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Mol Cell Biol, January 1998, p. 51-57, Vol. 18, No. 1
0270-7306/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
RNA Recognition Motif 2 of Yeast Pab1p Is Required
for Its Functional Interaction with Eukaryotic Translation
Initiation Factor 4G
Steven H.
Kessler and
Alan B.
Sachs*
Department of Molecular and Cell Biology,
University of California at Berkeley, Berkeley, California 94720
Received 22 August 1997/Returned for modification 1 October
1997/Accepted 10 October 1997
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ABSTRACT |
The eukaryotic mRNA 3' poly(A) tail and its associated
poly(A)-binding protein (Pab1p) are important regulators of gene
expression. One role for this complex in the yeast Saccharomyces
cerevisiae is in translation initiation through an interaction
with a 115-amino-acid region of the translation initiation factor
eIF4G. The eIF4G-interacting domain of Pab1p was mapped to its second
RNA recognition motif (RRM2) in an in vitro binding assay. Moreover,
RRM2 of Pab1p was required for poly(A) tail-dependent translation in
yeast extracts. An analysis of a site-directed Pab1p mutation which
bound to eIF4G but did not stimulate translation of uncapped,
polyadenylated mRNA suggested additional Pab1p-dependent events during
translation initiation. These results support the model that the
association of RRM2 of yeast Pab1p with eIF4G is a prerequisite for the
poly(A) tail to stimulate the translation of mRNA in vitro.
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INTRODUCTION |
The 3' poly(A) tail of eukaryotic
mRNA serves as an important regulator of gene expression. Both in vitro
and in vivo experiments have demonstrated a role for this structure in
translation (6, 15, 19, 20, 22). Particularly striking
examples of the role of the poly(A) tail in translation are found in
studies involving vertebrate oocytes, whose timing of progression
through meiosis relies on the regulated addition of poly(A) tails to
preexisting cytoplasmic mRNAs and their subsequent translational
activation (25). The poly(A) tail may also assist in the
nucleocytoplasmic transport of mRNA (9) and appears to
confer stability to cytoplasmic mRNA (4). To understand the
roles of the poly(A) tail more completely, we have analyzed the
structure and function of its major associated protein, the
poly(A)-binding protein (Pab1p). Pab1p has been found in all eukaryotes
examined thus far and is likely to mediate many of the cytoplasmic and
possibly some of the nuclear functions of the poly(A) tail. This study
focuses on the role of Pab1p in mediating the translational stimulation of mRNA by the poly(A) tail.
Although the function of the poly(A) tail in translation has been the
subject of research for many years (11, 21), a relevant target of Pab1p in the translation initiation pathway in yeast has only
recently been identified. This target is eukaryotic translation initiation factor 4G (eIF4G) (23). The eIF4G protein is part of the cytoplasmic 5' cap-binding complex eIF4F, which also contains the cap-binding protein eIF4E. eIF4G has been shown to bind to Saccharomyces cerevisiae Pab1p (23) and more
recently the wheat Pab1p (13) in vitro. The association of
yeast Pab1p with eIF4G has also been shown to mediate the poly(A) tail-
and Pab1p-dependent translational stimulation of mRNA in vitro
(24). Current models hold that Pab1p can stimulate
recruitment of the 40S ribosomal subunit to mRNA (22)
through its association with eIF4G. The eIF4G protein provides the link
to the 40S subunit since it can bind to the 40S-associated initiation
factor eIF3 (14). The Pab1p-binding site within yeast eIF4G
has been narrowed down to a 115-amino-acid region N terminal to the
binding site for eIF4E (23, 24). This study was designed to
define the region(s) of Pab1p that interacts with this subdomain of
eIF4G and thereby stimulates translation in vitro.
Pab1p is the founding member (1, 18) of a large family of
proteins containing an RNA recognition motif (RRM). Pab1p also contains
a less well defined carboxy-terminal region. The RRM consists of
approximately 90 amino acids, and nuclear magnetic resonance and
crystal structures of representative RRMs reveal a highly conserved
hydrophobic core with a less well conserved surface (reviewed in
reference 16). This latter feature undoubtedly supplies the specificity to each protein. Pab1p is one of few proteins
in the RRM family that contains four tandem copies of this domain.
While all four RRMs of Pab1p presumably share a common three-dimensional fold, they are quite divergent in sequence and therefore probably in function. We previously identified RRM2 of yeast
Pab1p as being primarily responsible for its high affinity and
specificity for poly(A) RNA (5). Here the importance of RRM2
and the other Pab1p domains in translation is addressed.
To identify domains of the protein that bind to eIF4G and are required
for poly(A) tail-dependent translation in vitro, a deletion analysis of
S. cerevisiae Pab1p was performed. Specifically, each Pab1
mutant protein was tested for its ability to bind to S. cerevisiae eIF4G in vitro and to stimulate poly(A) tail-dependent translation in yeast extracts. These experiments revealed that RRM2 of
Pab1p is required for both of these functions. Additionally, analysis
of a site-directed mutant of Pab1p enabled us to functionally separate
the binding of Pab1p to eIF4G from its activation of translation in
vitro. The results support the hypothesis that the association of RRM2
of Pab1p with eIF4G is a prerequisite for poly(A) tail-dependent
translation and that once associated, other regions of Pab1p and/or
eIF4G are needed to stimulate translation.
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MATERIALS AND METHODS |
Construction of Pab1p deletions.
PAB1-1
(5) was used as the template for all PAB1
plasmids created in this study. Of note, the PAB1-1 gene
encodes a His6 tag at the amino terminus of Pab1-1 and
contains unique restriction sites in the linkers between each of the
domains of PAB1. RRM1 was deleted by joining a
PvuII site at nucleotide (nt) 25 to a blunted
BamHI site at nt 372, thereby deleting amino acids 15 to
129. RRM2 was deleted by inserting OSK01 (GATCACAGGCCT) into the PAB1-1 plasmid with the following ends: a
BamHI site (nt 372) and a ClaI site (nt 632).
This results in a deletion of amino acids 132 to 216 and an insertion
of an alanine prior to amino acid 217. RRM3 was deleted by inserting
OSK03 (CGAAACAGTATGAAG) between the ClaI site (nt
632) and a StuI site (nt 927), thus removing amino acids 218 to 311. RRM4 was deleted by joining a blunted BamHI site at
nt 1266 to the StuI site (nt 927), which eliminates amino
acids 316 to 427. The carboxy-terminal truncation was constructed by
fusing blunted BamHI (nt 1266) and SpeI (nt 1819)
sites. The downstream BamHI site (nt 1266) was originally made in plasmid pJD13, which contains PAB1 modified only at
this site. The final amino acid is residue 429. pab1-105
(contains only RRM1 and RRM2) was made by fusing a blunted
ClaI site (nt 632) to a PvuII site at nt 1579. This protein contains a C-terminal LVKLLV hexapeptide following amino
acid 217. Finally, the gene encoding the protein containing just RRM2
was constructed in the same manner as pab1-105, with the
exception of the starting plasmid, which contained
pab1-
RRM1 instead of PAB1-1. All of the above were initially constructed in a yeast TRP1 CEN4 vector
(pAS414 [7]). These genes were also subcloned into
pET11d (Invitrogen) for bacterial overexpression followed by
Ni2+ affinity chromatography for purification (see
reference 5 for details). Table
1 summarizes the yeast and bacterial
strains containing the various pab1 genes.
RNA binding analysis.
Gel shifts were performed as described
by Deardorff and Sachs (5). Briefly, final buffer and salt
conditions were as follows: 10 mM Tris (pH 8.0), 80 mM potassium
acetate, 30 mM NaCl, 0.4 mM EDTA, 0.7 mM MgCl2, 0.6 mM
dithiothreitol, 2 µg of tRNA per ml, 0.6% glycerol, 15 µg of
bovine serum albumin per ml, and 1.5% polyvinyl alcohol. The samples
were run on a 4% acrylamide (40:1) native gel in 0.4×
Tris-borate-EDTA at 80 V for 50 min. Data were quantitated with a
Molecular Dynamics PhosphorImager and the ImageQuant program. The data
were then fit to the equation y = 1/[1 + (Kd/x)], where y is the fraction of
the oligo(A)20 shifted from the origin and x is
the free protein concentration. Binding to poly(A)-Sepharose (Pharmacia) was determined using 25 µl of resin with indicated concentrations of proteins in a final binding volume of 100 µl of
PBST (150 mM NaCl, 16 mM Na2HPO4, 4 mM
NaH2PO4, 0.1% Triton X-100 [pH 7.3]).
Following incubation for 1 h at 4°C, the resin was washed three
times in 750 µl of PBST. The resin was then boiled in 25 µl of
sodium dodecyl sulfate (SDS) gel loading buffer, of which 20 µl was
analyzed by SDS-polyacrylamide gel electrophoresis (PAGE) followed by
staining with Coomassie brilliant blue.
eIF4G binding analysis.
Glutathione S-transferase
(GST) fusions of the two yeast eIF4G Pab1p-binding sites were
overexpressed in Escherichia coli BAS3024 and BAS3035
(23). Bacterial cell lysates (5 µl) containing one of
these proteins were diluted 100-fold in PBST containing 1 mM
phenylmethylsulfonyl fluoride and incubated with 25 µl of glutathione-Sepharose (Pharmacia) for 1 h at 4°C. The resin was washed three times in 750 µl of PBST. Preincubated Pab1p-poly(A) (100 µl) was then added to the resin, which contained approximately 125 to
250 pmol of the eIF4G fragment, for 1 h at 4°C. The resin was
again washed three times in 750 µl of PBST and then boiled in 25 µl
of SDS gel loading buffer. Binding was measured by SDS-PAGE with 20 µl of the eluate for Coomassie brilliant blue staining or with 1 µl
of a 1:20 dilution of the eluate for Western analysis. Western blots
were performed with a polyclonal antibody to Pab1p and are as described
by Tarun and Sachs (23).
In vitro translation.
Translation extracts were prepared
from yeast cells as described previously (10, 22). For
studies using the addition of recombinant Pab1p variants, an extract
from YAS1874 (MATa MAK10::URA3 PEP4::HIS3 ade2 his3 leu2 trp1 ura3) was treated with 60 U of micrococcal nuclease per 100 µl of extract for 5 min at 26°C
(the reaction was quenched with 2 mM EGTA) and then with a 1:50
dilution of anti-Pab1p monoclonal antibody 1G1 (80 µg/µl)
(2). Various concentrations of the recombinant proteins were
incubated with 50 ng of polyadenylated luciferase (LUCpA) mRNA in a
7.5-µl mixture containing other translational components prior to the
addition of 7.5 µl of extract. Translation was allowed to proceed for
40 min at 26°C before quick freezing in liquid nitrogen. Translation was quantified by adding 10 µl of the above-described mixture to 50 µl of luciferase assay system mixture (Promega) and measuring activity in a TD-20e Luminometer (Turner).
Extracts were also prepared from YAS2261, YAS2235, YAS2236, YAS2237,
YAS2238, YAS2239, and YAS2025. These extracts were not treated with
nuclease or with the monoclonal antibody but were treated with EGTA to
a final concentration of 2 mM; 50 ng of either LUC (luciferase),
capLUC, LUCpA, or capLUCpA mRNA was added to the extracts. Translation
was measured as described above. All extracts used in this study had
optical densities at 260 nm of between 106 and 140.
Yeast methods.
The TRP1 CEN4 plasmids containing
the PAB1 variants were transformed into YAS2031
(MATa pab1::HIS3 ade2-1 his3-11 leu2-3,112 trp1-1 ura3-1 can1-100) containing plasmid
pPAB1URA3CEN. Trp+ transformants were selected
on solid YMD-Trp medium. These transformants were restruck onto YMD-Trp
medium containing 1 mg of 5-fluoro-orotic acid (8) per ml to
cure cells of pPAB1URA3CEN. Growth rates were determined by
growing these strains in liquid YMD-Trp medium at 30°C.
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RESULTS |
Purification of yeast Pab1p deletion variants.
We have
previously reported the construction of a modified yeast
PAB1 gene which contains convenient restriction enzyme sites between each of the four RRMs and encodes a hexahistidine tag at the
protein's N terminus (5). The presence of the restriction sites allowed for the exact deletions of each RRM, while the N-terminal histidine tag allowed for the rapid purification of the Pab1 protein from bacterial extracts by Ni2+-agarose affinity
chromatography. Figure 1A shows the
pab1 genes that were created for the experiments described
in this report. Both single- and multiple-domain dropouts were made,
and each was transformed into yeast cells and expressed as a
recombinant protein in E. coli. Figure 1B displays a
Coomassie blue-stained gel containing each of the purified recombinant
Pab1p variants isolated from the E. coli extracts. These
proteins were sufficiently pure to allow for further analysis.

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FIG. 1.
Construction and purification of Pab1p variants. (A)
Schematic diagram of the Pab1p deletion constructs used in this study.
The following amino acids were omitted from each of the constructs:
Pab1- RRM1p, 15 to 129; Pab1- RRM2p, 132 to 216; Pab1- RRM3p, 218 to 311; Pab1- RRM4p, 316 to 427; Pab1- Ctermp, 430 to 584; and
Pab1-105p, 218 to 584. WT, wild type. (B) Purified Pab1p variants. An
SDS-10% polyacrylamide gel stained with Coomassie brilliant blue is
shown. Positions of molecular weight standards are indicated to the
right.
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Poly(A)-binding properties of the Pab1p variants.
The
interaction between yeast Pab1p and eIF4G depends on the presence of
poly(A) RNA and on the ability of Pab1p to bind to the RNA
(23). To rule out the possibility that a Pab1p variant would
be unable to bind eIF4G as a result of its inability to associate with
poly(A), we assessed the poly(A)-binding activity of each variant. To
do so, a gel mobility shift assay was used to measure the equilibrium
dissociation constant (Kd) of each Pab1 protein
for oligo(A)20 as previously described (Fig.
2A; Table
2) (5). All of the
single-deletion Pab1p variants were able to bind to the RNA in these
assays with submicromolar Kds. Of these
proteins, the Pab1p missing RRM2 had the lowest affinity for
oligo(A)20 (approximately 10-fold lower than that of
wild-type Pab1p). This finding is consistent with results from previous work that examined the effects of deletions and of point mutations within each of Pab1p's RRMs on oligo(A) binding (3, 5, 12). Each of the other single-RRM deletion proteins exhibited
oligo(A)20 affinities that were intermediate in value to
the full-length Pab1 and the Pab1-
RRM2 proteins (Table 2).

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FIG. 2.
Poly(A) binding by the Pab1p variants. Determination of
equilibrium dissociation constants of Pab1p variants for
oligo(A)20 by gel mobility shift analysis. Shown are
representative autoradiograms for Pab1- Cterm (A), Pab1- RRM2 (B),
and Pab1- RRM4 (C). The analysis was also performed for each of the
Pab1p variants discussed in this study. 32P-labeled
oligo(A)20 was incubated with increasing amounts of the
indicated Pab1p variants. The percentage of radiolabeled RNA being
shifted was used to calculated the Kd values
(see Materials and Methods). These values are reported in Table 2. (D)
Binding of Pab1p variants to poly(A)-Sepharose. Eluates from
poly(A)-Sepharose resin incubated with the indicated Pab1p variants
were resolved by SDS-PAGE and visualized by Coomassie brilliant blue
staining. Initial binding concentrations of the Pab1 proteins were 3 µM for the wild type (WT), RRM2, and RRM4 and 6 µM for
Pab1-105p and Pab1-106p.
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The Pab1 protein truncated immediately C terminal to RRM2 (Pab1-105p)
exhibited a 40-fold decrease in affinity for oligo(A)20 (Table 2). This relatively poor affinity was unexpected since it was
previously shown that RRM2 is responsible for the high affinity of
Pab1p for poly(A) (3, 5, 12). Additionally, experiments
using a similar derivative of Pab1p from Xenopus laevis found it to exhibit near-wild-type affinity for
oligo(A)23 (12). Future work will be needed
to clarify the differences between these studies.
Both the in vitro association assays of Pab1p with eIF4G and the
stimulation of in vitro translation by the poly(A) tail use poly(A)
RNAs greater than 70 residues in length. Therefore, we also tested the
binding of some of the variants to poly(A)-Sepharose resin. This resin
has poly(A) RNAs of approximately 100 residues, and as a result assays
using it should more clearly reflect the ability of Pab1p to bind
poly(A) in the experiments described below. The Pab1p concentrations
used in this binding assay are also similar to those used in the eIF4G
binding assay and to the Pab1p concentrations in crude yeast extracts
(22). The Pab1p that was retained on the poly(A)-Sepharose
resin was eluted, resolved by SDS-PAGE, and then visualized by
Coomassie brilliant blue staining. As shown in Fig. 2D, all of the
Pab1p variants that were tested under these conditions bound to the
poly(A)-Sepharose resin with similar efficiencies. Specificity of
binding was shown by the inability of the Pab1-105 variant containing
RNA-binding inactivating mutations in each of its RRMs (Pab1-106p) to
bind to the resin (Fig. 2D). These experiments demonstrate that the
Pab1p variants are indeed able to bind to poly(A) RNA, and they
therefore eliminate the possibility that any failure to bind to eIF4G
would be due to a failure to bind poly(A).
RRM2 of Pab1p is required for association with yeast eIF4G.
Having established that all of the Pab1p variants bound to poly(A) with
reasonable affinity, we next investigated their ability to associate
with the Pab1p-binding regions of yeast eIF4G1 and eIF4G2. Each of the
two yeast homologs of eIF4G contains a 115-amino-acid region that binds
to Pab1p (23, 24). These 115-amino-acid fragments were
individually fused to GST, expressed in E. coli, and
immobilized on a glutathione-Sepharose resin. To define the region of
Pab1p that is responsible for the interaction, each Pab1p variant, at a
concentration of between 1.5 and 6 µM, was tested for its association
with the immobilized eIF4G. As shown in Fig.
3 and Table 2, all Pab1p variants
containing RRM2 were capable of associating with both eIF4G fragments,
while the Pab1p variant lacking RRM2 failed to bind at all
concentrations tested. None of the Pab1p variants bound to GST (data
not shown). Another aspect of the interaction between Pab1p and eIF4G
is the requirement for poly(A) binding by Pab1p. While the data shown
in Fig. 3 and elsewhere (23, 24) are consistent with this
requirement, a recent study (13) has reported that wheat
Pab1p does not require poly(A) binding in order to interact with wheat
eIF4F (the complex which contains eIF4G). Whether this discrepancy is
due to actual differences between Pab1p and eIF4G from yeast and wheat
has not yet been determined.

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FIG. 3.
RRM2 is required for Pab1p binding to eIF4G. Glutathione
resins containing the Pab1p-binding region of eIF4G1
(GST-eIF4G1/187-300p) (A) or eIF4G2 (GST-eIF4G2/200-315p) (B) were
incubated with poly(A) and the indicated Pab1p variant. Eluates from
these resins were then resolved by SDS-PAGE (12% gel) and visualized
by Coomassie brilliant blue staining. Initial concentrations for the
Pab1p variants in the binding reaction were 1.5 µM except for
Pab1- RRM1p and Pab1-105p, which were at 3 µM. Poly(A) was used at
a concentration of 58 µM AMP. WT, wild type.
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Of particular note, Pab1-105p, which contains only the two N-terminal
RRMs, also interacts with eIF4G (Fig. 3). This observation partially confirms the assignment of RRM2 of Pab1p as directly interacting with eIF4G. However, a recombinant fragment of Pab1p containing only RRM2 was unable to bind to the eIF4G fragments (data not shown). This inability may be due to a very weak
poly(A)-binding activity of the RRM2 protein
[Kd for oligo(A)20 of >10 µM
(data not shown)]. In summary, these eIF4G binding data indicate
that the eIF4G-binding site of Pab1p includes RRM2. They also indicate that this region of Pab1p interacts with both eIF4G1 and eIF4G2. Finally, the inefficient binding of Pab1p lacking RRM1 to eIF4G suggests that this region may also contribute to eIF4G binding.
RRM2 of Pab1p is also required for the high-affinity, specific binding
of Pab1p to poly(A) (3, 5, 12, 17). This could suggest that
the RRM2 requirement for Pab1p binding to eIF4G stems solely from the
poly(A) recognition activity of this domain and that this binding
enables another domain of Pab1p to bind to eIF4G. However, no other
domain of Pab1p is indispensable for eIF4G binding in our assays,
indicating that some feature of RRM2 of Pab1p is required for
contacting eIF4G. Another argument holds that binding to eIF4G merely
requires high affinity (i.e., Kd of <150 nM)
for oligo(A)20. Thus, all single-domain deletions other than Pab1-
RRM2p can bind to eIF4G. However, this seems unlikely because the Pab1-105p variant, which displays even lower affinity for oligo(A)20 than Pab1-
RRM2p (Table 2), still
efficiently associates with eIF4G.
Pab1p domain requirements for poly(A) tail-dependent
translation in vitro.
With the identification of RRM2 of Pab1p
as being required for binding to eIF4G, it was important to determine
whether this domain, and perhaps others, was necessary for the
stimulation of translation in vitro. To test the Pab1p deletion
variants for their ability to mediate poly(A) tail-dependent
translation, a varied approach was taken. The three assays reported
here are all based on a method that uses yeast extracts and a
luciferase reporter system (10). In these extracts, it was
shown that the poly(A) tail has a stimulatory activity independent of
the 5' cap structure and that these two structures can give rise to
synergistic effects (10, 22). Moreover, these two effects
are dependent on Pab1p (22, 24) and the Pab1p-binding site
on eIF4G (24). Initially, we tested for the ability of the
Pab1p deletion variants to rescue translation of uncapped,
polyadenylated (LUCpA) mRNA in an immunoneutralized wild-type extract.
Then, both poly(A) tail-dependent translation and the cap-poly(A) tail
synergism were analyzed in extracts prepared from strains harboring
each of the Pab1p variants. While these three tests are all based on published procedures, slight variations were used and will be discussed
when relevant.
The initial experiments with immunoneutralized extracts proved to be a
useful screening procedure for the activity of each of the Pab1p
variants. These tests enabled the use of a single wild-type extract
that was treated identically for all trials. Following a brief nuclease
treatment to rid the extract of endogenous mRNA (see Materials and
Methods), the endogenous Pab1p was neutralized with a monoclonal
antibody (2, 22) whose epitope is within RRM2 (data not
shown). Upon addition of recombinant full-length Pab1p, translation of
LUCpA mRNA was stimulated to levels approximately 40% of the level in
a nonneutralized extract (reference 22 and data not
shown). The Pab1p deletion variants that bound to eIF4G all displayed
activation to levels within 30 to 70% of that for the full-length
recombinant version (Fig. 4A; Table 2).
In contrast, Pab1-
RRM2p, which does not bind to eIF4G, was inactive
in this assay. This result is consistent with the requirement for the interaction of Pab1p with eIF4G for poly(A) tail-dependent translation. The observed activities in these tests were due to the recombinant proteins (and not titration of the antibody off of the endogenous Pab1p), as one Pab1p variant, Pab1-16p, was recognized by the antibody
(data not shown) but exhibited no activity in this assay (see below).
In addition, it has been previously shown that immunodepleted extracts
are also rescued by recombinant Pab1p (22).

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FIG. 4.
RRM2 is required for poly(A) tail-dependent translation
in vitro. (A) Reconstitution of translation in Pab1p immunoneutralized
extracts with the recombinant Pab1p variants and LUCpA mRNA. The
percentage of reconstitution, relative to the wild type (WT), achieved
by the addition of the indicated Pab1p variants to the
immunoneutralized extract is plotted on the y axis. Values
given are the averages of multiple experiments with three different
extracts. Each protein was tested over a range of concentrations, and
the maximal activation value was used to represent the percent
reconstitution. On average, a nonneutralized extract gave 150 U of
luminescence in the absence of added protein, and a neutralized extract
gave 2.2 U of luminescence. (B) Poly(A) tail-dependent translation in
extracts containing different Pab1p variants. Extracts from yeast
strains harboring the indicated Pab1p were prepared and assayed for the
indicated LUC mRNA translation. Values on the y axis
represent the ratio of LUCpA translation to capLUC translation. The
translation of capLUC mRNA serves as an internal standard to control
for variation in the overall translational activity of each extract.
(C) Synergistic activation of translation in extracts containing
different Pab1p variants. The ratio of the amount of translation of
capLUCpA mRNA to the sum of capLUC and LUCpA mRNA translation
[capLUCpA/(capLUC + LUCpA)] within the indicated extract is
plotted on the y axis. For panels B and C, the plotted
ratios represent the average of at least two experiments with each of
two independently prepared extracts. Representative luminescence values
for capLUC mRNA translation in each extract were as follows: WT, 39.8;
RRM1, 20.3; RRM2, 23.4; RRM3, 79.8; RRM4, 29.4; and
Cterm, 5.8.
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While the results presented above are consistent with our hypothesis
that binding to eIF4G by Pab1p is a prerequisite for poly(A)
tail-dependent translation, we wanted to be sure that no artifacts
resulted from the use of the anti-Pab1p antibody and recombinant Pab1
protein. Therefore, we prepared extracts from cells containing each of
the Pab1p deletion variants in place of the wild-type Pab1p. These
extracts allowed for the analysis of the translational activity of
these proteins in their own native-like environments. Furthermore,
since strains harboring Pab1p deleted for RRM2 are viable (see Table 2
for growth rates), it was important to determine whether extracts from
such strains were capable of mediating poly(A) tail-dependent
translation in vitro.
These new extracts afforded us the ability to test for both
stimulation of translation of LUCpA mRNA as well as capLUCpA
(capped and polyadenylated) mRNA. These two tests required neither the antibody nor recombinant protein. Furthermore, we found that nuclease treatment was not beneficial. In fact, while qualitatively similar results were achieved with nuclease treatment (data not shown), enhanced synergistic effects were observed without such treatment. The
nuclease treatment, however, has proved to be required for the
efficient reconstitution by Pab1p of Pab1p-immunoneutralized extracts.
As shown in Fig. 4B and summarized in Table 2, translation was
stimulated by the poly(A) tail only in extracts prepared from strains
producing Pab1p containing RRM2. This effect is most clearly exemplified by comparing the ratios of translational activity of
capped, unadenylated (capLUC) mRNA to that of LUCpA mRNA. The use of
capped transcripts provided an internal standard for each extract by
which to judge the tail-dependent effects. To address the possibility
that the extract harboring Pab1-
RRM2 is lacking some factor that
responds to the Pab1p-poly(A) signal, recombinant Pab1p was added to
these extracts. This addition was found to specifically rescue
translation of LUCpA and not unadenylated mRNA (data not shown),
suggesting that this extract is not deficient in something other than
the Pab1p activity. We did observe differences in the ability of
individual extracts to translate LUCpA versus capLUC mRNA. In
particular, extracts containing the Pab1-
RRM1 and Pab1-
Cterm
proteins had 7- and 10-fold reductions in their ability to translate
LUCpA relative to wild-type extracts (Fig. 4B; Table 2). The basis for
these differences in the translational activities among the extracts
awaits further investigation. Nonetheless, the present data strongly
support the notion that RRM2 of Pab1p is required for its translational
activity.
Another measure of Pab1p-dependent translation is the measure of
synergy between the 5' cap and poly(A) tail. Previously, it has been
shown that the presence of both a cap and a tail leads to synergistic
effects on translation in vitro (10, 22). Furthermore, this
synergy is dependent on Pab1p (22) and on its ability to interact with eIF4G (24). Synergy is measured as the ratio
of translation of capLUCpA mRNA to the sum of the translations of capLUC and LUCpA mRNAs. A ratio of 1.0 indicates that there is no
synergy between these two terminal mRNA structures. Again, we observed
a role for RRM2 of Pab1p in translational synergy since only the
extract containing Pab1-
RRM2p failed to exhibit significant synergy
(Fig. 4C; Table 2). The value for synergy in the Pab1-
RRM2p extract
slightly exceeds 1.0, perhaps due to a slight increase in the
functional half-life of capLUCpA over LUCpA and capLUC mRNAs
(21a). As with the poly(A) tail-dependent effects, it
is likely that the ability of Pab1p to interact with eIF4G via
RRM2 is a prerequisite for the cooperative effects of the cap and tail.
Binding to eIF4G is not sufficient for Pab1p-dependent
translation.
Having established that both the binding of Pab1p
to eIF4G and the activation of poly(A) tail-dependent translation by
Pab1p required RRM2, we evaluated the Pab1-16 protein. This protein contains the following substitutions within the highly conserved RNP1
motif of RRM1 and RRM2: Y83V and F170V, respectively (5). These substitutions result in an approximately 100-fold decrease in the
affinity of the recombinant Pab1-16 protein for oligo(A)20 (5). Cells harboring Pab1-16p grow more slowly than a
wild-type strain and become inviable when the eIF4E gene
CDC33 is also mutated (24).
Recombinant Pab1-16p did associate with the Pab1p-binding site of
eIF4G2 (Fig. 5A) and eIF4G1 in an
RNA-dependent manner (data not shown). However, this protein was unable
to restore poly(A) tail-dependent translation in immunoneutralized
extracts (Fig. 5B). Furthermore, extracts from cells containing
Pab1-16p exhibited nearly undetectable levels of LUCpA mRNA translation
(Fig. 5C) and only intermediate levels of synergy with the cap
structure (Fig. 5D). This intermediate value for synergy probably
indicates that these point mutations did not completely inactivate the
translational activity of the protein, as Pab1-16p still associated
with eIF4G. Similarly, partial loss-of-function mutations in the
Pab1p-binding site on eIF4G result in the loss of translation of LUCpA
mRNA without destroying the synergism between the cap and the poly(A) tail (24). Each of these observations on the properties of
Pab1-16p suggests that while the ability of Pab1p to associate with
eIF4G is a prerequisite for translational stimulation, there are
probably other regions of Pab1p and/or eIF4G that respond to this
binding event and then stimulate translation. We cannot, however, rule out at this time that Pab1-16p has a decreased affinity for eIF4G in
the extracts. Therefore, its deficiencies could result from inefficient
eIF4G binding.

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|
FIG. 5.
The Pab1-16 protein associates with eIF4G but does not
activate poly(A) tail-dependent translation. (A) Pab1-16p associates
with eIF4G. Glutathione resin containing the GST-eIF4G2/200-315p fusion
protein was incubated with poly(A) and the indicated Pab1 protein.
Eluates from these resins were then resolved by SDS-PAGE (10% gel).
The Pab1 proteins were visualized by Western analysis with a Pab1p
polyclonal antibody. The initial concentration for Pab1-16p in the
binding reaction was 3 µM; Pab1-1p and Pab1- RRM2p were at 1.5 µM. Poly(A) was used at a concentration of 58 µM AMP. WT, wild
type. (B) Pab1-16p fails to reconstitute Pab1p-dependent activation of
LUCpA translation. Immunoneutralized extracts were supplemented with
the indicated Pab1p and then assayed for their translation of LUCpA
mRNA. (C) Extracts containing Pab1-16p do not support LUCpA mRNA
translation. Translation extracts from strains harboring the
indicated Pab1 protein were programmed with either LUCpA or
capLUC mRNA. The ratio of the translation of these two mRNAs is
plotted. (D) Extracts containing Pab1-16p exhibit decreased levels of
translational synergy. The ratio of the amount of translation of
capLUCpA to the sum of capLUC and LUCpA mRNA translation within the
indicated extract is plotted on the y axis. A representative
of the values of capLUC mRNA translation in the Pab1-16p extracts used
for panels C and D was 15.6. (See the legend to Fig. 4 for details of
panels B to D.)
|
|
 |
DISCUSSION |
It has previously been shown that Pab1p from yeast can interact
with the 5' cap-binding complex eIF4F, which contains eIF4G (23,
24). Here, we extend this finding by showing that this function
requires RRM2 of Pab1p. The functional consequences of the interaction
between RRM2 and eIF4G are demonstrated by the need for RRM2 in poly(A)
tail-dependent translation in yeast extracts. Our analysis of the
Pab1-16p mutation also reveals that while association of Pab1p with
eIF4G is a prerequisite for translational stimulation, other features
of this interaction may also be required.
The most obvious finding of this study is the requirement for RRM2 of
Pab1p in mediating binding to eIF4G and in stimulating poly(A)
tail-dependent translation in vitro. What is less clear is the role of
the other domains of Pab1p, which include three RRMs and a 17-kDa
C-terminal region. Our in vitro translation data could suggest that
RRM1 and RRM4 and the C-terminal region of Pab1p are also involved in
mediating the Pab1p-poly(A) tail translation function. Specifically, we
found that deletion of RRM4 had an effect in the reconstitution assay,
while deletion of RRM1 had a significant effect in extracts prepared
from strains containing this Pab1p mutant (compare Fig. 4A and B).
Yeast RRM4 has been previously shown to have significant RNA-binding
activity (5), and this activity may contribute to the
translation function of the protein. As a result of its proximity to
RRM2, RRM1 may provide structural support to RRM2 and thereby enhance
the function of this latter domain. The C-terminal region of
Xenopus Pab1p has been suggested to mediate Pab1p
dimerization (12), and this could also serve to heighten the
translation function of Pab1p. Further experiments will be needed in
order to understand how other regions of Pab1p serve to enhance the
translational function of RRM2.
We are unable to conclude from our data that RRM2 directly contacts
eIF4G because of our inability to demonstrate an interaction between
the isolated RRM2 and eIF4G. One possible explanation for this
observation is that an isolated RRM2 lacks structural integrity.
Consistent with this proposal, we have been unable to observe
significant poly(A) binding by this domain in isolation (data not
shown), which presumably prevents its RNA-dependent interaction with
eIF4G. The minimal Pab1p which we could show has both eIF4G-binding
activity and translational activity (Pab1-105p) contains both RRM1 and
RRM2. Thus, it is possible that additional essential stabilizing
contacts with RRM2 are made through RRM1. Because RRM1 can be singly
deleted from Pab1p without destroying the interaction with eIF4G and
Pab1p-dependent translation, we assume that these proposed stabilizing
contacts can also be supplied by the other Pab1p RRMs.
Why does Pab1p require poly(A) in order for it to interact with eIF4G?
RNA binding may place Pab1p in an appropriate conformation to
bind to eIF4G. Alternatively, Pab1p may place the poly(A) into a
conformation suitable for contacting a latent eIF4G RNA-binding site.
The eIF4G protein may also contact both Pab1p and poly(A). The
requirement for a Pab1p-poly(A) complex for the interaction with eIF4G
may exist so as to prevent association of either non-mRNA-associated Pab1p or naked poly(A) with eIF4G. This would create a more stringent and specific requirement for Pab1p-dependent activation of translation.
An exciting yet unexpected result was provided by the analysis of
Pab1-16p. This protein was originally constructed with the goal of
disrupting its RNA-binding activity (5), but our
investigation has now suggested an additional role for its altered
residues in Pab1p-dependent translation. This protein exhibits a
reduction in the affinity for poly(A) RNA (5) yet still
interacts with eIF4G (Fig. 5A). However, this protein is incapable of
stimulating the translation of uncapped, polyadenylated (LUCpA) mRNA in
vitro (Fig. 5B and C). This result indicates that a simple binding
event is insufficient for mediating poly(A) tail-dependent translation. The nature of the defect of Pab1-16p will require further
investigation. As mentioned above, the possibility that Pab1-16p has a
decreased affinity for eIF4G will be pursued. The deficiency is
unlikely to be due to the reduction in affinity for poly(A), as
Pab1-105p has a similar affinity yet still activates translation in
vitro. This finding is also interesting in light of genetic analysis of
pab1-16. This allele exhibits synthetic lethality with
cdc33-1 (24), which is a mutant allele of the
gene encoding eIF4E. In the latter mutant, cap-dependent translation is
compromised. Thus, a possible reason for the observed synthetic
lethality is the deleterious effects of losing or reducing both
cap-dependent and poly(A) tail-dependent translation in vivo.
Future analysis of the interaction between Pab1p and eIF4G will involve
site-directed mutagenesis of Pab1p. This approach will allow for the
identification of the amino acid side chains that contact eIF4G, thus
more precisely defining the interaction surface. It should also
identify other residues within Pab1p that are dispensable for
association with eIF4G but are required for translational stimulation.
Site-directed mutagenesis, which has been used to examine the RNA
binding of Pab1p (5), should alleviate any potential
structural perturbations caused by the deletion of the ~90-amino-acid
RRMs and thus create fewer ambiguities in the data interpretation.
Nevertheless, the deletion analysis of Pab1p presented here has given
us the ability to define a region of the protein that is involved in
translation initiation in vitro and has therefore provided us with the
region of the protein which will be subject to more intensive
investigation.
 |
ACKNOWLEDGMENTS |
We thank members of the Sachs laboratory for thoughtful comments
on the manuscript.
This work was supported by grants to A.B.S. from the American Cancer
Society (82666) and the Hellman Family Fund.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Molecular and Cell Biology, University of California at Berkeley, 401 Barker Hall, Berkeley, CA 94720. Phone: (510) 643-7698. Fax: (510) 643-5035. E-mail: asachs{at}uclink4.berkeley.edu.
 |
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0270-7306/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
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