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. 2001 Jun;158(2):573–585. doi: 10.1093/genetics/158.2.573

Rpm2, the protein subunit of mitochondrial RNase P in Saccharomyces cerevisiae, also has a role in the translation of mitochondrially encoded subunits of cytochrome c oxidase.

V Stribinskis 1, G J Gao 1, S R Ellis 1, N C Martin 1
PMCID: PMC1461690  PMID: 11404323

Abstract

RPM2 is a Saccharomyces cerevisiae nuclear gene that encodes the protein subunit of mitochondrial RNase P and has an unknown function essential for fermentative growth. Cells lacking mitochondrial RNase P cannot respire and accumulate lesions in their mitochondrial DNA. The effects of a new RPM2 allele, rpm2-100, reveal a novel function of RPM2 in mitochondrial biogenesis. Cells with rpm2-100 as their only source of Rpm2p have correctly processed mitochondrial tRNAs but are still respiratory deficient. Mitochondrial mRNA and rRNA levels are reduced in rpm2-100 cells compared to wild type. The general reduction in mRNA is not reflected in a similar reduction in mitochondrial protein synthesis. Incorporation of labeled precursors into mitochondrially encoded Atp6, Atp8, Atp9, and Cytb protein was enhanced in the mutant relative to wild type, while incorporation into Cox1p, Cox2p, Cox3p, and Var1p was reduced. Pulse-chase analysis of mitochondrial translation revealed decreased rates of translation of COX1, COX2, and COX3 mRNAs. This decrease leads to low steady-state levels of Cox1p, Cox2p, and Cox3p, loss of visible spectra of aa(3) cytochromes, and low cytochrome c oxidase activity in mutant mitochondria. Thus, RPM2 has a previously unrecognized role in mitochondrial biogenesis, in addition to its role as a subunit of mitochondrial RNase P. Moreover, there is a synthetic lethal interaction between the disruption of this novel respiratory function and the loss of wild-type mtDNA. This synthetic interaction explains why a complete deletion of RPM2 is lethal.

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Selected References

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  1. Alconada A., Flores A. I., Blanco L., Cuezva J. M. Antibodies against F1-ATPase alpha-subunit recognize mitochondrial chaperones. Evidence for an evolutionary relationship between chaperonin and ATPase protein families. J Biol Chem. 1994 May 6;269(18):13670–13679. [PubMed] [Google Scholar]
  2. Attardi G., Schatz G. Biogenesis of mitochondria. Annu Rev Cell Biol. 1988;4:289–333. doi: 10.1146/annurev.cb.04.110188.001445. [DOI] [PubMed] [Google Scholar]
  3. Chacinska A., Boguta M., Krzewska J., Rospert S. Prion-dependent switching between respiratory competence and deficiency in the yeast nam9-1 mutant. Mol Cell Biol. 2000 Oct;20(19):7220–7229. doi: 10.1128/mcb.20.19.7220-7229.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chang S. C., Heacock P. N., Clancey C. J., Dowhan W. The PEL1 gene (renamed PGS1) encodes the phosphatidylglycero-phosphate synthase of Saccharomyces cerevisiae. J Biol Chem. 1998 Apr 17;273(16):9829–9836. doi: 10.1074/jbc.273.16.9829. [DOI] [PubMed] [Google Scholar]
  5. Chen D. C., Yang B. C., Kuo T. T. One-step transformation of yeast in stationary phase. Curr Genet. 1992 Jan;21(1):83–84. doi: 10.1007/BF00318659. [DOI] [PubMed] [Google Scholar]
  6. Chen X. J., Clark-Walker G. D. Alpha and beta subunits of F1-ATPase are required for survival of petite mutants in Saccharomyces cerevisiae. Mol Gen Genet. 1999 Dec;262(4-5):898–908. doi: 10.1007/s004380051156. [DOI] [PubMed] [Google Scholar]
  7. Chen X. J., Clark-Walker G. D. Specific mutations in alpha- and gamma-subunits of F1-ATPase affect mitochondrial genome integrity in the petite-negative yeast Kluyveromyces lactis. EMBO J. 1995 Jul 3;14(13):3277–3286. doi: 10.1002/j.1460-2075.1995.tb07331.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chen X. J., Clark-Walker G. D. The petite mutation in yeasts: 50 years on. Int Rev Cytol. 2000;194:197–238. doi: 10.1016/s0074-7696(08)62397-9. [DOI] [PubMed] [Google Scholar]
  9. Chupin V., Leenhouts J. M., de Kroon A. I., de Kruijff B. Secondary structure and topology of a mitochondrial presequence peptide associated with negatively charged micelles. A 2D H-NMR study. Biochemistry. 1996 Mar 12;35(10):3141–3146. doi: 10.1021/bi952482a. [DOI] [PubMed] [Google Scholar]
  10. Cliften P. F., Park J. Y., Davis B. P., Jang S. H., Jaehning J. A. Identification of three regions essential for interaction between a sigma-like factor and core RNA polymerase. Genes Dev. 1997 Nov 1;11(21):2897–2909. doi: 10.1101/gad.11.21.2897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Conrad-Webb H., Perlman P. S., Zhu H., Butow R. A. The nuclear SUV3-1 mutation affects a variety of post-transcriptional processes in yeast mitochondria. Nucleic Acids Res. 1990 Mar 25;18(6):1369–1376. doi: 10.1093/nar/18.6.1369. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Contamine V., Picard M. Maintenance and integrity of the mitochondrial genome: a plethora of nuclear genes in the budding yeast. Microbiol Mol Biol Rev. 2000 Jun;64(2):281–315. doi: 10.1128/mmbr.64.2.281-315.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Coruzzi G., Trembath M. K., Tzagoloff A. The isolation of mitochondrial and nuclear mutants of Saccharomyces cerevisiae with specific defects in mitochondrial functions. Methods Enzymol. 1979;56:95–106. doi: 10.1016/0076-6879(79)56012-1. [DOI] [PubMed] [Google Scholar]
  14. Costanzo M. C., Fox T. D. Control of mitochondrial gene expression in Saccharomyces cerevisiae. Annu Rev Genet. 1990;24:91–113. doi: 10.1146/annurev.ge.24.120190.000515. [DOI] [PubMed] [Google Scholar]
  15. Costanzo M. C., Fox T. D. Product of Saccharomyces cerevisiae nuclear gene PET494 activates translation of a specific mitochondrial mRNA. Mol Cell Biol. 1986 Nov;6(11):3694–3703. doi: 10.1128/mcb.6.11.3694. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Costanzo M. C., Seaver E. C., Fox T. D. At least two nuclear gene products are specifically required for translation of a single yeast mitochondrial mRNA. EMBO J. 1986 Dec 20;5(13):3637–3641. doi: 10.1002/j.1460-2075.1986.tb04693.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Dang Y. L., Martin N. C. Yeast mitochondrial RNase P. Sequence of the RPM2 gene and demonstration that its product is a protein subunit of the enzyme. J Biol Chem. 1993 Sep 15;268(26):19791–19796. [PubMed] [Google Scholar]
  18. Decoster E., Simon M., Hatat D., Faye G. The MSS51 gene product is required for the translation of the COX1 mRNA in yeast mitochondria. Mol Gen Genet. 1990 Oct;224(1):111–118. doi: 10.1007/BF00259457. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. Dieckmann C. L., Tzagoloff A. Analysis of yeast mitochondrial genes. Methods Enzymol. 1983;97:361–373. doi: 10.1016/0076-6879(83)97149-5. [DOI] [PubMed] [Google Scholar]
  21. Dunstan H. M., Green-Willms N. S., Fox T. D. In vivo analysis of Saccharomyces cerevisiae COX2 mRNA 5'-untranslated leader functions in mitochondrial translation initiation and translational activation. Genetics. 1997 Sep;147(1):87–100. doi: 10.1093/genetics/147.1.87. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Eilers M., Endo T., Schatz G. Adriamycin, a drug interacting with acidic phospholipids, blocks import of precursor proteins by isolated yeast mitochondria. J Biol Chem. 1989 Feb 15;264(5):2945–2950. [PubMed] [Google Scholar]
  23. Endo T., Eilers M., Schatz G. Binding of a tightly folded artificial mitochondrial precursor protein to the mitochondrial outer membrane involves a lipid-mediated conformational change. J Biol Chem. 1989 Feb 15;264(5):2951–2956. [PubMed] [Google Scholar]
  24. Fox T. D., Costanzo M. C., Strick C. A., Marykwas D. L., Seaver E. C., Rosenthal J. K. Translational regulation of mitochondrial gene expression by nuclear genes of Saccharomyces cerevisiae. Philos Trans R Soc Lond B Biol Sci. 1988 May 31;319(1193):97–105. doi: 10.1098/rstb.1988.0034. [DOI] [PubMed] [Google Scholar]
  25. Fox T. D., Folley L. S., Mulero J. J., McMullin T. W., Thorsness P. E., Hedin L. O., Costanzo M. C. Analysis and manipulation of yeast mitochondrial genes. Methods Enzymol. 1991;194:149–165. doi: 10.1016/0076-6879(91)94013-3. [DOI] [PubMed] [Google Scholar]
  26. Glerum D. M., Koerner T. J., Tzagoloff A. Cloning and characterization of COX14, whose product is required for assembly of yeast cytochrome oxidase. J Biol Chem. 1995 Jun 30;270(26):15585–15590. doi: 10.1074/jbc.270.26.15585. [DOI] [PubMed] [Google Scholar]
  27. Grivell L. A., Artal-Sanz M., Hakkaart G., de Jong L., Nijtmans L. G., van Oosterum K., Siep M., van der Spek H. Mitochondrial assembly in yeast. FEBS Lett. 1999 Jun 4;452(1-2):57–60. doi: 10.1016/s0014-5793(99)00532-3. [DOI] [PubMed] [Google Scholar]
  28. Groot G. S., Mason T. L., Van Harten-Loosbroek N. Var1 is associated with the small ribosomal subunit of mitochondrial ribosomes in yeast. Mol Gen Genet. 1979 Jul 24;174(3):339–342. doi: 10.1007/BF00267808. [DOI] [PubMed] [Google Scholar]
  29. Herbert C. J., Labouesse M., Dujardin G., Slonimski P. P. The NAM2 proteins from S. cerevisiae and S. douglasii are mitochondrial leucyl-tRNA synthetases, and are involved in mRNA splicing. EMBO J. 1988 Feb;7(2):473–483. doi: 10.1002/j.1460-2075.1988.tb02835.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Herrmann J. M., Neupert W. Protein transport into mitochondria. Curr Opin Microbiol. 2000 Apr;3(2):210–214. doi: 10.1016/s1369-5274(00)00077-1. [DOI] [PubMed] [Google Scholar]
  31. Herrmann J. M., Stuart R. A., Craig E. A., Neupert W. Mitochondrial heat shock protein 70, a molecular chaperone for proteins encoded by mitochondrial DNA. J Cell Biol. 1994 Nov;127(4):893–902. doi: 10.1083/jcb.127.4.893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Hill K., Model K., Ryan M. T., Dietmeier K., Martin F., Wagner R., Pfanner N. Tom40 forms the hydrophilic channel of the mitochondrial import pore for preproteins [see comment]. Nature. 1998 Oct 1;395(6701):516–521. doi: 10.1038/26780. [DOI] [PubMed] [Google Scholar]
  33. Kang P. J., Ostermann J., Shilling J., Neupert W., Craig E. A., Pfanner N. Requirement for hsp70 in the mitochondrial matrix for translocation and folding of precursor proteins. Nature. 1990 Nov 8;348(6297):137–143. doi: 10.1038/348137a0. [DOI] [PubMed] [Google Scholar]
  34. Kassenbrock C. K., Gao G. J., Groom K. R., Sulo P., Douglas M. G., Martin N. C. RPM2, independently of its mitochondrial RNase P function, suppresses an ISP42 mutant defective in mitochondrial import and is essential for normal growth. Mol Cell Biol. 1995 Sep;15(9):4763–4770. doi: 10.1128/mcb.15.9.4763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Kovác L., Lachowicz T. M., Slonimski P. P. Biochemical genetics of oxidative phosphorylation. Science. 1967 Dec 22;158(3808):1564–1567. doi: 10.1126/science.158.3808.1564. [DOI] [PubMed] [Google Scholar]
  36. 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]
  37. Lutz M. S., Ellis S. R., Martin N. C. Proteasome mutants, pre4-2 and ump1-2, suppress the essential function but not the mitochondrial RNase P function of the Saccharomyces cerevisiae gene RPM2. Genetics. 2000 Mar;154(3):1013–1023. doi: 10.1093/genetics/154.3.1013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Manning-Krieg U. C., Scherer P. E., Schatz G. Sequential action of mitochondrial chaperones in protein import into the matrix. EMBO J. 1991 Nov;10(11):3273–3280. doi: 10.1002/j.1460-2075.1991.tb04891.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Mayer A., Neupert W., Lill R. Mitochondrial protein import: reversible binding of the presequence at the trans side of the outer membrane drives partial translocation and unfolding. Cell. 1995 Jan 13;80(1):127–137. doi: 10.1016/0092-8674(95)90457-3. [DOI] [PubMed] [Google Scholar]
  40. Morales M. J., Dang Y. L., Lou Y. C., Sulo P., Martin N. C. A 105-kDa protein is required for yeast mitochondrial RNase P activity. Proc Natl Acad Sci U S A. 1992 Oct 15;89(20):9875–9879. doi: 10.1073/pnas.89.20.9875. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Mulero J. J., Fox T. D. PET111 acts in the 5'-leader of the Saccharomyces cerevisiae mitochondrial COX2 mRNA to promote its translation. Genetics. 1993 Mar;133(3):509–516. doi: 10.1093/genetics/133.3.509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Myers A. M., Pape L. K., Tzagoloff A. Mitochondrial protein synthesis is required for maintenance of intact mitochondrial genomes in Saccharomyces cerevisiae. EMBO J. 1985 Aug;4(8):2087–2092. doi: 10.1002/j.1460-2075.1985.tb03896.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. 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]
  44. Nelson N., Schatz G. Energy-dependent processing of cytoplasmically made precursors to mitochondrial proteins. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4365–4369. doi: 10.1073/pnas.76.9.4365. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Pel H. J., Grivell L. A. Protein synthesis in mitochondria. Mol Biol Rep. 1994 May;19(3):183–194. doi: 10.1007/BF00986960. [DOI] [PubMed] [Google Scholar]
  46. Philippsen P., Stotz A., Scherf C. DNA of Saccharomyces cerevisiae. Methods Enzymol. 1991;194:169–182. doi: 10.1016/0076-6879(91)94014-4. [DOI] [PubMed] [Google Scholar]
  47. Rapaport D., Mayer A., Neupert W., Lill R. cis and trans sites of the TOM complex of mitochondria in unfolding and initial translocation of preproteins. J Biol Chem. 1998 Apr 10;273(15):8806–8813. doi: 10.1074/jbc.273.15.8806. [DOI] [PubMed] [Google Scholar]
  48. Rapaport D., Neupert W., Lill R. Mitochondrial protein import. Tom40 plays a major role in targeting and translocation of preproteins by forming a specific binding site for the presequence. J Biol Chem. 1997 Jul 25;272(30):18725–18731. doi: 10.1074/jbc.272.30.18725. [DOI] [PubMed] [Google Scholar]
  49. Rothstein R. Targeting, disruption, replacement, and allele rescue: integrative DNA transformation in yeast. Methods Enzymol. 1991;194:281–301. doi: 10.1016/0076-6879(91)94022-5. [DOI] [PubMed] [Google Scholar]
  50. Slonimski P. P., Perrodin G., Croft J. H. Ethidium bromide induced mutation of yeast mitochondria: complete transformation of cells into respiratory deficient non-chromosomal "petites". Biochem Biophys Res Commun. 1968 Feb 15;30(3):232–239. doi: 10.1016/0006-291x(68)90440-3. [DOI] [PubMed] [Google Scholar]
  51. Stribinskis V., Gao G. J., Sulo P., Dang Y. L., Martin N. C. Yeast mitochondrial RNase P RNA synthesis is altered in an RNase P protein subunit mutant: insights into the biogenesis of a mitochondrial RNA-processing enzyme. Mol Cell Biol. 1996 Jul;16(7):3429–3436. doi: 10.1128/mcb.16.7.3429. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Subik J. A nuclear mutant of S. cerevisiae non-tolerating the cytoplasmic petite mutation. FEBS Lett. 1974 Jun 15;42(3):309–313. doi: 10.1016/0014-5793(74)80753-2. [DOI] [PubMed] [Google Scholar]
  53. Séraphin B., Simon M., Boulet A., Faye G. Mitochondrial splicing requires a protein from a novel helicase family. Nature. 1989 Jan 5;337(6202):84–87. doi: 10.1038/337084a0. [DOI] [PubMed] [Google Scholar]
  54. Séraphin B., Simon M., Faye G. MSS18, a yeast nuclear gene involved in the splicing of intron aI5 beta of the mitochondrial cox1 transcript. EMBO J. 1988 May;7(5):1455–1464. doi: 10.1002/j.1460-2075.1988.tb02963.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Terpstra P., Butow R. A. The role of var1 in the assembly of yeast mitochondrial ribosomes. J Biol Chem. 1979 Dec 25;254(24):12662–12669. [PubMed] [Google Scholar]
  56. Tzagoloff A. Ubiquinol-cytochrome-c oxidoreductase from Saccharomyces cerevisiae. Methods Enzymol. 1995;260:51–63. doi: 10.1016/0076-6879(95)60129-5. [DOI] [PubMed] [Google Scholar]
  57. 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]
  58. Underbrink-Lyon K., Miller D. L., Ross N. A., Fukuhara H., Martin N. C. Characterization of a yeast mitochondrial locus necessary for tRNA biosynthesis. Deletion mapping and restriction mapping studies. Mol Gen Genet. 1983;191(3):512–518. doi: 10.1007/BF00425771. [DOI] [PubMed] [Google Scholar]
  59. Valencik M. L., Kloeckener-Gruissem B., Poyton R. O., McEwen J. E. Disruption of the yeast nuclear PET54 gene blocks excision of mitochondrial intron aI5 beta from pre-mRNA for cytochrome c oxidase subunit I. EMBO J. 1989 Dec 1;8(12):3899–3904. doi: 10.1002/j.1460-2075.1989.tb08569.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Valencik M. L., McEwen J. E. Genetic evidence that different functional domains of the PET54 gene product facilitate expression of the mitochondrial genes COX1 and COX3 in Saccharomyces cerevisiae. Mol Cell Biol. 1991 May;11(5):2399–2405. doi: 10.1128/mcb.11.5.2399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Weber E. R., Hanekamp T., Thorsness P. E. Biochemical and functional analysis of the YME1 gene product, an ATP and zinc-dependent mitochondrial protease from S. cerevisiae. Mol Biol Cell. 1996 Feb;7(2):307–317. doi: 10.1091/mbc.7.2.307. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Westermann B., Gaume B., Herrmann J. M., Neupert W., Schwarz E. Role of the mitochondrial DnaJ homolog Mdj1p as a chaperone for mitochondrially synthesized and imported proteins. Mol Cell Biol. 1996 Dec;16(12):7063–7071. doi: 10.1128/mcb.16.12.7063. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Yuan H., Douglas M. G. The mitochondrial F1ATPase alpha-subunit is necessary for efficient import of mitochondrial precursors. J Biol Chem. 1992 Jul 25;267(21):14697–14702. [PubMed] [Google Scholar]
  64. Zinser E., Sperka-Gottlieb C. D., Fasch E. V., Kohlwein S. D., Paltauf F., Daum G. Phospholipid synthesis and lipid composition of subcellular membranes in the unicellular eukaryote Saccharomyces cerevisiae. J Bacteriol. 1991 Mar;173(6):2026–2034. doi: 10.1128/jb.173.6.2026-2034.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. van Wilpe S., Ryan M. T., Hill K., Maarse A. C., Meisinger C., Brix J., Dekker P. J., Moczko M., Wagner R., Meijer M. Tom22 is a multifunctional organizer of the mitochondrial preprotein translocase. Nature. 1999 Sep 30;401(6752):485–489. doi: 10.1038/46802. [DOI] [PubMed] [Google Scholar]

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