γ, which is known to be an important site for
GTP binding. 24 The N190D mutant mimics inactive
eIF2γ, and it exhibited reduced binding to AIMP3 in
comparison with WT eIF2γ in the IP assay (Fig. 3b).
These results demonstrated that AIMP3 was critical
for binding between MRS and eIF2γ, as well as for
the recruitment of active eIF2γ to the MRS–AIMP3
complex.
AIMP3 is important for formation of the TC
Because AIMP3 interacted with Met-tRNAiMet and
eIF2γ, we examined whether AIMP3 could play a
role in the formation of the TC via delivery of MettRNAiMet. HeLa cells were transfected with specific
siRNAs (small interfering RNAs) for knockdown of
MRS, AIMP3, eIF2α, and eIF2γ, and TC was
immunoprecipitated with eIF2β-specific antibody.
Translational Initiation Controlled by AIMP3/p18
479
Fig. 3. The effect of AIMP3 on
the interaction between MRS and
eIF2γ. (a) HeLa cells were transfected with si-control and siAIMP3. MRS was immunoprecipitated, and the bound proteins were
analyzed using Western blotting.
As MRS levels in the cells treated
with si-AIMP3 were reduced, minimum amounts of anti-MRS antibody (0.5 μg/500 μl lysate) were
used for the IP assays to equalize
the amounts of captured MRS
between the samples. (b) We transfected 293T cells with mCherry-tagged eIF2γ (WT or N190D mutant) and Flag-AIMP3 simultaneously, and the mCherryeIF2γ proteins were immunoprecipitated using anti-DsRed antibody for the analysis of bound Flag-AIMP3.
The amount of tRNAiMet bound to eIF2 complex was
analyzed, revealing that downregulation of AIMP3
decreased tRNAiMet in the eIF2 complex to the same
level as seen after eIF2γ knockdown (Fig. 4a). The
influence of MRS or eIF2α knockdown on the
amount of tRNAiMet was not as obvious as that of
AIMP3 knockdown.
Next, we carried out a gel‐filtration assay to
confirm the effect of AIMP3 knockdown on the
colocalization of eIF2 complex with ribosome. As
expected, reduced levels of AIMP3 decreased the
amounts of eIF2 subunits in the ribosomal fraction in
comparison with MRS knockdown (Fig. S4), suggesting that levels of AIMP3 affected TC formation,
which should be detected in the ribosomal
fraction. 25 Collectively, these results indicated that
AIMP3 played a crucial role in TC formation that
was linked to protein synthesis.
To investigate the effect of AIMP3 on global
translation, we calculated protein synthesis in the
AIMP3 MEF and HeLa cells using a Met incorporation assay. The AIMP3 +/− MEF cells exhibited about a
40% reduction in translation as compared with the
AIMP3 +/+ MEF cells (Fig. 4b), and similar results
were obtained with si-AIMP3-transfected HeLa cells
(Fig. 4c). Global translation was also reduced by
approximately 20% by knockdown of MRS; however,
the knockdown effect of AIMP3 on protein synthesis
was stronger. These results demonstrated the importance of Met-tRNAiMet delivery to eIF2 via AIMP3 in
global translation, even when Met-tRNAiMet seemed
abundant enough to negate a delay in TC formation.
Conclusions
Recently, another group reported a model that
explains how the TC binds the 40S ribosomal
subunit by identifying the binding motifs of eIF2γ
and 40S ribosome. 26 However, it is unclear how
Met-tRNAiMet moves to eIF2γ from MRS in the early
stage of translation initiation. We demonstrated here
that AIMP3, a binding partner of MRS in the MSC,
worked as a mediator of Met-tRNAiMet delivery
from MRS to eIF2. It is interesting that AIMP3
exhibits high affinity for Met-tRNAiMet but not for
Met-tRNAeMet , and it affected TC formation, which
is critical for translation initiation.
MRS acylates tRNAiMet and tRNAeMet, and among
the acylated tRNAs, only Met-tRNAiMet was recognized by AIMP3, suggesting that AIMP3 is probably
involved in the translation initiation but not in
elongation step. The GTP-bound form of eIF2γ can
also interact with Met-tRNAiMet through the recognition of Met moiety. 23 This suggests to us that
tRNA sequences and Met are important for binding
to AIMP3 and eIF2γ. While tRNAiMet and tRNAeMet
share the same anticodon sequences, there are
several differences between them (Fig. 1f). One of
the most distinctive features of tRNAiMet relates to
the acceptor stem, where the discriminating base
pair is located. tRNAiMet has an A1:U72 base pair in
its acceptor stem, whereas tRNAeMet has an G1:C72
base pair. 23,27 Because of this difference, eIF2γ can
discriminate Met-tRNA iMet from Met-tRNAeMet .
AIMP3 and eIF2γ may recognize Met-tRNAiMet in
a same way, although more study is required to
fully understand the Met-tRNA iMet delivery
mechanism.
It seems that MRS also interacts with eIF2γ. An
alternative way is the direct delivery of Met-tRNAiMet
from MRS to eIF2γ without the involvement of
AIMP3. However, AIMP3 involvement can inhibit
diffusion of Met-tRNAiMet by recruiting active eIF2γ
to the MRS–AIMP3 complex, thereby increases the
efficiency and accuracy of TC formation. AIMP3
involvement in Met-tRNAiMet transfer may be meaningful, considering the complicated regulatory mechanism of translation in higher eukaryotes. Generally,
translation is regulated by phosphorylation of eIF2α.
This phosphorylation prevents formation of the TC
and inhibits further rounds of translation initiation. In
addition, a recent study has suggested another
480
Translational Initiation Controlled by AIMP3/p18
Fig. 4. The effect of AIMP3 on
TC formation and global translation. (a) TC was immunoprecipitated with anti-eIF2β antibody from
the siRNA-transfected HeLa cells.
The bound RNA was purified using
Trizol, and the amounts of bound
tRNAiMet were analyzed using reverse transcription PCR. Actin was
used as a loading control. The
proteins were purified from the
Trizol-treated protein fractions and
analyzed by immunoblotting. The
relative amounts of bound tRNAiMet
from the samples treated by each
siRNA were presented in the bottom
panel. (b and c) Protein synthesis in
the AIMP3 +/+ and AIMP3+/− MEFs
(b) and siRNA-transfected HeLa cells
(c) was analyzed using a Met incorporation assay. Mean±SD of triplicate experiments are shown. The
differences between the samples
were significant (Pb0.05, one-way
ANOVA).
mechanism of translation control under UV stress. 19
According to Kwon et al., MRS phosphorylation
occurred simultaneously with eIF2α phosphorylation
and inhibited translation by reducing Met-tRNAiMet
production. The MRS phosphorylation site is critical
for tRNA binding; however, this residue is not
conserved in lower eukaryotes, such as yeast.
AIMP3 only exists in higher eukaryotes, but its
various functions are essential for the maintenance
of life in higher eukaryotes. 12–14 These studies suggest
that translational regulation mediated by MRS and
AIMP3 may be an adaptation by higher eukaryotes,
which developed more accurate and multistep
translational regulation during evolution. There is
still a possibility that AIMP3 can affect global
translation via unknown pathways. In the present
study, however, we elucidated the role of AIMP3 as a
subunit of MSC. Furthermore, we determined that
AIMP3 can capture the charged initiator tRNA and
deliver it to eIF2 by recruiting active eIF2γ. We also
determined that AIMP3 enables precise and efficient
formation of the TC and affects global translation.
Acknowledgements
This work was supported by the Global Frontier
Project grant NRF-M1AXA002-2011-0028417 and
National Research Foundation grants NRF-2011-
0005849 and NRF-2011-0028394 funded by the
Ministry of Education, Science and Technology of
Korea.
Supplementary Data
Supplementary data to this article can be
found online at http://dx.doi.org/10.1016/j.jmb.
2012.07.020
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