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J. Biol. Chem., Vol. 277, Issue 41, 37987-37990, October 11, 2002
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,§¶
From the Departments of Molecular and Cellular
Biology and § Biochemistry and Molecular Biophysics,
University of Arizona, Tucson, Arizona 85721
Received for publication, June 20, 2002, and in revised form, July 24, 2002
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ABSTRACT |
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 TOP
 ABSTRACT
 INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
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Expression of the yeast mitochondrial cytochrome
b gene (COB) is controlled by at least 15 nuclear-encoded proteins. One of these proteins, Cbp1, is required for
COB mRNA stability. The expression of mitochondrial genes at the level of
transcription, RNA processing, translation, post-translational
modification, and complex assembly depends on many nuclear-encoded
proteins that are synthesized in the cytoplasm and imported into
mitochondria (1-3). Mutations in these nuclear genes often lead to
respiratory deficiency, termed the
pet1 phenotype
because colonies are petite in size on fermentable glucose medium. To
understand how mitochondrial gene expression is regulated, the function
of these nuclear PET genes must first be understood.
The nuclear PET gene CBP1 encodes a protein that
is imported into mitochondria and is required for the stability of the
mitochondrial cytochrome b (COB) mRNA (4, 5).
COB mRNA is co-transcribed with the upstream
tRNAglu. The tRNA is processed from the initial transcript
by mitochondrial RNaseP and tRNA 3'-endonuclease, leaving a transcript
we have called the COB precursor RNA. The precursor is
further shortened at the 5'-end to produce what we have called the
mature COB mRNA. In a wild-type strain, there is
approximately five times more mature than precursor COB RNA.
In a cbp1 null strain, the mature COB mRNA is
undetectable, and precursor RNA is reduced 2- to 5-fold from wild-type
levels (Fig. 1) (6). cbp1 null
strains are respiratory-deficient, and no apocytochrome b is
synthesized, which suggests that: the 5'-extension on the precursor RNA
inhibits translation, the abundance of the precursor is below the
threshold required for respiration (about 4% of the levels of mature
mRNA in the wild-type strain), or Cbp1 is required for translation
of COB RNAs.
cbp1 null strains
fail to accumulate mature COB mRNA and cannot respire. Since cbp1 null strains lack mature COB
transcripts, the hypothesis that Cbp1 also plays a role in translation
of these mRNAs could not be tested previously. 5'-End trimming of
precursor COB RNA and other mitochondrial transcripts is
dependent on Pet127. pet127 mutants accumulate high levels
of precursor COB mRNA and have no mature mRNA.
pet127 mutants respire well; this phenotype implies that
COB precursor RNA is translated efficiently. With the
expectation that a cbp1pet127 strain might accumulate
substantial levels of COB RNA, the double null strain was
constructed and analyzed to test the hypothesis that Cbp1 is required
for translation of COB RNA. The
cbp1pet127 strain does accumulate levels of
COB precursor mRNA that are ~60% of the level of
COB mRNA in the wild-type strain. However, cytochrome
b protein is not synthesized, and thus the
cbp1pet127 strain does not respire. These results
suggest that Cbp1 is required for translation of COB RNAs.
INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
View larger version (12K):
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Fig. 1.
Processing of the upstream
region of the tRNAglu-COB transcript.
The upstream portion of the tRNAglu-COB
bicistronic transcription unit is depicted. Not shown are the exons and
introns of the COB gene, which extend in the rightward
direction. tRNAglu is processed from the initial transcript
by mitochondrial RNaseP (23) and tRNA 3'-endonuclease (24) to release
the upstream tRNA. The precursor RNA is trimmed at the 5'-end to
produce the mature mRNA. Pet127 is required for 5'-end trimming of
COB precursor RNA. Cbp1 is a nuclear-encoded protein that is
required for COB RNA stability. In a cbp1 mutant
strain, tRNAglu levels are similar to wild-type, whereas
precursor levels are reduced 2- to 5-fold and mature COB
mRNA is undetectable.
Evidence that precursor COB RNAs can be translated has come
from studies of Pet127, a nuclear-encoded protein that is localized to
mitochondria, where it plays a role in RNA processing. A
pet127 null strain exhibits a leaky non-respiratory
phenotype at 37 °C but respires well at 30 °C, the normal growth
temperature for yeast. In pet127 strains, 5'-end processing
of COB, VAR1, and ATP8/6
mRNAs and 15 S rRNA is blocked, and unprocessed COB
precursor RNAs accumulate to levels equivalent to those of processed
RNAs in wild-type strains (7). Since null pet127 strains
have no mature COB mRNA, but respire well, the
5'-unprocessed RNAs must be translated at sufficient levels to support
near wild-type respiratory capability.
Additional data suggestive of a requirement for Cbp1 in COB
RNA translation have come from analyses of point mutations in the
COB 5'-untranslated leader. Previously, we have defined a CCG trinucleotide in the otherwise AU-rich COB RNA leader
that is especially important for Cbp1-dependent
accumulation of COB RNAs. This CCG is located just
downstream of the 5'-end of mature COB mRNA (Fig. 1). We
have hypothesized that Cbp1 interacts with COB RNAs in the
region containing the CCG trinucleotide. ACG and CCU mutant strains are temperature-sensitive for
respiration and have very low levels of COB mRNA,
whereas the CAG mutant strain is respiratory-incompetent at
all temperatures and has undetectable levels of mRNA (8).
pet127 null mutations arose as spontaneous suppressors of
the conditionally respiratory-deficient ACG and CCU mutations but were unable to suppress the
CAG mutation. However, all three of the
pet127 mutant strains (ACG, CCU,
CAG) accumulated similar increased levels of COB
precursor RNA.2 Thus, the
accumulated COB precursor RNAs must be translated in the
pet127 ACG and CCU strains but
not in the CAG strain. We have interpreted the
respiratory-deficient phenotype of CAG as a loss of Cbp1
function in translation of COB RNAs.
As a more direct test of the activities of Cbp1, we made a deletion in
the CBP1 gene in a pet127 mutant strain with
the expectation that a cbp1pet127 strain would
accumulate enough COB precursor RNA to test our hypothesis
that Cbp1 is required for translation. Measurements of respiratory
capability, COB RNA accumulation, and synthesis of
cytochrome b apoprotein in the single cbp1 and pet127 and double null cbp1pet127 mutant
strains supports the hypothesis that Cbp1 is required for translation
of COB RNAs.
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EXPERIMENTAL PROCEDURES |
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TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
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Strains, Media, and Nomenclature-- The Saccharomyces cerevisiae strains used in this study are listed in Table I. The media in which the strains were grown are as follows: YPD (1% yeast extract, 2% peptone, 2% glucose), WO (0.67% yeast nitrogen base without amino acids, 2% glucose), and YEPG (1% yeast extract, 2% peptone, 3% glycerol). Amino acid supplements were added to suggested final concentrations (9). Wild-type nuclear and mitochondrial genes are represented by italicized, uppercase letters, i.e. CBP1, PET127, COB, and COX2. Genes with mutations are represented by italicized lowercase letters, i.e. cbp1 and pet127. rho refers to the mitochondrial genome. For example, rho+ denotes wild type, whereas rho0 indicates a lack of mitochondrial DNA. Other superscripts are used as descriptive names of mutant mitochondrial genomes.
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Construction of the Double Deletion Strain cbp1pet127
(uCBPET)--
Strain uCBP/rho+CCU
was made by transforming the uCCU strain with a 1.3-Kb
EcoRI fragment (cbp1::URA3) excised
from pFS10 and selecting for Ura+
transformants3. Double mutant
strain cbp1pet127/rho+CCU
(uCBPET/rho+CCU) was obtained by mating
haploid strain uCBP/rho+CCU to
pet127/rho0. The diploids were
selected under the microscope and sporulated in 1% potassium acetate
at 23 °C, and the tetrads were dissected. The double null
uCBPET/rho+CCU strain was obtained as a spore
from a non-parental ditype tetrad. The
uCBPET/rho+CCU strain was treated with
ethidium bromide to cause loss of mitochondrial DNA
(rho0) (10). Subsequently, strain
uCBPET/rho0 was crossed to a
kar1-1 strain JC3/rho+CCG
to yield uCBPET/rho+CCG.
Growth of Strains on Glycerol Plates-- The strains were cultured on glucose media at 30 °C to logarithmic phase. Cells were counted in a hemacytometer, and 1 × 106 cells were diluted in 100 µl of sterile water and serially diluted. Ten-µl drops of serial dilutions 105, 104, 103, 102, and 10 were spotted on glycerol plates and incubated at 25, 30, and 33 °C for 5 days.
Primer Extension Analysis of the 5'-Ends of COB
mRNAs--
Total RNA was isolated as described previously from
mid-logarithmic cultures grown in YPD (11). For quantitative analysis by primer extension, 8 µg of total RNA was hybridized to 10 pmol of
32P-radiolabeled COB "Cob6B" primer (12) and
COX2 "Cox4242" primer (13). The extension reactions were
carried out as described previously (12) using avian myeloblastosis
virus reverse transcriptase (Promega, Madison, WI) except that the
hybridization reaction was incubated at 47 °C for 90 min. 9 µl of
each of the reaction mixtures were loaded on a 7 M urea,
6% polyacrylamide wedged sequencing gel. The signals obtained from
precursor and mature COB mRNAs were quantitated
using a PhosphorImager (Amersham Biosciences) and normalized to
the signal from cytochrome c oxidase subunit II
(COX2) transcripts in the same strain. In
pet127 strains, COX2 levels are reduced
modestly. Northern analysis done in triplicate showed that the
COX2 mRNA level is 70% of wild-type in the
pet127 strain (data not shown). COB levels in
the primer extension analyses of pet127 strains were
corrected for this reduction in COX2 levels.
[35S]Methionine Labeling of Mitochondrial Gene
Products--
In vivo pulse-labeling of mitochondrial
proteins was performed as described previously (14). The cultures were
labeled with 12.5 µCi/ml [35S]methionine for 2 h
(Amersham Biosciences) in the presence of cycloheximide, which inhibits
cytosolic protein synthesis. Translation products were fractionated by
10% SDS-PAGE, dried, and visualized by exposing the gel to film for 14 days.
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RESULTS |
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TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
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The Double Deletion Strain cbp1pet127 Does Not
Respire--
Growth on media containing non-fermentable carbon sources
such as glycerol is a simple and very sensitive method for measuring respiratory capability. Metabolism of glycerol requires a functional respiratory chain and ATP synthase in the mitochondrial compartment. To
compare the respiration phenotype of the cbp1pet127
strain with that of the single mutant and wild-type controls, the
strains were grown overnight on rich glucose liquid medium (YPD) and
then serially diluted and spotted on rich glycerol plates (YEPG) and incubated at 25, 30, or 33 °C (Fig.
2). The wild-type and the pet127 strains grew very similarly at 30 °C on YEPG.
The wild-type strain grew slightly better than the pet127
strain at both 25 and 33 °C. The cbp1 and
cbp1pet127 strains did not grow on glycerol at any of
the three temperatures.
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The double cbp1pet127 deletion could lead to
respiratory incompetence by affecting the stability, processing, and/or
translation of COB transcripts. Either COB RNA is
destroyed (epistasis of the cbp1 COB RNA instability
phenotype) or COB RNA accumulates in the
cbp1pet127strain in an unprocessed form (epistasis of the pet127 unprocessed COB RNA phenotype) but is
not translated.
cbp1pet127 Accumulates High Levels of COB Precursor
RNA--
To determine whether the respiratory deficiency of the double
deletion strain cbp1pet127 was a result of the
instability of COB transcripts, the steady-state levels of
COB precursor and mature RNAs were determined by
quantitative primer extension analysis (Fig.
3). As observed previously, the
respiratory-deficient cbp1 strain had no detectable
mature COB mRNA and reduced levels of the COB
precursor RNA (6). The respiratory-competent pet127 strain had only COB precursor RNA at a level equal to the
sum of precursor and mature mRNA in the wild-type strain (128% of wild-type levels of mature COB mRNA). Like the
pet127 single mutant, the cbp1pet127
strain had no mature COB mRNA but had substantial levels
of COB precursor RNA (58% of wild-type levels of mature
COB message). Very slow respiratory growth on glycerol plates has been observed for strains that have as little as 4% of
wild-type levels of mature COB mRNA (12). The inability
of the cbp1pet127 strain to respire, despite
relatively high levels of COB precursor transcripts,
supports the hypothesis that Cbp1 is required for translation of
COB RNAs as well as their stability.
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Cytochrome b Protein Does Not Accumulate in the cbp1pet127
Strain--
To determine whether the cytochrome b protein
was present in the cbp1pet127 strain, mitochondrial
gene products in the double and single mutant strains were labeled
in vivo with [35S]methionine and analyzed by
SDS-PAGE (Fig. 4). As expected,
apocytochrome b protein was detected at robust levels in
both the wild-type and pet127 strains (lanes 2 and 3), confirming efficient translation of COB
precursor RNA in the pet127 strain. In contrast, no
apocytochrome b was detected in the
cbp1pet127 strain (Fig. 4, lane 4),
suggesting that Cbp1 is required for translation of COB
RNAs.
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The absence of cytochrome c oxidase subunit I (Cox1) in the
cbp1pet127 strain is another indicator that Cbp1 is
required for translation of COB RNAs, as opposed to
assembly/stability of cytochrome b protein. Translation of
an intron-excision maturase, encoded in the fourth intron of
COB (bi4), is required for splicing of the bi4 intron and
also for splicing of the fourth intron of COX1. Therefore,
if bi4 maturase is not translated from the COB precursor RNA
containing introns, fully spliced COX1 mRNA is not produced, and Cox1 protein cannot be translated (15).
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DISCUSSION |
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TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
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Nuclear-encoded factors that promote translation of specific
mitochondrial messenger RNAs have been described: for COB
mRNAs (Cbs1 and Cbs2), for ATP9 mRNAs (Aep1 and
Aep2), for COX1 mRNAs (Pet309), for
COX2 mRNAs (Pet111), for COX3 mRNAs
(Pet54, Pet494, and Pet122), and for ATP8/6 mRNAs
(Nca2/Nca3) (reviewed in Ref. 3). In many cases, the deletion of the
nuclear gene results in a decrease in the abundance of the
mitochondrial mRNA as well as a block to initiation of translation.
Here we have shown that Cbp1 falls into this class of "translational
activator" proteins as it affects both stability and translation of
COB RNAs. In respiratory-competent pet127
strains, COB precursor RNAs are translated to produce wild-type levels of cytochrome b protein. However, in
cbp1pet127 strains, precursor RNAs accumulate but are
not translated to produce either the COB-encoded maturases
or cytochrome b.
The translation of wild-type levels of cytochrome b in the
pet127 strain indicates that precursor RNAs with extended
5'-ends are translated as efficiently as 5'-trimmed mRNAs. All
evidence to date has pointed toward an internal entry mode of
translation initiation for mitochondrial mRNAs (3). For example,
mitochondrial mRNAs often have quite long 5'-untranslated
regions with multiple AUG sequences upstream of the bona
fide start codon. The messages do not have 5'-cap structures that
would be required for a cap-dependent initiation scheme
similar to that for eukaryotic cytoplasmic translation (16). Especially
for COX2 and COB, sites near the start codon have
been delineated through mutagenesis as being required for translation
initiation (17, 18). Thus, it should not be surprising that mRNAs
that are extended in length at the 5'-end, many nucleotides away from
the ribosome entry site, can be translated. It has been known for some
years that unspliced precursor mRNAs are translated; translation of
the maturases in the introns of COB and COX1 is required for subsequent excision of the introns (15).
So why do COB, ATP8/6, and VAR1 mRNAs have 5'-extensions that are shortened in a Pet127-dependent manner, whereas COX1, COX2, COX3, and ATP9 do not? COX1, COX2, COX3, and ATP9 may not be susceptible to shortening by Pet127 because they have 5'-triphosphate ends (the RNA is not processed after transcription). For example, Escherichia coli RNaseE is much more active on RNAs with monophosphate 5'-ends than triphosphate ends (19). COX3 transcripts are processed by cleavage of the upstream tRNAval. This 5'-processed mRNA may not be susceptible because the 5'-end is protected by RNA secondary structure or by proteins, such as the translational activators Pet494, Pet54, and Pet122 (20). COB, ATP8/6, and VAR1 mRNAs are susceptible up to the point where protection is provided. It may be that the sequences between the long and short mRNA 5'-ends of ATP8/6 and VAR1 are dispensable as has been shown for COB (13), but these sequences have not yet disappeared over evolutionary time, or there may be some subtle necessity for these sequences that has yet to be discovered.
COB precursor RNAs were 2-fold higher in the
pet127 than in the pet127cbp1 strain.
This implies that Cbp1 protects against one or more degradation
pathways that are not governed by Pet127, and/or the rate of
transcription of COB is decreased in cbp1 mutant strains. Lower rates of COB transcription could be a
specific effect of the loss of Cbp1, or they could be a general effect of the respiratory deficiency of this strain.
Does Cbp1 work together with the COB-specific translational
activators Cbs1 and Cbs2 to promote translation of the mRNAs? Cbp1
acts through a sequence that maps to the 5'-end of the mature COB mRNA (
961 to 898), whereas Cbs1 and Cbs2 act
through a site that maps to positions between 232 to 60 and 33 to
4 relative to the start codon at +1 (18). COB mRNA is
stable in cbs1 and cbs2 mutants, but the mRNA
is not translated (21). Cbp1 is found in the soluble fraction when
mitochondria are sonicated in buffer lacking
salt,4 whereas Cbs1 is firmly
embedded in the membrane and Cbs2 is peripherally attached (22). The
three proteins may interact at the surface of the inner membrane in a
complex that includes COB mRNA. Cbp1 could become
associated with the RNA during transcription, and through its affinity
for the other two proteins, it could deliver the RNA to the membrane
complex of Cbs1 and Cbs2, which promotes association with mitochondrial
ribosomes. Testing of this model requires further genetic and
biochemical experimentation.
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ACKNOWLEDGEMENTS |
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We thank Jacque Baca, Mike Rice, and Melissa Dellos for assisting with this manuscript.
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FOOTNOTES |
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* This work was supported by National Institutes of Health Grant GM34893 (to C. L. D.) and partially supported by a grant from Centro de Investigacion en Alimentacion y Desarrollo (CIAD), Mexico (to M. A. I. O).The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
¶ To whom correspondence should be addressed: Dept. of Biochemistry and Molecular Biophysics, University of Arizona, 1007 E. Lowell St., LSS Bldg. Room 454, Tucson, AZ 85721-0106. Tel.: 520-621-3569; Fax: 520-621-3709; E-mail: dieckman@u.arizona.edu.
Published, JBC Papers in Press, July 30, 2002, DOI 10.1074/jbc.M206132200
2 M. A. Islas-Osuna and C. L. Dieckmann, unpublished results.
3 F. A. Sibayan and C. L. Dieckmann, unpublished results.
4 K. Krause and C. L. Dieckmann, manuscript in preparation.
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ABBREVIATIONS |
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The abbreviations used are: pet, petite; COB, cytochrome b; COX1, cytochrome c oxidase subunit I; COX2, cytochrome c oxidase subunit II; COX3, cytochrome c oxidase subunit III.
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REFERENCES |
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TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
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T. P. Ellis, K. G. Helfenbein, A. Tzagoloff, and C. L. Dieckmann Aep3p Stabilizes the Mitochondrial Bicistronic mRNA Encoding Subunits 6 and 8 of the H+-translocating ATP Synthase of Saccharomyces cerevisiae J. Biol. Chem., April 16, 2004; 279(16): 15728 - 15733. [Abstract] [Full Text] [PDF]
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A. Fiori, T. L. Mason, and T. D. Fox Evidence that Synthesis of the Saccharomyces cerevisiae Mitochondrially Encoded Ribosomal Protein Var1p May Be Membrane Localized Eukaryot. Cell, June 1, 2003; 2(3): 651 - 653. [Abstract] [Full Text] [PDF]
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M. PELLETIER and L. K. READ RBP16 is a multifunctional gene regulatory protein involved in editing and stabilization of specific mitochondrial mRNAs in Trypanosoma brucei RNA, April 1, 2003; 9(4): 457 - 468. [Abstract] [Full Text] [PDF]
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