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Molecular and Cellular Biology, March 1999, p. 2220-2230, Vol. 19, No. 3
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Mammalian Staufen Is a Double-Stranded-RNA- and
Tubulin-Binding Protein Which Localizes to the Rough Endoplasmic
Reticulum
Louise
Wickham,1
Thomas
Duchaîne,1
Ming
Luo,1
Ivan R.
Nabi,2 and
Luc
DesGroseillers1,*
Departments of
Biochemistry1 and Pathology and Cell
Biology,2 University of Montreal, Montreal,
Quebec, Canada H3C 3J7
Received 9 September 1998/Returned for modification 23 October
1998/Accepted 17 November 1998
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ABSTRACT |
Staufen (Stau) is a double-stranded RNA (dsRNA)-binding protein
involved in mRNA transport and localization in Drosophila. To understand the molecular mechanisms of mRNA transport in mammals, we
cloned human (hStau) and mouse (mStau)
staufen cDNAs. In humans, four transcripts arise by
differential splicing of the Stau gene and code for two
proteins with different N-terminal extremities. In vitro, hStau and
mStau bind dsRNA via each of two full-length dsRNA-binding domains and
tubulin via a region similar to the microtubule-binding domain of
MAP-1B, suggesting that Stau cross-links cytoskeletal and RNA
components. Immunofluorescent double labeling of transfected mammalian
cells revealed that Stau is localized to the rough endoplasmic
reticulum (RER), implicating this RNA-binding protein in mRNA targeting
to the RER, perhaps via a multistep process involving microtubules.
These results are the first demonstration of the association of an
RNA-binding protein in addition to ribosomal proteins, with the RER,
implicating this class of proteins in the transport of RNA to its site
of translation.
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INTRODUCTION |
It is now believed that the
cytoskeleton is widely used to transport mRNAs between their
transcription and processing sites in the nucleus and their translation
and degradation sites in the cytoplasm (3, 42, 44). One
consequence of the interaction between mRNAs and the cytoskeleton is to
promote differential localization and/or transport of mRNAs in
subcellular compartments. Indeed, examples of mRNA targeting have been
observed in both germinal and somatic cells throughout the animal
kingdom (51, 55, 63). The universal use of this mechanism is
also apparent when we consider the nature of the proteins which are
coded by the transported mRNAs; asymmetric localization involving mRNAs coding for cytosolic, secreted, membrane-associated, or cytoskeletal proteins have all been reported. Localization of mRNAs in the cytoplasm
is now considered an essential step in the regulation of gene
expression and an efficient way to unevenly distribute proteins in
polarized cells. In general, it is believed that mRNA localization is
used to determine and/or regulate local sites of translation (46,
51, 55). Indeed, ribosomes and many translational cofactors were
found in association with the cytoskeletal elements, preventing both
mRNAs and translation factors from being diluted by the cellular fluid
(44). Transport and local translation of specific mRNAs have
been shown to play an important role in processes such as learning and
memory (38), synaptic transmission (9, 22, 26, 51,
61), axis formation during development (reviewed in reference
55), cell motility (30), and asymmetric cell division (7, 36, 37, 56).
The mechanisms underlying mRNA localization are not yet fully
understood, mainly because of the lack of information on the principal
constituents of the ribonucleoprotein (RNP) complexes involved in this
process. Nevertheless, it is known to involve both
cis-acting signals in mRNA and trans-acting
RNA-binding proteins which bind to this signal (55). The
signals that allow mRNAs to be recognized as targets for transport and
then to be localized have been mapped within their 3' untranslated
regions (UTRs) (55, 63). In contrast, the nature of the
RNA-binding proteins is still obscure. Recently, a 68-kDa protein which
binds the
-actin mRNA zipcode localization domain was
isolated and its transcript was cloned from chicken cDNA libraries
(47). This protein, which binds to microfilaments, contains
RNA-binding domains (RBDs) which share strong sequence similarities
with the RNP and KH motifs. In addition, 69- and 78 kDa proteins in
Xenopus laevis oocyte extracts have been shown to bind to
the localization signal of Vg1 mRNA (12, 50).
While the 69-kDa protein was shown to bind microtubules
(15), the 78-kDa Vera protein colocalized with a subdomain
of the smooth endoplasmic reticulum (SER) (12). Surprisingly, molecular cloning of the two proteins revealed that they
are identical and are similar to the chicken zipcode-binding protein
(13, 23).
Genetic and molecular studies have shown that the activity of the
staufen gene product in Drosophila is necessary
for the proper localization of bicoid and oskar
mRNAs to the anterior and posterior cytoplasm of oocytes, respectively,
and of prospero mRNA in neuroblasts (7, 16, 28, 36, 52,
53). Staufen (Stau), a member of the double-stranded RNA
(dsRNA)-binding protein family, contains (i) three copies of a domain
consisting of a 65- to 68-amino-acid consensus sequence which is
required to bind RNAs having double-stranded secondary structures and
(ii) two copies of a short domain which retains the last 21 amino acids at the C-terminal end of the complete motif (53, 54). In
vitro, it has been demonstrated that Stau binds directly to
bicoid and prospero mRNAs (36, 54).
However, since Stau seems to bind to any dsRNA in vitro, it is not
clear whether it binds directly to these RNAs in vivo or needs cellular
cofactors which make up part of a larger RNP complex to localize each
mRNA. Many experiments have demonstrated that the localization of
oskar, prospero, and bicoid mRNAs
occurs through a multistep mechanism of active transport that is
dependent on elements of the cytoskeleton (7, 17, 45, 55,
58).
To understand the mechanisms of mRNA transport in mammals and determine
the nature of both the RNAs and proteins in the RNA-protein complexes,
we began the cloning of the human and mouse staufen (hStau and mStau) cDNAs and the
characterization of their encoded proteins. Recently, we showed
by both Southern blot analysis of human DNA and fluorescent in
situ hybridization on human chromosomes in metaphase that the human
gene is present as a single copy in the human genome and is localized
in the middle of the long arm of chromosome 20 (11). We now
report the sequence of the hStau and mStau and show that the transcript
is found in all tested tissues. We further demonstrate that Stau binds
both dsRNA and tubulin in vitro via specific binding domains. Stau is
also shown to be present in the cytoplasm in association with the rough
endoplasmic reticulum (RER), implicating this protein in the targeting
of RNA to its site of translation.
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MATERIALS AND METHODS |
Molecular cloning and sequencing of the cDNAs.
To clone an
hStau homologue, we searched the GenBank database with
Drosophila dsRBD sequences to find consensus sequences and
eventually design degenerate oligonucleotide primers for reverse transcription (RT)-PCR. However, searching in the expressed sequence tag database identified a partial sequence, clone HFBDQ83 (GenBank accession no. T06248), with high homology to the Drosophila sequence. This clone was purchased from the American Type Culture Collection and used as a probe to screen both human brain (Clontech) and fetal total mouse (a generous gift from A. Royal) cDNA libraries as
described previously (62). DNA from the isolated
gt10
clones was subcloned into a pBluescript vector (Stratagene).
Double-stranded DNA (dsDNA) was sequenced by the
dideoxynucleotide method according to Sequenase protocols (United
States Biochemical Corp.).
Construction of fusion proteins.
The 1.2-kbp
BamHI fragment of the human HFBDQ83 cDNA was subcloned in
frame in either pQE32 (Qiagen) or pMAL-c (New England Biolabs), thus
generating the protein fused to a hexahistidine tag or to the
maltose-binding protein (MBP), respectively. The protein was expressed
in bacteria by induction with
isopropyl-
-D-thiogalactopyranoside (IPTG) as recommended
by the manufacturer.
Full-length and internal fragments of the mStau protein were PCR
amplified and cloned into pMal-c to produce MBP fusion proteins. For
the expression of the internal domains, which do not contain an
endogenous stop codon, the PCR fragments were cloned in a modified pMal-c vector (pMal-stop) in which stop codons were introduced at the
HindIII site, by the ligation of the annealed
complementary oligonucleotides 5'-AGCTTAATTAGCTGAC-3' and
5'-AGCTGTCAGCTAATTA-3'. The MBP-mStau fusion protein,
containing the full-length mStau sequence, was generated by PCR
amplification with Vent DNA polymerase (New England BioLabs), using the
primer pair 5'-CCTGGATCCGAAAGTATAGCTTCTACCATTG-3' plus
5'-TACATAAGCTTCTAGATGGCCAGAAAAGGTTCAGCA-3'. The resulting 1,562-bp fragment was digested with HindIII and
BamHI and ligated in the pMal-c vector. The C-terminal
fragment (mStau-C) was amplified with the primer pair
5'-GGATGAATCCTATTAGTAGACTTGCAC-3' plus
5'-TACATAAGCTTCTAGATGGCCAGAAAAGGTTCAGCA-3', digested with
HindIII, and cloned in the EagI* and
HindIII sites of pMal-c. EagI* was created by
filling in the cohesive ends of EagI-digested pMal-c vector,
using the Klenow fragment of DNA polymerase I. This fusion vector was
then digested with SacI and EcoRI, and the
resulting fragment was subcloned in the pMal-stop vector to generate
the mStau-RBD3 construct. The mStau-tubulin-binding domain (TBD)
construct was prepared by PCR using the primer pair 5'-GCTCTAGATTCAAAGTTCCCCAGGCGCAG-3' plus
5'-TTAAGCTTCTCAGAGGGTCTAGTGCGAG-3'; the product was digested
with XbaI and HindIII and cloned in the pMal-stop vector. mStau-RBD2 and mStau-RBD1 were constructed by first
amplifying a fragment using the primer pair
5'-CAATGTATAAGCCCGTGGACCC-3' and
5'-AAAAAGCTTGTGCAAGTCTACTAATAGGATTCATCC-3'. The resulting product was digested with HindIII and cloned in the
EagI* and HindIII sites of the pMal-stop
vector. This vector was then used to purify the 398-bp PstI
and HindIII fragment, which was subcloned in the
pMAL-stop vector to generate the mStau-RBD2 construct. In the same way,
the mStau-RBD1 vector was obtained by digestion with SmaI
and StuI, followed by recircularization of the digestion product using T4 DNA ligase. The mStau-RBD4 was PCR amplified by using
the primer pair 5'-ATAGCCCGAGAGTTGTTG-3' plus
5'-TACATAAGCTTCTAGATGGCCAGAAAAGGTTCAGCA-3'. The resulting
fragment was digested with HindIII and ligated in the
pMal-stop vector at the StuI and HindIII
sites. All MBP-Stau fusion plasmids were transformed in BL-21
Escherichia coli. The fusion proteins were obtained after
induction with 1 mM IPTG for 2 to 3 h. Cells were lysed in sodium
dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) loading
buffer for immediate use, or frozen at
80°C for storage.
Antibody production and Western blotting.
For the production
of antibodies, a large amount of the His-hStau fusion protein was
purified on Ni-nitrilotriacetic acid (NTA) resin (Qiagen) as
recommended by the manufacturer and injected into rabbits as done
previously (2). For Western blotting, cells were lysed in
1% n-octylglucoside-1 mM phenylmethylsulfonyl sulfoxide-aprotinin (1 µg/ml)-pepstatin A (1 µg/ml) in
phosphate-buffered saline (PBS). Protein extracts were quantified by
the Bradford method (Bio-Rad), and similar amounts of proteins were
separated on SDS-10% polyacrylamide gels and transferred onto
nitrocellulose membranes. Membranes were blocked for 30 min in TBS
(Tris-buffered saline; 10 mM Tris [pH 8.0], 150 mM NaCl)-5% dry
milk and incubated with primary antibodies in TBS-0.05% Tween for
1 h at room temperature. Detection was accomplished by incubating
the blots with peroxidase-conjugated anti-rabbit immunoglobulin G (IgG)
antibodies (Dimension Labs) followed by Supersignal Substrate (Pierce)
as recommended by the manufacturer.
RNA-binding assay.
Bacterial extracts from IPTG-induced
cultures were separated on SDS-10% polyacrylamide gels and the
proteins were transferred onto nitrocellulose membranes. Membranes were
incubated in the presence of 32P-labeled RNA probes in 50 mM NaCl-10 mM MgCl2-10 mM HEPES (pH 8.0)-0.1 mM EDTA-1
mM dithiothreitol-0.25% milk for 2 h at room temperature, washed
in the same buffer for 30 min, and exposed for autoradiography. For
competition assays, a 100- to 1,000-fold excess of cold homopolymers
(Pharmacia) was added to the hybridization mixture along with the
labeled probe. The 3' UTR of bicoid cDNA (positions 4016 to
4972), which was PCR amplified from Drosophila genomic DNA
and subcloned in the pBluescript vector, was transcribed by using T7
RNA polymerase in the presence of [
-32P]CTP. Synthetic
RNAs (Pharmacia) were labeled with T4 polynucleotide kinase in the
presence of [
-32P]ATP. The specific activities of the
bicoid and synthetic RNA probes were 1.4 × 106 and 0.5 × 106 cpm/µg, respectively.
For RNA-binding assay in solution, dilutions of the purified human
His-Stau fusion protein were incubated with in vitro-labeled
bicoid RNA (3' UTR), poly(rI)-poly(rC), poly(rI), or
poly(rC)
(20,000 cpm; specific activity, 10
6 cpm/µg) in
10 mM MgCl
2-50 mM NaCl-0.1 mM EDTA-1 mM
dithiothreitol-10
mM HEPES (pH 8.0) for 30 min at room temperature.
The RNA-protein
complexes were then filtered through a nitrocellulose
membrane
(0.45-µm pore size), washed, and counted. Analyses were done
with
the Graph Pad PRISM (version 2.01)
software.
Tubulin-binding assay.
Bacterial extracts from IPTG-induced
cultures were separated on SDS-10% polyacrylamide gels, and the
MBP-tagged proteins were transferred onto nitrocellulose membranes.
Membranes were incubated in TBS-1% Tween 20 for 45 min prior to an
overnight overlay with tubulin (7 µg/ml; Sigma) in TBS-0.2% Tween
20. Blots were washed several times in TBS-0.2% Tween 20 and then
incubated with a mixture of mouse monoclonal anti-
- and
anti-
-tubulin antibodies (ICN). Bound antibodies were detected with
secondary peroxidase-conjugated anti-mouse IgG antibodies (Dimension
Labs) and Supersignal substrate (Pierce) as stated previously. Separate
assays were performed with actin and antiactin antibodies (both from Sigma).
Immunofluorescence.
HStau-hemagglutinin (HA) and hStau-green
fluorescent protein (GFP) were constructed by PCR amplification of the
full-length cDNA, using the primer pair
5'-TACATGTCGACTTCCTGCCA/GGGCTGCGGG-3' plus
5'-TACAATCTAGATTATCAGCGGCCGCACCTCCCACACACAGACAT-3'. The 3' primer was synthesized with a NotI site just upstream from
the stop codon allowing ligation of a NotI cassette
containing either three copies of the HA tag or the GFP sequence. The
resulting fragment was cloned in pBluescript following digestion with
SalI and XbaI. The
KpnI/XbaI fragment was then subcloned in the
pCDNA3/RSV vector (25), and a NotI cassette was
introduced at the NotI site. For the TBD-GFP fusion protein,
the TBD was PCR amplified with oligonucleotides on each side of this
region (5'-TACATAAGCTTAAGCCACCATGGTCAAAGTTCCCCAGGCGC-3' and
5'-TACAATCTAGAGCGGCCGCGCTCAGAGGGTCTAGTGCGAG-3'). The sense primer contained an ATG initiation codon and the Kozak consensus sequence upstream from the TBD sequence. The antisense primer contained
a Not1 site just upstream from a stop codon. The resulting fragment was digested with HindIII and XbaI
and cloned into the pCDNA3/RSV vector. The GFP NotI cassette
was then introduced at the NotI site.
Mammalian cells were transiently transfected with the cDNAs by the
calcium phosphate precipitation technique, fixed in 4%
paraformaldehyde in PBS for 25 min at room temperature, and
permeabilized
with 0.3% Triton X-100 in PBS containing 0.1% bovine
serum albumin
(BSA). The cells were then blocked with 1% BSA in
PBS-0.3% Triton
X-100 and incubated with mouse anti-HA, rabbit
anticalreticulin,
or rabbit anticalnexin antibodies for 1 h at
room temperature,
as indicated. Cells were washed in permeabilization
buffer and
incubated with fluorescein-conjugated or Texas
red-conjugated
species-specific secondary antibodies (Jackson
Immunoresearch
Laboratories, West Grove, Pa.) in blocking buffer for
1 h. GFP
and GFP fusion proteins were detected by
autofluorescence. Mounting
was done in ImmunoFluor mounting medium
(ICN). For the analysis
of cytoskeleton-associated proteins,
transfected cells were first
extracted in 0.3% Triton X-100-130 mM
HEPES (pH 6.8)-10 mM EGTA-20
mM MgSO
4 for 5 min at 4°C
as previously described (
10). They
were then fixed in 4%
paraformaldehyde in PBS and processed for
immunofluorescence as
described above. Cells were visualized by
immunofluorescence, using the
63× planApochromat objective of
a Zeiss Axioskop fluorescence
microscope.
Confocal microscopy was performed with the 60× Nikon Plan Apochromat
objective of a dual-channel Bio-Rad 600 laser scanning
confocal
microscope equipped with a krypton-argon laser and the
corresponding
dichroid reflectors to distinguish fluorescein and
Texas red labeling.
No overlap was observed between the fluorescein
and Texas red channels.
Confocal images were printed with a Polaroid
TX1500 video
printer.
Nucleotide sequence GenBank accession numbers.
The human and
mouse sequences were deposited in the GenBank database under accession
no. AF061938, AF061939, AF061940, and AF061941 (human) and AF061942 (mouse).
 |
RESULTS |
Molecular cloning of mammalian staufen cDNAs.
To
understand the mechanism of mRNA transport in mammalian cells, we
cloned the human and mouse staufen homologues. Thirteen overlapping human cDNAs, ranging in size between 0.8 and 2.5 kb, were
isolated from a human central nervous system cDNA library, using the
expressed sequence tag HFBDQ83 cDNA as a probe (Fig. 1). Purified human HeLa cell
poly(A)+ RNAs were also reverse transcribed and PCR
amplified, using different 5' RACE (rapid amplification of 5' cDNA
ends) protocols, allowing us to clone the 5' end of the transcript. Two
different cDNAs of 3,217 and 3,506 nucleotides were identified from
overlapping clones (see below). One of the human cDNAs was then used to
screen a fetal total mouse cDNA library under low-stringency
conditions, which led to the isolation of a full-length cDNA
(mStau). The human and mouse proteins are 90% identical
(98% similarity).

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FIG. 1.
Amino acid sequences of the hStau cDNAs.
Shown is alignment of the cDNAs and PCR fragments with the translation
of the putative protein sequences. Numbers refer to the sequence of the
short cDNA. Positions of the four consensus dsRBDs (RBD1 to RBD4) and
of the TBD are indicated between brackets above the sequence.
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Hybridization of a human multiple-tissue Northern blot with a human
cDNA reveals that
hStau mRNA is found in every tested
tissue
(Fig.
2A), unlike the
Drosophila
staufen gene, which is
exclusively expressed in oocytes and in the
central nervous system
at the larval stage (
53). The size of
the cDNAs is close to
that of the transcripts, which migrate on a
Northern blot as an
unresolved large band of around 3.6 kb.

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FIG. 2.
Characterization of the hStau mRNA and
proteins. (A) Northern blot analysis of hStau expression in
human tissues. A human multiple-tissue Northern blot (Clontech) was
hybridized with the 1.2-kbp BamHI fragment of
hStau cDNA. Lane 1, brain; lane 2, pancreas; lane 3, heart;
lane 4, skeletal muscles; lane 5, liver; lane 6, placenta; lane 7, lung; lane 8, kidney. (B) Western blot experiment with anti-hStau
antibodies. Lane 1, HeLa cell extracts; lane 2, HEK 293 cell extracts.
(C) HEK 293 cells were transfected with cDNAs coding for either the
short (lane 2) or the long (lane 3) hStau isoform, lysed, and analyzed
by Western blotting using the anti-hStau antibodies. Mock-transfected
cells are shown in lane 1. (D) Schematic representation of the
Drosophila (accession no. M69111), human and mouse
(Hum/Mus), and C. elegans (accession no. U67949) Stau
proteins. The human protein P1 has an insertion of 81 amino acids at
its N-terminal extremity compared to protein P2. Large open and black
boxes represent the full-length and short dsRBDs, respectively. Small
boxes and lines are regions of high and low sequence similarity,
respectively. The hatched boxes indicate the position of the region
which is similar to the MAP1B microtubule-binding domain. The
percentage of identity between the domains of the human and
invertebrate proteins is indicated.
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A differential splicing event generates two hStau
proteins.
Characterization of the human cDNAs revealed the
presence of two types of transcripts which differ only by an insertion
of 289 bp at position 324 (T2 and T3 in Fig. 1). To confirm this result
and determine the relative expression of the two classes of
transcripts, we used RT-PCR to amplify the region of the transcript which overlaps the site of insertion. Unexpectedly, four different fragments were amplified. Cloning and sequencing of the fragments revealed that two correspond to the cDNA sequences (Fig. 1). Compared to the smallest cloned cDNA sequence (T2), a third fragment (T4) has an
insertion of 132 bp at position 249, which corresponds to an
Alu Sq sequence in an inverted orientation, while the other one (T1) has a deletion of 75 bp between positions 249 and 324. Within
a single tissue, the four bands are not expressed at the same level, T2
being the most abundant. However, from one tissue to the other, the
relative ratios of the four bands are roughly the same (not shown).
Translation of the cDNAs suggests that three of the four transcripts
(T1, T2, and T4) may give rise to a protein of 55 kDa.
Interestingly,
the DNA insertion in transcript T3 introduces an
ATG initiation codon
upstream from the first one found in the
other transcripts (Fig.
1).
This finding suggests that a second
putative protein of 63 kDa,
exhibiting an 81-amino-acid extension
at its N-terminal extremity
compared to the other protein, may
be translated. Using anti-hStau
antibodies in Western blot experiments,
we observed two protein bands
of around 63 and 55 kDa in human
cell extracts (Fig.
2B). To determine
whether our cDNAs could
account for the presence of the two proteins,
we subcloned the
T2 and T3 transcripts in an expression vector and
expressed them
in mammalian cells. As seen in Fig.
2C, each cDNA gives
rise to
a single overexpressed protein which perfectly comigrates with
one of the endogenous proteins. Altogether, these results demonstrate
that the
hstaufen gene produces four different transcripts
and
that the transcripts code for two highly homologous proteins which
differ in their N-terminal
extremities.
Comparison of the mammalian and Drosophila Stau
proteins.
The amino acid sequences of the mammalian proteins are
similar to that of the Drosophila Stau protein and of the
product of an uncharacterized open reading frame on the X chromosome of
Caenorhabditis elegans (Fig. 2D). The overall structures and
relative positions of the full-length and short RBDs are well
conserved, and high sequence identity is found between corresponding
dsRBDs. This is highly significant since an alignment of the domains
found in the members of the dsRNA-binding protein family shows an
average of only 29% amino acid identity to one another
(54). In addition, domains 1 and 4 in the human sequence,
which are short domains compared to the consensus, are nevertheless
highly similar to the corresponding fly sequences, even in the region
that extends far beyond the N-terminal side of the consensus sequence,
suggesting that they must play an essential role in Stau function.
Mammalian Stau does not contain the first dsRBD or the long N-terminal
sequence of the
Drosophila protein which was shown
to bind
to oskar protein (
5). In addition, a putative TBD located
between the third and fourth dsRBDs of mammalian Stau is not found
in
the
Drosophila protein, at least at the amino acid level.
This
region contains a stretch of 91 amino acids which show 25% amino
acid identity (66% similarity) to a microtubule-binding domain
of
microtubule-associated protein 1B (MAP1B) (
65). It is
meaningful
that the sequence similarity covers the full
microtubule-binding
domain of MAP1B and that it is restricted to this
domain. Putative
nuclear localization signals are also
present.
hStau and mStau bind dsRNAs.
As seen
in Fig. 2D, mammalian Stau proteins contain multiple dsRBDs. To
determine whether Stau binds RNAs, we used two bacterially expressed
fusion proteins, His-hStau and MBP-mStau, in an RNA-binding assay. The
fusion proteins were probed with in vitro-labeled bicoid mRNA, which is known to adopt an extensive secondary structure and to
strongly bind to Drosophila Stau protein, both in vivo and
in vitro (18, 54). Both fusion proteins strongly bind this
RNA. The binding is competed by a 100-fold excess of cold poly(rI)-poly(rC) but not by a 1,000-fold excess of poly(rI), poly(rC),
poly(rA), or poly(U) or by tRNA or dsDNA (Fig. 3A and B), suggesting that mammalian Stau
recognizes double-stranded structures in the RNA rather than a
sequence-specific region. Both fusion proteins also directly bind
labeled dsRNAs and RNA-DNA hybrids but not single-stranded RNA or DNA
homopolymers (Fig. 3A and C). As controls, bacterial extracts
containing overexpressed His-neutral endopeptidase or
MBP-aminopeptidase fusion proteins were also included on each blot;
they did not bind any of these nucleic acids. We also tested other in
vitro-labeled RNAs such as those coding for tubulin, neuropeptides from
Aplysia, and nuclear RNP B. All of these RNAs bind to Stau
in vitro, as reported previously for other members of the dsRNA-binding
protein family. This finding demonstrates that both hStau and mStau,
regardless of the protein to which they are fused, are able to bind
dsRNAs. However, there is no sequence specificity, as reported for
other members of the dsRNA-binding protein family (21, 54,
55).

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FIG. 3.
RNA-binding assay. Bacterially expressed His-hStau (A,
lanes S) and His-neutral endopeptidase (A, lane N) fusion proteins or
bacterially expressed MBP-mStau (B and C, lanes S) or
MBP-aminopeptidase (B and C, lanes A) fusion proteins were
electrophoresed on a polyacrylamide gel, transferred to nitrocellulose,
and incubated with 32P-labeled nucleic acids, in the
presence or absence of cold competitors, as indicated below each gel.
After extensive washing, binding was detected by autoradiography. A
representative Coomassie blue staining of the blots is shown on the
left (A and B). Arrows, positions of overexpressed Stau; arrowheads,
positions of overexpressed control proteins. Lanes M, molecular weight
markers.
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Filter binding assays, using Ni-NTA-purified His-hStau (inset), were
used to determine the binding affinity of Stau (Fig.
4). High-affinity binding, with a
Kd of about 10
9 M, was observed
when the 3' UTR of
bicoid or double-stranded
RNA was used as
a probe (Fig.
4A). The resulting sigmoidal curves
suggest that Stau
cooperatively binds dsRNAs. In contrast, only
low-affinity
binding was observed with single-stranded RNAs, confirming
that Stau
specifically binds dsRNAs (Fig.
4B).

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FIG. 4.
RNA-binding assay in solution. Dilutions of the purified
His-hStau fusion protein were incubated with fixed amounts of labeled
RNAs, and the RNA-protein complexes were filtered through
nitrocellulose membranes. (A) RNA-binding affinity to dsRNAs.
Triangles, 3' UTR of bicoid RNA; squares, poly(rI)-poly(rC).
The results are presented as a percentage of maximal retained probe and
are the averages of three independent experiments done in duplicate.
Inset, Coomassie blue staining of Ni-NTA-purified His/hStau after
separation by SDS-PAGE. (B) RNA-binding affinity to RNAs. Squares,
poly(rI)-poly(rC); triangles, poly(rI); inverted triangles, poly(rC);
diamonds, BSA with poly(rI)-poly(rC), used as a control. The results
are presented as a percentage of bound radioactivity and represent a
single experiment done in duplicate. The same results were obtained in
two other independent experiments.
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hStau and mStau bind tubulin in vitro.
As described above,
Stau contains a region which is similar to the microtubule-binding
domain of MAP1B. To determine whether mammalian Stau can bind tubulin,
bacterially expressed MBP-Stau fusion proteins were used in a
tubulin-binding assay. As shown in Fig.
5, hStau binds tubulin in vitro. As a
control, the bacterially expressed MBP-aminopeptidase fusion protein
was also included on the blot; it did not show any tubulin-binding
capability. Under the same conditions, hStau cannot bind actin (Fig.
5), which suggests that the binding of tubulin to Stau is specific. The
same results were obtained with the MBP-mStau fusion protein (Fig. 6B,
lane 1). Binding to mRNAs and
microtubules are two of the characteristics expected of localizing
proteins, making hStau and mStau very good candidates for mRNA
transport and localization in mammals.

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FIG. 5.
Tubulin-binding assay. Bacterially expressed MBP-hStau
(lanes S) or MBP-aminopeptidase (lanes A) fusion proteins were
electrophoresed on SDS-polyacrylamide gels, transferred to
nitrocellulose, and incubated with tubulin or actin. After extensive
washing, tubulin and actin were detected with monoclonal antitubulin
and antiactin antibodies, respectively. As controls, the same
experiments were performed in the absence of either tubulin or
antitubulin antibodies. Purified actin was also loaded on the gel as a
control (lane C). Sizes are indicated in kilodaltons.
|
|

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FIG. 6.
Molecular mapping of the dsRBD and TBD. Bacterially
expressed MBP-mStau (lanes 1), MBP-mStau deletion mutants (lanes 2 to
7), or MBP-aminopeptidase (lanes C) fusion proteins were
electrophoresed on a polyacrylamide gel, transferred to nitrocellulose,
incubated with either 32P-labeled 3'-UTR bicoid
RNA (A) or tubulin and antitubulin antibodies (B), and revealed as
described above. (C) Schematic representation of the mutant proteins.
Their RNA- and tubulin-binding responses are indicated.
|
|
Molecular mapping of the RBD and TBD.
To determine which Stau
domain(s) is involved in RNA and/or tubulin binding, the MBP-mStau
fusion protein was used to construct a series of deletion mutants (Fig.
6). The production and relative abundance of each fusion protein was
first verified by Western blotting (not shown). Using the RNA-binding
assay, we demonstrated that both of the full-size dsRBDs (dsRBD2 and
dsRBD3) are independently sufficient to bind bicoid RNA (Fig. 6A). In
contrast, the two short domains (dsRBD1 and dsRBD4) were unable to bind
dsRNA in this assay. We also demonstrated that the C-terminal half of
mStau is able to bind tubulin (Fig. 6B, lane 4). More specifically, the
region which is similar to the MAP1B microtubule-binding domain is
sufficient to bind tubulin (Fig. 6B, lane 6). These experiments confirm
that the regions that we identified by sequence comparison as putative
dsRBDs and TBDs are biochemically functional.
Stau is associated with the detergent-insoluble fraction in
vivo.
We next addressed the cellular distribution and cytoskeletal
association of the two hStau proteins in vivo. To do so, we fused GFP
or an HA tag to the 63- and 55-kDa hStau isoforms, respectively. Using
confocal microscopy, we first showed that the two fusion proteins
colocalize when coexpressed in mammalian cells (not shown). Then, we
showed that they are nonhomogeneously distributed throughout the
cytoplasm and label numerous vesicular and tubular structures which
concentrate in the perinuclear region (Fig.
7A). Minimal staining was found in the
nucleus. When the cells were treated with Triton X-100 prior to fixing,
allowing soluble proteins to be separated from the cytoskeleton and
cytoskeleton-associated proteins (44), the tubulovesicular
labeling was still present, demonstrating that hStau is associated with
the detergent-insoluble material in vivo (Fig. 7B). Labeled structures
were also present in cell processes, suggesting that Stau may target
mRNAs to peripheral ER elements. The same results were obtained
following expression of the GFP-mStau protein (not shown). The
association between hStau and the cytoskeletal-associated material was
confirmed by in vitro cell fractionation in the presence of Triton
X-100. In this assay, hStau partitioned mainly in the
cytoskeleton-associated fractions, although a significant fraction was
found in a soluble form, as judged by Western blotting (not shown).

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FIG. 7.
Subcellular localization of the hStau-GFP fusion
proteins. COS7 cells were transfected with cDNAs coding for either the
hStau-GFP (A and B) or TBD-GFP (C) fusion protein, or GFP alone (D).
Untreated (A, C, and D) or Triton X-100-treated (B) cells were fixed
and visualized by autofluorescence. Bar = 20 µm.
|
|
To determine whether the tubulin-binding domain identified in vitro is
truly involved in this function in vivo, we transfected
mammalian cells
with a cDNA coding for a fusion protein in which
the minimal TBD was
fused to GFP. In contrast to the full-length
protein, the TBD-GFP
fusion protein is randomly distributed in
the cytoplasmic and nuclear
domains of the cells (Fig.
7C), as
is the GFP protein used as a control
(Fig.
7D). This staining
was completely extracted by the Triton X-100
treatment (not shown),
suggesting that the minimal TBD found in vitro
is not sufficient
to render the protein insoluble and form a stable
association
with the microtubule network and/or the
cytoskeleton-associated
material.
Stau localizes to the RER in vivo.
Interestingly, the pattern
of localization of Stau resembles that of the ER. To test a putative
localization of Stau to the ER, we transfected mammalian cells with a
cDNA coding for a fusion protein in which a HA tag was introduced at
the C-terminal end of the short hStau protein. We then double labeled
transfected cells with anti-HA, to recognize hStau, and with
anticalreticulin or anticalnexin, two markers of the ER. Using a
confocal microscope, we showed that hStau completely colocalizes with
anticalreticulin, although HA-staining appears to be absent in some
parts of the ER, in particular around the nucleus (Fig. 8A to
C). To confirm these
results, we examined the colocalization of Stau and calnexin, a
specific marker for the RER (24) (Fig. 8D to F). The
patterns of staining obtained with anti-hStau and anticalnexin were
identical, demonstrating that hStau colocalizes exclusively with the
RER.

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FIG. 8.
Colocalization of hStau with markers of the RER by
confocal microscopy. A cDNA coding for an hStau-HA fusion protein was
transfected into COS7 cells. Triton X-100-treated cells were fixed and
double labeled with anti-HA (B) and anticalreticulin (A) or with
anti-HA (E) and anticalnexin (D). Anti-HA was detected with Texas
red-coupled anti-mouse IgG antibodies, using the Texas Red channel;
anticalreticulin and anticalnexin were detected with
fluorescein-conjugated anti-rabbit IgG antibodies, using the
fluorescein channel. Panels C and F are superpositions of panels
A plus B and D plus E, respectively. No overlap was observed between
the fluorescein and Texas red channels. Bar = 10 µm.
|
|
 |
DISCUSSION |
The transport and localization of specific mRNAs have important
functions in cell physiology. For example, mRNA targeting plays a key
role in the formation of cytoskeletal filaments and in the
establishment of morphogenetic gradients (55). However, the
nature of the RNP complexes as well as the mechanisms involved in these
processes are still largely uncharacterized. In this paper, we describe
a novel RNA-binding protein which localizes to the RER in mammalian
cells. Although its precise role is still unclear, its biochemical and
molecular properties strongly suggest that it is involved in mRNA
transport and/or localization. Consistent with such a role, we recently
demonstrated that hStau is involved in human immunodeficiency virus
type 1 genomic RNA encapsidation (41). Mammalian Stau was
also found in the dendrites of rat hippocampal neurons in culture, but
not in the axons, and colocalizes with RNPs known to contain mRNA,
ribosomes, and translation factors, suggesting a role for Stau in the
polarized transport and localization of mRNAs in mammalian neurons
(27).
A differential splicing event generates four hStau
transcripts.
The significance of the four different classes of
transcripts is unknown. They arise by differential splicing since each
of the inserts that appears in the 5' end of the cDNAs is flanked by
large introns containing typical consensus splicing sequences (6). They are observed in all the tissues tested by RT-PCR, suggesting that they are not cloning artifacts. The multiplicity of the
transcripts and the short size of the alternatively spliced exons may
explain the fact that a single but diffuse band is visible on the
Northern blot, despite the presence of four transcripts. This
alternative splicing, which changes the 5' UTR of the transcripts, could represent a mechanism by which translation is regulated, although
the presence of similar relative levels of the four transcripts in each
tissue argues against this possibility. Alternatively, these different
classes of transcripts may result from aberrant or incomplete splicing
events. In fact, an unusually large number of cDNA clones containing
intron sequences were isolated, and this may indicate that the splicing
of the premature transcripts is a slow process. The presence of an
Alu sequence in the 5' UTR may arise by the activation of a
resident intronic Alu element as an exon, as reported
previously (35). Many examples of recruitment, via splicing
or intron sliding, of a segment of a resident Alu element
into an mRNA have been reported. It is thought that the presence of a
polypyrimidine tract which is the complement of the A-rich tail of the
element when inserted in the reverse orientation contributes to the
creation of the splicing acceptor site. A point mutation, downstream
from this site, may generate the splicing donor site, as reported
previously. The presence of an old Alu subfamily sequence
and of only the right subunit segment of the Alu element is
consistent with this interpretation.
Structure and function of Stau.
We observed that mammalian
Stau, like all members of the dsRNA-binding protein family
(55), can bind any dsRNA or RNAs forming double-stranded
structures in vitro, regardless of its primary sequence, as well as
RNA-DNA hybrids. The latter adopt a conformation that is more closely
related to that of dsRNA than dsDNA, which probably explains why they
can bind to Stau. The fact that the full-length Stau protein, as
observed with single dsRBD, binds to any dsRNA in vitro suggests that
the correspondence between the position of the dsRBDs, and the
arrangement of double-stranded stems in the folded RNAs may not be
sufficient for specificity; posttranslational modifications and/or
essential cofactors capable of forming complex RNP structures along
with mRNA molecules could be necessary to discriminate between
different RNA secondary structures. Packaging of mRNAs into RNP
complexes (1, 18, 20, 32), the intermolecular dimerization
of the localization signal of bicoid mRNA (19),
and the involvement of untranslatable hnRNAs in mRNA transport
(31, 59, 60) are consistent with this interpretation. Until
now, specific mRNA-Stau interactions were shown in vivo only after
injection of different RNAs into Drosophila embryos, but the
mechanisms underlying the specificity are not known (18).
Since specific RNA binding cannot be obtained in vitro, it precludes
the use of classic techniques to isolate and identify relevant RNAs
which would bind staufen in vivo. Cross-linking of mRNA to Stau in vivo
and isolation of the resulting complexes will be necessary to identify
the nature of bound RNAs.
Regardless of their limitations, the in vitro assays did allow us to
map the molecular determinants which are necessary and
sufficient to
bind RNAs. The presence of two functional domains
in the mammalian Stau
contrasts with what has been reported for
other members of the
dsRNA-binding protein family, which contain
multiple full-length dsRBDs
but only one that is biochemically
functional (
21,
34,
39,
48). Interestingly, full-length
dsRBDs incapable to bind dsRNA by
themselves can do so when joined
to another inactive full-length
domain, suggesting that multiple
domains present in a given protein
exhibit cooperative binding
effect (
34,
48). Whether the two
mStau dsRBDs exhibit similar
or different affinities is not yet
clear.
We mapped the TBD to a region which is similar to a microtubule-binding
domain of MAP1B. Although this region can efficiently
bind tubulin in
vitro, it is not sufficient to bring a TBD-GFP
fusion protein to the
microtubule network. Binding of Stau to
microtubules in vivo may
involve more than one molecular determinant
or the proper localization
and folding of the TBD in the full-length
protein. Indeed, in our in
vitro assay, the fusion protein which
contains the C-terminal region in
addition to the TBD binds tubulin
more efficiently than does the TBD
alone, suggesting that this
region may be necessary for binding to
microtubules in vivo. Interestingly,
the corresponding region of the
Drosophila Stau protein was shown
to bind inscuteable
(
36), a protein with ankyrin domains which
is believed to
associate with the cytoskeleton (
33), suggesting
that
corresponding regions of the mammalian and
Drosophila
proteins
may have functional
similarities.
Alternatively, binding may be weak and/or transitory in vivo, for
example during the early steps of mRNA recruitment, during
mRNA
transport, and/or at mitosis, as found in
Drosophila
(
18,
45,
55). These steps may be difficult to observe by
immunofluorescence
in some cell lines (
18) and/or be masked
by the anchoring of
the protein to the RER. A similar conclusion was
reached when
binding of MAP1B to the microtubule network was studied
(
65),
suggesting that weak binding to the cytoskeleton may
be a characteristic
of proteins containing this type of TBD. These
steps may nevertheless
be necessary to allow the efficient and flexible
transport of
RNA along the cytoskeleton. Interestingly, the
immunoelectron
microscopic observation of dendrites of hippocampal
neurons in
culture showed the presence of abundant gold particles close
to
microtubules, strongly arguing in favor of a Stau-microtubule
association in these cells (
27). In
Drosophila,
there is no
evidence that Stau directly binds to the microtubule
network,
although Stau-dependent mRNA transport was shown to rely on
this
structure (
45,
55).
Our studies demonstrate that Stau is anchored to the RER and that the
putative TBD is not involved in this function. Indeed,
preliminary
results suggest that the binding of Stau to the RER
is carried out by
one of the RBDs (
40). Similar domains in other
members of
the dsRNA-binding proteins were previously shown to
be involved in
protein dimerization and/or in protein-protein
interactions (
4,
8). This finding also suggests that different
Stau molecular
determinants are necessary for binding to tubulin
and anchoring to the
RER. This is consistent with previous findings
demonstrating that in
Xenopus and
Drosophila, mRNA localization
was
likely to occur via successive steps involving different elements
of
the cytoskeleton and overlapping molecular determinants
(
55).
Localization of Stau to the RER.
When expressed in mammalian
cells, Stau isoforms show a tubulovesicular pattern of localization
which is found more abundantly in the perinuclear region. Besides
ribosomal proteins, Stau is the first RNA-binding protein shown to be
associated with the RER in mammals. No signal peptide or putative
hydrophobic transmembrane domains are present in either the long or
short Stau proteins, indicating that they are cytosolic proteins and
not residents of the RER and that their association to the RER is
likely to reflect their mRNA transport function. Two recent papers also suggest that mRNA transport may be linked to the ER or ER-like structures. In Xenopus oocytes, Vera, a Vg1
mRNA-binding protein, was shown to cosediment with TRAP
, a protein
associated with the protein translocation machinery of the ER. However,
in contrast to Stau, Vera-Vg1 complexes were found
associated only with a small subdomain of the ER, which was of the
smooth variety (12). Similarly, in Drosophila, at
least some steps in mRNA transport in nurse cells and oocytes seem to
occur within ER-like cisternae (64). As observed for the
Vg1 mRNA-SER interaction in Xenopus, this
structure seems to exclude most ribosomes, suggesting that translation
is not the major function of these associations.
hStau and mStau represent new members of a large family of proteins
involved in the transport and/or localization of mRNAs
to different
subcellular compartments and/or organelles. Stau,
the TAR RNA-binding
protein and
X. laevis homologue Xlrbpa, and
Spnr were shown
to colocalize with the RER (this paper), with
ribosomes and hnRNPs
(
14), and with the microtubular array of
spermatids
(
49), respectively. Our results strongly suggest
that
Stau-mRNA RNP complexes are transported along the microtubule
network
and then anchored to the RER. It is well known that the
ER is
associated with the microtubule cytoskeleton (
57).
Therefore,
a transient interaction between microtubules and Stau may
facilitate
the localization of Stau and the targeting of mRNA to the
RER.
One of the roles of Stau might be to transport and localize
specific
mRNAs to the RER, such as those coding for secreted or
membrane
proteins which have to be translocated to the RER. This would
bring them in proximity to the signal recognition particles and
RER,
thus facilitating translation and translocation. The presence
of Stau
in cell processes, in association with ER structures,
may represent a
first clue to understanding the role of many mRNAs
which were found to
be localized in neuronal processes (
51).
Stau may facilitate
the transport of mRNAs to cell processes to
ensure efficient local
translation and translocation. In addition,
the presence of multiple
Stau-like proteins in mammals creates
the possibility that different
members of the family can target
subclasses of mRNAs to different
subdomains of the ER. This phenomenon
has been described before and is
thought to be the first step
in the differential targeting of proteins
in polarized cells (
43).
We do not exclude the possibility that Stau plays additional roles in
mammals; Stau may first be linked to the RER for storage,
and then a
subset of molecules may be recruited by specific mRNAs
and/or cofactors
to form RNP complexes that will be transported
along microtubules
toward their final destination. The presence
of large amounts of Stau
in the perinuclear region, which could
be awaiting the
nucleocytoplasmic transport of mRNAs, is consistent
with this
possibility. The presence of a putative nuclear localization
signal
even suggests that Stau transits through the nucleus before
being
localized in the cytoplasm and plays a role in mRNA or rRNA
export.
Alternatively, Stau may play key roles in the translational
regulation
of localized mRNAs, as is the case for
Drosophila Stau,
which is essential for the translation of
oskar mRNA, once
it
is localized at the posterior pole (
29). Indeed, since
polysomes
and ER-bound ribosomes are not extracted by Triton X-100, it
is
possible that Stau is associated with the RER via ribosomes and/or
mRNAs. Characterization of mRNAs and putative cofactors which
bind to
staufen will be necessary to understand the
process.
In vertebrates, the mechanisms which underly the transport of mRNAs
have not yet been deciphered. Characterization of the
RNAs and proteins
involved in transport and localization is particularly
important since
understanding the mechanisms responsible for the
transport of mRNAs is
fundamental for learning more on the development
of polarity in cells,
both during mammalian development and in
somatic cells, at a time where
RNA-based gene therapy is being
considered as a possible approach to
cure different
disorders.
 |
ACKNOWLEDGMENTS |
We thank Luis Rokeach (Department of Biochemistry, University of
Montreal) for the anticalreticulin antibodies, John Bergeron (McGill
University) for the anticalnexin antibodies, and André Royal
(Department of Pathology and Cell Biology) for the mouse cDNA library.
We thank Luis Rokeach and Lea Brakier-Gingras for comments and
discussion and Michael Kiebler for sharing unpublished information.
The first two authors contributed equally to this work.
This work was supported by a Natural Sciences and Engineering Research
Council of Canada grant to L.D., a National Health Research Development
Program grant to L.D., and a Medical Research Council of Canada grant
to I.R.N.
 |
FOOTNOTES |
*
Corresponding author mailing address: Department of
Biochemistry, University of Montreal, P.O. Box 6128, Station Centre
Ville, Montreal, Quebec, Canada H3C 3J7. Phone: (514) 343-5802. Fax: (514) 343-2210. E-mail: desgros{at}bcm.umontreal.ca.
 |
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Molecular and Cellular Biology, March 1999, p. 2220-2230, Vol. 19, No. 3
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