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Originally published In Press as doi:10.1074/jbc.M201033200 on March 19, 2002
J. Biol. Chem., Vol. 277, Issue 21, 18665-18669, May 24, 2002
The 3'-Untranslated Region of Chloroplast psbA
mRNA Stabilizes Binding of Regulatory Proteins to the Leader of the
Message*
Yael S.
Katz and
Avihai
Danon§
From the Department of Plant Sciences, Weizmann Institute of
Science, Rehovot 76100, Israel
Received for publication, January 31, 2002
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ABSTRACT |
The 5'-leader and 3'-tail of chloroplast
mRNAs have been suggested to play a role in posttranscriptional
regulation of expression of the message. The regulation is thought to
be mediated, at least in part, by regulatory proteins that are encoded
by the nuclear genome and targeted to the chloroplast where they
interact with chloroplast mRNAs. Previous studies identified high
affinity binding of the 5'-untranslated region (UTR) of the chloroplast
psbA mRNA by Chlamydomonas reinhardtii
proteins. Here we tested whether the 3'-UTR of psbA
mRNA alone or linked in cis with the 5'-UTR of the
mRNA affects the high affinity binding of the message in vitro. We did not detect high affinity binding that is unique to
the 3'-UTR. However, we show that the cis-linked 3'-UTR
increases the stability of the 5'-UTR binding complex. This effect
could provide a means for translational discrimination against
mRNAs that are incorrectly processed.
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INTRODUCTION |
In initiation of translation, ribosomes bind to the
5'-untranslated region (UTR)1
of the mRNA and are consequently directed to the initiator codon of
the open reading frame. The 5'-UTR of several chloroplast mRNAs in
higher plants and in the unicellular green alga Chlamydomonas reinhardtii contain regions of inverted repeats and binding sites for nuclear encoded proteins. These interactions have been shown to be
involved not only in regulation of translation but also in processing
and stability of the message (1-10). It has been suggested that
ribosome association at the 5'-UTR may couple translation with mRNA
stability (11, 12). Most chloroplast mRNAs have an AU-rich 3'-UTR
with a terminal inverted repeat. This 3'-UTR inverted repeat has been
shown to play a role in the processing and stabilization of the
mRNA (13-17). Identification of interactions between the two
termini of cytoplasmic transcripts (18, 19) and examples of 3'-UTR
modulation of translation initiation in both eukaryotes (18, 20) and
prokaryotes (21-23) raise the possibility that interactions of the 5'-
and 3'-UTR of chloroplast mRNAs may influence their expression. In
support of this notion, recent results have shown that correct
processing of the 3'-UTR can promote translation initiation and
polysomal association (24).
Expression of the D1 protein, encoded by the chloroplast
psbA mRNA, is a prime example of the regulation of
translation involving the interaction of nuclear encoded factors and
regions of inverted repeats in the 5'-UTR of the transcript (3, 6,
25-27). In C. reinhardtii, the 5'-UTR of psbA
mRNA is the target for the light-regulated binding of a complex of
proteins of 38, 47, 55, and 60 kDa (3). These proteins interact with an
inverted repeat that is located upstream from a potential
Shine-Dalgarno-like site in the 5'-UTR (3, 7) and possibly with a
second site after psbA mRNA undergoes 5'-processing
(28). Assays of D1 synthesis in C. reinhardtii mutants, in
which the inverted repeat has been partially deleted or mutated,
indicate the importance of the stem-loop fold for the light-responsive
increase of D1 synthesis (7).
The central RNA-binding protein in the psbA 5'-binding
complex is the 47-kDa protein (RB47). RB47 is a nuclear encoded protein that shows high homology to poly(A)-binding proteins (29). Mutants in
which RB47 expression is low or lacking are defective in D1 translation, implicating RB47 as a message-specific translational factor (29-31). The 60-kDa protein (RB60) is a protein-disulfide isomerase-like protein also encoded by the nuclear genome (32). RB60
has been identified as the regulatory redox-active protein of the
psbA 5'-binding complex and is the likely candidate for perceiving the light-signal and modulating the binding of the complex
(33).
In addressing the potential modes of regulation of psbA
expression, we examined whether the 3'-UTR affects protein binding to
psbA mRNA. We report here a comparison of binding of
C. reinhardtii proteins to RNA probes of 5'-UTR, 3'-UTR, and
cis-linked 5'-UTR-3'-UTR. Our analysis indicated that the
high affinity binding to psbA mRNA is primarily via its
5'-UTR, whereas the presence of 3'-UTR in cis increases the
affinity of binding of the 5'-UTR-binding protein complex.
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EXPERIMENTAL PROCEDURES |
psbA RNA Constructs--
To assess the influence of
psbA 3'-UTR on binding of the psbA 5'-binding
complex, five types of RNA probes containing the psbA UTRs
were constructed as shown in Fig. 1. The 5' transcript (5'-T) included
the 5'-UTR and 36 bp downstream of the initiator codon, and the 3'
transcript (3'-T) contained 30 bp preceding the stop codon and the
3'-UTR. The fused 5'-UTR and 3'-UTR transcript (5'3'-T) was composed of
the combined 5'-T and 3'-T, in "sense" orientation. The 5'3'-NC-T
transcript lacked the 30-bp coding region proximal to the 3'-UTR and
the 5'3'-LC-T transcript included a longer segment of the 3'-coding
region (Fig. 1). The psbA UTR constructs were verified by sequence analysis.

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Fig. 1.
Schematic representation of the three
expression constructs used for in vitro
transcription. The 92 bp of the psbA 5'-UTR
(light gray box) and 36 bp from the coding region
(white box) were subcloned under the T7 promoter to form the
5' transcript (5'-T). The 52 bp of 3'-UTR (dark gray
box) and 30 bp of upstream coding region (hatch box)
were subcloned to form the 3' transcript (3'-T). Fusion in
sense orientation of the 5'-T and 3'-T created the 5'3'-T transcript
(5'3'-T). The 5'3'-NC-T transcript (5'3' NC-T)
lacked the 30-bp coding region proximal to the 3'-UTR, and the
5'3'-LC-T transcript (5'3' LC-T) included a longer segment
of the 3'-coding region. SacI, XbaI,
AccI, and BamHI denote restriction sites used for
building the constructs.
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Algae Growth Conditions and Purification of RNA-binding
Proteins--
C. reinhardtii 2137a cells were grown in TAP
medium (34), under continuous light at 25 °C, to a density of
~1 × 107 cells/ml. The C. reinhardtii
proteins were enriched for RNA-binding proteins by liquid
chromatography using a heparin-agarose column (3). Bound proteins were
eluted from the column with a potassium acetate gradient of 0.1-1.6
M (3). The recombinant RB47 protein (rRB47) containing a
His6 tag at its amino terminus was produced in
Escherichia coli and purified on a Ni-His trap column.
In Vitro Transcription, Gel Mobility Shift, and UV-cross-linking
Assays--
Each of the plasmids containing the psbA UTRs
was digested with either XbaI or BamHI
restriction enzyme and used as a template in run-off transcription
reactions containing [32P]UTP (3). Purified radiolabeled
RNA probes were used in gel mobility shift (GMS) assays to compare the
binding of the psbA 5', 3'- or 5'-3'-UTR RNA to proteins
extracted from C. reinhardtii.
In GMS experiments, the proteins were first incubated, at room
temperature, with 15 units of Prime-RNase inhibitor in 10 µl of
buffer containing 20 mM Tris (pH 7.5), 100 mM
potassium acetate, 0.2 mM EDTA, 5 mM
-mercaptoethanol, 4.5 mM MgCl2, 1.5 mM dithiothreitol, and 20% glycerol. Next, the proteins
were incubated with the 32P-labeled RNA transcripts and,
where specified, with nonlabeled RNA competitors. Nonspecific RNA
competitors that included 20 µg of tRNA (Sigma) and 2 µg of total
RNA isolated from a mutant cell line of C. reinhardtii that
lacks the psbA gene (FuD7) were included in both GMS and
UV-cross-linking assays. The products of GMS assays were separated on
5% native polyacrylamide gels (3), and formation of RNA-protein
complexes was visualized by autoradiography or by phosphorimaging.
In the UV-cross-linking assays, 32P-labeled RNA-protein
complexes were placed, on ice, 5 cm from the lamps of a Stratalinker device and irradiated for 30 min. The RNA transcripts were digested with 50 µg of RNase A (Sigma) for 30 min in the presence of 3 M urea, 3 mM EDTA at 55 °C. After adding SDS
and -mercaptoethanol to 2.5% final concentrations, proteins were
fractionated by 12% SDS-PAGE (35), and radiolabeled proteins were
detected by autoradiography.
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RESULTS |
C. reinhardtii Proteins Exhibit High Affinity Binding to cis-linked
UTRs--
C. reinhardtiiproteins partially purified by heparin
affinity chromatography were incubated with 32P-labeled
5'-T transcript and subjected to GMS assay. Total RNA, extracted from
the C. reinhardtii mutant cell line (FuD7) lacking the
psbA gene, was included in the binding reactions to compete out binding that was not psbA mRNA-specific. Protein
fractions, previously shown to contain the 47- and 60-kDa proteins (3), demonstrated prominent binding activity to the 5'-UTR of
psbA mRNA as expected (Fig.
2A). When the same protein
fractions were incubated with an equimolar concentration of
32P-labeled 3'-T transcript, only faint binding was
observed (Fig. 2B). This suggests that the protein(s)
binding to the 3'-UTR are either much less abundant or have
significantly lower affinity than those that bind the 5'-UTR.

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Fig. 2.
Gel mobility assays showing binding of
C. reinhardtii proteins to the three
psbA transcripts. Protein fractions from heparin
affinity chromatography were incubated with radiolabeled 5'-T
(A), 3'-T (B), 5'3'-T (C), 5'3'-NC-T
(D), or 5'3'-LC-T (E) RNAs, in the presence of
non-labeled tRNA and FuD7 RNA, and subjected to GMS assay. Fractions 14 and 15 contain high affinity binding activity to 5'-T and 5'3'-T.
Fractions 10-12 have RNase activity that causes degradation of the
free RNA probe. Longer incubation periods of radiolabeled RNA and
Fractions 14 and 15 prior to GMS assays verified lack of RNase activity
in these fractions (data not shown). RNA denotes sample
containing the labeled RNA transcript without protein. Column fractions
represent samples containing C. reinhardtii proteins of the
indicated fractions of heparin column chromatography.
Complex and Free mark the mobility of the
RNA-protein complex and the free RNA, respectively.
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Interestingly, a notably high binding signal was detected when
concentration of an equimolar 32P-labeled 5'3'-T transcript
was included in the GMS assay (Fig. 2C). This result implies
that the presence in cis of the 3' terminus of the message
resulted in formation of a higher affinity protein-RNA complex. To
establish whether this phenomenon is caused by the 3'-UTR or is unique
to the 5'3'-T, two additional 5'3' transcripts, 5'3'-NC-T (with no
3'-proximal coding region) and 5'3'-LC-T (with long 3'-proximal coding
region), were tested (Fig. 2, D and E). These two
5'3' transcripts also caused stabilization of the complex in comparison
with the 5'-T, assigning a primary role to the 3'-UTR in this
phenomenon. These results suggested three main alternatives: 1) the
presence in cis of 3'-UTR in the 5'3'-T transcript increases the affinity of the 5'-UTR binding activity; 2) the presence in cis of 5'-UTR increases the affinity of a novel binding to
the 3'-UTR; 3) a novel binding activity with high specificity to the 5'3'-T was detected in the GMS assay. To differentiate between these
alternatives the following experiments were performed.
Binding of cis-linked UTRs Is via RB47--
In a UV-cross-linking
(UVCL) assay, a radioactive label is transferred from the RNA to the
protein(s) that comes into close contact with the RNA molecule. The
labeled protein is then identified by autoradiography of
SDS-PAGE-fractionated proteins. We reasoned that if the high binding
activity observed with the 5'3'-T transcript is due to a novel binding
protein, specific either to the 3'-UTR or to the cis-linked
5'3'-T transcript, then the UVCL assay might detect it. UVCL assay with
32P-labeled 5'-T transcript, in the presence of tRNA and
FuD7 total RNA as competitors, typically labeled the RB47 protein (Fig.
3A).

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Fig. 3.
UVCL assay showing binding of C. reinhardtii proteins to the three transcripts.
Protein fractions from heparin affinity chromatography (column
fractions) were incubated with radiolabeled 5'-T (A), 3'-T
(B), or 5'3'-T (C), in the presence of
non-labeled tRNA and FuD7 RNA and subjected to UVCL assay. The pattern
of radiolabeled proteins is similar for the 5'-T and 5'3'-T, with a
primary label transfer to a 47-kDa protein (RB47) from fractions 14 and
15.
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In agreement with the results of the GMS analysis, only a faint signal
corresponding to the 47-kDa protein was detected with 32P-labeled 3'-T transcript in the UVCL assay (Fig.
3B). The pattern of proteins labeled by cross-linking to the
5'- or 5'-3'-RNA was similar (Fig. 3, A and C).
There was no notable difference of protein bands to account for the
influence of the 3'-UTR on the 5'3'-T binding in GMS assays. However,
this does not exclude binding that may occur in an RNA region that does
not have enough uridine bases to cause strong labeling of the
protein(s) or protein-protein interactions that may affect the RNA
binding. These results suggest that the binding to the 5'3'-T is also
by RB47 and its associated proteins and mainly via the 5'-UTR. To
confirm this, the specificity of the binding to the transcripts was
addressed further using affinity and competition assays.
Specificity and Affinity of cis-linked UTR Binding
Activity--
In competition assays, the specificity of RNA binding is
evaluated by including increasing amounts of non-labeled competitor RNAs in the binding reactions. A higher capacity of a non-labeled RNA
to compete with the radioactive RNA for the binding activity ranks it
higher in specificity. If the binding to the transcript containing the
cis-linked 5'- and 3'-UTRs is principally via the 5'-UTR,
then this RNA should compete better than the 3'-UTR. To assess the
specificity of binding to the 5'3'-T RNA, GMS assays containing either
the 32P-labeled 5'-T transcript or the 5'3'-T transcript
were performed in the presence of 5-, 25-, 50-, 100-, 200-, and
400-fold excess of non-labeled 5'-T or 3'-T RNAs (Fig.
4A). The non-labeled 5'-UTR transcript competed with the radiolabeled 5'-T or 5'3'-T RNAs. In
contrast, the 3'-UTR did not effectively compete with binding of either
the 5'-UTR or 5'3'-T transcript. Similar results were obtained when
5'-T or 3'-T competitors were included in UVCL assays (Fig.
4B). These results show that specificity of RB47 protein and
its associated proteins is primarily to the 5'-UTR, rather than the
3'-UTR, and strongly argue for its binding the 5'3'-T transcript mainly
via the segment containing the 5'-UTR.

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Fig. 4.
Specificity of binding of 5'-UTR and
5'3'-T. Comparison of the competition by non-labeled 5'- or 3'-RNA
transcripts was analyzed by GMS assay performed with radiolabeled 5'-T
or 5'3'-T (A). Minimal protein concentrations required for
complex formation with each of the 5'-T and 5'3'-T transcripts were
used as determined in Fig. 5 (a 3-fold higher protein concentration in
5'-T assays than in 5'3'-T assays). Non-labeled 5'-T competed
effectively for the binding of C. reinhardtii proteins,
whereas 3'-T did not. Native complex and Free
mark the mobility of the native RNA-protein complex and the free RNA,
respectively. Competition assays performed in a UV-cross-linking assay
(B) also demonstrated that the 5'-T, but not the 3'-T,
effectively competed for RB47 labeling.
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If RB47 and its associated proteins bind the psbA 5'-UTR
segment of 5'-T and 5'3'-T RNAs then what is the mechanism for enhanced binding of 5'3'-T? One possibility is that the cis-linked
3'-UTR increases the affinity of the native protein complex to the RNA. To compare the affinity of 5'-T and 5'3'-T binding, decreasing amounts
of C. reinhardtii proteins were mixed with equimolar
concentrations of each type of RNA and subjected to GMS assay. The
results in Fig. 5 show that an ~3-fold
lower concentration of proteins, containing an estimated concentration
of 0.07 µM RB47, was required for 50% native complex
formation with the radiolabeled 5'3'-T RNA than with the 5'-UTR alone.
This shows that the RB47 and its associated proteins bind the 5'3'-T
with higher affinity than the 5'-T alone. Therefore, although the
3'-UTR itself exhibits only minor protein binding in GMS or UVCL
assays, its fusion to the 5'-UTR seems to stimulate the binding of the
native protein complex.

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Fig. 5.
Affinity of 5'-UTR and
cis-linked UTR binding activities. The protein
concentration that resulted in 50% binding of either the 5'-UTR
(A) or the cis-linked 5'-3'-UTRs (B)
was determined by incubating each radiolabeled RNA with decreasing
amounts of C. reinhardtii proteins and analyzing the
formation of protein-RNA complexes by GMS assay. The combined results
of three independent experiments are presented in a graph
(C). Approximately 3-fold higher concentrations of proteins
were required for 50% binding of the native complex to 5'-T than to
5'3'-T. RNA denotes sample containing the labeled RNA
transcript without protein. µg protein represents samples
containing C. reinhardtii proteins of Fraction 14 of heparin
column chromatography. Native complex and Free
mark the mobility of the native RNA-protein complex and the free RNA,
respectively.
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rRB47 Does Not Bind the cis-linked UTRs with Preferential
Affinity--
RB47 was the primary binding protein identified in
assays containing 5'-T and 5'3'-T RNAs. To determine whether binding of RB47 on its own is sufficient for the preferential affinity to the
cis-linked transcript, we assayed whether purified
recombinant RB47 (rRB47) can mimic the binding of the native complex
containing RB47 in GMS assays. Binding of rRB47 to 5'-T or 5'3'-T
formed complexes that migrated faster than the corresponding native
complex (Fig. 6A), suggesting
that the complex formed by the intrinsic binding contained additional
proteins. Further, in contrast to the preferential affinity of the
native complex to the 5'3'-T, the binding of rRB47 to both 5'- and
5'3'-RNA is of similar affinity (Fig. 6, B and
C). In fact, on its own rRB47 displayed a slight preference
to the 5'-T (Fig. 6C), further supporting the different nature of binding of rRB47 and the native complex. Together, these results suggest that an additional protein(s) associated with RB47 is
necessary for the preferential binding to the cis-linked 5'-3'-UTRs as compared with the 5'-UTR and that the presence in cis of the 3'-UTR promotes the binding of the native complex
comprised of RB47 and its cognate proteins. We tested whether the
inclusion of recombinant RB60 (rRB60) with rRB47 mimics the binding of
the native complex. However, rRB60 and rRB47 together also did not result in preferential binding of the cis-linked 5'3'-T RNA
(data not shown) suggesting that the addition of RB60 was either not required or not sufficient.

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Fig. 6.
rRB47 binding to 5'-T and 5'3'-T
transcripts. Comparison of the binding of recombinant RB47
(rRB47) to the 5'-T and 5'3'-T RNAs with binding of C. reinhardtii heparin column chromatography fraction 14 (Hep) by GMS assay (A). RNA denotes
sample containing the labeled RNA transcript without protein. The
affinity of rRB47 binding to the 5' of 5'-3'-RNA was examined by
determining the concentration of rRB47 that results in 50% binding of
either the 5'-T and 5'3'-T RNAs (B). The combined results of
three independent experiments are presented in a graph (C).
Binding of rRB47 to 5'-T and 5'3'-T transcripts displayed similar
affinities. Native complex, rRB47 complex, and
Free mark the mobility of the native RNA-protein complex,
the RNA-rRB47 complex, and the free RNA, respectively.
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DISCUSSION |
Here we show that the presence in cis of the 3'-UTR of
psbA mRNA is required for high affinity binding of the
native complex, containing the RB47 protein, to the 5'-UTR. Several
modes of action could explain the effect of the 3'-UTR on the binding
of the proteins to the 5'-UTR of psbA mRNA. A change in
the affinity of an RNA-protein complex may result from a conformational
shift in the RNA and/or from an altered binding of the protein. Our
results, so far, do not exclude either possibility. The 3'-UTR of
psbA mRNA may interact directly with the 5'-UTR of the
message, thereby inducing it to form a structural motif with high
affinity to the native complex containing RB47. Such long range RNA-RNA
interactions have been found to affect translational efficiency in
prokaryotes (22). It should be noted that the MFOLD computer program
for RNA structure analysis (36) did not predict any such 5'-UTR-3'-UTR
interactions (data not shown). Alternatively, because low affinity
binding of RB47 to the 3'-UTR was also found (Fig. 3), it is possible that RB47 may bind both UTRs of psbA mRNA when they are
present in cis. This may not be entirely surprising as the
3'-UTR is AU-rich, and RB47 shares high homology with poly(A)-binding
proteins (31). In this scheme, the simultaneous binding of RB47 and its
associated proteins to the 5'- and 3'-UTRs forms a high affinity
complex (Fig. 2).
Previous characterization of the 5'-UTR binding activity by GMS, UVCL,
and psbA RNA-affinity chromatography assays suggested that
it is composed of four proteins (3). The UVCL assay, which labels
proteins that are in direct contact with the RNA, showed that RB47 is
the primary RNA-binding protein of the complex (Fig. 3 and Ref. 3), and
cloning of RB47 showed that it contains RNA-binding domains (31).
Extraction of the proteins that were complexed with the 5'-UTR of
psbA mRNA in the GMS assay revealed that RB60 is also
associated with the RNA, potentially via protein-protein interactions
with RB47 (3). Based on these results, it was suggested that the
complex contains four proteins of which only binding of RB47 and RB60
was resistant to the conditions of the GMS (3).
A comparison of mobility shift of 5'-T and 5'3'-T RNAs by either rRB47
or by the partially purified C. reinhardtii proteins showed
that the native proteins form complexes with slower mobility (Fig. 6),
further indicating that the native complex contains additional
protein(s), such as RB60, RB38, or RB55. The higher affinity of the
binding of the native complex to the cis-linked 5'- and
3'-UTRs than to the 5'-T transcript indicates that the presence in
cis of the 3'-UTR promotes the binding of the native complex
comprised of RB47 and its cognate proteins. Interestingly, the
recombinant RB47 binds the 5'-T and the 5'3'-T at similar high
affinities (compare Figs. 5 and 6), suggesting that the lower affinity
of the native complex in the absence of the 3'-UTR is a result of
action of the proteins associated with RB47.
The activity of the proteins that bind the 5'-UTR psbA
mRNA correlates with the translation rate of the D1 protein in
C. reinhardtii cells (3). Therefore, the increased affinity
of 5'-UTR psbA mRNA-binding proteins conferred by the
3'-UTR may suggest that the 3'-UTR influences D1 synthesis by
stimulating binding of the native complex, comprised of RB47 and its
cognate proteins, to the 5'-UTR. Correct processing of the 3'-UTR was
suggested to be required for high levels of translation initiation and
polysomal association in C. reinhardtii cells (24). Recent
results from tobacco transformants in which the influence of the
psbA UTRs on translation of a reporter gene were studied
indicated that including the psbA 3'-UTR resulted in a
3-4-fold enhancement of translation (25). In another study, deletion
of the inverted repeat of the 3'-UTR of petD mRNA led to
a reduction in petD expression beyond that expected by the
decrease in mRNA accumulation alone, indicating that the 3'-UTR may
also contribute to efficient translation (37). These findings suggest
that the 3'-UTR of chloroplast messages is required for optimal
translation, in addition to its role in determination of mRNA
stability. Collectively, these results suggest that the impaired
binding of the native complex, comprised of RB47 and its associated
proteins, to a psbA mRNA lacking an intact 3'-UTR may
discriminate it from efficient translation.
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FOOTNOTES |
*
This work was supported by Grant 651/00 from the Israel
Science Foundation and a grant from the Minerva Foundation.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.
Recipient of a Feinberg Graduate School Fellowship.
§
Holder of the Judith and Martin Freedman Career Developmental
Chair. To whom correspondence should be addressed. Tel.:
972-8-934-2382; Fax: 972-8-934-4181; E-mail:
avihai.danon@weizmann.ac.il.
Published, JBC Papers in Press, March 19, 2002, DOI 10.1074/jbc.M201033200
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ABBREVIATIONS |
The abbreviations used are:
UTR, untranslated
region;
GMS, gel mobility shift;
UVCL, UV-cross-linking;
r, recombinant.
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