Skip to main content
Log in

Yme2p is a mediator of nucleoid structure and number in mitochondria of the yeast Saccharomyces cerevisiae

  • Research Article
  • Published:
Current Genetics Aims and scope Submit manuscript

Abstract

A large number of gene products have been identified that either directly or indirectly alter the inheritance of mitochondrial DNA. In yeast, we have used a unique genetic screen based on the transfer of DNA from mitochondria to nucleus to identify nuclear-encoded gene products that are targeted to mitochondria and impact the stable inheritance of mitochondrial DNA. A specific allele of one of these genes, yme2-4, prevents even the low wild-type rate of mitochondrial DNA transfer to the nucleus and imparts significant temperature-sensitive and respiratory-growth defects. Intra- and extragenic suppressors of the yme2-4 growth phenotypes were isolated and analysis of these interacting genes reveals that both YME2 and its suppressors influence the structure and number of mitochondrial nucleoids. The yme2-4 allele decreases the average number of mtDNA nucleoids found in cells and the sensitivity of DNA in toluene-treated mitochondria to digestion by DNA exonuclease, effects reversed by intra- and extragenic suppressors. The extragenic suppressor, a missense allele of ILV5, encodes an enzyme of the branched-chain amino acid biosynthetic pathway that is also a component of mitochondrial nucleoids. A null allele of ILV5 suppresses transfer of mitochondrial DNA to the nucleus and displays synthetic interactions with yme2-4.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Albring M, Griffith J, Attardi G (1977) Association of a protein structure of probable membrane derivation with HeLa cell mitochondrial DNA near its origin of replication. Proc Natl Acad Sci USA 74:1348–1352

    Article  PubMed  CAS  Google Scholar 

  • Bateman JM, Perlman PS, Butow RA (2002) Mutational bisection of the mitochondrial DNA stability and amino acid biosynthetic functions of i1v5p of budding yeast. Genetics 161(3):1043–1052

    PubMed  CAS  Google Scholar 

  • Birney E, Kumar S, Krainer AR (1993) Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Res 21:5803–5816

    Article  PubMed  CAS  Google Scholar 

  • Boldogh IR, Nowakowski DW, Yang HC, Chung H, Karmon S, Royes P, Pon LA (2003) A protein complex containing Mdm10p, Mdm12p, and Mmm1p links mitochondrial membranes and DNA to the cytoskeleton-based segregation machinery. Mol Biol Cell 14:4618–4627

    Article  PubMed  CAS  Google Scholar 

  • Burgess SM, Delannoy M, Jensen RE (1994) MMM1 encodes a mitochondrial outer membrane protein essential for establishing and maintaining the structure of yeast mitochondria. J Cell Biol 126:1375–1391

    Article  PubMed  CAS  Google Scholar 

  • Chen XJ, Wang X, Kaufman BA, Butow RA (2005) Aconitase couples metabolic regulation to mitochondrial DNA maintenance. Science 307:714–717

    Article  PubMed  CAS  Google Scholar 

  • Cho JH, Ha SJ, Kao LR, Megraw TL, Chae CB (1998) A novel DNA-binding protein bound to the mitochondrial inner membrane restores the null mutation of mitochondrial histone Abf2p in Saccharomyces cerevisiae. Mol Cell Biol 18:5712–5723

    PubMed  CAS  Google Scholar 

  • Diffley JFX, Stillman B (1991) A close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. Proc Natl Acad Sci USA 88:7864–7868

    Article  PubMed  CAS  Google Scholar 

  • Echeverria M, Robert D, Carde JP, Litvak S (1991) Isolation from wheat mitochondria of a membrane-associated high molecular weight complex involved in DNA synthesis. Plant Mol Biol 16:301–315

    Article  PubMed  CAS  Google Scholar 

  • Hall RM, Mattick JS, Marzuki S, Linnane AW (1975) Evidence for a functional association of DNA synthesis with the membrane in mitochondria of Saccharomyces cerevisiae. Mol Biol Rep 2:101–106

    Article  PubMed  CAS  Google Scholar 

  • Hanekamp T, Thorsness PE (1996) Inactivation of YME2/RNA12, which encodes an integral inner mitochondrial membrane protein, causes increased escape of DNA from mitochondria to the nucleus in Saccharomyces cerevisisae. Mol Cell Biol 16:2764–2771

    PubMed  CAS  Google Scholar 

  • Hanekamp T, Thorsness PE (1999) YNT20, a bypass suppressor of yme1 yme2, encodes a putative 3’-5- exonuclease localized in mitochondria of Saccharomyces cerevisiae. Curr Genet 34:438–448

    Article  PubMed  CAS  Google Scholar 

  • Hanekamp T, Thorsness MK, Rebbapragada I, Fisher EM, Seebart C, Darland MR, Coxbill JA, Updike DL, Thorsness PE (2002) Maintenance of mitochondrial morphology is linked to maintenance of the mitochondrial genome in Saccharomyces cerevisiae. Genetics 162:1147–1156

    PubMed  CAS  Google Scholar 

  • Hillar M, Rangayya V, Jafar BB, Chambers D, Vitzu M, Wyborny LE (1979) Membrane-bound mitochondrial DNA: isolation, transcription and protein composition. Arch Int Physiol Biochim 87:29–49

    Article  PubMed  CAS  Google Scholar 

  • Hobbs AE, Srinivasan M, McCaffery JM, Jensen RE (2001) Mmm1p, a mitochondrial outer membrane protein, is connected to mitochondrial DNA (mtDNA) nucleoids and required for mtDNA stability. J Cell Biol 152:401–410

    Article  PubMed  CAS  Google Scholar 

  • Kaufman BA, Newman SM, Hallberg RL, Slaughter CA, Perlman PS, Butow RA (2000) In organello formaldehyde crosslinking of proteins to mtDNA: identification of bifunctional proteins. Proc Natl Acad Sci USA 97:7772–7777

    Article  PubMed  CAS  Google Scholar 

  • Kaufman BA, Kolesar JE, Perlman PS, Butow RA (2003) A function for the mitochondrial chaperonin Hsp60 in the structure and transmission of mitochondrial DNA nucleoids in Saccharomyces cerevisiae. J Cell Biol 163:457–461

    Article  PubMed  CAS  Google Scholar 

  • Leonhard K, Herrmann JM, Stuart RA, Mannhaupt G, Neupert W, Langer T (1996) AAA proteases with catalytic sites on opposite membrane surfaces comprise a proteolytic system for the ATP-dependent degradation of inner membrane proteins in mitochondria. EMBO J 15:4218–4229

    PubMed  CAS  Google Scholar 

  • Liang S, Alksne L, Warner JR, Lacroute F (1992) rna12+, a gene of Saccharomyces cerevisiae involved in pre-rRNA maturation. Characterization of a temperature-sensitive mutant, cloning and sequencing of the gene. Mol Gen Genet 232:304–312

    PubMed  CAS  Google Scholar 

  • Lockshon D, Zweifel SG, Freeman-Cook LL, Lorimer HE, Brewer BJ, Fangman WL (1995) A role for recombination junctions in the segregation of mitochondrial DNA in yeast. Cell 81:947–955

    Article  PubMed  CAS  Google Scholar 

  • MacAlpine DM, Perlman PS, Butow RA (2000) The numbers of individual mitochondrial DNA molecules and mitochondrial DNA nucleoids in yeast are co-regulated by the general amino acid control pathway. Embo J 19:767–775

    Article  PubMed  CAS  Google Scholar 

  • Meeusen S, Tieu Q, Wong E, Weiss E, Schieltz D, Yates JR, Nunnari J (1999) Mgm101p is a novel component of the mitochondrial nucleoid that binds DNA and is required for the repair of oxidatively damaged mitochondrial DNA. J Cell Biol 145:291–304

    Article  PubMed  CAS  Google Scholar 

  • Mollapour M, Piper PW (2001) The ZbYME2 gene from the food spoilage yeast Zygosaccharomyces bailii confers not only YME2 functions in Saccharomyces cerevisiae, but also the capacity for catabolism of sorbate and benzoate, two major weak organic acid preservatives. Mol Microbiol 42:919–930

    Article  PubMed  CAS  Google Scholar 

  • Newman SM, Zelenaya-Troitskaya O, Perlman PS, Butow RA (1996) Analysis of mitochondrial DNA nucleoids in wild-type and a mutant strain of Saccharomyces cerevisiae that lacks the mitochondrial HMG box protein Abf2p. Nucleic Acids Res 24:386–393

    Article  PubMed  CAS  Google Scholar 

  • Philippsen P, Stotz A, Scherf C (1991) DNA of Saccharomyces cerevisiae. Methods Enzymol 194:169–182

    PubMed  CAS  Google Scholar 

  • Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277

    Article  PubMed  CAS  Google Scholar 

  • Shafer KS, Hanekamp T, White KH, Thorsness PE (1999) Mechanisms of mitochondrial DNA escape to the nucleus in the yeast Saccharomyces cerevisiae. Curr Genet 36:183–194

    Article  PubMed  CAS  Google Scholar 

  • Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Cold Spring Harbor, New York

    Google Scholar 

  • Thorsness MK, White KH, Thorsness PE (2002) Migration of mtDNA into the nucleus. Methods Mol Biol 197:177–186

    PubMed  CAS  Google Scholar 

  • Thorsness PE, Fox TD (1993) Nuclear mutations in Saccharomyces cerevisiae that affect the escape of DNA from mitochondria to the nucleus. Genetics 134:21–28

    PubMed  CAS  Google Scholar 

  • Van Tuyle GC, McPherson ML (1979) A compact form of rat liver mitochondrial DNA stabilized by bound proteins. J Biol Chem 254:6044–6053

    PubMed  Google Scholar 

  • Yaffe MP (1991) Analysis of mitochondrial function and assembly. Methods Enzymol 194:627–643

    Article  PubMed  CAS  Google Scholar 

  • Zelenaya-Troitskaya O, Perlman PS, Butow RA (1995) An enzyme in yeast mitochondria that catalyzes a step in branched-chain amino acid biosynthesis also functions in mitochondrial DNA stability. EMBO J 14:3268–3276

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We dedicate this work to the memory of Dr. Theodor Hanekamp. We thank Karen White, Brian Francis, Mary Brownson, and Christopher Smith for their many thoughtful suggestions. This work was supported by National Institutes of Health Grant GM047390.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Peter E. Thorsness.

Additional information

Communicated by Carla Koehler

Rights and permissions

Reprints and permissions

About this article

Cite this article

Park, S., Hanekamp, T., Thorsness, M.K. et al. Yme2p is a mediator of nucleoid structure and number in mitochondria of the yeast Saccharomyces cerevisiae . Curr Genet 50, 173–182 (2006). https://doi.org/10.1007/s00294-006-0087-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00294-006-0087-9

Keywords

Navigation