, Volume 52, Issue 12, pp 1148–1157 | Cite as

Molecular genetics of the peptidyl transferase center and the unusual Var1 protein in yeast mitochondrial ribosomes

  • T. L. Mason
  • C. Pan
  • M. E. Sanchirico
  • K. Sirum-Connolly
Milti-Author Reviews


Mitochondria posses their own ribosomes responsible for the synthesis of a small number of proteins encoded by the mitochondrial genome. In yeast,Saccharomyces cerevisiae, the two ribosomal RNAs and a single ribosomal protein, Varl, are products of mitochondrial genes, and the remaining approximately 80 ribosomal proteins are encoded in the nucleus. The mitochondrial translation system is dispensable in yeast, providing an excellent experimental model for the molecular genetic analysis of the fundamental properties of ribosomes in general as well as adaptations required for the specialized role of ribosomes in mitochondria. Recent studies of the peptidyl transferase center, one of the most highly conserved functional centers of the ribosome, and the Varl protein, an unusual yet essential protein in the small ribosomal subunit, have provided new insight into conserved and divergent features of the mitochondrial ribosome.

Key words

Saccharomyces cerevisiae mitochondrial ribosomes peptidyl transferase Varl ribosomal protein gene relocation posttranscriptional rRNA modification 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Myers, A. M., Pape, L. K. and Tzagoloff A. (1985) Mitochondrial protein synthesis is required for maintenance of intact mitochondrial genomes inSaccharomyces cerevisiae. EMBO J.4: 2087–2092PubMedGoogle Scholar
  2. 2.
    Kitakawa, M., and Isono, K. (1991) The mitochondrial ribosomes. Biochimie73: 813–825CrossRefPubMedGoogle Scholar
  3. 3.
    Mason, T. L., and Sirum-Connolly K. (1996) Expression of rRNA genes in mitochondria and chloroplasts. In: Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis, pp. 421–449. Zimmermann, R. A. and Dahlberg, A. E. (ed.), RCR Press, Boca Raton, FloridaGoogle Scholar
  4. 4.
    Fox, T. D. (1996) Genetics of mitochondrial translation. In: Translational Control, pp. 733–758, Hershey, J. W. B., Matthews, M. B., and Sonenberg, N. (eds), Cold Spring Harbor Press, Cold Spring Harbor, New York.Google Scholar
  5. 5.
    Grivell, L. A. (1995) Nucleo-mitochondrial interactions in mitochondrial gene expression. Crit. Rev. Biochem. Molec. Biol.30: 121–164Google Scholar
  6. 6.
    Dieckmann, C. L. and Staples, R. R. (1984) Regulation of mitochondrial gene expression inSaccharomyces cerevisiae. Int. Rev. Cytol.152: 145–181Google Scholar
  7. 7.
    Noller, H. F. (1993) Peptidyl transferase: protein, ribonucleoprotein, or RNA? J Bacteriol.175: 5297–5300PubMedGoogle Scholar
  8. 8.
    Noller, H. F. (1993) tRNA-rRNA interactions and peptidyl transferase. Faseb J.7: 87–89PubMedGoogle Scholar
  9. 9.
    Lieberman, K. R., and Dahlberg, A. E. (1995) Ribosome-catalyzed peptide-bond formation. In: Progress in Nucleic Acid Research and Molecular Biology, vol. 50, pp. 1–23, Cohn W. E. and Moldave, K. (eds). Academic Press Inc, 525 B Street, Suite 1900, San Diego, California 92101-4495Google Scholar
  10. 10.
    Garrett, R. A. and Rodriguez-Fonseca, C. (1996) The peptidyl transferase center. In: Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis pp. 327–355, Zimmermann, R. A. and Dahlberg A. E. (eds.), CRC Press, Boca Raton, FloridaGoogle Scholar
  11. 11.
    Noller, H. F., Hoffarth, V. and Zimniak, L. (1992) Unusual resistance of peptidyl transferase to protein extraction procedures [see comments]. Science256: 1416–1419PubMedGoogle Scholar
  12. 12.
    Garrels, J. (1995) YPD—A database for the proteins ofSaccharomyces cerevisiae. Nucl. Acids Res.24: 46–49.CrossRefGoogle Scholar
  13. 13.
    Pan, C., Sirum-Connolly, K., and Mason, T. L. (1993) Essential features of the peptidyl transferase center in the yeast mitochondrial ribosome. In: The Translational Apparatus. Structure, Function, Regulation, Evolution, pp. 587–598, Nierhaus, K. H., Franceschi, F., Subramanian, A. R., Erdmann, V. A. and Wittmann-Liebold B. (eds), Plenum Press, New YorkGoogle Scholar
  14. 14.
    Fearon, K., and Mason, T. L. (1988) Structure and regulation of a nuclear gene inSaccharomyces cerevisiae that specifies MRP7, a protein of the large subunit of the mitochondrial ribosome. Molec. Cell. Biol.8: 3636–3646PubMedGoogle Scholar
  15. 15.
    Pan, C. and Mason, T. L. (1995) Identification of the yeast nuclear gene for the mitochondrial homologue of bacterial ribosomal protein L16. Nucl. Acids Res.23: 3673–3677PubMedGoogle Scholar
  16. 16.
    Egebjerg, J., Christiansen, J. and Garrett, R. A. (1991) Attachment sites of primary binding protein-L1, protein-L2 and protein-L23 on 23-S ribosomal RNA ofEscherichia-coli. J. Molec. Biol.222: 251–264CrossRefPubMedGoogle Scholar
  17. 17.
    Cooperman, B.S., Wooten, T., Romero, D. P. and Traut R. R. (1966) Histidine 229 in protein L2 is apparently essential for 50S peptidyl transferase activity. Biochem. Cell. Biol.73: 1087–1094Google Scholar
  18. 18.
    Pan C. (1994) Molecular genetic dissection of nuclear genes for proteins in the peptidyl transferase center of the yeast mitochondrial ribosome, PhD Thesis, University of MassachusettsGoogle Scholar
  19. 19.
    Wower, J., Wower, I. K., Kirillov, S. V., Rosen, K. V., Hixon, S. S. and Zimmermann, R. A. (1996) Peptidyl transferase and beyond. Biochem. Cell. Biol.73: 1041–1047Google Scholar
  20. 20.
    Wower, J., Sylvers, L. A., Rosen, K. V., Hixson, S. S. and Zimmermann, R. A. (1993) A model of the tRNA binding sites on theEscherichia coli ribosome. In: The Translational Apparatus. Structure, Function, Regulation, Evolution, pp. 455–464, Nierhaus, K. H., Franceschi, F., Subramanian, A. R., Erdmann, V. A. and Wittmann-Liebold B. (eds), Plenum Press, New YorkGoogle Scholar
  21. 21.
    Walleczek, J., Martin, T., Redl, B. Stoffler-Meilicke, M. and Stoffler, G. (1989) Comparative cross-linking study on the 50S ribosomal subunit fromEscherichia coli. Biochemistry28: 4099–4105CrossRefPubMedGoogle Scholar
  22. 22.
    Walleczek J., Redl B, Stoffler-Meilicke M. and Stoffler G. (1989) Protein-protein cross-linking of the 50S ribosomal subunit ofEscherichia coli using 2-iminothiolane. Identification of cross-links by immunoblotting techniques. J. Biol. Chem.264: 4231–4237PubMedGoogle Scholar
  23. 23.
    Redl, B., Walleczek, J., Stoffler-Meilicke, M., and Stoffler, G. (1989) Immunoblotting analysis of protein-protein crosslinks within the 50S ribosomal subunit ofEscherichia coli. A study using dimethylsuberimidate as crosslinking reagent. Eur. J. Biochem.181: 351–356CrossRefPubMedGoogle Scholar
  24. 24.
    Garrett R. A., Muller, S., Spiercer P. and Zimmermann R. A. (1974) Binding of 50S ribosomal subunit proteins to 23S RNA ofEscherichia coli. J. Molec. Biol.88 553–557CrossRefPubMedGoogle Scholar
  25. 25.
    Wower I., Wower J., Meinke M. and Brimacombe R. (1981) The use of 2-iminothiolane as an RNA-protein cross-linking agent inEscherichia coli ribosomes, and the localization on 23S RNA of sites cross-linked to proteins L4, L6, L21, L23, L27 and L29. Nucl. Acids Res.9: 4285–4302PubMedGoogle Scholar
  26. 26.
    Gulle H., Hoppe E., Osswald M., Greuer B., Brimacombe R. and Stoffler G. (1988) RNA-protein cross-linking inEscherichia coli 50S ribosomal subunits; determination of sites on 23S RNA that are cross-linked to proteins L2, L4, L24 and L27 by traetment with 2-iminothiolane. Nucl. Acids Res.16: 815–832PubMedGoogle Scholar
  27. 27.
    Osswald M., Greuer B. and Brimacombe R. (1990) Localization of a series of RNA-protein cross-link sites in the 23S and 5S ribosomal RNA fromEscherichia coli, induced by treatment of 50S subunits with three different bifunctional reagents. Nucl. Acids Res.18: 6755–6760PubMedGoogle Scholar
  28. 28.
    Schulze H. and Nierhaus K. H. (1982) Minimal set of ribosomal components for reconstitution of the peptidyltransferase activity. EMBO J.1: 609–613PubMedGoogle Scholar
  29. 29.
    Dabbs E. R., Hasenbank R., Kastner B., Pak K.-H., Wartusch B. and Stoffler G. (1983) Immunological studies ofEscherichia coli mutants lacking one or two ribosomal proteins. Molec. Gen. Genet.192: 301–308CrossRefPubMedGoogle Scholar
  30. 30.
    Fearon K. (1989) Nuclear genes inSaccharomyces cerevisiae that encode proteins of the large subunit of the mitochondrial ribosome., Ph.D. Thesis, University of MassachusettsGoogle Scholar
  31. 31.
    Huff M. O., Hanic-Joyce P. J., Dang H., Rodrigues L. A. and Ellis S. R. (1993) Two inactive fragments derived from the yeast mitochondrial ribosomal protein MrpS28 function in trans to support ribosome assembly and respiratory growth. J. Molec. Biol.233: 597–605CrossRefPubMedGoogle Scholar
  32. 32.
    Thurlow D. L., Mason T. L. and Zimmermann R. A. (1984) 5S RNA-like structures in large ribosomal subunit RNAs of fungal mitochondria. FEBS Letters173: 277–282CrossRefGoogle Scholar
  33. 33.
    Lang B. F., Cedergren R. and Gray M. W. (1987) The mitochondrial genome of the fission yeast,Schizosaccharomyces pombe. Sequence of the large-subunit ribosomal RNA gene, comparison of potential secondary structure in fungal mitochondrial large-subunit rRNAs and evolutionary considerations. Eur. J. Biochem.169: 527–537CrossRefPubMedGoogle Scholar
  34. 34.
    Dontsova O., Tishkov V., Dokudovskaya, S. Bogdanov A., Doring T., Rinkeappel J., Thamm S., Greuer B., and Brimacombe R. (1994) Stem-loop IV of 5S rRNA lies close to the peptidyltransferase center. Proc. Natl. Acad. Sci. USA91: 4125–4129PubMedGoogle Scholar
  35. 35.
    Dokudovskaya S., Dontsova O., Shpanchenko O., Bogdanov A. and Brimacombe R. (1996) Loop IV of 5S ribosomal RNA has contacts both to domain II and to domain V of the 23S RNA. RNA2: 146–152PubMedGoogle Scholar
  36. 36.
    Moore P. B. (1966) The structure and function of 5S ribosomal RNA. In: Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis, pp. 199–236 Zimmermann R. A. and Dahlberg A. E. (eds) CRC Press, Boca Raton, FloridaGoogle Scholar
  37. 37.
    Sirum-Connolly K., Peltier J. M., Crain P. F., McCloskey J. A. and Mason T. L. (1995) Implications of a functional large ribosomal RNA with only three modified nucleotides. Biochimie77: 30–39CrossRefPubMedGoogle Scholar
  38. 38.
    Klootwijik J., Klein I. and Grivell L. A. (1975) Minimal post-transcriptional modification of yeast mitochondrial ribosomal RNA. J. Molec. Biol.97: 337–350PubMedGoogle Scholar
  39. 39.
    Bakin A., Lane B. G. and Ofengand J. (1994) Clustering of pseudouridine residues around the peptidyltransferase center of yeast cytoplasmic and mitochondrial ribosomes. Biochemistry.33: 13475–13483CrossRefPubMedGoogle Scholar
  40. 40.
    Sirum-Connolly K. and Mason T. L. (1993) Functional requirement of a site-specific ribose methylation in ribosomal RNA. Science262; 1886–1889PubMedGoogle Scholar
  41. 41.
    Moazed D. and Noller H. F. (1989) Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell57: 585–597CrossRefPubMedGoogle Scholar
  42. 42.
    Samaha R. R., Green R. R. and Noller H. F. (1995) A base pair between tRNA and 23S rRNA in the peptidyle transferase centrer of the ribosome. Nature377: 309–314CrossRefPubMedGoogle Scholar
  43. 43.
    Krzyzosiak W., Denman R., Nurse K., Hellman W., Boublik M. Gehrke C. W., Agris P. F. and Ofengand J. (1987) In vitro synthesis of 16S ribosomal RNA containing single base changes and assembly into a functional 30S ribosome. Biochemistry26: 2353–2364CrossRefPubMedGoogle Scholar
  44. 44.
    Pinkham J. L., Dudley A. M. and Mason T. L. (1994) T7 RNA polymerase-dependent expression ofCOXII in yeast mitochondria. Molec. Cell. Biol.14: 4643–4652PubMedGoogle Scholar
  45. 45.
    Lane B. G., Ofengand J. and Gray M. W. (1995) Pseudouridine and 2′-O-methlated nucleosides. Significance of their selective occurrence in rRNA domains that function in ribosome-catalyzed synthesis of the peptide bounds in proteins. Biochimie77: 7–15CrossRefPubMedGoogle Scholar
  46. 46.
    Maden B. E. H., Corbett M. E., Heeney P. A., Pugh K. and Ajuh P. M. (1985) Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA. Biochimie77: 22–29CrossRefGoogle Scholar
  47. 47.
    Kiss-Laszlo Z., Henry Y., Bachellerie J.-P., Caizergues-Ferrer M. and Kiss T. (1996) Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell85: 1077–1088CrossRefPubMedGoogle Scholar
  48. 48.
    Sanchirico M., Tzellas A., Fox T. D., Conrad-Webb H., Perlman P. S. and Mason T. L. (1995) Relocation of the unusualVAR1 gene from the mitochondrion to the nucleus. Biochem. Cell. Biol.73: 987–995PubMedGoogle Scholar
  49. 49.
    Groot G. S. P., Mason T. L. and VanHarten-Loosbroek N. (1979) Varl is associated with the small ribosomal subunit of mitochondrial ribosomes in yeast. Molec. Gen. Genet.174: 339–342CrossRefPubMedGoogle Scholar
  50. 50.
    Terpstra P. and Butow R. A. (1979) The role of varl in the assembly of yeast mitochondrial ribosomes. J. Biol. Chem.254: 12662–12669PubMedGoogle Scholar
  51. 51.
    Douglas M. G. and Butow R. A. (1976) Variant forms of mitochondrial translation products in yeast: evidence for location of determinants on mitochondrial DNA. Proc. Natl. Acad. Sci. U.S.A.73: 1083–1086PubMedGoogle Scholar
  52. 52.
    Butow R. A., Perlman P. S. and Grossman L. I. (1985) The unusualvarl gene of yeast mitochondrial DNA. Science228: 1496–1501PubMedGoogle Scholar
  53. 53.
    Hudspeth M. E., Ainley W. M., Shumard D. S., Butow R. A. and Grossman L. I. (1982) Location and structure of theVAR1 gene on yeast mitochondrial DNA: nucleotide sequence of the 40.0 allele. Cell30: 617–626CrossRefPubMedGoogle Scholar
  54. 54.
    Murphy K., Choo K. B., Macreadie I. Marzuki S., Lukins H. B., Nagley P. and Linnane A. W. (1980) Biogenesis of mitochondria: a temperature sensitivity mutation affecting the mitochondrially synthesized Varl protein ofSaccharomyces cerevisiae. Arch. Biochem. Biophys.203: 260–270CrossRefPubMedGoogle Scholar
  55. 55.
    Zassenhaus H. P. and Perlman P. S. (1982) Respiration deficient mutants in the A/T-rich region on the yeast mitochondrial DNA containing thevar1 gene. Curr. Genetics,6: 179–188CrossRefGoogle Scholar
  56. 56.
    Butow R. A., Perlman P. S. and Grossman L. I. (1985) The unusualVAR1 gene of yeast mitochondrial DNA. Science228: 1496–1501PubMedGoogle Scholar
  57. 57.
    Davis S. C. and Ellis S. R. (1995) Incorporation of the yeast mitochondrial ribosomal protein Mrp2 into ribosomal subunits requires the mitochondrially encoded Var1 protein. Molec. Gen. Genet.247: 379–386CrossRefPubMedGoogle Scholar
  58. 58.
    Haffter P., McMullin T. W. and Fox T. D. (1990) A genetic link between an mRNA-specific translational activator and the translation system in yeast mitochondria. Genetics,125: 495–503PubMedGoogle Scholar
  59. 59.
    Haffter P. and Fox T. D. (1992) Suppression of carboxy-terminal truncations of the yeast mitochondrial mRNA-specific translational activator PET122 by mutations in two new genes, MRP17 and PET127. Molec. Gen. Genet.235: 64–73CrossRefPubMedGoogle Scholar
  60. 60.
    McMullin T. W., Haffter P. and Fox T. D. (1990) A novel small-subunit ribosomal protein of yeast mitochondria that interacts functionally with an mRNA-specific translational activator. Molec. Cell. Biol.10: 4590–4595PubMedGoogle Scholar
  61. 61.
    Conrad-Webb H., Perlman P. S., Zhu H., and Butow R. A. (1990) The nuclearSUV3-1 mutation affects a variety of post-transcriptional processes in yeast mitochondria. Nucl. Acids Res.18: 1369–1376PubMedGoogle Scholar
  62. 62.
    Steele D. F., Butler C. A. and Fox T. D. (1996) Expression of a recoded nuclear gene inserted into yeast mitochondrial DNA is limited by mRNA-specific translational activation. Proc. Natl. Acad. Sci. USA93: 5253–5257CrossRefPubMedGoogle Scholar
  63. 63.
    Attardi G. and Schatz G. (1988) Biogenesis of mitochondria. A. Rev. Cell. Biol.4: 289–333Google Scholar
  64. 64.
    Claros M. G., Perea J., Shu Y., Samatey F. A., Popot J.-L. and Jacq C. (1995) Limitations to in vitro import of hydrophobic proteins into yeast mitochondria: the case of a cytoplasmically synthesized apocytochromeb. Eur. J. Biochem.228: 762–771CrossRefPubMedGoogle Scholar
  65. 65.
    Grohmann L., Graack H. R., Kruft V., Choli T, Goldschmidtreisin S. and Kitakawa M. (1991) Extended N-terminal sequencing of proteins of the large ribosomal subunit from yeast mitochondria. FEBS Letters284: 51–56CrossRefPubMedGoogle Scholar
  66. 66.
    Olsen G. J., Overbeek R., Larsen N., Marsh T. L., Mccaughey M. J., Maciukenas M. A., Kuan W. M., Macke T. J., Xing Y. Q. and Woese C. R. (1992) The Ribosomal Database Project. Nucl. Acids Res.20: 2199–2200PubMedGoogle Scholar

Copyright information

© Berkhäuser Verlag Basel 1996

Authors and Affiliations

  • T. L. Mason
    • 1
    • 2
  • C. Pan
    • 1
    • 2
  • M. E. Sanchirico
    • 1
    • 2
  • K. Sirum-Connolly
    • 1
    • 2
  1. 1.Department of Biochemistry and Molecular BiologyUniversity of MassachusettsAmherstUSA
  2. 2.Graduate Program in Molecular and Cellular BiologyUniversity of MassachusettsAmherstUSA

Personalised recommendations