Institut National de la Recherche
Agronomique, Unité d'Endocrinologie Cellulaire, Laboratoire de
Différenciation Cellulaire et Croissance, 34060 Montpellier Cedex
1, France,1 and Physiologisches
Institut, Universität Heidelberg, D-69120 Heidelberg,
Germany2
Received 11 March 1999/Returned for modification 28 April
1999/Accepted 1 September 1999
 |
INTRODUCTION |
The regulation of mitochondrial
activity by thyroid hormone is well documented. Triiodothyronine (T3)
increases the number of mitochondria (20, 24-25) and
mitochondrial protein synthesis (33). This hormone is thus
considered to be a major regulator of mammalian mitochondrial
biogenesis (33). T3 also stimulates mitochondrial metabolism
(46) and, in particular, oxidative phosphorylation (48,
50). Some of these effects could involve activation of
mitochondrial genome transcription induced by T3 (10, 29,
34). However, the molecular nature of these influences remains
highly controversial. In particular, the evidence of mitochondrial high-affinity T3 binding sites which has been provided (19, 23,
49) leads to the proposition of direct action of the hormone on
the organelle. Unfortunately, conflicting data and the controversial identification of the ADP/ATP translocator as a T3 mitochondrial receptor has complicated interpretation of this hypothesis. In parallel, the observation that T3 could activate a nuclear gene encoding mt-TFA (18), a potent mitochondrial transcription
factor (13, 14), suggests that almost all aspects of the
regulation of mitochondrial activity by thyroid hormone could involve
the nuclear pathway. However, a recent study by Enriquez et al.
(11) demonstrated that T3 acts directly at mitochondrial
level to regulate RNA synthesis in the organelle.
In line with this work, previous studies have shed new light on the
action of T3 at the mitochondrial level. First, in addition to the
47-kDa full-length T3 nuclear receptor c-ErbA
1, Bigler and Eisenman
(4) reported the occurrence of several smaller size cellular
c-ErbA
proteins in chicken erythroid cells, some of which displayed
an extranuclear location. Moreover, these authors demonstrated that
these proteins are synthesized by the use of internal AUGs identified
in the c-erbA
1 mRNA (5). Second, by a number
of convergent experimental approaches, we established that a 43-kDa
protein related to c-ErbA
1 is located in the mitochondrial matrix
(54), i.e., via Western blots with highly purified rat liver
mitochondrial extracts and two different antisera raised against
c-ErbA, immunoprecipitation of a T3-binding 43-kDa mitochondrial protein with one of these antisera, and electron microscopy. In addition, by using DNA binding analysis, we presented evidence that
this mitochondrial protein specifically bound to a natural or a
synthetic T3 response element (T3RE). Finally, in CV1 cells, by using
an expression vector driving the synthesis of a 43-kDa c-ErbA
1
protein from an internal AUG identified by Bigler et al.
(5), we found that this protein was localized in the
mitochondrion. Interestingly, a recent report of Andersson and
Vennström (1) also pointed out that such a protein
displays an extranuclear location. Moreover, overexpression of the
protein in the same cells induced significant stimulation of
mitochondrial activity (54). These data lead us to propose
that this truncated c-ErbA protein we called p43 could be a
mitochondrial T3 receptor involved in some aspects of the direct
influence of the hormone on the organelle (54).
On the basis of these observations, in the present experiments we
tested mitochondrial import of p43 and its transcriptional activity by
using isolated rat liver mitochondria or living cells. We report here
that p43 is a potent T3-dependent transcription factor of the
mitochondrial genome, thus clearly demonstrating the existence of
direct T3 regulation of mitochondrial gene expression.
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MATERIALS AND METHODS |
Construction of plasmids and reporter genes.
The mouse D
loop was generated by PCR (5'-ACATCAAGAAGAAGGAGCTACTCCC
[positions 15347 to 15372] and 3'-CGGT-CTATGGAGGTTTGCATGTG [positions 113 to 136]) from the pST41 plasmid encoding the
complete mouse mitochondrial genome (3), kindly provided by
D. Ricquier (Centre National de la Recherche Scientifique Meudon,
France), and cloned into the pBluescript SK vector. The pD-loop-tk-CAT reporter gene was constructed by insertion of a 1.1-kb
HindIII-BamHI fragment of the
SK-D-loop into the HindIII-BamHI site of
pBL-CAT8+. pDR2-tk-CAT and pRSV-tk-CAT reporter plasmids were
constructed by insertion of an oligonucleotide sequence containing
natural T3REs (DR2 oligonucleotide,
5'-AGCTTGTCAAGGCATGAAGGTCAGCACG-3'; RSV oligonucleotide,
5'-AGCTTGTCATGCCTTCCTCAACATAGCCGTCAAGGCATGAAGG-3'), found in the rat D loop, into the
HindIII-BamHI sites of pBL-CAT. pSG5-FE6,
pSG5-
1, and pSG5-
2 were constructed by insertion of the 1.5-, 1.1-, and 1.0-kb EcoRI fragments, respectively, encoding c-ErbA
1, p43, and p43-
DBD into the EcoRI site of pSG5.
The inserts were generated by EcoRI digestion of the pF1,
pF1
met1, and pF1
met2 plasmids, kindly provided by J. Bigler and
R. N. Eisenman (5). pSG5-mtTFA was constructed by
insertion of a 1.3-kb BamHI-BglII fragment of the
pQE9-hmtTFA plasmid encoding h-mtTFA into the BamHI-BglII sites of pSG5.
Mitochondrial import.
Import experiments were performed
according to the method of Komiya and Mihara (26) by using
highly purified isolated rat liver mitochondria (54).
Mitochondria were incubated for 45 min in the presence of 5% rabbit
reticulocyte lysate containing [35S]methionine-labeled
proteins (c-ErbA
, c-ErbA
0, c-ErbA
1, p43, p43-
DBD, mt-TFA,
and pO-DHFR synthesized from the SG5-THR
, SG5-THR
0, SG5-FE6,
SG5-
1, SG5-
2, SG5-h-mtTFA, and sp64-pO-DHFR plasmids, respectively, the latter kindly provided by G. C. Shore)
(45). After import experiments, mitochondria were treated
with proteinase K as previously described (26). Then, 10%
of the amount of reticulocyte lysate added to mitochondria for the
import experiments was loaded in the control lane. To assess the
presence of p43 in the mitochondrial matrix, matrix extracts were
prepared after p43 import studies by using an osmotic shock procedure
as described by Goglia et al. (19). Purity of matrix
extracts was assessed by measurement of cytochrome oxidase activity,
which remained lower than the limit of detection of the assay. As
indicated in the legend, mitoplasts were prepared by digitonin
treatment as previously described by Darley-Usmar et al.
(9), mitochondria and rabbit reticulocyte lysates were
depleted for ATP and ADP by apyrase treatment, or the membrane
potential was decreased by 1 µM fluoryl cyanide
m-chlorophenylhydrazone (FCCP) as previously described
(26).
Cytoimmunofluorescence.
Stable transfection of CV1 cells and
cytoimmunofluorescence studies of p43 were performed as described by
Wrutniak et al. (54). Staining was performed with a
monoclonal antibody raised against a mitochondrial antigen (Anti-Mitok
[Chemicom International, Inc.]; final dilution, 1/30) and with a
polyclonal antibody raised against the c-ErbA carboxy-terminal domain
(rabbit RHT II antiserum [54]), kindly provided by M. Dauça (Université de Nancy, France) (final dilution,
1/100).
Electromobility shift assays (EMSAs).
Gel retardation
experiments were performed according to the method of Wrutniak et al.
(54), with 32P-labeled oligonucleotide probes
corresponding to the mitochondrial T3RE-like sequences identified on
the Rattus norvegicus mitochondrial genome (16):
DR0 (ACGTTAGGTCAAGGTGTAGCC; mitochondrial genome positions 743 to 764), Ipal7
(AGCGCGACCTATTTAAGAGTTCATATC;
positions 2371 to 2397), DR2
(GTCAAGGCATGAAGGTCAGCAC; positions
15928 to 15949), and RSV1-TRE
(TTGATGCCTTCCTCAACATAGCCGTCAAGGCATGAAG;
positions 15904 to 15941). A perfect DR4 sequence
(TCAGGTCACAGGAGGTCA) was used as control probe, and a sequence belonging to the myogenin promoter (AGCTTCTCTGTGATTTAATGCCAGCGCG) was used as an unrelated
probe. A 0.7-µg portion of highly purified mitochondrial protein
extracts prepared on heparin agarose columns, as described by Wrutniak et al. (54), was added to each lane. The presence of p43 in the binding complex was assessed by using a monoclonal antibody (LA038
[Quality Biotechnology]; final dilution, 1/10) raised against a
specific sequence of the DNA-binding domain of c-ErbA
(KSFFRRTIQKNLHPTYSC). A full-length c-ErbA
1 protein synthesized in a
baculovirus system was used where indicated (kindly provided by J. Ghysdael, Orsay, France).
T3 binding assays.
p43 affinity for T3
(Ka) was measured in saturation experiments by
using 125I-labeled T3 (3.3 mCi/µg; NEN Life Science
Products) according to the method of Daadi et al. (8).
Nonspecific binding was assessed in simultaneous assays in which a 1 µM concentration of cold T3 was added. Bound and free T3 were
separated by using a Sephadex G-50 column.
Cell cultures and transcriptional activation assays.
Myoblasts of the QM7 cell line (2) were grown in Earle's
199 medium supplemented with 0.2% tryptose phosphate broth, penicillin (100 IU/ml), and 10% T3-depleted fetal calf serum. Serum was T3 depleted according to the method of Samuels et al. (40).
However, after hormonal depletion, significant free T3 and T4 levels
were still detected by radioenzymology (3 and 15 pM, respectively, in
the depleted serum against 6.8 and 86 pM in the control serum).
Transient-transfection assays were performed with QM7 cells by using
expression plasmids and chloramphenicol acetyltransferase (CAT)
reporter genes previously described, in addition to a Rous sarcoma
virus (RSV)-
-galactosidase expression vector, according to the
method of Cassar-Malek et al. (7). Where indicated, 10
8 M T3 was added to the culture medium. All
transfections were normalized according to
-galactosidase activity,
and results were expressed as a percentage of the control value. Data
are presented as the means ± the standard errors of the means
(SEM) of five separate experiments.
In vitro protein synthesis.
Proteins were synthesized
by using the rabbit reticulocyte lysate transcription-translation
TNT kit (Promega) according to the manufacturer's instructions.
For import experiments, reactions were performed by using
[35S]methionine-labeled p43, p43-
DBD, c-ErbA
1,
c-ErbA
, c-ErbA
0, and mt-TFA (pSG5-
1, pSG5-
2,
pSG5-FE6, pSG5-THR
, pSG5-THR
0, pSG5-h-mtTFA, and
psp64-pO-DHFR vectors, respectively).
In organello mitochondrial transcription and translation
assays.
Transcription and translation assays were performed by
using isolated rat liver mitochondria over a 60-min period at 37°C, as described by Ostronoff et al. (37), in the presence of
2% rabbit reticulocyte lysate (containing p43, p43-
DBD, or mt-TFA; unprogrammed lysate for control). Mitochondrial RNA was extracted twice
at room temperature (37). Translation reactions were
performed in the presence of [35S]methionine; newly
synthesized mitochondrial proteins were precipitated with
trichloroacetic acid (TCA) on a Whatman filter 41, washed five times
with 5% TCA-0.1% methionine, twice with ethanol, and dried.
Radioactivity was measured by liquid scintillation counting.
Mitochondrial DNA probes and Northern blot analysis.
DNA
probes were constructed by specific digestion of the pST41 plasmid,
which contains the mouse mitochondrial DNA, and purification of the
specific insert by using the Qiaex II kit (Qiagen). Digestion by
HincII gave a 1,494-pb insert encoding 12S and 16S rRNA.
Specific DNA probes for the mouse mitochondrial cytochrome b
(Cytb), cytochrome c oxidase subunit III (COX III), and
cytochrome c oxidase subunit I (COX I) were generated by PCR
from the pST41 plasmid with the following primers: Cytb
(5'-CCTACCTGCCCCATCCAACAT and
3'-ATGGTTAGAGTCCTTAATAGC), COX III
(5'-CAAACTCATGCATATCACATA and
3'-ATCTGCATTAGACTGAAAAGG), and COX I
(5'-AATCGTTGATTATTCTCAACC and
3'-GTGTAAGCTCCTTGGTTGGAT). S26 ribosomal protein DNA probe
was used as an invariant control as previously described
(52). After in organello mitochondrial transcription
studies, total mitochondrial RNA was analyzed by electrophoresis
through 1.4% formaldehyde-agarose gels or through 1.4% agarose gels
in the presence of deionized CH3HgOH (12) and
then transferred to a nylon membrane. Membranes were prehybridized at
65°C for 30 min (0.5 M phosphate buffer, 1 mM EDTA, 7% sodium dodecyl sulfate [SDS], 1% bovine serum albumin [BSA]), and
[32P]dCTP-labeled DNA probes were added. Hybridization
was carried out at 65°C for 24 h. After hybridization, membranes
were washed according to the following protocol: 2× SSC buffer (25 mM
phosphate buffer, 0.25% SDS) (1× SSC is 150 mM NaCl plus 15 mM sodium
citrate) for 5 min at 65°C, 0.6× SSC buffer (two times) for 20 min
at 65°C, and 0.1× SSC buffer for 5 min at 65°C. Membranes were
exposed to X-ray films and analyzed by densitometric scanning.
Western blot analysis.
A 100-µg portion of control or
p43-overexpressing CV1 cells was analyzed by using RHTII antiserum
raised against c-ErbA. Portions (100 µg) of control or
p43-overexpressing QM7 cells were analyzed with rabbit antiserum raised
against mt-TFA produced by injections of recombinant protein obtained
by purification by Ni2+ affinity chromatography after
E. coli transformation with pQE9-mt-TFA.
 |
RESULTS |
p43 displays a binding affinity for T3 that is similar to that of
the c-ErbA
1 nuclear receptor.
In order to define the p43
binding affinity for T3, we performed saturation experiments with
[125I]T3. After Scatchard analysis, we found that p43
displayed a strong affinity (Ka = 2 · 109 M
1) for the hormone (Fig.
1), a finding similar to that previously recorded for the c-ErbA
1 nuclear receptor
(Ka = 3 · 109
M
1 [42]). This result indicated that
deletion of the amino-terminal domain of c-ErbA
1 did not alter its
ability to bind T3.

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FIG. 1.
Binding affinity of p43 for triiodothyronine. (A)
Saturation experiments were performed with p43 synthesized in rabbit
reticulocyte lysate and labeled with [125I]T3. (B) The
affinity constant (Ka) was estimated by using a
Scatchard linearization of saturation experiments (43). Data
are the means ± the SEM of three separate experiments.
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In contrast to full-length c-ErbA T3 nuclear receptors, p43 is
imported into mitochondria.
The mitochondrial import of p43 or of
the full-length c-ErbA
1 and c-ErbA
1 T3 receptors was studied by
using purified isolated rat liver mitochondria and in vitro-synthesized
35S-labeled proteins in rabbit reticulocyte lysate. As a
positive control, the simultaneous import of the mitochondrial
transcription factor mt-TFA was observed. In addition, at the end of
the experiment, the mitochondrial pellet was subjected to a proteinase
K treatment in order to prevent any possible contamination of
mitochondria by nonimported proteins (26).
As previously reported by Bigler et al. (5), translation
with the pSG5-FE6 vector gave rise to two major c-ErbA
1 proteins with molecular masses of 47 kDa (the full-length T3 nuclear receptor) and 43 kDa (p43), as illustrated in Fig.
2A. Using reticulocyte lysates containing
the two proteins, we detected only the shorter form in the organelle
after import experiments (Fig. 2B, lane 2). Data obtained by using a
35S-labeled p43 protein synthesized from another vector,
pSG5-
1, established the specific mitochondrial import of this
protein as follows: (i) p43 is highly sensitive to proteinase K
treatment (Fig. 2C, lane 2), and (ii) it was protected from proteolysis after the import experiment (Fig. 2C, lane 3). At this step,
solubilization of mitochondria by Tris-NP-40 restored the sensitivity
of p43 to proteinase K (Fig. 2C, lane 4). By contrast, we failed to
detect any significant import of the c-ErbA
1 form of the T3 nuclear receptor (Fig. 2B, lane 4), in agreement with our previous work where
this protein was not detected in mitochondrial extracts (54). However, most nonmammalian vertebrates express a
c-ErbA
0 variant with a very short amino terminus, showing an
important homology with p43 (15). To test the possibility
that c-ErbA
0 could enter into mitochondria, we performed import
experiments with 35S-labeled TR
0 protein synthesized
from the pSG5-THR
0 plasmid. As observed for p43, THR
0 is imported
into mitochondria (Fig. 2B, lane 6). Finally, as expected, mt-TFA was
imported with the predicted protein cleavage (38), thus
validating the experimental procedure (Fig. 2B, lane 8). All of these
results demonstrated that, in contrast to the full-length c-ErbA
1 or
the c-ErbA
1 T3 receptors, the 43-kDa c-ErbA
1 protein is imported
into the mitochondrial matrix.

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FIG. 2.
Import of full-length thyroid hormone receptors
(c-ErbA 1, c-ErbA 1, and c-ErbA 0) and mt-TFA into mitochondria.
(A) p43 is synthesized through the use of an internal AUG of
c-erbA 1 mRNA. (B) Import experiments (+) were performed
with isolated rat liver mitochondria in the presence of 5% rabbit
reticulocyte lysate containing 35S-labeled proteins and
incubated at 30°C for 50 min. Import reactions were stopped by
cooling on ice, and samples were treated with proteinase K to prevent
contamination by nonimported proteins. Mitochondria were collected by
centrifugation, and after SDS-polyacrylamide gel electrophoresis, the
presence of labeled proteins was assessed by exposure to X-ray films.
(C) Sensitivity of p43 to proteinase K before and after mitochondrial
import. Lanes: 1, 10% of the amount of labeled proteins used in import
experiments was loaded; lane 2, treatment of p43 with proteinase K;
lane 3, p43 import experiment; lane 4, treatment with proteinase K
after p43 import and solubilization of mitochondrial membranes by
Tris-NP-40. , Control lane (10% of the amount of labeled proteins
used in import experiments was loaded; +, import experiment; p47,
c-ErbA 1 nuclear receptor; p43, mitochondrial c-ErbA 1 protein; p,
precursor protein; m, mature protein.
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Typical steps involved in mitochondrial protein import have already
been described: (i) binding of the protein to a mitochondrial outer
membrane receptor; (ii) translocation through the outer and inner
mitochondrial membranes, a process generally driven by the
mitochondrial membrane potential; and (iii) unfolding to an active
conformation involving ATP-dependent interactions with mitochondrial
heat shock proteins. In addition, the targeting sequence of almost all
mitochondrial protein imported is cleaved by matrix proteases; however,
if this sequence is included in the mature protein sequence, protein
import does not lead to a reduction in protein size (35).
To assess the involvement of several of these steps in p43
mitochondrial import, we studied the influence of apyrase (used to
deplete ATP and ADP stores) or FCCP (used to decrease the mitochondrial membrane potential). The efficiency of such treatment was validated in
our experimental conditions by using pO-DHFR (a protein where the
matrix targeting signal of mitochondrial preornithine carbamyl transferase was fused to dihydrofolate reductase
[45]). As previously shown (45), pO-DHFR
import occurred with the predicted protein cleavage (Fig.
3A, lane 2) and was strongly inhibited by
apyrase (Fig. 3A, lane 3) or FCCP (Fig. 3A, lane 4). First, p43 size
did not decrease after mitochondrial protein import (Fig. 3B, lane 2),
thus ruling out the pre-sequence cleavage pathway for this protein.
Moreover, removal of the outer membrane by treatment with digitonin
before import did not significantly affect the amounts of p43 recovered
in the matrix extract (Fig. 3B, lane 3), suggesting that interaction of
p43 with the outer mitochondrial receptor is not a prerequisite for its
translocation. In addition, reduction of the mitochondrial membrane
potential by FCCP or depletion of mitochondrial ATP stores by apyrase
did not affect p43 import (Fig. 3B, lanes 5 and 4). Finally, exogenous
T3 addition did not influence p43 import (Fig. 3B, lane 6).

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FIG. 3.
p43 import takes place through an unusual pathway. (A)
pO-DHFR import. p, precursor protein; m, mature protein. (B) p43 import
was studied as described in the legend to Fig. 2. After import and
proteinase K treatment, matrix proteins were specifically extracted by
osmotic shock and loaded in each well. A total of 10% of the amount of
labeled p43 used in import experiments was loaded in the control lane
(lane 1). Prior to import, when indicated, mitoplast and ATP-depleted
mitochondria were obtained respectively after digitonin and apyrase
treatments. Mitochondrial membrane potential was dissipated by the
addition of FCCP prior to import experiments. (C) Time-related changes
in the amount of labeled p43 imported into mitochondria and relative
p43 import expressed as the percentage of the value recorded after 60 min of incubation. Mitochondrial proteins were collected after
increasing times of incubation at 30°C.
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A study of the time course of p43 import demonstrated that the protein
was rapidly imported (Fig. 3C). Significant import was detected within
the first minute of the experiment; in addition, the maximal
mitochondrial p43 level was recorded after 15 min of incubation and did
not change thereafter. In agreement with these data, comparison of the
total amount of p43 present in the reaction medium with the amount of
imported p43 suggested the involvement of a saturable process. To test
this hypothesis, we overexpressed p43 by stable transfection of simian
CV1 cells, which do not express high levels of c-ErbA proteins. In
cytoimmunofluorescence experiments that used the same procedure
(54) no staining was observed with the c-ErbA preabsorbed
RHTII antiserum in control cells tranfected with empty vector (Fig.
4A1). By contrast, with RHTII antiserum
we found a slight labeling (Fig. 4A2). Moreover, as previously
demonstrated when p43 is moderately expressed, the protein was
predominantly localized in the mitochondrion (Fig. 4A3). However, when
it was strongly overexpressed, the protein displayed both a
mitochondrial and a nuclear location (Fig. 4A4). In the present
experiments, the use of an antibody raised against a mitochondrial
antigen (Fig. 4A5) confirmed the colocalization of p43 and mitochondria
(Fig. 4A4 to 4A7). In addition, Western blot experiments were performed
with control or p43 overexpressing CV1 cells in order to assess that
the main protein overexpressed is 43 kDa (Fig. 4B). All of these data
indicate that mitochondrial p43 import is a saturable process and that
the protein is essentially imported into the nucleus after
mitochondrial import saturation. Interestingly, in agreement with the
nuclear location of a testis-specific mt-TFA isoform previously
reported by Larsson et al. (27), we also observed that
significant amounts of mt-TFA reached the nucleus after overexpression
of this mitochondrial transcription factor (data not shown), thus
suggesting that such a feature is not specific to p43.

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FIG. 4.
p43 mitochondrial import occurs according to a saturable
process. (A) Panels: 1, staining of CV1 cells with a c-ErbA-preabsorbed
RHTII antiserum (antibody raised against c-ErbA; final dilution,
1/100); 2, staining of control CV1 cells transfected with empty vector;
3 to 7, staining of CV1 cells overexpressing p43 after stable
transfection; 2 to 4, staining with rabbit RHTII antiserum (final
dilution, 1/100); 3, mild p43 overexpression level leads to a major
mitochondrial p43 location; 4, high p43 overexpression level leads to
simultaneous mitochondrial and nuclear p43 locations; 5, staining with
an antibody raised against a mitochondrial antigen (Anti-Mitok; final
dilution, 1/30) (same microscopic field as in panel 4) (magnification,
×400); 6 and 7, magnification of microscopic fields 4 and 5 demonstrating colocalization of the two antigens. (B) High p43
overexpression in CV1 cells. Western blot experiments were performed
with RHTII antiserum. Proteins (100 µg) were loaded into each lane.
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p43 binds to specific sequences of the mitochondrial genome.
The mitochondrial 43-kDa c-ErbA
1 protein is truncated by a number of
amino acids upstream of the DNA-binding domain of the T3 nuclear
receptor. In addition, we have previously demonstrated that p43
specifically binds to a synthetic palindromic and a natural nuclear
T3RE sequence or to a DR2 sequence identified in the mitochondrial genome (54). This led us to search for other mitochondrial
T3RE (mt-T3RE) sequences. In addition to the initial DR2 sequence, we
found three other potential binding sequences with high similarity to
other T3REs described to date (Fig. 5A):
(i) a DR0 sequence (6) located in the gene encoding 12S
rRNA; (ii) an Ipal7 (inverted palindrome [44]) located
in the gene encoding 16S rRNA; and (iii) a perfect RSV-T3RE-like
sequence differing from that previously published only by the number of
nucleotides between the two half-sites (39). Interestingly,
two of these sequences (DR2 and RSV-T3RE) are located in the D loop
which contains the promoters used by mt-TFA to induce transcription of
the mitochondrial genome.

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FIG. 5.
p43 specifically binds to the four T3RE-like sequences
recorded in the rat mitochondrial genome. (A) T3RE-like sequences
recorded in the rat mitochondrial genome; the first and last
nucleotides of the sequences are numbered according to the
mitochondrial genome sequence reported by Bibb et al. (3).
(B to D) EMSAs were performed with highly purified rat liver
mitochondrial extracts and 32P-labeled nucleotidic probes.
(B) When indicated, an excess of cold T3RE probe or unrelated probe was
added to assess the specificity of binding ("+" = 200-fold molar
excess). (C) When indicated, a monoclonal antibody raised against a
specific sequence of the DNA-binding domain of c-ErbA (LA038; final
dilution, 1/10) was incubated for 15 min with the mitochondrial extract
prior to the addition of the labeled probe. The DR4 probe is used as a
positive control. (D) Comparison of the binding patterns to a DR4 probe
of the full-length c-ErbA 1 protein (synthesized in baculovirus) and
the p43 mitochondrial complex. Bands: 1, c-ErbA 1 monomer; 2, c-ErbA 1 homodimer. The electrophoretic mobility of the mitochondrial
complex is similar to that recorded for the c-ErbA 1 homodimer.
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We performed EMSAs with highly purified mitochondrial extracts by using
these mitochondrial sequences as probes (mt-T3REs). We found that a
mitochondrial protein complex bound to all mt-T3REs, as well as to a
DR4 sequence used as a positive control (Fig. 5B and C). The
specificity of the binding was demonstrated by the strong inhibition of
binding resulting from the addition of an excess of the corresponding
cold probe (Fig. 5B, lanes 3, 6, 9, and 12) and by the inability of an
unrelated DNA probe to compete for binding (Fig. 5B, lanes 2, 5, 8, and
11). Interestingly, whatever the T3RE probe used in the EMSAs, this
mitochondrial complex displayed the same migration pattern, thus
suggesting that a common complex binds to all T3REs. In addition,
preincubation of mitochondrial extracts with an antibody raised against
c-ErbA fully abrogated the binding of the mitochondrial complex to
mt-T3REs, as well as to a DR4 T3RE (Fig. 5C, lanes 2, 4, 6, 8, and 10),
whereas nonrelated antibodies (raised against ADP/ATP translocator or myosin heavy chain) did not (data not shown), demonstrating that p43 is
a major component of this complex. Comparison of the respective binding
patterns of this mitochondrial complex and an in vitro-synthesized full-length c-ErbA
1 protein (TR
) with a DR4-T3RE provided
additional information. As expected, TR
monomer and dimer were
easily detected; in addition, the mitochondrial complex displayed an
electrophoretic mobility similar to that observed for the TR
homodimer (Fig. 5D).
All of these data indicating that p43 is a mitochondrial DNA-binding
protein led us to test its possible transcriptional activity in mitochondria.
p43 is a T3-dependent transcription factor in the mitochondrial
context.
To examine more directly the ability of p43 to activate
mitochondrial transcription, we performed in organello transcription experiments with isolated rat liver mitochondria and p43 or mt-TFA proteins synthesized in rabbit reticulocyte lysate.
By using a COX III probe, two precursor transcripts of >13 kb were
detected on Northern blots after 20 min of film exposure in
mitochondria incubated in the presence of p43 or mt-TFA (Fig. 6A). These transcripts were difficult to
detect in mitochondria incubated in the presence of unprogrammed
reticulocyte lysate, requiring a much longer film exposure (up to 3 days) to obtain evidence of their presence (Fig. 6A). These data
indicate that, like mt-TFA, p43 induced a strong increase in the levels
of mitochondrial precursor transcripts in the presence of exogenous T3.
A reduced p43 influence was observed in the absence of exogenous T3, in agreement with the fact that mitochondria are a major compartment of T3
accumulation in the cell (32, 49). In addition, all of the
precursor transcripts induced by p43 or mt-TFA were also detected in
Northern blots performed with other mitochondrial probes (Cytb, ND 5, ND 4, ATPase 6/COX II, ND 6L, COX I, ND 2, or ND 1; Fig. 6B and data
not shown). However, we failed to detect the precursor transcript
population with the 12S and 16S rRNA probes. Interestingly, the size of
precursor transcripts detected in control mitochondria after 3 days of
film exposure corresponded to that obtained in the presence of p43 and
mt-TFA (Fig. 6A). In addition, we found that in the presence of
exogenous T3, p43 induced a strong rise in precursor transcript levels
within 5 min of incubation; such a strong increase was not recorded in the absence of the hormone (Fig. 6C). Overall, these observations agree
with our data from transient-transfection assays (see below) showing
that p43 is a mitochondrial T3-dependent transcription factor. Finally,
although p43-
DBD was imported in significant amounts into the
mitochondrial matrix (data not shown), incubation of mitochondria in
the presence of this protein did not induce any rise in the
accumulation of precursor transcripts levels (Fig. 6D), thus
establishing the absolute requirement of the p43 DNA-binding domain for
transcriptional activity.

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FIG. 6.
p43 induces a T3-dependent increase in mitochondrial
transcripts levels. (A to E) In organello transcription experiments
were performed as described by Ostronoff et al. (37) with
purified rat liver mitochondria in the presence of 2% rabbit
reticulocyte lysate (unprogrammed lysate for control mitochondria, p43,
or mt-TFA) and incubated at 37°C for 60 min. When indicated,
10 8 M T3 was added to the incubation medium.
Transcription experiments were stopped by cooling on ice. Mitochondria
were collected by centrifugation, and mitochondrial RNA was extracted
twice at room temperature. (A to D) After in organello transcription
experiments, precursor transcripts were detected by Northern blotting
with the indicated mitochondrial probes. Duration of film exposure is
indicated under the probe. (A and B) Precursor transcript levels
recorded after 60 min of in organello transcription. (C) Time-related
changes in precursor transcript levels in the presence of p43
(±10 8 M T3). Transcription experiments were performed in
the presence of cold p43 and incubated at 37°C for increasing times.
(D) Transcription experiments were performed in the presence of cold
p43 or p43- DBD and then incubated at 37°C for 60 min with T3
(10 8 M). (E) Northern blot experiments were performed
with agarose slab gels containing deionized CH3HgOH after
in organello transcription studies. Mature transcripts are detected by
hybridization with the indicated mitochondrial probes after 60 min of
in organello transcription. (F) Influence of T3 and/or p43 on the value
of the mitochondrial mRNA/rRNA ratio. The ratios were obtained after
densitometric analysis of CytB and 12S plus 16S rRNA.
|
|
In further experiments, we studied the appearance of mature transcripts
by using 16S and 12S rRNA and Cytb probes in Northern blot experiments.
As expected, mt-TFA stimulated accumulation of these transcripts
independently of the presence of exogenous T3 (31). A
similar influence was observed for p43, and it was potentiated by
exogenous T3 (Fig. 6E). Therefore, these data demonstrated that p43 and
mt-TFA induced 16S and 12S rRNA transcription despite their not being
detected in the precursor transcript population. As previously
described (11), when the relative amount of mRNA was
compared with the amount of rRNAs, T3 addition induced a twofold increase in the value of the mRNA/rRNA ratio relative to that of the
control (Fig. 6F). Interestingly, we found that this hormonal influence
was moderately potentiated by the presence of p43, increasing this
ratio up to fourfold (Fig. 6F). These alterations in the mRNA/rRNA
ratio suggest that this T3 receptor is involved in the hormone-induced
shift of the relative expression of mitochondrial mRNA and rRNA.
In addition, using the same experimental procedure, we tested the
influence of p43 on mitochondrial protein translation by measuring
[35S]methionine incorporation. Whereas mitochondrial
translation was efficiently inhibited by chloramphenicol in these
experiments (data not shown), incorporation of labeled methionine was
stimulated threefold by mt-TFA (Fig. 7).
Interestingly, in the presence of T3, p43 also enhanced this
incorporation up to threefold compared to the level of incorporation of
control mitochondria (Fig. 7). As expected from the previous results,
p43-
DBD had no influence on methionine incorporation (Fig. 7).

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FIG. 7.
p43 induces a T3-dependent increase in mitochondrial
translation. In organello translation experiments were performed as
described for Fig. 6 in the presence of [35S]methionine
and incubated at 37°C for 120 min. Translation experiments were
stopped by cooling on ice. Mitochondria were collected by
centrifugation, and mitochondrial proteins were TCA precipitated on
Whatman filter 41, washed five times with 5% TCA, and then washed
twice with ethanol. Radioactivity was measured by liquid scintillation
counting. [35S]methionine incorporation into
mitochondrial proteins was expressed as a percentage of control values.
Data are presented as the means ± the SEM of five separate
experiments. When indicated, 10 8 M T3 was added to the
incubation medium.
|
|
Transient-transfection experiments indicate that mt-T3REs located
in the mitochondrial D loop are involved in p43 transcriptional
activity.
Taking advantage of the fact that strong overexpression
of p43 and mt-TFA results both in a mitochondrial and a nuclear
location of the protein, we performed transient-transfection
experiments with QM7 myoblasts to assess the involvement of the mt-T3RE
located in the mitochondrial sequences in the transcriptional activity of p43. For this purpose, CAT reporter genes under the control of the
mitochondrial D loop or the two sequences of mt-T3RE located in the D
loop (RSV-T3RE and DR2) were constructed (Fig.
8A) and cotransfected with an expression
vector for p43 or mt-TFA (pSG5-mt-TFA). Stimulatory activities of p43
and mt-TFA used as a positive control were simultaneously observed. In
addition, a deleted p43 protein without a DNA-binding domain
(p43-
DBD) was also expressed in these experiments to assess the
direct involvement of p43 DNA binding in transcriptional activation.

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FIG. 8.
p43 expression induces a T3-dependent stimulation of the
activity of reporter genes driven by the D loop or mitochondrial T3REs.
(A) Representation of the construction used in CAT assays. (B)
Transient-transfection assays were performed with T3-deprived QM7 cells
by using the expression vectors and CAT reporter genes indicated in the
figure. All results were normalized according to the -galactosidase
activity and are expressed as percentages of the control value. Data
are presented as the means ± the SEM of five separate
experiments. When indicated, 10 8 M T3 was added to the
culture medium.
|
|
When a reporter gene driven by the mitochondrial D loop was used,
expression of mt-TFA induced a twofold stimulation of reporter gene
activity (Fig. 8B1). Interestingly, p43 expression induced a fourfold
induction of CAT activity dependent on the presence of T3. Moreover, in
experiments with reporter genes under the control of the mt-DR2 or the
mt-RSV-T3RE sequences, where mt-TFA was devoid of any transcriptional
activity, p43 displayed activity similar to that recorded for the
D-loop construct (Fig. 8B2 and 8B3). In all experiments, p43-
DBD
failed to stimulate reporter gene activity, thus demonstrating that p43
binding to its response element is needed to induce gene reporter
activation. Overall, these data suggest that p43 could be a
T3-dependent transcription factor of the mitochondrial genome using
response elements located in the D loop which differ from those used by
mt-TFA.
p43 overexpression increases mitochondrial transcript levels in
living cells.
To test p43 mitochondrial transcriptional activity
in living cells, we stably overexpressed p43 in QM7 myoblasts. In these QM7 cells cultured in a T3-depleted medium, Northern blot analysis with
a COX I probe demonstrated that mitochondrial mRNA levels were enhanced
by p43 overexpression in the presence of exogenous T3 (Fig.
9A). To exclude the possibility that this
influence is mediated by stimulation of mt-TFA expression at the
nuclear level, we performed Western blot experiments with cellular
extracts and an antibody raised against mt-TFA (Fig. 9B). We found that
p43 overexpression and/or T3 have no influence on mt-TFA protein
expression.

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FIG. 9.
Stable p43 overexpression in QM7 cells increases COX I
mRNA levels without affecting mt-TFA expression. QM7 cells were
cultured in a T3-depleted medium according to the method of Samuels et
al. (40), and, when indicated, 10 8 M T3 was
added to the incubation medium. (A) Northern blot analysis with total
RNA extracted from the control or from p43-overexpressing QM7 cells
demonstrated that p43 overexpression increases COX I mRNA levels in the
presence of exogenous T3; amounts of RNA loaded in each lane were
assessed by using S26 mRNA as a control. (B) p43 overexpression in QM7
cells and/or exogenous T3 do not influence mt-TFA protein. Western blot
experiments were performed with an antiserum raised against mt-TFA.
Proteins (100 µg) were loaded in each lane.
|
|
 |
DISCUSSION |
The influence of thyroid hormone at the mitochondrial level
remains a complex and poorly understood field of research. Several kinds of action have been reported, obviously involving different pathways with regard to their respective latency periods (for a review,
see reference 53). For instance, stimulation of
oxidative phosphorylation occurs within minutes of thyroid hormone
treatment (48, 50), whereas a significant enhancement of
mitochondriogenesis is not recorded until after several days
(20). Mitochondrial biogenesis is the result of complex
mechanisms involving, in particular, a coordinated rise in the
expression of nuclear genes encoding mitochondrial proteins and in the
expression of the mitochondrial genome. This observation shows the
importance of the regulation of mitochondrial transcription by T3.
Interestingly, numerous studies report that thyroid hormone stimulates
mitochondrial genome expression (10, 17, 29, 34). This
influence could be partly explained by the finding that T3 increases
the steady-state levels of mt-TFA mRNA (18), encoding a
mitochondrial transcription factor. However, this pathway involving T3
nuclear receptors does not provide a convincing explanation of the
short-term stimulation of mitochondrial transcription induced by T3 in
isolated mitochondria in the absence of nuclear influence (29). Therefore, one attractive possibility is that a
T3-dependent transcription factor directly acts inside the organelle, a
possibility supported by the recent data of Enriquez et al.
(11).
The identification by our laboratory of a 43-kDa c-ErbA
1 protein
located in the mitochondrial matrix displaying simultaneous DNA- and
T3-binding activities (p43, 54) led to the
hypothesis that p43 was similar to a truncated c-ErbA
1 protein
previously characterized by Bigler et al. (5), synthesized
by the use of an internal AUG of the c-erbA
1 messenger. Moreover, we
found that stable overexpression of p43 in CV1 cells stimulated
mitochondrial activity (54), suggesting that this
mitochondrial T3-binding protein was directly involved in some aspects
of the influence of the hormone on mitochondrial activity. This led us
to study the mitochondrial import and function of p43.
In the present study, we first showed that the binding affinity of p43
for T3 is similar to that of the c-ErbA
1 nuclear receptor (42). This result indicated that the amino-terminal deletion occurring in p43 did not alter the T3-binding activity of the protein.
p43 is imported into mitochondria by an unusual pathway previously
reported for a yeast mitochondrial transcription factor.
Import
experiments with isolated mitochondria revealed several interesting
points. First, the inability of the full-length T3 nuclear receptors
c-ErbA
1 and
1 to be imported into mitochondria explains the
previous failure to detect these proteins in the organelle
(54). Second, the rapid import of p43 into the organelle suggests that the amino terminus of the nuclear receptor c-ErbA
1 efficiently abrogates the mitochondrial translocation of the protein. Finally, study of the time course of p43 import suggests that the
protein is internalized into mitochondria according to a saturable process, in agreement with our cytoimmunofluorescence data indicating that p43 displays both a mitochondrial and a nuclear location only when
highly overexpressed. As in our previous work (54), we
failed to detect p43 in rat liver nuclei; p43 nuclear import probably
does not occur under physiological conditions. However, these findings
are in line with the study of Andersson and Vennström (1) indicating that, when overexpressed, a truncated
c-ErbA
1 protein corresponding to p43 could display both a nuclear
and an undefined cytoplasmic location. Moreover, comparison of
c-ErbA
1 and p43 overexpression led these researchers to conclude
that the T3 receptor amino terminus is needed to induce an exclusive nuclear location, in agreement with the present results. Interestingly, the mitochondrial import of TR
0 observed in the present work is also
in line with the results of Andersson and Vennström
(1), indicating that, when overexpressed, the protein
displays a nuclear and a cytoplasmic location. Therefore, these data
suggest that p43 is probably not a unique receptor in mitochondria.
Another set of data demonstrates that p43 import is not affected by
experimental alterations of several important factors normally involved
in mitochondrial protein import, including interaction with the outer
membrane receptor, membrane potential, or mitochondrial ATP stores.
Several studies have underlined that the import of some mitochondrial
proteins could be independent of one or more of the parameters studied.
For instance, cytochrome c or cytochrome c
oxidase subunit Va does not interact with the outer mitochondrial membrane receptor (30, 36, 51), whereas the import of
apocytochrome c is also independent of the mitochondrial
membrane potential (51). More interesting is the observation
that import of the yeast mitochondrial transcription factor MTF1
(28) is similar to that recorded here for p43
(41). Therefore, although quite unusual, p43 mitochondrial
import occurs according to a process already described. Finally, this
import is not affected by hormone, indicating that T3 does not affect
p43 activity by regulating its intramitochondrial level. However,
import mechanisms of MTF1 or p43 are still unknown.
p43 specifically binds to mitochondrial DNA sequences related to
T3REs.
We have previously shown that, in addition to a natural or
a synthetic T3RE sequence, p43 specifically binds to a DR2 sequence located in the D loop of the mitochondrial genome (54). This led us to search for other T3RE-related sequences in the mitochondrial genome by using the following criteria: (i) the presence of two half-sites and (ii) the presence of no more than one base mutation in
each half-site by comparison with the consensus sequence. These are
more stringent criteria than those fulfilled by some natural nuclear
T3REs. In addition to the DR2 motif, three other sequences fit these criteria.
In EMSA where the mt-DR2 and a DR4 sequence were used as positive
controls, a mitochondrial protein complex specifically bound to all
sequences. The abrogation of DNA binding by an antibody raised against
c-ErbA demonstrated that p43 is a major component of the
mt-T3RE-binding complex. In addition, the electrophoretic mobilities
were similar with all probes, suggesting that the same complex binds to
all T3REs. Finally, comparison of the respective electrophoretic
mobilities of the mitochondrial complex and of the full-length
c-ErbA
1 homodimer after DNA binding clearly suggests that p43 does
not bind to mt-T3REs as a monomer. This result agrees with a recent
study indicating that deletion of a sequence included in the c-ErbA
1
amino terminus strongly favors formation of homodimeric complexes
(22). Moreover, this observation raised the question of the
mitochondrial partner(s) involved in this binding. In Western blot
studies, we failed to detect RXR isoforms in rat liver mitochondrial extracts (data not shown). Therefore, we conclude that the p43 mitochondrial complex does not include this major partner of T3 nuclear receptors.
p43 is a mitochondrial T3-dependent transcription factor.
These data led us to study the possible transcriptional activity of p43
mediated by binding to the previously identified mitochondrial DNA
sequences. Using isolated rat liver mitochondria, we found that in the
presence of exogenous T3 p43 induced a dramatic rise in the levels of
mitochondrial precursor transcripts recorded after 60 min of
incubation. In agreement with a previous study of T3 transcriptional
activity in the organelle (29), these changes were detected
after no more than 5 min of incubation. A weaker, more delayed rise in
precursor transcript levels was also detected in the absence of
exogenous T3, possibly as a result of the influence of T3 mitochondrial
stores (32, 49). Overall, the extent and rapidity of the
increase in precursor transcript levels rule out the possibility that
changes in mitochondrial RNA stability are a major factor involved in
the influence of p43 and T3. In addition, this conclusion is also
supported by the observation that the half-lives of mitochondrial rRNA
and mRNA are increased in hypothyroid rats (11).
Finally, the failure of p43-
DBD to stimulate precursor transcript
accumulation indicates that p43 DNA binding is absolutely needed to
induce transcriptional activation. Therefore, p43 fulfills all of the
experimental criteria to be considered as a T3-dependent transcription
factor of the mitochondrial genome: (i) binding to specific
mitochondrial DNA sequences and (ii) T3-dependent transcriptional
activity induced by binding to DNA. Interestingly, these data may also
explain the earlier finding of a previously uncharacterized protein
with a molecular mass of ca. 43 kDa in the mt-TFA-containing fraction
that induces mitochondrial genome transcription (13).
In addition, Northern blot experiments indicated that the precursor
transcripts induced by p43 contain all mitochondrial genes tested
except for the 12S and 16S rRNAs. Such data suggest that these
precursor transcripts detected in our experiments are partially processed. However, since p43 binds to a T3RE located in the DNA region
coding for the 16 rRNA, the possibility that use of this response
element induces transcription of a subunit of the mitochondrial genome,
including all transcripts except the 12S and 16S rRNAs, cannot be
excluded. Despite the lack of previous experimental evidence, this
possibility could satisfactory explain the shift in the mRNA/rRNA ratio
induced by T3 (reference 11 and the present study).
In parallel with the increase in precursor transcripts levels, mt-TFA,
or p43 in the presence of exogenous T3, also induces a significant rise
in the levels of mitochondrial mature transcripts. However, this
influence was smaller than that on the accumulation of precursor
transcripts, suggesting that cleavage of precursor transcripts is a
limiting step for protein synthesis in isolated mitochondria.
Interestingly, p43 induces a stimulation of mitochondrial protein
synthesis to an extent similar to that recorded for mature transcripts.
This observation suggests that, at least in these experimental
conditions, mitochondrial transcription is a crucial target for
regulators of mitochondrial activity.
Taking advantage of the nuclear location of mt-TFA or p43 after
overexpression experiments, we used transfection assays to study the
involvement in p43 transcriptional activity of the two mt-T3RE
sequences located on the mitochondrial D loop. In these experiments,
mt-TFA induced a significant activation of a D-loop reporter gene.
However, mt-TFA activity was restricted to this reporter. By contrast,
p43 stimulated all reporter genes driven by the D loop or mt-T3REs only
in the presence of T3. Therefore, although transcriptional activity of
both mt-TFA and p43 is mediated by the D loop, it appears that the
response elements used by these two factors are not similar. In
addition, these data demonstrate that the two mt-T3RE sequences located
in the D loop support the mitochondrial transcriptional activity of p43.
Finally, stable overexpression of p43 in QM7 cells in the presence of
exogenous T3 increased the levels of mitochondrial mRNAs, without
involving an induction of mt-TFA, suggesting that direct stimulation of
mitochondrial transcription by p43 is functional in living cells.
Reduced stimulation of COX I mRNA by p43 was also recorded in the
absence of exogenous T3. However, the remaining activity could be
explained by the limited T3 levels measured in the culture medium after
hormonal depletion and by the fact that mitochondria are a major
compartment of T3 accumulation in the cell (32, 49). In
agreement with this possibility, it has been shown that very low levels
of T3 could significantly influence transcription with isolated
mitochondria (11). However, reduced p43 T3-independent
activity cannot be completely ruled out in the mitochondrial context.
Overall, in conjunction with in organello transcription assays, the
data obtained in living cells clearly support the proposition that p43
is a potent mitochondrial transcription factor. However, while it
provides an understanding of some aspects of T3 action on mitochondria,
our work does not explain short-term hormonal influences, including the
stimulation of oxidative phosphorylation, which occurs within minutes
of T3 treatment and is insensitive to inhibitors of protein synthesis
(48). Clearly, other pathways inducing activation of
preexisting mitochondrial proteins are probably involved in such effects.
In conclusion, the present study emphasizes the mitochondria are a
direct target of T3. Moreover, the presence of a c-ErbA
1-related protein in the organelle, and the additional observation that c-ErbA
0 is also imported into mitochondria, suggest that other hormonal receptors belonging to the nuclear receptor subfamily could
also be located in the organelle. Finally, the finding that the
c-erbA
gene simultaneously encodes mitochondrial and
nuclear T3 receptors reveals an interesting pathway involved in the
coordination of the expression of (i) nuclear genes encoding
mitochondrial proteins and (ii) the mitochondrial genome (Fig.
10). Such coordination is probably
needed for the stimulation of mitochondrial biogenesis (25,
46), and our data provide a significant explanation for the major
influence of T3 on mitochondrial activity.

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FIG. 10.
The c-ErbA gene encodes a mitochondrial and a nuclear
T3 receptor. With the nuclear receptor, T3 increases the expression of
genes encoding the mitochondrial proteins. With the mitochondrial
receptor, T3 stimulates mitochondrial genome expression. This mechanism
could provide the basis for coordination of nuclear and mitochondrial
transcription needed for stimulation of mitochondrial biogenesis.
|
|
This work was supported by grants from the Institut National de la
Recherche Agronomique (INRA), the Association Française contre
les Myopathies, the Association de Recherche contre le Cancer, and the
Deutsche Forschungsgemeinschaft WI 889/3-2. François Casas,
Pierrick Rochard, and Anne Rodier are recipients of fellowships from,
respectively, INRA and the Direction Générale de
l'Enseignement et de la Recherche, the Ministère de la Recherche
et de l'Enseignement, and the Ligue Nationale contre le Cancer.
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