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Different Roles of Eukaryotic MutS and MutL Complexes in Repair of Small Insertion and Deletion Loops in Yeast


DNA mismatch repair greatly increases genome fidelity by recognizing and removing replication errors. In order to understand how this fidelity is maintained, it is important to uncover the relative specificities of the different components of mismatch repair. There are two major mispair recognition complexes in eukaryotes that are homologues of bacterial MutS proteins, MutSα and MutSβ, with MutSα recognizing base-base mismatches and small loop mispairs and MutSβ recognizing larger loop mispairs. Upon recognition of a mispair, the MutS complexes then interact with homologues of the bacterial MutL protein. Loops formed on the primer strand during replication lead to insertion mutations, whereas loops on the template strand lead to deletions. We show here in yeast, using oligonucleotide transformation, that MutSα has a strong bias toward repair of insertion loops, while MutSβ has an even stronger bias toward repair of deletion loops. Our results suggest that this bias in repair is due to the different interactions of the MutS complexes with the MutL complexes. Two mutants of MutLα, pms1-G882E and pms1-H888R, repair deletion mispairs but not insertion mispairs. Moreover, we find that a different MutL complex, MutLγ, is extremely important, but not sufficient, for deletion repair in the presence of either MutLα mutation. MutSβ is present in many eukaryotic organisms, but not in prokaryotes. We suggest that the biased repair of deletion mispairs may reflect a critical eukaryotic function of MutSβ in mismatch repair.


Vyšlo v časopise: Different Roles of Eukaryotic MutS and MutL Complexes in Repair of Small Insertion and Deletion Loops in Yeast. PLoS Genet 9(10): e32767. doi:10.1371/journal.pgen.1003920
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003920

Souhrn

DNA mismatch repair greatly increases genome fidelity by recognizing and removing replication errors. In order to understand how this fidelity is maintained, it is important to uncover the relative specificities of the different components of mismatch repair. There are two major mispair recognition complexes in eukaryotes that are homologues of bacterial MutS proteins, MutSα and MutSβ, with MutSα recognizing base-base mismatches and small loop mispairs and MutSβ recognizing larger loop mispairs. Upon recognition of a mispair, the MutS complexes then interact with homologues of the bacterial MutL protein. Loops formed on the primer strand during replication lead to insertion mutations, whereas loops on the template strand lead to deletions. We show here in yeast, using oligonucleotide transformation, that MutSα has a strong bias toward repair of insertion loops, while MutSβ has an even stronger bias toward repair of deletion loops. Our results suggest that this bias in repair is due to the different interactions of the MutS complexes with the MutL complexes. Two mutants of MutLα, pms1-G882E and pms1-H888R, repair deletion mispairs but not insertion mispairs. Moreover, we find that a different MutL complex, MutLγ, is extremely important, but not sufficient, for deletion repair in the presence of either MutLα mutation. MutSβ is present in many eukaryotic organisms, but not in prokaryotes. We suggest that the biased repair of deletion mispairs may reflect a critical eukaryotic function of MutSβ in mismatch repair.


Zdroje

1. FishelR, LescoeMK, RaoMRS, CopelandNG, JenkinsNA, et al. (1993) The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer. Cell 75: 1027–1038.

2. LeachFS, NicolaidesNC, PapadopoulosN, LiuB, JenJ, et al. (1993) Mutations of a mutS homolog in hereditary nonpolyposis colorectal cancer. Cell 75: 1215–1225.

3. HemminkiA, PeltomäkiP, MecklinJ-P, JärvinenH, SalovaaraR, et al. (1994) Loss of the wild type MLH1 gene is a feature of hereditary nonpolyposis colorectal cancer. Nature Genet 8: 405–409.

4. NicolaidesNC, PapadopoulosN, LiuB, WeiY-F, CarterKC, et al. (1994) Mutations of two PMS homologues in hereditary nonpolyposis colon cancer. Nature 371: 75–80.

5. PapadopoulosN, NicolaidesNC, WeiY-F, RubenSM, CarterKC, et al. (1994) Mutation of a mutL homolog in hereditary colon cancer. Science 263: 1625–1629.

6. BronnerCE, BakerSM, MorrisonPT, WarrenG, SmithLG, et al. (1994) Mutation in the DNA mismatch repair gene homologue hMLH1 is associated with hereditary non-polyposis colon cancer. Nature 368: 258–261.

7. LiGM (2008) Mechanisms and functions of DNA mismatch repair. Cell Res 18: 85–98.

8. IyerRR, PluciennikA, BurdettV, ModrichPL (2006) DNA mismatch repair: functions and mechanisms. Chem Rev 106: 302–323.

9. JiricnyJ (2006) The multifaceted mismatch-repair system. Nat Rev Mol Cell Biol 7: 335–346.

10. HarringtonJM, KolodnerRD (2007) Saccharomyces cerevisiae Msh2-Msh3 acts in repair of base-base mispairs. Mol Cell Biol 27: 6546–6554.

11. StrandM, EarleyMC, CrouseGF, PetesTD (1995) Mutations in the MSH3 gene preferentially lead to deletions within tracts of simple repetitive DNA in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 92: 10418–10421.

12. NewL, LiuK, CrouseGF (1993) The yeast gene MSH3 defines a new class of eukaryotic MutS homologues. Mol Gen Genet 239: 97–108.

13. MarraG, IaccarinoI, LettieriT, RoscilliG, DelmastroP, et al. (1998) Mismatch repair deficiency associated with overexpression of the MSH3 gene. Proc Natl Acad Sci USA 95: 8568–8573.

14. DrummondJT, GenschelJ, WolfE, ModrichP (1997) DHFR/MSH3 amplification in methotrexate-resistant cells alters the hMutSα/hMutSβ ratio and reduces the efficiency of base-base mismatch repair. Proc Natl Acad Sci USA 94: 10144–10149.

15. GhaemmaghamiS, HuhW, BowerK, HowsonRW, BelleA, et al. (2003) Global analysis of protein expression in yeast. Nature 425: 737–741.

16. TomeS, SimardJP, SleanMM, HoltI, MorrisGE, et al. (2013) Tissue-specific mismatch repair protein expression: MSH3 is higher than MSH6 in multiple mouse tissues. DNA Repair (Amst) 12: 46–52.

17. LinZ, NeiM, MaH (2007) The origins and early evolution of DNA mismatch repair genes–multiple horizontal gene transfers and co-evolution. Nucleic Acids Res 35: 7591–7603.

18. SiaEA, KokoskaRJ, DominskaM, GreenwellP, PetesTD (1997) Microsatellite instability in yeast: Dependence on repeat unit size and DNA mismatch repair genes. Mol Cell Biol 17: 2851–2858.

19. JohnsonRE, KovvaliGK, PrakashL, PrakashS (1996) Requirement of the yeast MSH3 and MSH6 genes for MSH2-dependent genomic stability. J Biol Chem 271: 7285–7288.

20. HarfeBD, MinesingerBK, Jinks-RobertsonS (2000) Discrete in vivo roles for the MutL homologs Mlh2p and Mlh3p in the removal of frameshift intermediates in budding yeast. Curr Biol 10: 145–148.

21. Flores-RozasH, KolodnerRD (1998) The Saccharomyces cerevisiae MLH3 gene functions in MSH3-dependent suppression of frameshift mutations. Proc Natl Acad Sci USA 95: 12404–12409.

22. ErdenizN, DudleyS, GealyR, Jinks-RobertsonS, LiskayRM (2005) Novel PMS1 alleles preferentially affect the repair of primer strand loops during DNA replication. Mol Cell Biol 25: 9221–9231.

23. KowYW, BaoG, ReevesJW, Jinks-RobertsonS, CrouseGF (2007) Oligonucleotide transformation of yeast reveals mismatch repair complexes to be differentially active on DNA replication strands. Proc Natl Acad Sci USA 104: 11352–11357.

24. HarfeBD, Jinks-RobertsonS (1999) Removal of frameshift intermediates by mismatch repair proteins in Saccharomyces cerevisiae. Mol Cell Biol 19: 4766–4773.

25. GreeneCN, Jinks-RobertsonS (1997) Frameshift intermediates in homopolymer runs are removed efficiently by yeast mismatch repair proteins. Mol Cell Biol 17: 2844–2850.

26. KimN, AbdulovicAL, GealyR, LippertMJ, Jinks-RobertsonS (2007) Transcription-associated mutagenesis in yeast is directly proportional to the level of gene expression and influenced by the direction of DNA replication. DNA Repair (Amst) 6: 1285–1296.

27. MarsischkyGT, KolodnerRD (1999) Biochemical characterization of the interaction between the Saccharomyces cerevisiae MSH2-MSH6 complex and mispaired bases in DNA. J Biol Chem 274: 26668–26682.

28. RodriguezGP, RomanovaNV, BaoG, RoufNC, KowYW, et al. (2012) Mismatch repair dependent mutagenesis in nondividing cells. Proc Natl Acad Sci USA 109: 6153–6158.

29. PangQS, ProllaTA, LiskayRM (1997) Functional domains of the Saccharomyces cerevisiae Mlh1p and Pms1p DNA mismatch repair proteins and their relevance to human hereditary nonpolyposis colorectal cancer-associated mutations. Mol Cell Biol 17: 4465–4473.

30. GuptaS, GellertM, YangW (2012) Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops. Nat Struct Mol Biol 19: 72–78.

31. DowenJM, PutnamCD, KolodnerRD (2010) Functional studies and homology modeling of Msh2-Msh3 predict that mispair recognition involves DNA bending and strand separation. Mol Cell Biol 30: 3321–3328.

32. GueneauE, DherinC, LegrandP, Tellier-LebegueC, GilquinB, et al. (2013) Structure of the MutLalpha C-terminal domain reveals how Mlh1 contributes to Pms1 endonuclease site. Nat Struct Mol Biol 20: 461–468.

33. KellisM, PattersonN, EndrizziM, BirrenB, LanderES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241–254.

34. KadyrovFA, HolmesSF, AranaME, LukianovaOA, O'DonnellM, et al. (2007) Saccharomyces cerevisiae MutLα Is a mismatch repair endonuclease. J Biol Chem 282: 37181–37190.

35. NishantKT, PlysAJ, AlaniE (2008) A mutation in the putative MLH3 endonuclease domain confers a defect in both mismatch repair and meiosis in Saccharomyces cerevisiae. Genetics 179: 747–755.

36. HombauerH, CampbellCS, SmithCE, DesaiA, KolodnerRD (2011) Visualization of eukaryotic DNA mismatch repair reveals distinct recognition and repair intermediates. Cell 147: 1040–1053.

37. MoldovanGL, PfanderB, JentschS (2007) PCNA, the maestro of the replication fork. Cell 129: 665–679.

38. LeeSD, AlaniE (2006) Analysis of interactions between mismatch repair initiation factors and the replication processivity factor PCNA. J Mol Biol 355: 175–184.

39. JohnsonRE, KovvaliGK, GuzderSN, AminNS, HolmC, et al. (1996) Evidence for involvement of yeast proliferating cell nuclear antigen in DNA mismatch repair. J Biol Chem 271: 27987–27990.

40. UmarA, BuermeyerAB, SimonJA, ThomasDC, ClarkAB, et al. (1996) Requirement for PCNA in DNA mismatch repair at a step preceding DNA resynthesis. Cell 87: 65–73.

41. ChenC, MerrillBJ, LauPJ, HolmC, KolodnerRD (1999) Saccharomyces carevisiae pol30 (proliferating cell nuclear antigen) mutations impair replication fidelity and mismatch repair. Mol Cell Biol 19: 7801–7815.

42. PluciennikA, DzantievL, IyerRR, ConstantinN, KadyrovFA, et al. (2010) PCNA function in the activation and strand direction of MutLα endonuclease in mismatch repair. Proc Natl Acad Sci USA 107: 16066–16071.

43. AminNS, NguyenMN, OhS, KolodnerRD (2001) exo1-Dependent mutator mutations: Model system for studying functional interactions in mismatch repair. Mol Cell Biol 21: 5142–5155.

44. BowersJ, TranPT, JoshiA, LiskayRM, AlaniE (2001) MSH-MLH complexes formed at a DNA mismatch are disrupted by the PCNA sliding clamp. J Mol Biol 306: 957–968.

45. ClarkAB, ValleF, DrotschmannK, GaryRK, KunkelTA (2000) Functional interaction of proliferating cell nuclear antigen with MSH2-MSH6 and MSH2-MSH3 complexes. J Biol Chem 275: 36498–36501.

46. Flores-RozasH, ClarkD, KolodnerRD (2000) Proliferating cell nuclear antigen and Msh2p-Msh6p interact to form an active mispair recognition complex. Nature Genet 26: 375–378.

47. HargreavesVV, PutnamCD, KolodnerRD (2012) Engineered disulfide-forming amino acid substitutions interfere with a conformational change in the mismatch recognition complex Msh2-Msh6 required for mismatch repair. J Biol Chem 287: 41232–41244.

48. LauPJ, Flores-RozasH, KolodnerRD (2002) Isolation and characterization of new proliferating cell nuclear antigen (POL30) mutator mutants that are defective in DNA mismatch repair. Mol Cell Biol 22: 6669–6680.

49. IyerRR, PluciennikA, GenschelJ, TsaiMS, BeeseLS, et al. (2010) MutLα and proliferating cell nuclear antigen share binding sites on MutSβ. J Biol Chem 285: 11730–11739.

50. LauPJ, KolodnerRD (2003) Transfer of the MSH2.MSH6 complex from proliferating cell nuclear antigen to mispaired bases in DNA. J Biol Chem 278: 14–17.

51. KumarP, NagarajaramHA (2012) A study on mutational dynamics of simple sequence repeats in relation to mismatch repair system in prokaryotic genomes. J Mol Evol 74: 127–139.

52. ShellSS, PutnamCD, KolodnerRD (2007) Chimeric Saccharomyces cerevisiae Msh6 protein with an Msh3 mispair-binding domain combines properties of both proteins. Proc Natl Acad Sci USA 104: 10956–10961.

53. LopezCA, ClearyJD, PearsonCE (2010) Repeat instability as the basis for human diseases and as a potential target for therapy. Nat Rev Mol Cell Biol 11: 165–170.

54. ShahSN, HileSE, EckertKA (2010) Defective mismatch repair, microsatellite mutation bias, and variability in clinical cancer phenotypes. Cancer Res 70: 431–435.

55. EzzatizadehV, PintoRM, SandiC, SandiM, Al-MahdawiS, et al. (2012) The mismatch repair system protects against intergenerational GAA repeat instability in a Friedreich ataxia mouse model. Neurobiol Dis 46: 165–171.

56. LangWH, CoatsJE, MajkaJ, HuraGL, LinY, et al. (2011) Conformational trapping of mismatch recognition complex MSH2/MSH3 on repair-resistant DNA loops. Proc Natl Acad Sci U S A 108: E837–E844.

57. PanigrahiGB, SleanMM, SimardJP, GileadiO, PearsonCE (2010) Isolated short CTG/CAG DNA slip-outs are repaired efficiently by hMutSβ, but clustered slip-outs are poorly repaired. Proc Natl Acad Sci USA 107: 12593–12598.

58. GuoJ, ZhengL, LiuW, WangX, WangZ, et al. (2011) Frequent truncating mutation of TFAM induces mitochondrial DNA depletion and apoptotic resistance in microsatellite-unstable colorectal cancer. Cancer Res 71: 2978–2987.

59. DuvalA, HamelinR (2002) Mutations at coding repeat sequences in mismatch repair-deficient human cancers: Toward a new concept of target genes for instability. Cancer Res 62: 2447–2454.

60. HeganDC, NarayananL, JirikFR, EdelmannW, LiskayRM, et al. (2006) Differing patterns of genetic instability in mice deficient in the mismatch repair genes Pms2, Mlh1, Msh2, Msh3 and Msh6. Carcinogen 27: 2402–2408.

61. HansenRS, ThomasS, SandstromR, CanfieldTK, ThurmanRE, et al. (2010) Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci USA 107: 139–144.

62. RothsteinR (1990) Targeting, disruption, replacement, and allele rescue: integrative DNA transformation in yeast. Methods Enzymol 194: 281–301.

63. DattaA, Jinks-RobertsonS (1995) Association of increased spontaneous mutation rates with high levels of transcription in yeast. Science 268: 1616–1619.

64. AbdulovicAL, MinesingerBK, Jinks-RobertsonS (2008) The effect of sequence context on spontaneous Pol ζ -dependent mutagenesis in Saccharomyces cerevisiae. Nucleic Acids Res 36: 2082–2093.

65. WinzelerEA, ShoemakerDD, AstromoffA, LiangH, AndersonK, et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901–906.

66. StoriciF, LewisLK, ResnickMA (2001) In vivo site-directed mutagenesis using oligonucleotides. Nat Biotechnol 19: 773–776.

67. RodriguezGP, SongJB, CrouseGF (2012) Transformation with oligonucleotides creating clustered changes in the yeast genome. PLoS ONE 7: e42905.

68. ShermanF (1991) Getting started with yeast. Methods Enzymol 194: 3–21.

69. SikorskiRS, HieterP (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19–27.

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