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J. Biol. Chem., Vol. 277, Issue 41, 37987-37990, October 11, 2002

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Cbp1 Is Required for Translation of the Mitochondrial Cytochrome b mRNA of Saccharomyces cerevisiae^*

Maria A. Islas-Osuna, Timothy P. Ellis^§, Lorraine L. Marnell^§, Telsa M. Mittelmeier^§, and Carol L. Dieckmann^§¶

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

	ABSTRACT

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS DISCUSSION REFERENCES

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. 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

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 tRNA^glu. 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.

View larger version (12K): [in this window] [in a new window]   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.

	EXPERIMENTAL PROCEDURES

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS DISCUSSION REFERENCES

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.

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.

	RESULTS

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS DISCUSSION REFERENCES

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.

View larger version (26K): [in this window] [in a new window]   Fig. 2.   Growth on medium requiring respiration. The strains wild type (WT), cbp1, pet127, and cbp1pet127 were cultured in YPD media to logarithmic phase. Cells were washed, diluted in water, counted, and serially diluted. 10 µl of the dilutions were spotted on YEPG plates to yield dots with 105, 104, 103, 102, and 10 cells. The plates were incubated for 5 days at 25, 30, and 33 °C.

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.

View larger version (37K): [in this window] [in a new window]   Fig. 3.   Primer extension analysis of 5'-ends of COB transcripts. Total RNA was isolated from the strains, annealed to end-labeled COB (cob6B) and COX2 (cox4242) primers simultaneously, and extended by reverse transcriptase. The corresponding positions of the 5'-ends of the COB pre-mRNA (Pre-COB), mature COB mRNA (Mat-COB), and COX2 are marked on the left. As a control for the amount of RNA loaded, COX2 (the mitochondrial gene coding for cytochrome c oxidase subunit II) was extended together with COB RNAs. The COB levels were normalized with respect to COX2 levels with the appropriate correction for differences of COX2 levels in the pet127 strains (see "Experimental Procedures"). The level of mature COB mRNA in the wild-type (WT) strain was set to 100%, and the level of mature and COB pre-mRNA in the mutant strains was compared with it. Numbers were obtained from the averages and standard deviations of three gels. COB precursor RNA levels are: wild type, 18.6 ± 11.6; cbp1, 9.1 ± 6.2; pet127, 128.0 ± 44.3; and cbp1pet127, 58.0 ± 6.2.

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.

View larger version (47K): [in this window] [in a new window]   Fig. 4.   [35S] methionine-labeled mitochondrial gene products. Mitochondrial gene products in the mutant strains were labeled with [35S] methionine in the presence of cycloheximide, an inhibitor of cytoplasmic translation. Mitochondria isolated from each strain were suspended in Laemmli buffer, and the labeled proteins were separated by 10% SDS-PAGE. The positions of major mitochondrial gene products are indicated on the left, whereas the positions and sizes of protein molecular size standards are indicated on the right. WT, wild type.

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).

	DISCUSSION

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS DISCUSSION REFERENCES

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 tRNA^val. 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.

	ACKNOWLEDGEMENTS

We thank Jacque Baca, Mike Rice, and Melissa Dellos for assisting with this manuscript.

	FOOTNOTES

^* 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.

	ABBREVIATIONS

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.

	REFERENCES

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS DISCUSSION REFERENCES

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This Article Abstract Full Text (PDF) All Versions of this Article: 277/41/37987    most recent M206132200v1 Submit a Letter to Editor Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Request Permissions Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Islas-Osuna, M. A. Articles by Dieckmann, C. L. Search for Related Content PubMed PubMed Citation Articles by Islas-Osuna, M. A. Articles by Dieckmann, C. L. Social Bookmarking                      What's this?