Department of Cell Biology, Cleveland Clinic
Foundation, Lerner Research Institute, Cleveland, Ohio 44195
Received 2 October 2000/Returned for modification 7 November
2000/Accepted 29 November 2000
The cotranslational incorporation of the unusual amino acid
selenocysteine (Sec) into both prokaryotic and eukaryotic proteins requires the recoding of a UGA stop codon as one specific for Sec. The
recognition of UGA as Sec in mammalian selenoproteins requires a Sec
insertion sequence (SECIS) element in the 3' untranslated region as
well as the SECIS binding protein SBP2. Here we report a detailed
analysis of SBP2 structure and function using truncation and
site-directed mutagenesis. We have localized the RNA binding domain to
a conserved region shared with several ribosomal proteins and
eukaryotic translation termination release factor 1. We also identified
a separate and novel functional domain N-terminal to the RNA binding
domain which was required for Sec insertion but not for SECIS binding.
Conversely, we showed that the RNA binding domain was necessary but not
sufficient for Sec insertion and that the conserved glycine residue
within this domain was required for SECIS binding. Using glycerol
gradient sedimentation, we found that SBP2 was stably associated with
the ribosomal fraction of cell lysates and that this interaction was
not dependent on its SECIS binding activity. This interaction also
occurred with purified components in vitro, and we present data which
suggest that the SBP2-ribosome interaction occurs via 28S rRNA. SBP2
may, therefore, have a distinct function in selecting the ribosomes to
be used for Sec insertion.
 |
INTRODUCTION |
There are many examples of
translational regulation that involve RNA binding proteins
interacting with specific sequences in the 3' untranslated
regions (UTRs) of various mRNAs (10, 18). A
specialized case of this is found in the incorporation of
selenocysteine (Sec) into a select group of eukaryotic proteins where a
sequence specific 3' UTR binding protein is required for Sec insertion
at its cognate UGA codon (6). The Sec-containing proteins
that have been characterized perform myriad biological functions
including oxidant defense and hormone maturation (reviewed in
references 9 and 20). While mice deficient in
the selenoprotein glutathione peroxidase are viable (11),
one or more selenoproteins are apparently required for early
development, as elimination of the tRNASec gene in mice
causes early embryo lethality (3).
While the incorporation of Sec into the Escherichia coli
formate dehydrogenase isozymes is fairly well characterized
(2), the system which governs mammalian Sec insertion has
only been partially elucidated. Several essential components of what we here term the Sec insertion complex (SIC) have been identified. These
include the UGA codon that encodes Sec (13), the Sec
insertion sequence (SECIS) element found in all selenoprotein 3' UTRs
(1), and the recently identified SECIS binding protein
(SBP2), which we demonstrated to be required for Sec insertion in vitro
(6). A fourth component of the SIC that is also likely to
be required for Sec incorporation is the Sec-specific elongation factor
(eEFsec) that has been recently shown to be functional in transfected
cells (7, 21). Because Sec is encoded by what is
ordinarily a stop codon, the mechanism of Sec insertion is likely to
involve direct competition with translation termination. The SIC may
therefore interact with or regulate the interactions of the release
factors required for translation termination.
This work focuses on the RNA binding protein SBP2, a novel 94-kDa
protein that shares a 32-amino acid motif with several ribosomal proteins and eukaryotic translation termination release factor 1 (eRF-1). eRF-1 functionally and structurally mimics a tRNA molecule that is specific for stop codons and in this fashion binds the ribosomal A site and terminates chain elongation (19). The
fact that SBP2 and eRF-1 share this sequence suggests that they also share a common class of targets, which may shed light on the molecular basis for the competition between Sec insertion and termination. This
conserved sequence has been proposed to be a novel RNA binding motif
(12) and has recently been demonstrated to be involved in
the binding of ribosomal protein L30 to its own mRNA (15). In this report, we establish that this motif, which we will refer to as
the L30 RNA binding domain, is required for SBP2 RNA binding activity
and function as measured by the ability to incorporate Sec in vitro. In
addition, we have identified a nonoverlapping functional domain that is
required for Sec insertion but not RNA binding. Further analysis
indicates that SBP2 is stably associated with the ribosomal fraction in
transfected cells and in vitro, and that this interaction may be
mediated by 28S rRNA. We hypothesize that SBP2 may be involved in
selecting a subset of ribosomes which are competent for Sec insertion.
 |
MATERIALS AND METHODS |
Mutagenesis.
All truncated SBP2 constructs were derived from
internal PCR primers (Table 1) which
added a methionine to the N terminus. Annealing sites were chosen so
that the optimal initiation sequence ATGG would be present for all
truncation mutants except TM535-846, which used a naturally occurring
ATG. PCR fragments were TA cloned into pCR3.1 (Invitrogen). Point
mutations were made with an Altered Sites II Ex-1 mutagenesis kit
(Promega). Mutant constructs were sequenced in their entirety by
automated DNA sequencing. The human SBP2-like protein (hSLP) was
derived from human hypothetical protein KIAA0256 (GenBank accession no.
6634006) obtained from the Kazusa DNA Research Institute (Kisarazu,
Japan). This study made use of the C-terminal half of hSLP, which is
similar to SBP2. It was obtained by PCR using primers hSLP-5' and
hSLP-3' (Table 1).
RNA probes and binding assays.
32P-labeled
wild-type and mutant phospholipid hydroperoxide glutathione peroxidase
(PHGPx) 3' UTR probes were synthesized exactly as described elsewhere
(5). Electrophoretic mobility shift assays (EMSA) included
4.4 fmol of in vitro-translated SBP2 as indicated for the figures and
20 fmol of wild-type or mutant PHGPx 3' UTR in 1× phosphate-buffered
saline (PBS) supplemented with 250 µg of E. coli tRNA per
ml. 10 mM dithiothreitol (DTT), and 5 µg of soybean trypsin inhibitor
(Sigma) per ml. Complexes were formed at 37°C for 30 min and then
resolved on 4% nondenaturing polyacrylamide gels, which were dried and
exposed to a PhosphorImager cassette (Molecular Dynamics).
In vitro translation.
Plasmid DNAs containing wild-type and
mutant SBP2 constructs were linearized with XbaI and used as templates
for in vitro transcription with T7 RNA polymerase (Ribomax T7; Promega)
in the presence of m7G(5')ppp(5')G (AP Biotech). A 50-ng
aliquot of each SBP2 RNA was used in 12.5 or 25-µl rabbit
reticulocyte lysate in vitro translation reactions in the presence of
[35S]Met as described by the manufacturer (Promega).
Translation products were resolved by sodium dodecyl
sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) on a 12% gel and
quantitated by PhosphorImager analysis. The amount of each protein was
determined by quantitation of known amounts of [35S]Met
spotted on 3-mm filter paper and calculated based on an endogenous
concentration of 5 µM cold Met in the lysate (as specified by the manufacturer).
Expression of recombinant SBP2.
For the construction of
(Strep-tagged C-terminal SBP2, the original ATCC clone
corresponding to expressed sequence tag H31811 was digested with
EcoRI and XhoI and subcloned into the
EcoRI and XhoI sites of pASK-IBA7 (Strep-tag II;
Genosys). This vector added to the N terminus of the SBP2 clone
the amino acid sequence MASWSHPQFEKIEGRRDRGP
(the Strep tag sequence is underlined), which begins with amino
acid 399.
Glycerol gradients.
McArdle 7777 cells, a rat hepatoma cell
line, were transiently transfected with wild-type and mutant SBP2
clones using LipofectAMINE (Life Technologies); 40 h posttransfection,
the cells were washed and then harvested by scraping into PBSD (1×
PBS, 2 mM DTT). The cells were disrupted by 15 strokes with a
high-clearance Dounce homogenizer. The extracts were spun at
14,000 × g for 10 min at 4°C. The supernatants were
diluted to 1 mg/ml, and 500 µl of each was loaded onto 10 to 30%
linear glycerol gradients made in PBSD plus or minus NaCl or EDTA as
indicated. For in vitro complex assembly, 5 µg of purified
Strep-tagged SBP2 was incubated with or without 2.0 A260 units of salt-washed ribosomes purified
from rabbit reticulocyte lysate (generously provided by W. Merrick, Case Western Reserve University) in a total volume of 0.5 ml diluted with PBSD. The mixture was incubated at 37°C for 5 min, placed on ice
for 10 to 15 min, and then loaded onto a 10 to 30% linear glycerol
gradient made in PBSD. All gradients were spun at 210,000 × g in a SW41 rotor for 3.5 h (McArdle cell gradients) or 4.5 h
(in vitro complexes) at 4°C. Fractions (0.6 ml) were pulled from the
top of each gradient, and 200 µl from each fraction was subjected to
trichloroacetic acid (TCA) precipitation (10% TCA, 0.05% Tween 20).
Fractions from gradients that contained Strep-tagged recombinant SBP2
alone were supplemented with 5 µg of pure soybean trypsin inhibitor
(Sigma) as a carrier. Precipitated proteins were resolved by SDS-PAGE
(12% gel), blotted to nitrocellulose, blocked with 3% BSA in PBST
(1× PBS plus 0.2% Tween 20), and, for Strep-tagged proteins, probed
with a 1:4,000 dilution of alkaline phosphatase-conjugated streptavidin
(AP Biotech). For untagged proteins, the blots were probed with a
1:2,000 dilution of anti-SBP2 polyclonal antibody followed by a 1:5,000
dilution of alkaline phosphatase-conjugated anti-rabbit immunoglobulin
G secondary antibody. Blots were developed in nitroblue
tetrazolium-5-bromo-4-chloro-3-indolylphosphate (Promega).
PHGPx translation assay.
PHGPx translation was monitored
essentially as described previously (6), except that the
protein was labeled with [35S]Met instead of
[75Se]Sec. Our previous results showed that the
incorporation of 75Se-labeled Sec was both codon and SECIS
element dependent (6). PHGPx translation can also be
assayed by [35S]Met labeling, which is also codon and
SECIS element dependent and which yields exactly the same results as
75Se labeling. Briefly, 4.4-fmol aliquots of in
vitro-translated SBP2 proteins were added in a total volume of 2 µl
(brought to volume with fresh rabbit reticulocyte lysate) to a standard
12.5-µl assay including 5 µCi of [35S]Met. PHGPx
translation products were purified from the entire reaction using
bromosulfophthalein S-glutathione (BSP)-agarose, and the
bound proteins were resolved by SDS-PAGE (15% gel) followed by
autoradiography or PhosphorImager analysis.
 |
RESULTS |
Analysis of SBP2 truncation mutants.
In earlier work, we
showed that the N-terminal half of SBP2 is dispensable for both SECIS
binding and selenoprotein synthesis (6). To gain more
insight into the mechanism of SBP2 action, we constructed a series of
truncation mutants in the C-terminal half of SBP2 in an effort to
define domains necessary for RNA binding and functional activity. The
truncation mutants (diagrammed in Fig. 2) are termed
TMx-y, where x-y refers to
the positions of the remaining amino acids derived from full-length
SBP2. All constructs were efficiently translated in rabbit reticulocyte lysate (Fig. 1A) except for full-length
SBP2 (lane 10). This is consistent with our difficulty in expressing
full-length SBP2 in bacteria, but the basis for reduced translation is
unknown. Excess SBP2 (4.4 fmol) protein was used in the following
assays; the exception was the full-length protein, of which only 0.9 fmol was used. This amount of full-length SBP2 is still in excess for the functional assay but is within the lower portion of the linear range of the RNA binding assay (data not shown). As we previously reported, the apparent and predicted molecular masses of SBP2 are not
in agreement and differ by approximately 26 kDa. The truncation mutants
described above help to delineate the origin of this anomaly, as the
difference in molecular mass between TM517-846 and TM585-846 is
predicted to be only 7.4 kDa but is observed to be approximately 20 kDa
by SDS-PAGE (Fig. 1). It should be noted that the major contaminating
lower-molecular-mass band at 52 kDa is likely the result of internal
initiation at Met 535. To test the contribution of this contaminant to
SBP2 RNA binding and functional activity, TM535-846 (Fig. 1A, lane 11)
was engineered to begin with Met 535 and runs at exactly the same
molecular weight as the lower-molecular-weight band in lanes 1 to 3.

View larger version (63K):
[in this window]
[in a new window]
|
FIG. 1.
Expression and activity of SBP2 truncation mutants. (A)
[35S]Met-labeled in vitro-translated SBP2 resolved by
SDS-PAGE. Mutants are identified by the amino acid positions indicated.
(B) In vitro PHGPx translation assay in which 4.4 fmol of each SBP2
protein was added in the presence of [35S]Met. PHGPx was
purified from the reaction using BSP-agarose. Lane 12 contains no SBP2.
(C) EMSA for the mutants listed in panel A. 35S-labeled
SBP2 (4.4 fmol) was incubated with 20 fmol of wild-type
32P-labeled PHGPx 3' UTR, and the complexes were resolved
on a 4% nondenaturing gel. The asterisk indicates the position of a
SECIS-specific complex in nonsupplemented reticulocyte lysate. (D) Same
as panel C except that the probe was an AUGA deletion mutant of the
PHGPx 3' UTR (14).
|
|
To assay SBP2 function, equimolar amounts of in vitro-translated SBP2
protein were added to a PHGPx translation assay. The results are shown
in Fig. 1B and summarized in Fig. 2,
where the data are expressed as a percentage of the wild-type activity
derived from the addition of C-terminal SBP2 (TM399-846). As mentioned above, the elimination of amino acids 1 to 398 has no effect on activity. Elimination of amino acids 1 to 458 (mutant TM459-846; lane
2) results in a 50% reduction in activity, and the elimination of
amino acids 1 to 516 (mutant TM517-846; lane 3) results in a nearly
complete loss of activity. Interestingly, neither of these mutations
has an effect on SECIS binding activity (see below). Elimination of the
C-terminal amino acids 778 to 846 (mutant TM399-777; lane 7) has no
effect on activity, but removal of 49 additional amino acids
(TM399-728; lane 8) eliminates both function and RNA binding activity.
From these data we conclude that amino acids 399 to 517 are
specifically required for Sec insertion and as such can be considered a
distinct functional domain.

View larger version (20K):
[in this window]
[in a new window]
|
FIG. 2.
Summary of SBP2 truncation mutant data. RNA binding and
functional activity (Fig. 1) and ribosome binding activity (Fig. 6) are
summarized to the right of the diagram of each SBP2 truncation mutant.
The values for functional activity represent the percentage of the
wild-type activity normalized to that found with the addition of
C-terminal SBP2 (TM399-846); those for binding activity represent the
percentage of wild-type probe shifted to slower-migrating species
normalized to the shift observed with TM399-846. All quantitation was
performed by PhosphorImager analysis. The putative functional domain as
determined from the mutant data is indicated at the bottom. The hatched
box on the full-length diagram represents the conserved L30 RNA binding
domain. Constructs that were not tested in the ribosome binding assay
are marked "ND."
|
|
To assay RNA binding, in vitro-translated SBP2 was incubated with
radiolabeled PHGPx 3' UTR RNA and analyzed by EMSA. RNA binding
activities of wild-type and mutant SBP2 proteins are shown in Fig. 1C.
All of the expressed proteins that bind the PHGPx 3' UTR do so
specifically, as shown by the lack of binding to a mutant 3' UTR from
which the conserved AUGA element has been deleted (Fig. 1D). The
elimination of amino acids 1 to 534 (mutant TM535-846; lane 11) as
well as 778-846 (mutant TM399-728; lane 8) severely reduces binding
efficiency, indicating that the RNA binding domain encompasses the
region from 517 to 777. The SECIS binding data are presented
numerically in Fig. 2 as the percentage of wild-type probe shifted to
slower-migrating species normalized to the binding activity of
TM399-846. It is noteworthy that any mutation which eliminates RNA
binding also eliminates Sec insertion activity, suggesting that RNA
binding is absolutely required for Sec insertion. The mutant which
corresponds to an internal initiation at M535 does not contribute
significantly to the RNA binding activity (Fig. 1C, lane 11) and lacks
any detectable functional activity (Fig. 1B, lane 11). Interestingly,
the region that appears to be responsible for the aberrant migration
during SDS-PAGE overlaps with part of the RNA binding domain, and the
modification or unique structure which causes the aberration may be
necessary for proper SBP2 function. Overall, these results indicate
that the RNA binding domain resides between amino acids 517 and 777, a
region which includes the putative RNA binding motif known to be
required for ribosomal protein L30 RNA binding activity
(15). In addition, it appears that the SBP2 functional
domain (amino acids 399 to 517) does not overlap with the RNA binding
domain and may represent the site of interaction with another component
of the Sec insertion machinery.
Analysis of SBP2 point mutants.
To further characterize the
RNA binding domain, we introduced point mutations in the stretch of
amino acids that is conserved among the sequences shown in the
alignment of what we here term the L30 RNA binding motif (Fig.
3). No other significant similarity among
these proteins exists. As shown in Fig. 3, SBP2 contains a Cys residue
at position 25 (SBP2 position 684) that is unique among the group. To
test if this unique Cys residue is required for binding, C684 was
changed to the more commonly observed Leu or to a potentially
disruptive Trp residue. As shown in Fig.
4B and C, neither mutant was
significantly diminished in its ability to bind the PHGPx 3' UTR or
enhance PHGPx translation. Quantitation of the effects indicates a
slightly lower amount of both activities for the C684W mutant (Fig. 4).
We suspect that the introduction of a bulky aromatic side group into
the conserved RNA binding domain may cause some disruption of the local
structure. Binding specificity is also not affected by these mutations,
as shown in Fig. 4D, in which a PHGPx 3' UTR with a mutant SECIS
element was used. These data indicate that the unique Cys residue found in SBP2 is not required for RNA binding activity.

View larger version (70K):
[in this window]
[in a new window]
|
FIG. 3.
Alignment of amino acids contained within the L30 RNA
binding motif. Sequences are grouped according to similarity. The top
group consists of the omnipotent suppressors of translation termination
(SUP1) which have since been identified as eRF-1. The second group
consists of the ribosomal protein L30 sequences. The third group
consists of SBP2 and hSLP. The remaining groups consist of ribosomal
proteins and RimK. Conserved amino acids are in boldface. Species noted
include Trypanosoma cruzi, Methanococcus
vannielii, Suefolobus acidocaldarius, Haloarcula
marismortui, Bacillus subtilis, and Trypanosoma
brucei.
|
|

View larger version (35K):
[in this window]
[in a new window]
|
FIG. 4.
Analysis of SBP2 point mutants and hSLP. (A)
[35S]Met-labeled SBP2 proteins were resolved by SDS-PAGE.
(B) Assay of PHGPx expression as describe for Fig. 1B. Lane 8 contains
no SBP2. (C) EMSA for SBP2 mutant proteins as described for Fig. 1C.
(D) Same as panel C except that the probe was an AUGA deletion mutant
of the PHGPx 3' UTR. Lane 7 contains 2 µl of rabbit reticulocyte
lysate without SBP2; lane 8 contains probe in the absence of rabbit
reticulocyte lysate. (E) Quantitation of the results in panels B and C
expressed as percentage of activity (%Act) or percentage of binding
(%Binding) as described for Fig. 2.
|
|
We also wished to determine if the invariant Gly residue at position 10 (SBP2 position 669) is required for RNA binding activity. Alteration of
this Gly residue to Arg (G669R) completely abrogated both binding
activity and function, while a G669A mutation eliminated all detectable
binding activity but not all of the detectable enhancement of PHGPx
translation (Fig. 4B and C). To test the idea that any of the conserved
domains shown in Fig. 3 might suffice for PHGPx 3' UTR binding, the
SBP2 analog known as human hypothetical protein KIAA0256 (here termed
human SBP2-like protein, or hSLP) was subcloned and expressed in vitro.
This does not appear to be the human SBP2 homologue, as sequences which
are greater than 90% identical to rat SBP2 are present in the human
expressed sequence tag database. The hSLP construct used here consists
of the C-terminal 428 amino acids which are 46% identical to the
C-terminal 447 amino acids of SBP2, with 75% identity in the L30 RNA
binding domain (6). As with the SBP2 mutants, hSLP was
expressed in rabbit reticulocyte lysate and tested for its ability to
bind the PHGPx 3' UTR and enhance PHGPx translation. Expression of hSLP
in rabbit reticulocyte lysate yields a protein with an apparent molecular mass exceeding 85 kDa (Fig. 4A), which is almost double the
predicted molecular mass. As mentioned above, the C-terminal portion of
SBP2 is involved in its anomalous migration during SDS-PAGE, and this
appears to be the case for hSLP as well. As shown in Fig. 4C, lane 6, hSLP binds the PHGPx 3' UTR very weakly, albeit specifically (compare
to Fig. 4D, lane 6), and does not support PHGPx translation (Fig. 4B).
Thus, the possession of a conserved motif is not sufficient for full
RNA binding activity. These results are consistent with the truncation
data, which indicated that a significant amount of sequence surrounding
the conserved motif is required for RNA binding activity.
Interaction of SBP2 with ribosomes.
Our current model of Sec
incorporation employs SBP2 in preventing termination while perhaps
simultaneously delivering a functional SBP2-eEFsec-Sec-tRNASec complex to the ribosomal A site.
To test whether SBP2 is stably associated with ribosomes, we used
glycerol gradients to study SBP2 sedimentation after transient
transfection of wild-type and mutant SBP2 constructs. Our initial
attempts to use standard sucrose-based polysome gradients failed due to
the sensitivity of the SBP2 complex to the artificially high magnesium
concentration necessary to stabilize polysomes (data not shown).
Therefore, the conditions used for this experiment do not show an
analysis of mRNAs stably associated with the ribosomal fraction.
Strep-tagged C-terminal SBP2 (TM399-846) was transiently transfected
into the rat hepatoma cell line McArdle 7777. After 40 h, extracts
from these cells were fractionated on 10 to 30% glycerol gradients.
Fractions were collected and precipitated with TCA followed by Western
blot analysis using an anti-Strep tag probe. Figure
5 shows the results of three gradients
run under various conditions. Figure 5A indicates that the vast
majority of Strep-tagged SBP2 sediments with the heavier fractions
(numbers 8 to 10) under low-stringency conditions (PBS-2 mM DTT). The
addition of 0.5 M NaCl to the extraction and gradient buffers resulted
in complete disruption of the complex, as shown in Fig. 5B. Complex
formation was not sensitive to 5 mM EDTA (Fig. 5C), suggesting that
divalent metal ions are not necessary for this interaction. Reprobing
of these blots with anti-SBP2 antibody indicates that all detectable
endogenous SBP2 is found to cofractionate with fractions 8 to 10 (data
not shown). It is unlikely that transfected SBP2 is "pulling"
endogenous SBP2 onto the ribosomes because our analysis of cells
transfected with the N-terminal half of SBP2, which is not ribosome
associated, also shows that the endogenous protein sediments with
ribosomes (data not shown). Staining of the blot in Fig. 5A for total
protein demonstrated that most protein sedimented in the first five
fractions of the gradient (Fig. 5F). To ascertain whether or not a
SECIS element was involved in this interaction, we extracted RNA from
the EDTA-containing gradient fractions and analyzed the distribution of
PHGPx mRNA by Northern blot analysis. PHGPx mRNA was chosen because it
is expressed to relatively high levels in McArdle cells
(8) and because GPx mRNA was not detectable in this
experiment, which contains limited amounts of mRNA. As shown in Fig.
5D, the bulk of PHGPx mRNA does not cosediment with SBP2, suggesting
that SBP2 is not stably associated with SECIS elements and the ribosome
simultaneously. This was a surprising result and may reflect an effect
of the methods used, but it may suggest that SBP2 preferentially binds
to ribosomes and interacts with SECIS elements only after translation
initiation. PHGPx mRNA sedimentation was the same as that of
nonselenoprotein (glyceraldehyde-3-phosphate dehydrogenase) mRNA
(data not shown). To analyze the positions of the ribosomal
subunits, the Northern gel described above was stained with ethidium
bromide to allow visualization of the positions of the 18S and 28S
rRNAs in the gradient, which indicates the positions of the 40 and
60/80S ribosomal subunits (Fig. 5E). These results suggest that SBP2 is
stably associated with either 60S or 80S, but not isolated 40S,
ribosomal subunits.

View larger version (65K):
[in this window]
[in a new window]
|
FIG. 5.
Sedimentation of SBP2 in glycerol gradients.
Strep-tagged TM399-846 was transiently transfected into McArdle 7777 cells, and 500-µg aliquots of extracted proteins were loaded onto 10 to 30% linear glycerol gradients. Fractions (0.6 ml) were collected
from the top of each gradient. Proteins were TCA precipitated, resolved
by SDS-PAGE, blotted to nitrocellulose, and probed with alkaline
phosphatase-conjugated streptavidin, which recognizes the Strep tag. (A
to C) Gradients run in PBSD, PBSD plus 0.5 M NaCl, and PBSD plus 5 mM
EDTA respectively. (D) RNA was extracted from the fractions run in 5 mM
EDTA, resolved on a 1% denaturing agarose gel, blotted to nylon, and
probed for PHGPx mRNA. (E) Gel in panel D stained with ethidium
bromide. (F) Blot in panel A stained with India ink.
|
|
To determine which domain of SBP2 is required for ribosome interaction,
we expressed several SBP2 mutant proteins in McArdle 7777 cells, and
analyzed complex formation on glycerol gradients as described above.
The results from these experiments are shown in Fig.
6 and are summarized in Fig. 2. As best
indicated by the G669R mutant, SECIS binding activity is not required
for complex formation. Mutations which eliminate activity but not RNA
binding (e.g., TM517-846) are impaired for complex formation, as the
majority of the protein is not associated with fractions 8 to 10. In
addition, the mutation which eliminates part of the RNA binding domain
(TM399-728) is also reduced in its ability to form complexes. These
results suggest that both the putative functional domain and the RNA
binding domain are crucial for the SBP2-ribosome interaction. Because the G669R mutant still binds ribosomes, however, we conclude that the
RNA binding domain and the ribosome binding domain are not identical.

View larger version (35K):
[in this window]
[in a new window]
|
FIG. 6.
Sedimentation of SBP2 mutants in glycerol gradients.
McArdle 7777 cell extracts containing the mutant SBP2 proteins
indicated to the right were loaded onto glycerol gradients as described
for Fig. 5. TM399-846, G669R, and TM1-397 are Strep-tagged proteins
detected with alkaline phosphatase-conjugated streptavidin. The
remainder of the proteins were untagged and detected with anti-SBP2
antibodies.
|
|
To verify that the complex we have identified in glycerol gradients is
due to ribosomes and not self-association or other interactions,
purified recombinant Strep-tagged TM399-846 (6) was
analyzed in the presence or absence of purified salt-washed ribosomes
derived from rabbit reticulocytes (16). Interestingly, purified TM399-846 alone sediments in fractions 3 and 4 (Fig. 7A), while the addition of 2 A260 units of ribosomes moves the SBP2 to
fractions 10 to 12 (Fig. 7B; SBP2 is found further down the gradient
than described above due to a longer spinning time used to increase
resolution). The addition of 0.5 M NaCl to the gradient results in a
complete disruption of the complex and moves SBP2 to the first two
fractions of the gradient. These results suggest that SBP2 is, indeed,
interacting with ribosomes and is also self-associated into a
salt-sensitive complex in the absence of ribosomes.

View larger version (8K):
[in this window]
[in a new window]
|
FIG. 7.
Sedimentation of recombinant SBP2 and purified
ribosomes. (A) Purified Strep-tagged C-terminal SBP2 (TM399-846; 5 µg) was layered onto a 10 to 30% glycerol gradient. Fractions
processed as described for Fig. 5. (B) Purified SBP2 (TM399-846; 5 µg) was incubated with 2.0 A260 units of
purified salt-washed ribosomes from rabbit reticulocyte lysate and then
layered onto a glycerol gradient and processed as for panel A. (C) Same
as panel B except that 0.5 M NaCl was added to the reaction mix.
|
|
SBP2 interacts with rRNA.
Because the RNA binding domain of
SBP2 is required for ribosome binding and because ribosomal protein L30
uses a similar domain to interact with its own mRNA as well as 28S rRNA
(15, 22), we decided to test for the ability of SBP2 to
bind rRNA in vitro. Toward this end, Strep-tagged TM399-846 was
incubated with rRNA extracted from the purified salt-washed ribosomes
used for Fig. 7 and subjected to glycerol gradient fractionation. As
shown in Fig. 8A, SBP2 is not found in
the early fractions (numbers 3 and 4) where the 18S rRNA alone is
present. However, SBP2 does form a complex with 28S rRNA or the
combination of 28S and 18S rRNAs which, as shown in Fig. 8B, is present
in fractions 6 to 9. While we cannot rule out that this interaction
requires the presence of both rRNA species, it is likely that the
SBP2-ribosome interaction depends on SBP2 binding to 28S rRNA.

View larger version (38K):
[in this window]
[in a new window]
|
FIG. 8.
Cosedimentation of SBP2 and purified rRNA. Purified
Strep-tagged C-terminal SBP2 (TM399-846; 5 µg) was incubated with
purified total rRNA and fractionated on a 10 to 30% glycerol gradient.
Gradient fractions were analyzed for SBP2 content by Western blotting
(A) and rRNA content by agarose gel electrophoresis and ethidium
bromide staining (B).
|
|
 |
DISCUSSION |
The recent discovery of two novel factors involved in mammalian
selenoprotein synthesis, SBP2 and eEFSec, has shed significant light on
the mechanism of Sec incorporation. The latter of these factors has
been described as the Sec-specific elongation factor which is required
for delivering the Sec-tRNASec to the ribosomal A site. The
role of SBP2 is much less clear, and we have previously hypothesized
that it is involved in the other major dynamic presumed to be required
for Sec insertion, competition with translation termination. Here we
describe the beginning of a detailed investigation of the structure and
function of SBP2 in order to elucidate its role in Sec insertion. From this and previous work, we know that SBP2 is a multifunctional protein
that binds to SECIS elements, interacts with eEFSec, and also binds
stably to ribosomes.
As shown in Fig. 3, SBP2 shares a sequence motif with a variety of
eukaryotic and prokaryotic proteins. The best-studied member of this
family is ribosomal protein L30 which is involved in its own splicing
and translational regulation by means of binding to its own pre-mRNA
and mRNA, respectively. The fact that the L30 RNA binding domain is
involved in RNA binding has been established by extensive nuclear
magnetic resonance analysis on the L30 protein and mRNA target
(15). While there is no sequence similarity between the
L30 mRNA and a SECIS element, the overall structures of both SBP2 and
L30 binding sites can be described as a bulge flanked on both sides by
paired sequences (5, 15), and both sequences may form the
GA quartet that is known to be essential for Sec insertion.
Interestingly, the L30 target site on 25S rRNA from Saccharomyces
cerevisiae has also recently been determined and found to be very
similar to the L30 mRNA binding site in both primary and secondary
structures (22). The truncation and point mutants
described in this report establish that the L30 RNA binding domain is
required for SBP2 RNA binding and functional activity. However,
mutations which eliminate SECIS binding do not eliminate ribosome
association, suggesting that this motif is not strictly relegated
to ribosome-rRNA interactions. In addition, the conserved motif is not
sufficient for sequence specific binding, as demonstrated by the
truncation mutants which still retain the motif but are unable to
sustain binding activity. Furthermore, the SBP2-related protein
that was tested here was barely able to bind the PHGPx 3' UTR,
suggesting that even a related sequence is not sufficient for specific
binding. This point is further supported by the fact that the L30
nuclear magnetic resonance data indicate that residues C terminal to
the conserved region are involved in protein-RNA contacts
(15). These residues are not conserved in SBP2.
In terms of SBP2 function, it is clear from the data presented here
that RNA binding activity is required for function and that a
functional domain can be identified as a discrete stretch of amino
acids. This region, however, is not a member of any known sequence
families and thus does not shed light on its mechanism of action. It is
likely that this region is involved in the interactions necessary for
Sec insertion, and so our current efforts are involved in identifying
the critical residues in this region and testing mutants for their
ability to interact with eEFSec. It is possible, for example, that this
region is involved directly with preventing termination either by
binding to the release factor(s) directly or by blocking access of
eRF-1 to the ribosomal A site. We have thus far been unable to
demonstrate any interaction between SBP2 and either of the eukaryotic
release factors (eRF-1 or eRF-3), but work is still in progress on that front.
Perhaps the most significant finding from this work is that SBP2 is
stably associated with the ribosomal fraction of glycerol gradients
both in vivo and in vitro. This interaction appears to be direct, as
purified SBP2 is able to interact with salt-washed purified ribosomes.
It is striking that the point mutant that fails to bind the SECIS
element still associates with the ribosome, but that deletions which
encroach on the RNA binding domain greatly reduce ribosome association.
In light of these results, we propose that the ribosome binding domain
and SECIS binding domain overlap but are not identical. Considering
that SBP2 appears to form a homomeric complex based on its
sedimentation in glycerol gradients in the absence of any other
factors, it is tempting to suggest that an SBP2 dimer in a head-to-head
orientation uses one RNA binding domain to interact with the ribosome
and the other to interact with the SECIS element.
These results lead us to speculate that SBP2 may be involved in
selecting ribosomes for Sec insertion. That is, by binding to a subset
of ribosomes without discrimination, SBP2 is making that pool of
ribosomes competent for Sec insertion. This model would predict,
therefore, that selenoproteins translated on ribosomes lacking SBP2
will terminate at the Sec codon, while those being translated on
SBP2-containing ribosomes will bypass termination and insert Sec. While
the data presented here do not directly support the idea that SBP2 is
involved in preventing termination, we anticipate that future work
which will define the site of the SBP2-ribosome interaction should shed
light on potential interactions with the termination mechanism. The
binding of SBP2 to the ribosome being the first step, a second step
will likely consist of quaternary complex formation (SBP2, SECIS
element, eEFSec, and Sec-tRNASec), and that this step will
also be regulated by SBP2 by means of differential affinity for the
various SECIS elements. Thus, it is conceivable that SBP2 is the major
determinant of the efficiency of selenoprotein synthesis, and that it
may be involved in the differential stability of selenoprotein mRNA
that is known to be highly regulated during selenium deficiency
(4, 17). In reticulocyte lysates SBP2 is the clearly
limiting factor, and this may also be true in tissues that have limited
selenoprotein synthesis capacity.
We thank Bill Merrick for providing purified reticulocyte
ribosomes as well as Julia Fletcher and Carri Gerber for a critical review of the manuscript.
This work was supported by Public Health Service grants
HL29582 (D. M. D.) and F32 DK09878-01 (P.R.C.) from the
National Institutes of Health.
| 1.
|
Berry, M. J.,
L. Banu,
Y. Y. Chen,
S. J. Mandel,
J. D. Kieffer,
J. W. Harney, and P. R. Larsen.
1991.
Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3' untranslated region.
Nature
353:273-276[CrossRef][Medline].
|
| 2.
|
Bock, A.
2000.
Biosynthesis of selenoproteins an overview.
Biofactors
11:77-78[Medline].
|
| 3.
|
Bosl, M. R.,
K. Takaku,
M. Oshima,
S. Nishimura, and M. M. Taketo.
1997.
Early embryonic lethality caused by targeted disruption of the mouse selenocysteine tRNA gene (Trsp).
Proc. Natl. Acad. Sci. USA
94:5531-5534[Abstract/Free Full Text].
|
| 4.
|
Brigelius-Flohe, R.
1999.
Tissue-specific functions of individual glutathione peroxidases.
Free Radic. Biol. Med.
27:951-965[CrossRef][Medline].
|
| 5.
|
Copeland, P. R., and D. M. Driscoll.
1999.
Purification, redox sensitivity, and RNA binding properties of SECIS-binding protein 2, a protein involved in selenoprotein biosynthesis.
J. Biol. Chem.
274:25447-25454[Abstract/Free Full Text].
|
| 6.
|
Copeland, P. R.,
J. E. Fletcher,
B. A. Carlson,
D. L. Hatfield, and D. M. Driscoll.
2000.
A novel RNA binding protein, SBP2, is required for the translation of mammalian selenoprotein mRNAs.
EMBO J.
19:306-314[CrossRef][Medline].
|
| 7.
|
Fagegaltier, D.,
N. Hubert,
K. Yamada,
T. Mizutani,
P. Carbon, and A. Krol.
2000.
Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation.
EMBO J.
19:4796-4805[CrossRef][Medline].
|
| 8.
|
Fletcher, J. E.,
P. R. Copeland, and D. M. Driscoll.
2000.
Polysome distribution of phospholipid hydroperoxide glutatione peroxidase mRNA: evidence for a block in elongation at the UGA/selenocysteine codon.
RNA
6:1573-1584[Abstract].
|
| 9.
|
Gladyshev, V. N., and D. L. Hatfield.
1999.
Selenocysteine-containing proteins in mammals.
J. Biomed. Sci.
6:151-160[CrossRef][Medline].
|
| 10.
|
Gray, N. K., and M. Wickens.
1998.
Control of translation initiation in animals.
Annu. Rev. Cell Dev. Biol.
14:399-458[CrossRef][Medline].
|
| 11.
|
Ho, Y. S.,
J. L. Magnenat,
R. T. Bronson,
J. Cao,
M. Gargano,
M. Sugawara, and C. D. Funk.
1997.
Mice deficient in cellular glutathione peroxidase develop normally and show no increased sensitivity to hyperoxia.
J. Biol. Chem.
272:16644-16651[Abstract/Free Full Text].
|
| 12.
|
Koonin, E. V.,
P. Bork, and C. Sander.
1994.
A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme?
Nucleic Acids Res.
22:2166-2167[Abstract/Free Full Text].
|
| 13.
|
Lee, B. J.,
P. J. Worland,
J. N. Davis,
T. C. Stadtman, and D. L. Hatfield.
1989.
Identification of a selenocysteyl-tRNA (Ser) in mammalian cells that recognizes the nonsense codon, UGA.
J. Biol. Chem.
264:9724-9727[Abstract/Free Full Text].
|
| 14.
|
Lesoon, A.,
A. Mehta,
R. Singh,
G. M. Chisolm, and D. M. Driscoll.
1997.
An RNA-binding protein recognizes a mammalian selenocysteine insertion sequence element required for cotranslational incorporation of selenocysteine.
Mol. Cell. Biol.
17:1977-1985[Abstract].
|
| 15.
|
Mao, H.,
S. A. White, and J. R. Williamson.
1999.
A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex.
Nat. Struct. Biol.
6:1139-1147[CrossRef][Medline].
|
| 16.
|
Merrick, W. C.
1979.
Assays for eukaryotic protein synthesis.
Methods Enzymol.
60:108-123[Medline].
|
| 17.
|
Moriarty, P. M.,
C. C. Reddy, and L. E. Maquat.
1998.
Selenium deficiency reduces the abundance of mRNA for Se-dependent glutathione peroxidase 1 by a UGA-dependent mechanism likely to be nonsense codon-mediated decay of cytoplasmic mRNA.
Mol. Cell. Biol.
18:2932-2939[Abstract/Free Full Text].
|
| 18.
|
Sachs, A. B.,
P. Sarnow, and M. W. Hentze.
1997.
Starting at the beginning, middle, and end: translation initiation in eukaryotes.
Cell
89:831-838[CrossRef][Medline].
|
| 19.
|
Song, H.,
P. Mugnier,
A. K. Das,
H. M. Webb,
D. R. Evans,
M. F. Tuite,
B. A. Hemmings, and D. Barford.
2000.
The crystal structure of human eukaryotic release factor eRF1 mechanism of stop codon recognition and peptidyl-tRNA hydrolysis.
Cell
100:311-321[CrossRef][Medline].
|
| 20.
|
Stadtman, T. C.
2000.
Selenium biochemistry. Mammalian selenoenzymes.
Ann. N.Y. Acad. Sci.
899:399-402[Free Full Text].
|
| 21.
|
Tujebajeva, R. M.,
P. R. Copeland,
X.-M. Xu,
B. A. Carlson,
J. W. Harney,
D. M. Driscoll,
D. L. Hatfield, and M. J. Berry.
2000.
Decoding apparatus for eukaryotic selenocysteine insertion.
EMBO Rep.
1:1-6[CrossRef].
|
| 22.
|
Vilardell, J.,
S. J. Yu, and J. R. Warner.
2000.
Multiple functions of an evolutionarily conserved RNA binding domain.
Mol. Cell
5:761-766[CrossRef][Medline].
|