Skip to main content
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1997 Aug;17(8):4199–4207. doi: 10.1128/mcb.17.8.4199

Premature 3'-end formation of CBP1 mRNA results in the downregulation of cytochrome b mRNA during the induction of respiration in Saccharomyces cerevisiae.

K A Sparks 1, S A Mayer 1, C L Dieckmann 1
PMCID: PMC232273  PMID: 9234677

Abstract

The yeast mitochondrial genome encodes only seven major components of the respiratory chain and ATP synthase; more than 200 other mitochondrial proteins are encoded by nuclear genes. Thus, assembly of functional mitochondria requires coordinate expression of nuclear and mitochondrial genes. One example of coordinate regulation is the stabilization of mitochondrial COB (cytochrome b) mRNA by Cbp1, the product of the nuclear gene CBP1 (cytochrome b processing). CBP1 produces two types of transcripts with different 3' ends: full-length 2.2-kb transcripts and 1.2-kb transcripts truncated within the coding sequence of Cbp1. Upon induction of respiration, the steady-state level of the long transcripts decreases while that of the short transcripts increases reciprocally, an unexpected result since the product of the long transcripts is required for COB mRNA stability and thus for respiration. Here we have tested the hypothesis that the short transcripts, or proteins translated from the short transcripts, are also required for respiration. A protein translated from the short transcripts was not detected by Western analysis, although polysome gradient fractions were shown to contain both long and short CBP1 transcripts. A mutant strain in which production of the short transcripts was abolished showed wild-type growth properties, indicating that the short transcripts are not required for respiration. Due to mutation of the carbon source-responsive element, the long transcript level in the mutant strain did not decrease during induction of respiration. The mutant strain had increased levels of COB RNA, suggestive that production of short CBP1 transcripts is a mechanism for downregulation of the levels of long CBP1 transcripts, Cbp1, and COB mRNA during the induction of respiration.

Full Text

The Full Text of this article is available as a PDF (1.1 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Baim S. B., Pietras D. F., Eustice D. C., Sherman F. A mutation allowing an mRNA secondary structure diminishes translation of Saccharomyces cerevisiae iso-1-cytochrome c. Mol Cell Biol. 1985 Aug;5(8):1839–1846. doi: 10.1128/mcb.5.8.1839. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ballinger D. G., Pardue M. L. The control of protein synthesis during heat shock in Drosophila cells involves altered polypeptide elongation rates. Cell. 1983 May;33(1):103–113. doi: 10.1016/0092-8674(83)90339-2. [DOI] [PubMed] [Google Scholar]
  3. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2(2):95–113. [PubMed] [Google Scholar]
  4. Buckholz R. G., Cooper T. G. Oxalurate induction of multiple URA3 transcripts in Saccharomyces cerevisiae. Mol Cell Biol. 1983 Nov;3(11):1889–1897. doi: 10.1128/mcb.3.11.1889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chen J. Y., Martin N. C. Biosynthesis of tRNA in yeast mitochondria. An endonuclease is responsible for the 3'-processing of tRNA precursors. J Biol Chem. 1988 Sep 25;263(27):13677–13682. [PubMed] [Google Scholar]
  6. Chen W., Dieckmann C. L. Cbp1p is required for message stability following 5'-processing of COB mRNA. J Biol Chem. 1994 Jun 17;269(24):16574–16578. [PubMed] [Google Scholar]
  7. Christianson T., Edwards J. C., Mueller D. M., Rabinowitz M. Identification of a single transcriptional initiation site for the glutamic tRNA and COB genes in yeast mitochondria. Proc Natl Acad Sci U S A. 1983 Sep;80(18):5564–5568. doi: 10.1073/pnas.80.18.5564. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Craigen W. J., Caskey C. T. The function, structure and regulation of E. coli peptide chain release factors. Biochimie. 1987 Oct;69(10):1031–1041. doi: 10.1016/0300-9084(87)90003-4. [DOI] [PubMed] [Google Scholar]
  9. Crivellone M. D., Wu M. A., Tzagoloff A. Assembly of the mitochondrial membrane system. Analysis of structural mutants of the yeast coenzyme QH2-cytochrome c reductase complex. J Biol Chem. 1988 Oct 5;263(28):14323–14333. [PubMed] [Google Scholar]
  10. Decker C. J., Parker R. A turnover pathway for both stable and unstable mRNAs in yeast: evidence for a requirement for deadenylation. Genes Dev. 1993 Aug;7(8):1632–1643. doi: 10.1101/gad.7.8.1632. [DOI] [PubMed] [Google Scholar]
  11. Dieckmann C. L., Gandy B. Preferential recombination between GC clusters in yeast mitochondrial DNA. EMBO J. 1987 Dec 20;6(13):4197–4203. doi: 10.1002/j.1460-2075.1987.tb02767.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dieckmann C. L., Koerner T. J., Tzagoloff A. Assembly of the mitochondrial membrane system. CBP1, a yeast nuclear gene involved in 5' end processing of cytochrome b pre-mRNA. J Biol Chem. 1984 Apr 25;259(8):4722–4731. [PubMed] [Google Scholar]
  13. Dieckmann C. L., Staples R. R. Regulation of mitochondrial gene expression in Saccharomyces cerevisiae. Int Rev Cytol. 1994;152:145–181. doi: 10.1016/s0074-7696(08)62556-5. [DOI] [PubMed] [Google Scholar]
  14. Elble R., Tye B. K. Both activation and repression of a-mating-type-specific genes in yeast require transcription factor Mcm1. Proc Natl Acad Sci U S A. 1991 Dec 1;88(23):10966–10970. doi: 10.1073/pnas.88.23.10966. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Finnegan P. M., Payne M. J., Keramidaris E., Lukins H. B. Characterization of a yeast nuclear gene, AEP2, required for accumulation of mitochondrial mRNA encoding subunit 9 of the ATP synthase. Curr Genet. 1991 Jul;20(1-2):53–61. doi: 10.1007/BF00312765. [DOI] [PubMed] [Google Scholar]
  16. Gietz R. D., Schiestl R. H. Applications of high efficiency lithium acetate transformation of intact yeast cells using single-stranded nucleic acids as carrier. Yeast. 1991 Apr;7(3):253–263. doi: 10.1002/yea.320070307. [DOI] [PubMed] [Google Scholar]
  17. Guo Z., Sherman F. 3'-end-forming signals of yeast mRNA. Trends Biochem Sci. 1996 Dec;21(12):477–481. doi: 10.1016/s0968-0004(96)10057-8. [DOI] [PubMed] [Google Scholar]
  18. Hann B. C., Walter P. The signal recognition particle in S. cerevisiae. Cell. 1991 Oct 4;67(1):131–144. doi: 10.1016/0092-8674(91)90577-l. [DOI] [PubMed] [Google Scholar]
  19. Hatfield L., Beelman C. A., Stevens A., Parker R. Mutations in trans-acting factors affecting mRNA decapping in Saccharomyces cerevisiae. Mol Cell Biol. 1996 Oct;16(10):5830–5838. doi: 10.1128/mcb.16.10.5830. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Hollingsworth M. J., Martin N. C. RNase P activity in the mitochondria of Saccharomyces cerevisiae depends on both mitochondrion and nucleus-encoded components. Mol Cell Biol. 1986 Apr;6(4):1058–1064. doi: 10.1128/mcb.6.4.1058. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Keller W. No end yet to messenger RNA 3' processing! Cell. 1995 Jun 16;81(6):829–832. doi: 10.1016/0092-8674(95)90001-2. [DOI] [PubMed] [Google Scholar]
  22. Kukuruzinska M. A., Robbins P. W. Protein glycosylation in yeast: transcript heterogeneity of the ALG7 gene. Proc Natl Acad Sci U S A. 1987 Apr;84(8):2145–2149. doi: 10.1073/pnas.84.8.2145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Köhrer K., Domdey H. Preparation of high molecular weight RNA. Methods Enzymol. 1991;194:398–405. doi: 10.1016/0076-6879(91)94030-g. [DOI] [PubMed] [Google Scholar]
  24. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  25. Liu Y. X., Dieckmann C. L. Overproduction of yeast viruslike particles by strains deficient in a mitochondrial nuclease. Mol Cell Biol. 1989 Aug;9(8):3323–3331. doi: 10.1128/mcb.9.8.3323. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Mann K. P., Weiss E. A., Nevins J. R. Alternative poly(A) site utilization during adenovirus infection coincides with a decrease in the activity of a poly(A) site processing factor. Mol Cell Biol. 1993 Apr;13(4):2411–2419. doi: 10.1128/mcb.13.4.2411. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Martin N. C., Miller D. L., Underbrink K., Ming X. Structure of a precursor to the yeast mitochondrial tRNAMetf. Implications for the function of the tRNA synthesis locus. J Biol Chem. 1985 Feb 10;260(3):1479–1483. [PubMed] [Google Scholar]
  28. Mayer S. A., Dieckmann C. L. The yeast CBP1 gene produces two differentially regulated transcripts by alternative 3'-end formation. Mol Cell Biol. 1989 Oct;9(10):4161–4169. doi: 10.1128/mcb.9.10.4161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Mayer S. A., Dieckmann C. L. Yeast CBP1 mRNA 3' end formation is regulated during the induction of mitochondrial function. Mol Cell Biol. 1991 Feb;11(2):813–821. doi: 10.1128/mcb.11.2.813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Minvielle-Sebastia L., Winsor B., Bonneaud N., Lacroute F. Mutations in the yeast RNA14 and RNA15 genes result in an abnormal mRNA decay rate; sequence analysis reveals an RNA-binding domain in the RNA15 protein. Mol Cell Biol. 1991 Jun;11(6):3075–3087. doi: 10.1128/mcb.11.6.3075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Mittelmeier T. M., Dieckmann C. L. CBP1 function is required for stability of a hybrid cob-oli1 transcript in yeast mitochondria. Curr Genet. 1990 Dec;18(5):421–428. doi: 10.1007/BF00309911. [DOI] [PubMed] [Google Scholar]
  32. Mittelmeier T. M., Dieckmann C. L. In vivo analysis of sequences necessary for CBP1-dependent accumulation of cytochrome b transcripts in yeast mitochondria. Mol Cell Biol. 1993 Jul;13(7):4203–4213. doi: 10.1128/mcb.13.7.4203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Mittelmeier T. M., Dieckmann C. L. In vivo analysis of sequences required for translation of cytochrome b transcripts in yeast mitochondria. Mol Cell Biol. 1995 Feb;15(2):780–789. doi: 10.1128/mcb.15.2.780. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Mueller D. M., Getz G. S. Steady state analysis of mitochondrial RNA after growth of yeast Saccharomyces cerevisiae under catabolite repression and derepression. J Biol Chem. 1986 Sep 5;261(25):11816–11822. [PubMed] [Google Scholar]
  35. Mueller D. M., Getz G. S. Transcriptional regulation of the mitochondrial genome of yeast Saccharomyces cerevisiae. J Biol Chem. 1986 Sep 5;261(25):11756–11764. [PubMed] [Google Scholar]
  36. Myers A. M., Crivellone M. D., Tzagoloff A. Assembly of the mitochondrial membrane system. MRP1 and MRP2, two yeast nuclear genes coding for mitochondrial ribosomal proteins. J Biol Chem. 1987 Mar 5;262(7):3388–3397. [PubMed] [Google Scholar]
  37. Nakai T., Yasuhara T., Fujiki Y., Ohashi A. Multiple genes, including a member of the AAA family, are essential for degradation of unassembled subunit 2 of cytochrome c oxidase in yeast mitochondria. Mol Cell Biol. 1995 Aug;15(8):4441–4452. doi: 10.1128/mcb.15.8.4441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Nonet M., Scafe C., Sexton J., Young R. Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol Cell Biol. 1987 May;7(5):1602–1611. doi: 10.1128/mcb.7.5.1602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Oba T., Andachi Y., Muto A., Osawa S. CGG: an unassigned or nonsense codon in Mycoplasma capricolum. Proc Natl Acad Sci U S A. 1991 Feb 1;88(3):921–925. doi: 10.1073/pnas.88.3.921. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Passmore S., Maine G. T., Elble R., Christ C., Tye B. K. Saccharomyces cerevisiae protein involved in plasmid maintenance is necessary for mating of MAT alpha cells. J Mol Biol. 1988 Dec 5;204(3):593–606. doi: 10.1016/0022-2836(88)90358-0. [DOI] [PubMed] [Google Scholar]
  41. Shah H. C., Carlson G. P. Alteration by phenobarbital and 3-methyl-cholanthrene of functional and structural changes in rat liver due to carbon tetrachloride inhalation. J Pharmacol Exp Ther. 1975 Apr;193(1):281–292. [PubMed] [Google Scholar]
  42. St John T. P., Davis R. W. The organization and transcription of the galactose gene cluster of Saccharomyces. J Mol Biol. 1981 Oct 25;152(2):285–315. doi: 10.1016/0022-2836(81)90244-8. [DOI] [PubMed] [Google Scholar]
  43. Staples R. R., Dieckmann C. L. Generation of temperature-sensitive cbp1 strains of Saccharomyces cerevisiae by PCR mutagenesis and in vivo recombination: characteristics of the mutant strains imply that CBP1 is involved in stabilization and processing of cytochrome b pre-mRNA. Genetics. 1993 Dec;135(4):981–991. doi: 10.1093/genetics/135.4.981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Staples R. R., Dieckmann C. L. Suppressor analyses of temperature-sensitive cbp1 strains of Saccharomyces cerevisiae: the product of the nuclear gene SOC1 affects mitochondrial cytochrome b mRNA post-transcriptionally. Genetics. 1994 Nov;138(3):565–575. doi: 10.1093/genetics/138.3.565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Stone E. M., Swanson M. J., Romeo A. M., Hicks J. B., Sternglanz R. The SIR1 gene of Saccharomyces cerevisiae and its role as an extragenic suppressor of several mating-defective mutants. Mol Cell Biol. 1991 Apr;11(4):2253–2262. doi: 10.1128/mcb.11.4.2253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Tanguay R. L., Gallie D. R. Translational efficiency is regulated by the length of the 3' untranslated region. Mol Cell Biol. 1996 Jan;16(1):146–156. doi: 10.1128/mcb.16.1.146. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Tate W. P., Brown C. M. Translational termination: "stop" for protein synthesis or "pause" for regulation of gene expression. Biochemistry. 1992 Mar 10;31(9):2443–2450. doi: 10.1021/bi00124a001. [DOI] [PubMed] [Google Scholar]
  48. Tzagoloff A., Dieckmann C. L. PET genes of Saccharomyces cerevisiae. Microbiol Rev. 1990 Sep;54(3):211–225. doi: 10.1128/mr.54.3.211-225.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Ulery T. L., Jang S. H., Jaehning J. A. Glucose repression of yeast mitochondrial transcription: kinetics of derepression and role of nuclear genes. Mol Cell Biol. 1994 Feb;14(2):1160–1170. doi: 10.1128/mcb.14.2.1160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Weber E. R., Dieckmann C. L. Identification of the CBP1 polypeptide in mitochondrial extracts from Saccharomyces cerevisiae. J Biol Chem. 1990 Jan 25;265(3):1594–1600. [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES