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Originally published In Press as doi:10.1074/jbc.M004304200 on August 1, 2000
J. Biol. Chem., Vol. 275, Issue 41, 32268-32276, October 13, 2000
Cap-Poly(A) Synergy in Mammalian Cell-free Extracts
INVESTIGATION OF THE REQUIREMENTS FOR POLY(A)-MEDIATED
STIMULATION OF TRANSLATION INITIATION*
Yanne M.
Michel,
Didier
Poncet ,
Maria
Piron §,
Katherine M.
Kean¶, and
Andrew M.
Borman
From the Unité de Génétique Moléculaire des
Virus Respiratoires, CNRS URA 1966, Institut Pasteur, 25 rue du Dr.
Roux, 75724 Paris Cedex 15 and the Laboratoire de
Virologie et Immunologie Moléculaires INRA, CRJJ, Domaine de
Vilvert, 78352 Jouy-en-Josas Cedex, France
Received for publication, May 19, 2000, and in revised form, July 25, 2000
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ABSTRACT |
The 5' cap and 3' poly(A) tail of eukaryotic
mRNAs cooperate to stimulate synergistically translation initiation
in vivo, a phenomenon observed to date in vitro
only in translation systems containing endogenous competitor mRNAs.
Here we describe nuclease-treated rabbit reticulocyte lysates and HeLa
cell cytoplasmic extracts that reproduce cap-poly(A) synergy in the
absence of such competitor RNAs. Extracts were rendered
poly(A)-dependent by ultracentrifugation to partially
deplete them of ribosomes and associated initiation factors. Under
optimal conditions, values for synergy in reticulocyte lysates
approached 10-fold. By using this system, we investigated the molecular
mechanism of poly(A) stimulation of translation. Maximal cap-poly(A)
cooperativity required the integrity of the eukaryotic initiation
factor 4G-poly(A)-binding protein (eIF4G-PABP) interaction, suggesting
that synergy results from mRNA circularization. In addition,
polyadenylation stimulated uncapped cellular mRNA translation and
that driven by the encephalomyocarditis virus internal ribosome entry
segment (IRES). These effects of poly(A) were also sensitive to
disruption of the eIF4G-PABP interaction, suggesting that 5'-3' end
cross-talk is functionally conserved between classical mRNAs and an
IRES-containing mRNA. Finally, we demonstrate that a rotaviral
non-structural protein that evicts PABP from eIF4G is capable of
provoking the shut-off of host cell translation seen during rotavirus infection.
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INTRODUCTION |
The 5' ends of all eukaryotic mRNAs are modified
post-transcriptionally to carry a methylated cap structure,
m7GpppN (1). Aside from roles in RNA splicing,
stabilization, and transport, the cap structure significantly enhances
the recruitment of the 40 S ribosomal subunit to the mRNA 5' end
during translation initiation. The latter function requires recognition
of the cap by the eukaryotic initiation factor
(eIF)1 4F. The eIF4F
holoenzyme complex consists of the cap-binding protein eIF4E and an
ATP-dependent RNA helicase (eIF4A) bound toward the N- and
C-terminal ends, respectively, of a scaffold molecule eIF4G (for review
see Ref. 2). The C-terminal domain of eIF4G also interacts with eIF3, a
complex that associates directly with the 40 S ribosomal subunit.
Most mRNAs carry a poly(A) tail at their 3' ends, which determines
mRNA stability (for review see Ref. 3) and enhances translation
initiation efficiency (4). However, reports concerning the actual
extent of enhancement of translation initiation by the poly(A) tail are
somewhat contradictory, depending on the system used. Moderate
poly(A)-mediated stimulation of translation can occur in the absence of
a cap structure or functional eIF4E, but a cap is absolutely required
for optimal poly(A)-mediated translation stimulation (5, 6). Studies
performed in the rabbit reticulocyte lysate (RRL) and other
nuclease-treated cell-free extracts demonstrated that the stimulation
of translation upon capping and poly(A) tailing were additive phenomena
(7, 8). In contrast, in vivo translation studies have
demonstrated that the poly(A) tail and cap interact synergistically to
stimulate translation initiation in yeast, plant spheroplasts, and
mammalian cells (5, 6, 9). Synergy between the cap and poly(A) tail in
promoting translation has also been observed in non-nucleased yeast and
Drosophila cell-free translation extracts (6, 8, 10).
However, synergy was abrogated by disruption of endogenous mRNA
translation in yeast cells (9) or by nuclease treatment of yeast
cell-free extracts unless such extracts were supplemented with excess
competitor mRNAs (6). It was thus suggested that an RNA requires
the poly(A) tail for translation only when it is competing with other
capped and polyadenylated RNAs for limiting concentrations of ribosomes
or translation factors. Support for this suggestion came from the
demonstration that mutations that affect polyadenylation only
significantly reduce translation when introduced into yeast strains
harboring low concentrations of ribosomal subunits (11).
Biochemical analyses clearly demonstrated that poly(A) tail-mediated
translation stimulation involves increased 40 S subunit recruitment to
mRNAs and requires the intervention of poly(A) tail-binding protein
(PABP) (5). PABP was recently demonstrated to interact physically with
the N-terminal region of eIF4G from yeast (12) and from mammals (13).
Thus, a closed loop model of translation initiation on capped,
polyadenylated mRNAs was postulated (3). Formal proof of mRNA
circularization via the cap-eIF4E-eIF4G-PABP-poly(A) interaction was
provided by atomic force microscopy of mRNAs complexed with
purified recombinant proteins (14). However, the functional
consequences of mRNA circularization have not been directly
addressed experimentally.
Since the closed loop model of translation initiation depends upon
interactions between the 5'-terminal cap structure and the 3' poly(A)
tail, the subset of eukaryotic and viral mRNAs that are either
uncapped or non-polyadenylated are difficult to accommodate within this
model. For certain viral mRNAs, an alternative means of closing the
loop has already been proposed. For instance, for capped,
non-polyadenylated rotaviral mRNAs, the viral non-structural protein NSP3 binds the conserved rotaviral RNA 3' end and can interact
with eIF4G and displace PABP from the eIF4F complex (15, 16). However,
the case for picornaviral RNAs remains unresolved. Whereas these viral
RNAs are polyadenylated, they are uncapped, and translation initiation
is independent of the RNA 5' end. In fact, ribosome entry on
these RNAs occurs internally, several hundred nucleotides downstream of
the 5' end, and is driven by a complex RNA signal of some
400-500 nt, coined the IRES (internal ribosome entry segment) (for
review see Ref. 17).
Here, we describe mammalian cell-free translation systems that exhibit
cap-poly(A) synergy in the absence of added competitor mRNAs. These
systems, derived from extracts in which IRES-driven translation is
routinely studied, were used to examine the molecular mechanism of
poly(A) tail-mediated translational stimulation on classical eukaryotic
mRNAs and on an mRNA harboring an IRES.
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EXPERIMENTAL PROCEDURES |
Plasmid Constructions--
Plasmids were derived from the
previously described pXLJCon clone (18), which contains the cDNA
for Xenopus laevis cyclin B2 (including the 5' and 3'-UTRs)
under the control of the bacteriophage T7 promoter, followed by a short
artificial polylinker and then the cDNA corresponding to a
truncated coding region and the 3'-UTR of the influenza virus NS
protein. For the present study, the NS-coding region of pXLJCon was
replaced by the gene encoding the p24 capsid protein of human
immunodeficiency virus type I (HIV-ILAI; see Ref. 19). The
different resulting constructs are represented schematically in Fig. 1.
In a first step, the NS-coding region and 3'-UTR were excised by
digestion with BamHI and EcoRI and replaced by a
PCR-generated fragment corresponding to the 150-nt NS 3'-UTR (sense
primer, 5' ATGGATCCCGGGTGAAGAAGTGAGACACAAAC 3'; antisense primer SP6
primer; 30 cycles: 96 °C 30 s, 55 °C 45 s, 72 °C 1 min) to generate pXLinker. In a second step, a PCR fragment containing
the entire p24-coding region was generated to contain unique
NcoI and SmaI restriction sites at the 5' and 3'
ends, respectively (PCR primers p24sense 5' CCATGGATCCTATAGTGCAGAACATA 3' and p24antisense 5' TCCCCCGGGCAAAACTCTTGCCTTATG 3'; 30 cycles: 96 °C 30 s, 55 °C 45 s, 72 °C 2 min). Introduction
of the NcoI-SmaI-digested PCR product into
pXLinker digested with the same enzymes results in the fusion of p24 in
frame between the polylinker ATG initiation codon and the TGA stop
codon that precedes the NS 3'-UTR, producing pB2Op24. The resulting p24
gene product thus carries 2 amino acid extensions at each of the N and
C termini. For the construction of pB2 IRESp24, nucleotides 10-547
of the human rhinovirus type 2 5'-UTR were excised from the previously
described pXLJ10-547 (18) by digestion with SalI and
BamHI and were inserted into pB20p24 digested with the same
enzymes. The monocistronic p0p24 plasmid was constructed by replacing
the small SalI-EcoRI fragment of pJCon (18) with
that from pB20p24. To insert the entire EMCV IRES (from the poly(C)
tract to nt 848) into p0p24 (to produce pEMCVp24), the in-filled
EcoRI-NcoI small fragment from p-CITE (Novagen)
was inserted into the in-filled BamHI site of p0p24.
To produce a plasmid encoding only cyclin B2, and with 5'- and 3'-UTRs
identical to those in pB20p24, the full 5'-UTR and cyclin B2-coding
region up to the stop codon was amplified by PCR so as to contain a
unique SmaI site at its 3' end (sense primer T7 promoter,
antisense primer 5' TCTTCACCCGGGAGAGAGACTTGCAGCAAG 3'; 30 cycles:
96 °C 30 s, 55 °C 45 s, 72 °C 2 min). The
Asp718I-SmaI internal fragment of this PCR
product that includes the 3' end of the coding region was then used to
replace the full Asp718-SmaI region of the
pB20p24 construct. The resulting pB2 construct thus contains the
cyclin-coding region, with a 2-amino acid C-terminal extension, fused
in frame with the NS stop codon and 3'-UTR (Fig. 1).
Versions of all of these constructions carrying poly(A) stretches were
constructed by inserting annealed 5' AATTA50G 3' and 5' AATTCT50 3' oligonucleotides into the unique
EcoRI site at the 3' end of the NS 3'-UTR. This gives an
A50 followed directly by a unique EcoRI
site, 24 nt downstream of the authentic polyadenylation signal.
Constructs were verified by automatic sequencing.
Antibodies and Recombinant Proteins--
Human rhinovirus 2A
proteinase, expressed in Escherichia coli and purified
exactly as described previously (20), was a gift from T. Skern. A
recombinant fragment of rotavirus NSP3 protein encompassing amino acids
163-313 was overexpressed in E. coli and purified exactly
as described previously (16, 21). Both NSP3 and 2A proteinase were
dialyzed against H100 buffer (10 mM HEPES-KOH, pH 7.5, 100 mM KCl, 1 mM MgCl2, 0.1 mM EDTA, and 7 mM -mercaptoethanol) prior to
use. Rabbit anti-eIF4G peptide 7 antiserum (raised against residues
327-342) was a gift of R. Rhoads. Monoclonal antibody 10E10 against
human PABP was a gift of M. Görlach.
Preparation of Translation Extracts--
Nuclease-treated RRL
was partially depleted of ribosomes by ultracentrifugation. Briefly,
2-ml volumes of flexi-reticulocyte lysate (Promega) were centrifuged at
90,000 rpm for 15-20 min in a Beckman TL-100 benchtop ultracentrifuge.
The supernatant was removed, aliquoted, and stored at 80 °C. The
ribosomal pellets were resuspended in 1/10 volume (with respect to the
initial volume of lysate) of H100 buffer and frozen at 80 °C.
Non-nucleased HeLa cell S10 extracts were prepared exactly as described
previously (22) and were dialyzed overnight against H100 buffer.
Translation-competent HeLa cell S10 extracts were prepared and treated
with micrococcal nuclease as described (23) except that dialysis was
performed against H100 buffer. Ribosome depletion of
translation-competent HeLa cell S10 extracts was performed as described
above for RRL.
In Vitro Transcriptions and Translations--
In
vitro transcriptions and translations were performed as described
previously (24) except that artificially capped transcripts were
synthesized in the presence of 0.8 mM cap analogue (Ambion Inc.). Transcription reactions included trace quantities of
[ -32P]UTP to allow accurate quantification of RNA
yields. All RNAs were purified on G-50 Sephadex spin columns (Roche
Molecular Biochemicals) to eliminate non-incorporated cap analogue and
nucleotides prior to ethanol precipitation and washing with 70% ethanol.
In vitro translation reactions were performed in the
presence of [35S]methionine. RRL-based reactions
contained 50% by volume of flexi-reticulocyte lysate (Promega) or
ribosome-depleted RRL and 33% by volume of H100 buffer or
non-nucleased HeLa cell S10 extract in H100 buffer, and were programmed
with the indicated concentrations of in vitro transcribed
mRNAs. Final concentrations, respectively, of added KCl and
MgCl2 were 102 and 0.8 mM (for the experiments
presented in Fig. 2) and 115 and 0.9 mM in all subsequent
reactions. For translation reactions performed in translation-competent
HeLa cell extracts, reactions containing 40% of HeLa cell extract were programmed with 6.5 µg/ml of in vitro transcribed
mRNAs. In certain experiments, translation reactions were
supplemented with ribosomal pellet resuspended in H100 buffer, or
purified recombinant proteins (2A proteinase or a fragment of NSP3)
also in H100 buffer.
Translations were performed for 90 min at 30 °C, and the translation
products were analyzed by SDS-polyacrylamide gel electrophoresis as
described previously (25), using gels containing 20% w/v acrylamide.
Dried gels were exposed to Hyperfilm -max (Amersham Pharmacia
Biotech) typically for 12-16 h. Densitometric quantification of
translation products was as described previously (24) using multiple
exposures of each gel to ensure that the linear response range of the
film was respected and that low levels of translation could be
accurately quantified. In some experiments, the total radioactivity
incorporated into proteins was assayed by trichloroacetic acid
precipitation exactly as described (26). The data presented in each
figure are representative of at least three independent translation assays.
Sucrose Gradient Analysis of Ribosome
Profiles--
Quantification of 40 S and 60 S ribosomal subunits in
translation extracts was performed exactly as described previously
(27), using 110-µl aliquots of RRL or translation-competent HeLa cell S10 extract (20-30 A260 units).
Co-immunoprecipitation and Western Blotting--
Translation
reactions (200 µl) were incubated with and without recombinant NSP3
for 30 min at 30 °C before immunoprecipitation as described
previously (16) with 1 µl per reaction of rabbit anti-eIF4G peptide 7 antisera. Western blot analysis of immunoprecipitated proteins was
exactly as described (24). Membranes were incubated with mouse
anti-PABP primary antibody, followed by horseradish peroxidase-linked
goat anti-mouse secondary antibodies, and were revealed by enhanced
chemiluminescence (ECLplus, Amersham Pharmacia Biotech).
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RESULTS |
To date, several cell-free translation extracts have been
described that reproduce the cap-poly(A) synergistic stimulation of
translation previously observed in vivo (6, 8, 10). However,
synergy was only observed in these cell-free extracts in the presence
of competitor mRNAs (6), which complicates a dissection of the
molecular basis of synergy. The primary aim of the study presented here
was to develop cell-free extracts from mammals that would exhibit
synergy between the cap and poly(A) tail in the absence of added
competitor mRNAs, and therefore could be used to examine the
molecular mechanism of cap-poly(A) cooperativity.
Development of an RRL-based Translation System That Exhibits
Cap-Poly(A) Synergy--
The effects of the poly(A) tail on
translation can be measured in two ways: by comparing the translation
efficiency of uncapped mRNAs with and without a poly(A) tail, or by
examining the synergy obtained upon addition of both poly(A) and a cap
to an mRNA (28). To carry out a comprehensive analysis, we compared
the translation efficiency of four versions of a given mRNA as
follows: neither capped nor polyadenylated ( / ), capped and
non-polyadenylated (+/ ), uncapped and polyadenylated ( /+), and both
capped and polyadenylated (+/+). These were synthesized in
vitro from cDNA transcription templates that only differed by
an oligonucleotide-derived homopolymer A50 insertion
preceding a unique EcoRI site at the end of a 150-nt 3'-UTR
(pB2; see "Experimental Procedures" and Fig.
1). Thus, the polyadenylated mRNAs
described here terminate with an A50- GAAUU tail.
It has previously been shown that a short 3' end heterologous
sequence does not affect poly(A) tail-promoted translation (6),
and that 50 A residues suffice to demonstrate the roles of the
poly(A) tail in translation initiation (9, 29).

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Fig. 1.
Schematic representation of plasmids used in
this work. The X. laevis cyclin B2 and HIV-I p24-coding
regions and the regions corresponding to the active EMCV and inactive
HRV2 IRESes are shown as open boxes. Numbers
below coding regions refer to the first and last amino acids of each
reporter gene product; for the HRV2 and EMCV IRESes, the numbering is
based on the viral genome sequence and denotes the first and last
nucleotides of viral sequence. Other 5'- and 3'-UTRs are depicted as
thick lines; the ATG codon that serves to initiate HIV-I p24
synthesis is shown in bold; restriction sites and stop
codons are underlined. Clones were constructed in duplicate,
differing only in the presence or absence of anA50
insertion (bracketed) at the EcoRI site used for
linearization prior to transcription.
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B2 RNAs were first translated in a nuclease-treated RRL in
vitro translation system, in the absence of added competitor RNAs (see Fig. 2A, RRL + 0%
HeLaS10 lanes). As expected, translation of capped B2 mRNA in this
system was some 30-fold more efficient than that of the uncapped
equivalent (compare +/ and / lanes). Polyadenylation
of uncapped B2 mRNA stimulated its translation approximately 6-fold
(compare /+ and / lanes). Moreover, additive stimulation of translation was achieved by polyadenylation and capping
(compare the +/+ lane with the sum of the +/ and /+ lanes), in accordance with previous reports (7, 8). Since poly(A)-mediated synergistic stimulation of translation in
nuclease-treated yeast extracts required the presence of competitor
RNAs (6), we next measured the translation activity of the B2 mRNAs
in RRL supplemented with increasing amounts of non-nucleased HeLa cell S10 extract. Non-nucleased cell extract was employed rather than purified poly(A) RNA to ensure that physiological cell equivalents of
mRNA were added. Global translation efficiency was significantly lowered in such conditions (Fig. 2A, RRL compare 0, 16.5 and 33 HeLaS10 lanes). Furthermore, the
stimulatory effects of addition of a cap or poly(A) tail alone were
then reduced (see values for Relative Stimulation, Fig.
2A). In contrast, slight cap-poly(A) synergy (calculated as
the relative stimulation of +/+ RNA divided by the sum of the relative
stimulations of /+ and +/ RNAs) was reproducibly observed. This
increased concomitantly with the quantity of added competitor but never
reached 2-fold.

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Fig. 2.
Development of an RRL-based translation
system that exhibits cap-poly(A) synergy. A, standard
RRL or ribosome-depleted RRL were supplemented with 33% (v/v) of
non-nucleased HeLa cell S10 extract (33 lanes), H100 buffer
(0 lanes), or 1:1 of S10 extract and H100 buffer (16.5 lanes). Reactions were programmed with RNAs (6.5 µg/ml)
transcribed in vitro from pB2 in four distinct versions as
indicated above each lane. Control reactions were programmed
with water (no RNA lanes). Translations were processed as described
under "Experimental Procedures." The autoradiograph of the dried
20% polyacrylamide gel is shown. The position of the cyclin B2
translation product is marked. Translation efficiency derived from
densitometric quantification is plotted below each lane.
Relative stimulation of translation was calculated by comparing the
translation efficiency of capped and/or polyadenylated RNA to that of
the / RNA (arbitrary units for the / RNAs from left to
right of 0.11, 0.12, 0.06, 0.06, 0.05, and 0.07). B,
sucrose gradient analysis of the proportions of 40 S and 60 S
ribosomal subunits in equivalent volumes of standard RRL (upper
plot), ribosome-depleted RRL (middle plot), or RRL
supplemented with 33% of non-nucleased HeLa cell S10 extract
(lower plot). Absorbance at 254 nm (y axis) is
plotted against gradient fraction number. The positions of the 40 S,
60 S, and 80 S peaks and the top and bottom of the gradients are
indicated. C, ribosome-depleted RRL supplemented with H100
buffer (0×) or ribosomes recovered from RRL after
ultracentrifugation (final concentrations of 0.8 or 1.6× with respect
to intact RRL; see "Experimental Procedures") and programmed with
the indicated versions of B2 RNA as in A. The data are
presented as in A. Arbitrary units for the / lanes were
0.16, 0.17, and 0.33.
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It has been suggested that the concentration of free ribosomes
per se determines the magnitude of poly(A)-mediated
translation stimulation (11). Thus, in an attempt to amplify
cap-poly(A) synergy in the RRL system, and to circumvent the need for
addition of competitor RNAs, RRL was partially depleted of ribosomes by ultracentrifugation (see "Experimental Procedures"). Translation efficiency was dramatically reduced in reactions containing the ultracentrifugation supernatant compared with those based on intact RRL
(Fig. 2A, compare ribosome-depleted RRL and
RRL lanes; 0% HeLaS10). The stimulatory effects
of capping non-polyadenylated mRNA and polyadenylating uncapped
mRNA were also reduced as compared with the reactions performed in
standard RRL. However, cap-poly(A) cooperative stimulation of
translation was observed (synergy of approximately 3-fold). Whereas the
addition of a non-nucleased HeLa cell S10 extract to ribosome-depleted
RRL moderately improved global translation efficiency, it did not
affect the synergy (see Fig. 2A, right-hand side),
presumably because the positive effects of the added competitor
mRNAs in increasing synergy are negated by the free ribosomes and
initiation factors present in the HeLa cell extract. Thus, all further
studies using the RRL system were performed with ribosome-depleted RRL,
without HeLa cell extract supplementation.
Sucrose gradient analysis was performed to determine the proportions of
40 S and 60 S ribosomal subunits present in the different translation
systems used (Fig. 2B). The concentration of 60 S and 40 S
ribosomal subunits in ribosome-depleted RRL was below the detection
limit of the assay (middle plot), whereas, compared with RRL
(upper plot), larger 40 S and 60 S peaks and an additional peak corresponding to 80 S ribosomes could be detected in RRL supplemented with non-nucleased HeLa cell extract (lower
plot). As an additional control of the ribosome-depleted system,
it was verified that ultracentrifugation had not irreversibly altered the nature of the translation extracts. Indeed, back-addition of the
ribosomes pelleted during ultracentrifugation totally restored translation activity to levels observed in control RRL (Fig.
2C and data not shown). More importantly, cap-poly(A)
synergy was reduced when 0.8× ribosomes (with respect to starting
extract) were included in the reaction and was abolished when 1.6×
ribosomes were added back.
Examination of Cap and Poly(A) Cooperativity in Human Cell-free
Extracts--
We next examined whether a similar strategy for inducing
poly(A) dependence could be used with other cell-free extracts.
Similarly to standard RRL, only a minor translational advantage is
conferred upon polyadenylation of a capped B2 RNA in a nuclease-treated translation-competent HeLa S10 extract (Fig.
3A, 2 left-hand lanes). When
HeLa cell extracts were submitted to ultracentrifugation, supernatants
were totally lacking in translation activity (Fig. 5A, 0×
lanes) unless they were supplemented with a fraction of the
ribosomes recovered from the ultracentrifugation pellet (Fig. 3A,
0.3 and 0.6× lanes). Sucrose gradient analysis,
performed to control extract composition, confirmed the significantly
reduced concentrations of free 40 S and 60 S ribosomal subunits in
the depleted extracts (Fig. 3A). In depleted extracts
reconstituted with 0.3× ribosomes, polyadenylation increased
translation efficiency of a capped mRNA 3-4-fold. Moreover, a
modest cap-poly(A) synergy was observed (approximately 2.5-fold, see
Fig. 3B), demonstrating that the ability to render extracts
poly(A)-dependent by ultracentrifugation is not a
peculiarity of the RRL system.

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Fig. 3.
Cap-poly(A) synergy in a human cell-free
extract. A, nuclease-treated translation-competent HeLa
cell S10 extract (HeLaS10) or ribosome-depleted HeLa S10
supplemented with either H100 buffer (0×) or ribosomes
recovered from HeLa cell S10 extract after ultracentrifugation (final
concentrations with respect to control HeLa cell S10 extract) were
programmed with 6.5 µg/ml capped, B2 RNAs in non-polyadenylated or
polyadenylated form (as indicated). Translation products were analyzed
as described in the legend to Fig. 2. Sucrose gradient analysis of the
proportions of 40 S and 60 S ribosomal subunits in equivalent volumes
of nuclease-treated translation-competent HeLa cell S10 extract
(upper plot), or ribosome-depleted HeLa S10 supplemented
with ribosomes recovered from the centrifugation pellet (final
concentration of 0.3× with respect to intact HeLa cell S10 extract;
lower plot) was performed as described under "Experimental
Procedures." Data are presented as in Fig. 2. B,
ribosome-depleted HeLa S10 supplemented with 0.3× ribosomes was
programmed with 6.5 µg/ml of the various in vitro
transcribed B2 mRNAs as shown above each lane.
Translation products were analyzed as described in the legend to Fig.
2.
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Synergy in Ribosome-depleted RRL Is Sensitive to mRNA
Concentration--
The levels of synergy reported above in
ribosome-depleted RRL (2-3-fold) were rather modest when compared with
those observed from in vivo studies (see for example Ref.
9). In an attempt to increase synergy in the RRL system, we first
optimized the concentrations of added KCl and MgCl2 with
respect to +/+ mRNA translation (data not shown; optima of 115 and
0.9 mM respectively, as opposed to 102 and 0.8 mM used for the experiments shown in Fig. 2) and then
examined the effects of RNA concentration on synergy. A second series
of mRNAs transcribed from p0p24 cDNAs (Fig. 1) was included in
the analysis to show that the effects observed so far were not
an artifact of the pB2 constructs. Whereas the B2 and 0p24 RNAs share
an identical 150-nt 3'-UTR/poly(A) tract, the cyclin B2 5'-UTR and
coding region in the 0p24 mRNAs are replaced by a short
oligonucleotide-derived 5'-UTR preceding the HIV-I p24-coding region.
B2 and 0p24 mRNAs were thus used to program ribosome-depleted RRL
translation reactions at a range of final RNA concentrations, and the
degree of cap-poly(A) synergy was calculated at each concentration (Fig. 4). Similar levels of synergy were
observed with equivalent molar concentrations of the 0p24 and B2
mRNAs (950 and 1450 nt long, respectively), indicating that
cap-poly(A) cooperativity is likely to be a general phenomenon on
mRNAs translated in this system. It should be noted that kinetic
experiments failed to detect any differences in the functional
half-lives between RNAs that were capped, polyadenylated, or both (data
not shown), even when extremely low concentrations of programming RNA
were used. Thus, synergy does not result from significant differences
in mRNA stability in these extracts. More important, although
virtually no synergy was evidenced with near-saturating concentrations
of the B2 and 0p24 mRNAs, synergy increased significantly as the RNA concentration was reduced and reached almost 8- and 10-fold, respectively, at the lowest concentrations tested. This increase in
observed synergy stemmed from the extremely inefficient translation of
the +/ RNAs at all but the highest RNA concentrations. Indeed, in all
such experiments, the dose responses for +/ mRNAs showed significant non-linearity at the lower end of the RNA concentration range (see also for example Fig. 7). It is plausible that this non-linearity reflects the inability of the +/ mRNAs to compete with the endogenous RNA fragments generated by nuclease treatment of
the lysate. It is also interesting that synergy is highest when low RNA
concentrations are used to program ribosome-depleted RRL, whereas no
synergy is observed in standard RRL at any RNA concentration (Fig. 2,
and data not shown). Although we have no concrete explanation for this
discrepancy, these data imply that the factors that are limiting in
ribosome-depleted RRL are never limiting in standard RRL. In the light
of the data presented above, subsequent translation experiments in
depleted RRL were performed with optimal KCl and MgCl2
concentrations and a compromise of mRNAs concentrations that allow
significant synergy while yielding easily detectable amounts of
translation products.

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Fig. 4.
Sensitivity of cap-poly(A) synergy to RNA
concentration in ribosome-depleted RRL. Ribosome-depleted RRL was
programmed with different final concentrations of mRNAs derived
either from pB2 (left-hand side) or from p0p24
(right-hand side) transcribed in the form indicated
alongside each panel. Final RNA concentrations were 10, 5, 2.5, or 1.25 µg/ml for B2 mRNAs and 6.3, 3.15, or 1.575 µg/ml for 0p24
mRNAs. Translation products were analyzed as described in the
legend to Fig. 2. For reactions programmed with / and /+ 0p24
mRNAs, a second panel is shown that corresponds to an 8-fold
overexposure of the gel (long expo. panels). The translation
efficiencies of the various RNAs (squares, / ;
circles, /+; diamonds, +/ ; and
triangles, +/+) plotted as a function of RNA concentration
and the cap-poly(A) synergy calculated at each RNA concentration are
shown below the two series of panels.
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The PABP-eIF4G Interaction Mediates the Translational Effects of
the Poly(A) Tail--
To characterize the molecular requirements for
cap-poly(A) synergy in the RRL-based system, we employed the group A
rotavirus NSP3 protein. In addition to binding specifically a conserved sequence present at the 3' end of all rotaviral mRNAs (15), NSP3
was recently shown to interact directly with the N-terminal part of
eIF4G and, in doing so, to evict PABP from the eIF4F complex (16).
Thus, if cap-poly(A) synergy depends on mRNA circularization mediated by the eIF4G-PABP interaction, it should be abolished by NSP3.
For the study presented here, a truncated form of recombinant NSP3
spanning amino acids 163-313 was used. This fragment is deleted for
the rotaviral RNA binding domain but is still capable of disrupting the
eIF4G-PABP interaction (16, 21).
First, the effects of NSP3 on the translation of a pool of cellular
mRNAs were determined, by including pure protein in standard RRL
reactions containing non-nucleased HeLa cell S10 extract as a source of
mRNAs. NSP3 significantly inhibited global protein synthesis in a
dose-dependent manner, with inhibition attaining over 70%
when NSP3 concentrations exceeded 12 µg/ml (Fig.
5A). It was confirmed that the
recombinant NSP3 fragment was displacing PABP from the eIF4F complex in
this system by immunoprecipitating the eIF4F complex with antibodies
directed against eIF4G, and analyzing the immunocomplexes by Western
blotting with antibodies raised against PABP (Fig. 5B).
Inclusion of NSP3 in translation reactions dramatically reduced the
quantity of PABP which co-immunoprecipitated with eIF4G. These data,
together with results of similar experiments performed with
rotavirus-infected cell extracts (16), demonstrate that in the absence
of the eIF4G-PABP interaction the RNA-protein interactions alone are
not sufficiently stable to withstand the precipitation conditions. This
is possibly because the affinities of the separated proteins for
mRNA ends are lower than those of the intact eIF4G·PABP
complex (see "Discussion"). Interestingly, even with high
concentrations of added NSP3, PABP eviction from eIF4G was not
complete. Effectively, co-immunoprecipitation of PABP with eIF4G from
translation reactions containing 50 µg/ml of added NSP3 approached
20% of that observed in reactions without NSP3. This is the first
direct demonstration that NSP3 can inhibit translation of cellular
mRNAs, presumably via its interaction with eIF4G and displacement
of PABP.

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Fig. 5.
NSP3 evicts PABP from eIF4G and inhibits
endogenous mRNA translation. A, standard RRL
reactions were programmed with the endogenous mRNAs present in
non-nucleased HeLa cell S10 extract (33% v/v S10 extract) and received
recombinant truncated rotavirus NSP3 protein in H100 buffer
(concentrations in µg/ml, indicated above each lane) or
H100 buffer alone (0 lane). The exposure shown is 8-fold
longer than when in vitro transcribed RNAs were analyzed.
Alongside is plotted the radioactivity incorporated into proteins as
determined by trichloroacetic acid precipitation. B,
translation reactions (150 µl) were assembled as described in
A in the presence of the indicated concentrations of NSP3,
prior to immunoprecipitation with antibody against eIF4G and Western
blotting with antibodies (Ab) against PABP (see
"Experimental Procedures"). A control reaction contained no
anti-eIF4G antibody. RRL (0.25 µl) was loaded alongside to serve as a
marker for the position of endogenous PABP (RRL lane). The
percentage of PABP in the immunoprecipitate is indicated
below each lane (100% is the value obtained in the absence
of NSP3).
|
|
Next, the effect of NSP3 on each of the four different forms of
in vitro transcribed B2 and 0p24 mRNAs was examined in
standard and ribosome-depleted RRL (Fig.
6). The final concentration of NSP3 used
(5 µg/ml) corresponds to the minimal concentration required to reduce
translation of cellular mRNAs by 50% and to displace 80% of PABP
from the eIF4F complex (see Fig. 5). NSP3 had no significant effect on
the translation efficiency of the non-polyadenylated RNAs in either
translation system (Fig. 6, A and B, see
/ and +/ lanes). In contrast,
NSP3 reduced the translation efficiency of each capped polyadenylated
RNA to approach that of its non-polyadenylated counterpart in
ribosome-depleted RRL (Fig. 6, A and B,
+/+ and +/ lanes), severely
diminishing cap-poly(A) synergy. These results strongly suggest that
synergy requires mRNA circularization mediated by the eIF4G-PABP
interaction. Interestingly, NSP3 inclusion in standard RRL reactions
reduced the translation efficiency of polyadenylated RNAs to approach
that of their non-polyadenylated equivalents, irrespective of the
mRNA cap status. These data imply that poly(A) tail-mediated
stimulation of translation in standard RRL also requires the PABP-eIF4G
interaction. This hypothesis is indirectly supported by results
obtained using the human rhinovirus 2A proteinase, which cleaves eIF4G
such that its PABP/eIF4E-binding domain is separated from the region
that fixes the ribosome-associated eIF3 complex (13, 20, 30). Not only
did this proteinase dramatically inhibit translation of capped B2 RNAs
in either system, it also showed the same effects as NSP3 on
translation of uncapped polyadenylated B2 RNA in RRL, i.e.
the efficiency was reduced to approach that of uncapped
non-polyadenylated RNA (Fig. 6A, 2A lanes).

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Fig. 6.
Cap-poly(A) synergy requires the interaction
between PABP and eIF4G. Standard or ribosome-depleted RRL was
programmed with B2 (A), 0p24 (B), or EMCVp24
(C) mRNAs. Final RNA concentrations were 3 µg/ml (for
0p24 mRNAs) and 6.2 µg/ml (for EMCVp24 mRNAs), and for B2
mRNAs were 2.6 µg/ml (in ribosome-depleted RRL) or 6.5 µg/ml in
standard RRL (to facilitate the detection of B2 translation products in
RRL reactions treated with 2A proteinase). Reactions were supplemented
with H100 buffer ( lanes), recombinant
truncated NSP3 protein (5 µg/ml; N lanes), or rhinovirus
2A proteinase (10 µg/ml; 2A lanes) each in H100 buffer.
Translation products were analyzed as described in the legend to Fig.
2. Calculated cap-poly(A) synergies for the B2 and 0p24 mRNAs in
ribosome-depleted RRL were, respectively, 5.1- and 5.9-fold in the
absence of NSP3, as compared with 1.3- and 1.8-fold in the presence of
NSP3. Poly(A)-mediated stimulation of EMCVp24 was 3.7-fold in the
absence and 1.8-fold in the presence of NSP3. In three independent
experiments, poly(A) stimulation of EMCV IRES-driven translation in
depleted RRL was 3-, 3.7-, and 4.5-fold.
|
|
The standard RRL system is often used to study the translation of
non-classical IRES-containing mRNAs. We evaluated whether one such
IRES, that of encephalomyocarditis virus (EMCV, a picornavirus), would
still be translationally active in the ribosome-depleted RRL system.
The full EMCV IRES was inserted into the oligonucleotide linker of
p0p24 such that p24 synthesis will be driven from the authentic viral
AUG at the 3' end of the IRES (Fig. 1). Since picornaviral RNAs are
naturally uncapped, only two versions of the EMCVp24 RNA were
generated, differing in the presence or absence of the 3' poly(A) tail.
The corresponding transcripts were translated in either standard or
ribosome-depleted RRL, with and without 5 µg/ml of added NSP3 (Fig.
6C). The efficiency of EMCVp24 translation was significantly
reduced in ribosome-depleted as compared with standard RRL (Fig.
6C). However, we consider that the EMCV IRES was still
functional in the depleted extract since the uncapped, non-polyadenylated version of this RNA was translated some 15-fold better than the equivalent / 0p24 mRNA (Fig. 6). In addition, the EMCV IRES is still functional in ribosome-depleted RRL when inserted between the two cistrons of a dicistronic mRNA, confirming that it is behaving as an IRES (data not shown).
Polyadenylation of the uncapped EMCVp24 mRNA reproducibly
stimulated translation 3-4-fold in the ribosome-depleted extract, whereas it had only a slight positive effect on IRES activity in
standard RRL reactions. Inclusion of NSP3 in the reactions abolished
the modest poly(A)-mediated stimulation of translation driven from the
EMCV IRES in RRL and also significantly reduced the stimulation seen in
ribosome-depleted RRL (Fig. 6C, N lanes), demonstrating that
the eIF4G-PABP interaction is required for maximal poly(A)-mediated
stimulation of translation on this uncapped, IRES-containing mRNA.
Cap-Poly(A) Synergy Is Not Affected by Increasing the Distance
between the Open Reading Frame and the Poly(A) Tail--
One possible
result of circularization of mRNAs with relatively short 3'-UTRs is
that terminating ribosomes are in the proximity of the mRNA 5' end,
which could serve to facilitate recycling of ribosomal subunits from
the mRNA 3' end back to the 5' cap (for reviews see Refs. 3 and
31). Thus, we investigated the impact of the length of the mRNA
that separates the end of the open reading frame from the poly(A) tail
on cap-poly(A) cooperativity. Toward this end, a dicistronic mRNA
transcribed from pB20p24 (see Fig. 1) was generated, which has the same
5' and 3'-UTRs as the monocistronic B2 mRNA, but carries a second
translatable cistron encoding the HIV-I p24 protein preceded by a short
polylinker. This could be used to determine whether ribosome arrival
near the mRNA 3' end is required for cap-poly(A) synergy, since the RRL translation system is inefficient in reinitiating translation of
downstream cistrons in polycistronic messages. However, since it is
formally possible that ribosomes could scan past the start site of the
second cistron without re-initiating translation, a cDNA was
constructed such that dicistronic RNAs would contain a truncated,
inactive IRES from human rhinovirus type 2 between the two cistrons
(Fig. 1, pB2 IRESp24). We have previously
demonstrated that this inactive IRES presents a barrier to ribosomal
scanning and downstream cistron translation without competing
significantly with the upstream cistron for translation components
(18).
RNAs with the four different combinations of cap and/or poly(A) tail
were transcribed from these different cDNAs and used to program
ribosome-depleted RRL translation reactions at a range of molar
equivalent RNA concentrations. No p24 synthesis could be evidenced in
reactions programmed with the dicistronic B20p24 or B2 IRESp24 RNAs,
confirming the absence of reinitiation and downstream cistron
translation in the ribosome-depleted extracts (Fig.
7). Of more interest, the B2 cistron of
the B2, B20p24, and B2 IRESp24 RNAs was translated with very similar
efficiency in the three cases, and the three mRNAs behaved almost
identically with respect to the cooperative effects of the cap and
poly(A) tail at the different mRNA concentrations. These
results infer that cap-poly(A) cooperativity is insensitive to
increasing the distance that separates the termination codon and the
poly(A) tail and that there is no advantage for a capped-polyadenylated RNA if ribosomes terminate translation 150 nt (on B2 RNA) rather than
1200 nt (in the case of the B2 IRESp24 RNA) upstream of the mRNA
3' end.

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Fig. 7.
Cap-poly(A) synergy is not quantitatively
affected on dicistronic mRNAs with downstream silent open reading
frames. Ribosome-depleted RRL extracts were programmed with
equivalent molar concentrations of B2, B20p24, or B2 IRESp24
mRNAs as described in the legend to Fig. 4 (RNA concentrations in
µg/ml: 6.2, 3.1, and 1.55 for B2; 10, 5.0, and 2.5 for B20p24; and
12.5, 6.25, and 3.125 for B2 IRESp24). A control reaction was
programmed with water (no RNA lane). A reaction programmed
with 0p24 mRNA was loaded alongside to indicate the position of the
p24 gene product (0p24 lane). Presentation of the data is
exactly as in the legend to Fig. 4. Curves for / mRNAs were
omitted for clarity.
|
|
 |
DISCUSSION |
To our knowledge, the translation systems described here are the
first mammalian in vitro extracts that support cap-poly(A) synergistic stimulation of translation in the absence of intact competitor RNAs. RRL extracts were rendered
poly(A)-dependent by partial depletion of ribosomal
subunits, and presumably their tightly associated translation factors,
via ultracentrifugation. Control experiments based on high salt
treatment of cell extracts before ultracentrifugation suggest that
reduced concentrations of both ribosomes and initiation factors
contribute to synergy.2
However, it cannot be ruled out that ultracentrifugation also serves to
remove certain general RNA-binding proteins that could reduce the
effects of the mRNA poly(A) tail on translation in non-depleted
extracts. Under optimal conditions, the ribosome-depleted RRL extracts
exhibited levels of synergy (8-10-fold) comparable to those reported
for Drosophila embryo and yeast cell-free extracts (synergies of 3-15-fold depending on the system), in which mRNA competition was used to confer poly(A) dependence (6, 8, 10, 28). It
should be noted that global translation efficiency of in
vitro transcribed mRNAs was significantly lower in
ribosome-depleted as opposed to intact RRL. We believe that this is not
a major concern, since, when compared with the highly competitive
environment of the intact cell, standard RRL exhibits extremely
elevated translation levels for a given RNA species.
Translation-competent HeLa cell S10 extracts could also be rendered
moderately poly(A)-dependent (synergy of 2.5-fold) by
ultracentrifugation. However, due to the intrinsically lower
translation activity of HeLa cell extracts in our hands as compared
with RRL, it was difficult to reproducibly improve synergy by reducing
mRNA concentration (data not shown).
The ability to generate poly(A)-dependent extracts without
intact competitor RNA addition allowed us to address the question of
mRNA circularization as the molecular basis of cap-poly(A) cooperativity. We used the rotaviral NSP3 protein to interrupt the
PABP-eIF4G interaction invoked in the closed loop model of translation
initiation. To date, this is the only known initiation factor complex
affected by NSP3, although it cannot be formally excluded that other
protein-protein interactions are also sensitive to the rotaviral
protein. Cap-poly(A) synergy in poly(A)-dependent extracts
was severely reduced (although not completely abolished) by NSP3,
demonstrating that the PABP-eIF4G interaction is required for maximal
synergy. In favor of the hypothesis that cap-poly(A) cooperativity
relies on eIF4F/PABP-mediated mRNA circularization, it has been
reported that the interaction of wheat germ PABP with eIF4F increases
the affinity of eIF4E for cap analogue by some 40-fold, and conversely
that the affinity of eIF4F-complexed plant PABP for poly(A) is greater
than that of free PABP (32, 33). It also seems plausible from our data
that the additive effects of capping and polyadenylation in standard
RRL result from mRNA circularization, since they were abolished by
NSP3. However, the translational advantage conferred by circularization
in this case is minimal, presumably because ribosomes and associated
translation factors are not limiting.
The poly(A) tail also moderately stimulated translation initiation on
uncapped RNAs, in accordance with previous reports (6, 8). However,
compared with control RRL, this stimulation was reduced when extracts
were partially depleted of ribosomes. Interestingly, the
poly(A)-mediated stimulation of uncapped RNA translation also requires
intact eIF4G complexed to PABP, as indicated by sensitivity to the NSP3
and 2A proteins (see Fig. 6). These results are in agreement with those
of Ref. 28, where eIF4G mutations were used to interrupt the eIF4G-PABP
interaction in yeast. It is possible that the eIF4G·PABP complex also
induces circularization of uncapped-polyadenylated RNAs. However, it
remains to be determined whether eIF4G complexed to PABP can bind RNA
directly, for instance via its RNA recognition motif (2, 34).
Another aspect of the experiments reported here concerns the general
inhibition of in vitro translation of a pool of cellular mRNAs by purified recombinant rotaviral NSP3 protein. Once again, the known physiological properties of NSP3 support the concept that
actively translated cellular mRNAs are circularized via a cap-eIF4E-eIF4G-PABP-poly(A) interaction. Furthermore, these data constitute the first direct evidence that NSP3 alone is sufficient to
provoke the shut-off of host cell translation seen during rotavirus infection. Inhibition of in vitro translation of endogenous
mRNAs by recombinant NSP3 reproducibly reached a plateau at around
70% inhibition. The residual translation reflected a global
inefficient translation of mRNAs within the pool rather than
continued translation of a specific subpopulation of mRNAs, and
thus probably corresponds to the efficiency of
"poly(A)-independent" translation in this system. However,
NSP3-induced displacement of PABP from eIF4G was not total and reached
a plateau at around 80% displacement (see Fig. 5). The subpopulation
of the eIF4F-PABP complex that resists NSP3 might be partly responsible
for the residual translation observed with endogenous mRNAs
in NSP3-treated extracts (Fig. 5A). Similarly, it could
explain why NSP3 did not totally abolish cap-poly(A) synergy (Fig. 6).
Further studies will be required to dissect the nature of this
apparently NSP3-resistant proportion of the eIF4F·PABP complex.
We have also shown that the introduction of a barrier to 40 S
ribosomal scanning followed by a second, non-translated open reading
frame between the reporter gene and the poly(A) tail does not
quantitatively affect translation efficiency or cap-poly(A) cooperativity. These data imply that the length of the effective 3'-UTR
is of little importance to mRNA 5'-3' end interplay, which is
directly relevant to the many natural mRNAs that have extremely long 3'-UTRs containing silent open reading frames. In addition, these
data argue against the simplistic hypothesis that synergy results from
post-termination 40 S ribosomal subunits reaching the poly(A) tail and
then being directly transferred back to the 5' cap. Instead one might
speculate that, if ribosome recycling occurs, it is either indirect
preferential re-recruitment of dissociated ribosomal subunits that
remain in the proximity of the "donor" mRNA or direct recycling
from the vicinity of the termination codon. In this respect, it is
interesting to note that PABP was recently shown to interact with a
component of the eukaryotic translation termination machinery (35). To
resolve completely the mechanism resulting in synergy, it would be
advantageous to determine whether an RNA behaves "catalytically" or
"stoichiometrically" in the depleted extract. Unfortunately, from
the data presented here, it is difficult to discriminate convincingly
between these two types of behavior. The dose responses of the
different mRNAs translated in depleted extract all exhibit some
non-linearity, which could be interpreted as indicative of catalytic
action. However, as we have already pointed out (see "Results,"
this non-linearity could equally reflect competition between the added
transcripts and fragments of endogenous mRNA generated by
micrococcal nuclease treatment of the translation extracts. Further
studies will be required to address fully this question.
Finally, we demonstrated that the effects of polyadenylation on
non-classical, IRES-containing mRNAs can be studied in these systems. EMCV IRES-driven translation was stimulated severalfold by
addition of a poly(A) tail to the uncapped IRES-carrying mRNA, an
effect that was diminished by NSP3. These results suggest that the
mechanism of 5'-3' end cross-talk operative on classical cellular mRNAs is at least partly conserved for certain IRES-containing messages. We are currently evaluating the effects of polyadenylation on
the IRES activities of other members of the picornavirus family, many
of whom are known to induce the cleavage of PABP and/or eIF4G during
infection of the host cell.
 |
ACKNOWLEDGEMENTS |
We acknowledge the skillful technical
assistance of N. Castagné. We also thank Sylvie van der Werf and
Cécile Malnou for their interest in this work. Work in the
laboratory of K. M. K. was supported by the Program de Recherche
Clinique de l'Institut Pasteur and by Grant 6495 from the Association
Française Contre les Myopathies.
 |
FOOTNOTES |
*
This work was supported in part by a grant from the Program
de Recherches Fondamentales en Microbiologie, Maladies Infectieuses et
Parasitologie from the MENRT (to D. P.).The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
§
Present address: Dept. Medecine Interne-Hepatology, Vall
D'Hebron Hospital, 08035 Barcelona, Spain.
¶
To whom correspondence should be addressed. Tel.: 33 1 40 61 33 55; Fax: 33 1 40 61 30 45; E-mail: kathiemb@pasteur.fr.
Published, JBC Papers in Press, August 1, 2000, DOI 10.1074/jbc.M004304200
2
Borman, A. M., Michel, Y. M., and Kean, K. M. (2000) Nucleic Acids Res., in press.
 |
ABBREVIATIONS |
The abbreviations used are:
eIF, eukaryotic
initiation factor;
PABP, poly(A)-binding protein;
IRES, internal
ribosome entry segment;
UTR, untranslated region;
HIV-I, human
immunodeficiency virus type I;
nt, nucleotide;
PCR, polymerase chain
reaction;
NSP, non-structural protein;
NS, non-structural;
EMCV, encephalomyocarditis virus.
 |
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Copyright © 2000 by The American Society for Biochemistry and Molecular Biology, Inc.

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