Abstract
Killer toxins from Kluyveromyces lactis (zymocin) and Pichia acaciae (PaT) were found to disable translation in target cells by virtue of anticodon nuclease (ACNase) activities on tRNAGlu and tRNAGln, respectively. Surprisingly, however, ACNase exposure does not only impair translation, but also affects genome integrity and concomitantly DNA damage occurs. Previously, it was shown that homologous recombination protects cells from ACNase toxicity. Here, we have analyzed whether other DNA repair pathways are functional in conferring ACNase resistance as well. In addition to HR, base excision repair (BER) and postreplication repair (PRR) promote clear resistance to either, PaT and zymocin. Comparative toxin sensitivity analysis of BER mutants revealed that its ACNase protective function is due to the endonucleases acting on apurinic (AP) sites, whereas none of the known DNA glycosylases is involved. Because PaT and zymocin require the presence of the ELP3/TRM9-dependent wobble uridine modification 5-methoxy-carbonyl-methyl (mcm5) for tRNA cleavage, we analyzed toxin response in DNA repair mutants additionally lacking such tRNA modifications. ACNase resistance caused by elp3 or trm9 mutations was found to rescue hypersensitivity of DNA repair defects, consistent with DNA damage to occur as a consequence of tRNA cleavage. The obtained genetic evidence promises to reveal new aspects into the mechanism linking translational fidelity and genome surveillance.
Similar content being viewed by others
References
Alseth I, Eide L, Pirovano M, Rognes T, Seeberg E, Bjørås M (1999) The Saccharomyces cerevisiae homologues of endonuclease III from Escherichia coli, Ntg1 and Ntg2, are both required for efficient repair of spontaneous and induced oxidative DNA damage in yeast. Mol Cell Biol 19:3779–3787
Andersen PL, Xu F, Xiao W (2008) Eukaryotic DNA damage tolerance and translesion synthesis through covalent modifications of PCNA. Cell Res 18:162–173
Barbour L, Xiao W (2003) Regulation of alternative replication bypass pathways at stalled replication forks and its effects on genome stability: a yeast model. Mutat Res 532:137–155
Blastyák A, Pintér L, Unk I, Prakash L, Prakash S, Haracska L (2007) Yeast Rad5 protein required for postreplication repair has a DNA helicase activity specific for replication fork regression. Mol Cell 28:167–175
Broomfield S, Hryciw T, Xiao W (2001) DNA postreplication repair and mutagenesis in Saccharomyces cerevisiae. Mutat Res 486:167–184
Butler AR, O’Donnell RW, Martin VJ, Gooday GW, Stark MJR (1991) Kluyveromyces lactis toxin has an essential chitinase activity. Eur J Biochem 199:483–488
Chen J, Derfler B, Maskati A, Samson L (1989) Cloning a eukaryotic DNA glycosylase repair gene by the suppression of a DNA repair defect in Escherichia coli. Proc Natl Acad Sci USA 86:7961–7965
Dornfeld K, Johnson M (2005) AP endonuclease deficiency results in extreme sensitivity to thymidine deprivation. Nucleic Acids Res 33:6644–6653
Downs JA, Lowndes NF, Jackson SP (2000) A role for Saccharomyces cerevisiae histone H2A in DNA repair. Nature 408:1001–1004
Eide L, Bjørås M, Pirovano M, Alseth I, Berdal KG, Seeberg E (1996) Base excision of oxidative purine and pyrimidine DNA damage in Saccharomyces cerevisiae by a DNA glycosylase with sequence similarity to endonuclease III from Escherichia coli. Proc Natl Acad Sci USA 93:10735–10740
Frohloff F, Fichtner L, Jablonowski D, Breunig KD, Schaffrath R (2001) Saccharomyces cerevisiae elongator mutations confer resistance to the Kluyveromyces lactis zymocin. EMBO J 20:1993–2003
Gietz RD, Schiestl RH (1995) Transforming yeast with DNA. Methods Mol Cell Biol 5:255–269
Gueldener U, Heinisch J, Koehler GJ, Voss D, Hegemann JH (2002) A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Res 30:e23
Guillet M, Boiteux S (2002) Endogenous DNA abasic sites cause cell death in the absence of Apn1, Apn2 and Rad1/Rad10 in Saccharomyces cerevisiae. EMBO J 21:2833–2841
Gunge N, Tamaru A, Ozawa F, Sakaguchi K (1981) Isolation and characterization of linear deoxyribonucleic acid plasmids from Kluyveromyces lactis and the plasmid-associated killer character. J Bacteriol 145:382–390
Guzder SN, Torres-Ramos C, Johnson RE, Haracska L, Prakash L, Prakash S (2004) Requirement of yeast Rad1–Rad10 nuclease for the removal of 3′-blocked termini from DNA strand breaks induced by reactive oxygen species. Genes Dev 18:2283–2291
Higgins DR, Prakash S, Reynolds P, Prakash L (1983) Molecular cloning and characterization of the RAD1 gene of Saccharomyces cerevisiae. Gene 26:119–126
Hoege C, Pfander B, Moldovan GL, Pyrowolakis G, Jentsch S (2002) RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 419:135–141
Huang B, Johansson MJ, Byström AS (2005) An early step in wobble uridine tRNA modification requires the elongator complex. RNA 11:424–436
Huang B, Lu J, Byström AS (2008) A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. RNA 14:2183–2194
Jablonowski D, Fichtner L, Martin VJ, Klassen R, Meinhardt F, Stark MJR, Schaffrath R (2001) Saccharomyces cerevisiae cell wall chitin, the potential Kluyveromyces lactis zymocin receptor. Yeast 18:1285–1299
Jentsch S, McGrath JP, Varshavsky A (1987) The yeast DNA repair gene RAD6 encodes a ubiquitin-conjugating enzyme. Nature 329:131–134
Johnson AW, Demple B (1988) Yeast DNA diesterase for 3′-fragments of deoxyribose: purification and physical properties of a repair enzyme for oxidative DNA damage. J Biol Chem 263:18009–18016
Johnson RE, Torres-Ramos CA, Izumi T, Mitra S, Prakash S, Prakash L (1998) Identification of APN2, the Saccharomyces cerevisiae homolog of the major human AP endonuclease HAP1, and its role in the repair of abasic sites. Genes Dev 12:3137–3143
Kalhor HR, Clarke S (2003) Novel methyltransferase for modified uridine residues at the wobble position of tRNA. Mol Cell Biol 23:9283–9292
Kämper J, Esser K, Gunge N, Meinhardt F (1991) Heterologous gene expression on the linear DNA killer plasmids from Kluyveromyces lactis. Curr Genet 19:109–118
Karumbati AS, Wilson TE (2005) Abrogation of the Chk1-Pds1 checkpoint leads to tolerance of persistent single-strand breaks in Saccharomyces cerevisiae. Genetics 169:1833–1844
Karumbati AS, Deshpande RA, Jilani A, Vance JR, Ramotar D, Wilson TE (2003) The role of yeast DNA 3′-phosphatase Tpp1 and Rad1/Rad10 endonuclease in processing spontaneous and induced base lesions. J Biol Chem 278:31434–31443
Klassen R, Meinhardt F (2005) Induction of DNA damage and apoptosis in Saccharomyces cerevisiae by a yeast killer toxin. Cell Microbiol 7:393–401
Klassen R, Teichert S, Meinhardt F (2004) Novel yeast killer toxins provoke S-phase arrest and DNA damage checkpoint activation. Mol Microbiol 53:263–273
Klassen R, Krampe S, Meinhardt F (2007) Homologous recombination and the yKu70/80 complex exert opposite roles in resistance against the killer toxin from Pichia acaciae. DNA Repair (Amst) 6:1864–1875
Klassen R, Paluszynski JP, Wemhoff S, Pfeiffer A, Fricke J, Meinhardt F (2008) The primary target of the killer toxin from Pichia acaciae is tRNAGln. Mol Microbiol 69:681–697
Lu J, Huang B, Esberg A, Johansson MJ, Byström AS (2005) The Kluyveromyces lactis gamma-toxin targets tRNA anticodons. RNA 11:1648–1654
Ma W, Resnick MA, Gordenin DA (2008) Apn1 and Apn2 endonucleases prevent accumulation of repair-associated DNA breaks in budding yeast as revealed by direct chromosomal analysis. Nucleic Acids Res 36:1836–1846
Meadows KL, Song B, Doetsch PW (2003) Characterization of AP lyase activities of Saccharomyces cerevisiae Ntg1p and Ntg2p: implications for biological function. Nucleic Acids Res 31:5560–5567
Nash HM, Bruner SD, Schärer OD, Kawate T, Addona TA, Spooner E, Lane WS, Verdine GL (1996) Cloning of a yeast 8-oxoguanine DNA glycosylase reveals the existence of a base-excision DNA-repair protein superfamily. Curr Biol 6:968–980
Ogawa T, Tomita K, Ueda T, Watanabe K, Uozumi T, Masaki H (1999) A cytotoxic ribonuclease targeting specific transfer RNA anticodons. Science 283:2097–2100
Percival KJ, Klein MB, Burgers PM (1989) Molecular cloning and primary structure of the uracil-DNA-glycosylase gene from Saccharomyces cerevisiae. J Biol Chem 264:2593–2598
Popoff SC, Spira AI, Johnson AW, Demple B (1990) Yeast structural gene (APN1) for the major apurinic endonuclease: homology to Escherichia coli endonuclease IV. Proc Natl Acad Sci USA 87:4193–4197
Prakash S, Johnson RE, Prakash L (2005) Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function. Annu Rev Biochem 74:317–353
Scheller J, Schürer A, Rudolph C, Hettwer S, Kramer W (2000) MPH1, a yeast gene encoding a DEAH protein, plays a role in protection of the genome from spontaneous and chemically induced damage. Genetics 155:1069–1081
Schiestl RH, Prakash S, Prakash L (1990) The SRS2 suppressor of rad6 mutations of Saccharomyces cerevisiae acts by channeling DNA lesions into the RAD52 DNA repair pathway. Genetics 124:817–831
Schürer KA, Rudolph C, Ulrich HD, Kramer W (2004) Yeast MPH1 gene functions in an error-free DNA damage bypass pathway that requires genes from homologous recombination, but not from postreplicative repair. Genetics 166:1673–1686
Sentürker S, van der Kemp Auffret P, You HJ, Doetsch PW, Dizdaroglu M, Boiteux S (1998) Substrate specificities of the Ntg1 and Ntg2 proteins of Saccharomyces cerevisiae for oxidized DNA bases are not identical. Nucleic Acids Res 26:5270–5276
Singh KK, Sigala B, Sikder HA, Schwimmer C (2001) Inactivation of Saccharomyces cerevisiae OGG1 DNA repair gene leads to an increased frequency of mitochondrial mutants. Nucleic Acids Res 29:1381–1388
Stark MJR, Boyd A (1986) The killer toxin of Kluyveromyces lactis: characterization of the toxin subunits and identification of the genes which encode them. EMBO J 5:1995
Stark MJR, Boyd A, Mileham AJ, Romanos MA (1990) The plasmid encoded killer system of Kluyveromyces lactis: a review. Yeast 6:1–29
Stelter P, Ulrich HD (2003) Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation. Nature 425:188–191
Tokunaga M, Kawamura A, Hishinuma F (1989) Expression of pGKL killer 28 K subunit in Saccharomyces cerevisiae: identification of 28 K subunit as a killer protein. Nucleic Acids Res 17:3435–3446
Tomita K, Ogawa T, Uozumi T, Watanabe K, Masaki H (2000) A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops. Proc Natl Acad Sci USA 97:8278–8283
Tomkinson AE, Bardwell AJ, Bardwell L, Tappe NJ, Friedberg EC (1993) Yeast DNA repair and recombination proteins Rad1 and Rad10 constitute a single-stranded-DNA endonuclease. Nature 362:860–862
Ulrich HD (2005) The RAD6 pathway: control of DNA damage bypass and mutagenesis by ubiquitin and SUMO. Chembiochem 6:1735–1743
Unk I, Haracska L, Prakash S, Prakash L (2001) 3′-phosphodiesterase and 3′→5′ exonuclease activities of yeast Apn2 protein and requirement of these activities for repair of oxidative DNA damage. Mol Cell Biol 21:1656–1661
Van der Kemp PA, Thomas D, Barbey R, de Oliveira R, Boiteux S (1996) Cloning and expression in Escherichia coli of the OGG1 gene of Saccharomyces cerevisiae, which codes for a DNA glycosylase that excises 7, 8-dihydro-8-oxoguanine and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine. Proc Natl Acad Sci USA 93:5197–5202
Van Dijken JP, Bauer J, Brambilla L, Duboc P, Francois JM, Gancedo C, Giuseppin ML, Heijnen JJ, Hoare M, Lange HC, Madden EA, Niederberger P, Nielsen J, Parrou JL, Petit T, Porro D, Reuss M, van Riel N, Rizzi M, Steensma HY, Verrips CT, Vindelov J, Pronk JT (2000) An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb Technol 26:706–714
Worsham PL, Bolen PL (1990) Killer toxin production in Pichia acaciae is associated with linear DNA plasmids. Curr Genet 18:77–80
Xiao W, Chow BL, Hanna M, Doetsch PW (2001) Deletion of the MAG1 DNA glycosylase gene suppresses alkylation-induced killing and mutagenesis in yeast cells lacking AP endonucleases. Mutat Res 487:137–147
You HJ, Swanson RL, Doetsch PW (1998) Saccharomyces cerevisiae possesses two functional homologues of Escherichia coli endonuclease III. Biochemistry 37:6033–6040
You HJ, Swanson RL, Harrington C, Corbett AH, Jinks-Robertson S, Sentürker S, Wallace SS, Boiteux S, Dizdaroglu M, Doetsch PW (1999) Saccharomyces cerevisiae Ntg1p and Ntg2p: broad specificity N-glycosylases for the repair of oxidative DNA damage in the nucleus and mitochondria. Biochemistry 38:11298–11306
Acknowledgments
Thanks are due to Dr. W. Kramer (Göttingen, Germany) for providing yeast strains. Financial support by the Deutsche Forschungsgemeinschaft (DFG) Grant no. ME 1142/5-1 is gratefully acknowledged.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by A. Aguilera.
Rights and permissions
About this article
Cite this article
Klassen, R., Wemhoff, S., Krause, J. et al. DNA repair defects sensitize cells to anticodon nuclease yeast killer toxins. Mol Genet Genomics 285, 185–195 (2011). https://doi.org/10.1007/s00438-010-0597-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00438-010-0597-5