Dominant Mutations in Identify the Mlh1-Pms1 Endonuclease Active Site and an Exonuclease 1-Independent Mismatch Repair Pathway
Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC) is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR) caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A) that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway.
Vyšlo v časopise:
Dominant Mutations in Identify the Mlh1-Pms1 Endonuclease Active Site and an Exonuclease 1-Independent Mismatch Repair Pathway. PLoS Genet 9(10): e32767. doi:10.1371/journal.pgen.1003869
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1003869
Souhrn
Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC) is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR) caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A) that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway.
Zdroje
1. de la ChapelleA (2004) Genetic predisposition to colorectal cancer. Nat Rev Cancer 4: 769–780.
2. PeltomakiP, VasenHF (1997) Mutations predisposing to hereditary nonpolyposis colorectal cancer: database and results of a collaborative study. The International Collaborative Group on Hereditary Nonpolyposis Colorectal Cancer. Gastroenterology 113: 1146–1158.
3. BorresenAL, LotheRA, MelingGI, LystadS, MorrisonP, et al. (1995) Somatic mutations in the hMSH2 gene in microsatellite unstable colorectal carcinomas. Hum Mol Genet 4: 2065–2072.
4. KaneMF, LodaM, GaidaGM, LipmanJ, MishraR, et al. (1997) Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines. Cancer Res 57: 808–811.
5. Network TCGA (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature 487: 330–337.
6. Network TCGA (2013) Integrated genomic characterization of endometrial carcinoma. Nature 497: 67–73.
7. PeltomakiP (2003) Role of DNA mismatch repair defects in the pathogenesis of human cancer. J Clin Oncol 21: 1174–1179.
8. DattaA, AdjiriA, NewL, CrouseGF, Jinks RobertsonS (1996) Mitotic crossovers between diverged sequences are regulated by mismatch repair proteins in Saccaromyces cerevisiae. Mol Cell Biol 16: 1085–1093.
9. MaticI, RayssiguierC, RadmanM (1995) Interspecies gene exchange in bacteria: the role of SOS and mismatch repair systems in evolution of species. Cell 80: 507–515.
10. PutnamCD, HayesTK, KolodnerRD (2009) Specific pathways prevent duplication-mediated genome rearrangements. Nature 460: 984–989.
11. IyerRR, PluciennikA, BurdettV, ModrichPL (2006) DNA mismatch repair: functions and mechanisms. Chem Rev 106: 302–323.
12. KolodnerRD, MarsischkyGT (1999) Eukaryotic DNA mismatch repair. Curr Opin Genet Dev 9: 89–96.
13. KunkelTA, ErieDA (2005) DNA mismatch repair. Annu Rev Biochem 74: 681–710.
14. LahueRS, AuKG, ModrichP (1989) DNA mismatch correction in a defined system. Science 245: 160–164.
15. LamersMH, PerrakisA, EnzlinJH, WinterwerpHH, de WindN, et al. (2000) The crystal structure of DNA mismatch repair protein MutS binding to a G×T mismatch. Nature 407: 711–717.
16. ObmolovaG, BanC, HsiehP, YangW (2000) Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Nature 407: 703–710.
17. AcharyaS, FosterPL, BrooksP, FishelR (2003) The coordinated functions of the E. coli MutS and MutL proteins in mismatch repair. Mol Cell 12: 233–246.
18. WelshKM, LuAL, ClarkS, ModrichP (1987) Isolation and characterization of the Escherichia coli mutH gene product. J Biol Chem 262: 15624–15629.
19. BurdettV, BaitingerC, ViswanathanM, LovettST, ModrichP (2001) In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair. Proc Natl Acad Sci U S A 98: 6765–6770.
20. AcharyaS, WilsonT, GradiaS, KaneMF, GuerretteS, et al. (1996) hMSH2 forms specific mispair-binding complexes with hMSH3 and hMSH6. Proc Natl Acad Sci U S A 93: 13629–13634.
21. MarsischkyGT, FilosiN, KaneMF, KolodnerR (1996) Redundancy of Saccharomyces cerevisiae MSH3 and MSH6 in MSH2-dependent mismatch repair. Genes Dev 10: 407–420.
22. ProllaTA, PangQ, AlaniE, KolodnerRD, LiskayRM (1994) MLH1, PMS1, and MSH2 interactions during the initiation of DNA mismatch repair in yeast. Science 265: 1091–1093.
23. MendilloML, MazurDJ, KolodnerRD (2005) Analysis of the interaction between the Saccharomyces cerevisiae MSH2-MSH6 and MLH1-PMS1 complexes with DNA using a reversible DNA end-blocking system. J Biol Chem 280: 22245–22257.
24. BlackwellLJ, WangS, ModrichP (2001) DNA chain length dependence of formation and dynamics of hMutSalpha.hMutLalpha.heteroduplex complexes. J Biol Chem 276: 33233–33240.
25. KadyrovFA, DzantievL, ConstantinN, ModrichP (2006) Endonucleolytic function of MutLalpha in human mismatch repair. Cell 126: 297–308.
26. KadyrovFA, HolmesSF, AranaME, LukianovaOA, O'DonnellM, et al. (2007) Saccharomyces cerevisiae MutLalpha is a mismatch repair endonuclease. J Biol Chem 282: 37181–37190.
27. AminNS, NguyenMN, OhS, KolodnerRD (2001) exo1-Dependent mutator mutations: model system for studying functional interactions in mismatch repair. Mol Cell Biol 21: 5142–5155.
28. TishkoffDX, BoergerAL, BertrandP, FilosiN, GaidaGM, et al. (1997) Identification and characterization of Saccharomyces cerevisiae EXO1, a gene encoding an exonuclease that interacts with MSH2. Proc Natl Acad Sci U S A 94: 7487–7492.
29. WeiK, ClarkAB, WongE, KaneMF, MazurDJ, et al. (2003) Inactivation of Exonuclease 1 in mice results in DNA mismatch repair defects, increased cancer susceptibility, and male and female sterility. Genes Dev 17: 603–614.
30. ConstantinN, DzantievL, KadyrovFA, ModrichP (2005) Human mismatch repair: reconstitution of a nick-directed bidirectional reaction. J Biol Chem 280: 39752–39761.
31. Flores-RozasH, ClarkD, KolodnerRD (2000) Proliferating cell nuclear antigen and Msh2p-Msh6p interact to form an active mispair recognition complex. Nat Genet 26: 375–378.
32. LinYL, ShivjiMK, ChenC, KolodnerR, WoodRD, et al. (1998) The evolutionarily conserved zinc finger motif in the largest subunit of human replication protein A is required for DNA replication and mismatch repair but not for nucleotide excision repair. J Biol Chem 273: 1453–1461.
33. 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.
34. ZhangY, YuanF, PresnellSR, TianK, GaoY, et al. (2005) Reconstitution of 5′-directed human mismatch repair in a purified system. Cell 122: 693–705.
35. XieY, CounterC, AlaniE (1999) Characterization of the repeat-tract instability and mutator phenotypes conferred by a Tn3 insertion in RFC1, the large subunit of the yeast clamp loader. Genetics 151: 499–509.
36. DzantievL, ConstantinN, GenschelJ, IyerRR, BurgersPM, et al. (2004) A defined human system that supports bidirectional mismatch-provoked excision. Mol Cell 15: 31–41.
37. LongleyMJ, PierceAJ, ModrichP (1997) DNA polymerase delta is required for human mismatch repair in vitro. J Biol Chem 272: 10917–10921.
38. HombauerH, CampbellCS, SmithCE, DesaiA, KolodnerRD (2011) Visualization of eukaryotic DNA mismatch repair reveals distinct recognition and repair intermediates. Cell 147: 1040–1053.
39. HombauerH, SrivatsanA, PutnamCD, KolodnerRD (2011) Mismatch repair, but not heteroduplex rejection, is temporally coupled to DNA replication. Science 334: 1713–1716.
40. LangstonLD, O'DonnellM (2006) DNA replication: keep moving and don't mind the gap. Mol Cell 23: 155–160.
41. BenkovicSJ, ValentineAM, SalinasF (2001) Replisome-mediated DNA replication. Annu Rev Biochem 70: 181–208.
42. LibertiSE, LarreaAA, KunkelTA (2013) Exonuclease 1 preferentially repairs mismatches generated by DNA polymerase alpha. DNA Repair (Amst) 12: 92–96.
43. PluciennikA, DzantievL, IyerRR, ConstantinN, KadyrovFA, et al. (2010) PCNA function in the activation and strand direction of MutLalpha endonuclease in mismatch repair. Proc Natl Acad Sci U S A 107: 16066–16071.
44. GenschelJ, ModrichP (2003) Mechanism of 5′-directed excision in human mismatch repair. Mol Cell 12: 1077–1086.
45. KadyrovFA, GenschelJ, FangY, PenlandE, EdelmannW, et al. (2009) A possible mechanism for exonuclease 1-independent eukaryotic mismatch repair. Proc Natl Acad Sci U S A 106: 8495–8500.
46. 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.
47. NamaduraiS, JainD, KulkarniDS, TabibCR, FriedhoffP, et al. (2010) The C-terminal domain of the MutL homolog from Neisseria gonorrhoeae forms an inverted homodimer. PLoS One 5: e13726.
48. PillonMC, LorenowiczJJ, UckelmannM, KlockoAD, MitchellRR, et al. (2010) Structure of the endonuclease domain of MutL: unlicensed to cut. Mol Cell 39: 145–151.
49. TranPT, ErdenizN, SymingtonLS, LiskayRM (2004) EXO1-A multi-tasking eukaryotic nuclease. DNA Repair (Amst) 3: 1549–1559.
50. TranPT, ErdenizN, DudleyS, LiskayRM (2002) Characterization of nuclease-dependent functions of Exo1p in Saccharomyces cerevisiae. DNA Repair (Amst) 1: 895–912.
51. PangQ, 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.
52. Nick McElhinnySA, StithCM, BurgersPM, KunkelTA (2007) Inefficient proofreading and biased error rates during inaccurate DNA synthesis by a mutant derivative of Saccharomyces cerevisiae DNA polymerase delta. J Biol Chem 282: 2324–2332.
53. Nick McElhinnySA, KumarD, ClarkAB, WattDL, WattsBE, et al. (2010) Genome instability due to ribonucleotide incorporation into DNA. Nat Chem Biol 6: 774–781.
54. Nick McElhinnySA, WattsBE, KumarD, WattDL, LundstromEB, et al. (2010) Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases. Proc Natl Acad Sci U S A 107: 4949–4954.
55. PursellZF, IsozI, LundstromEB, JohanssonE, KunkelTA (2007) Regulation of B family DNA polymerase fidelity by a conserved active site residue: characterization of M644W, M644L and M644F mutants of yeast DNA polymerase epsilon. Nucleic Acids Res 35: 3076–3086.
56. DeschenesSM, TomerG, NguyenM, ErdenizN, JubaNC, et al. (2007) The E705K mutation in hPMS2 exerts recessive, not dominant, effects on mismatch repair. Cancer Lett 249: 148–156.
57. ZakharyevichK, TangS, MaY, HunterN (2012) Delineation of joint molecule resolution pathways in meiosis identifies a crossover-specific resolvase. Cell 149: 334–347.
58. BrownMS, LimE, ChenC, NishantKT, AlaniE (2013) Genetic Analysis of mlh3 Mutations Reveals Interactions Between Crossover Promoting Factors During Meiosis in Baker's Yeast. G3 (Bethesda) 3: 9–22.
59. HunterN, BortsRH (1997) Mlh1 is unique among mismatch repair proteins in its ability to promote crossing-over during meiosis. Genes Dev 11: 1573–1582.
60. DuppatlaV, BoddaC, UrbankeC, FriedhoffP, RaoDN (2009) The C-terminal domain is sufficient for endonuclease activity of Neisseria gonorrhoeae MutL. Biochem J 423: 265–277.
61. FukuiK, NishidaM, NakagawaN, MasuiR, KuramitsuS (2008) Bound nucleotide controls the endonuclease activity of mismatch repair enzyme MutL. J Biol Chem 283: 12136–12145.
62. IinoH, KimK, ShimadaA, MasuiR, KuramitsuS, et al. (2011) Characterization of C- and N-terminal domains of Aquifex aeolicus MutL endonuclease: N-terminal domain stimulates the endonuclease activity of C-terminal domain in a zinc-dependent manner. Biosci Rep 31: 309–322.
63. KosinskiJ, PlotzG, GuarneA, BujnickiJM, FriedhoffP (2008) The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family. J Mol Biol 382: 610–627.
64. HargreavesVV, ShellSS, MazurDJ, HessMT, KolodnerRD (2010) Interaction between the Msh2 and Msh6 nucleotide-binding sites in the Saccharomyces cerevisiae Msh2-Msh6 complex. J Biol Chem 285: 9301–9310.
65. UmezuK, SugawaraN, ChenC, HaberJE, KolodnerRD (1998) Genetic analysis of yeast RPA1 reveals its multiple functions in DNA metabolism. Genetics 148: 989–1005.
66. GerikKJ, GarySL, BurgersPM (1997) Overproduction and affinity purification of Saccharomyces cerevisiae replication factor C. J Biol Chem 272: 1256–1262.
67. AyyagariR, ImpellizzeriKJ, YoderBL, GarySL, BurgersPM (1995) A mutational analysis of the yeast proliferating cell nuclear antigen indicates distinct roles in DNA replication and DNA repair. Mol Cell Biol 15: 4420–4429.
68. FienK, StillmanB (1992) Identification of replication factor C from Saccharomyces cerevisiae: a component of the leading-strand DNA replication complex. Mol Cell Biol 12: 155–163.
69. BrungerAT, AdamsPD, CloreGM, DeLanoWL, GrosP, et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54: 905–921.
70. McReeDE (1999) XtalView/Xfit–A versatile program for manipulating atomic coordinates and electron density. J Struct Biol 125: 156–165.
71. Bennett-LovseyRM, HerbertAD, SternbergMJ, KelleyLA (2008) Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins 70: 611–625.
72. SieversF, WilmA, DineenD, GibsonTJ, KarplusK, et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2013 Číslo 10
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- Dominant Mutations in Identify the Mlh1-Pms1 Endonuclease Active Site and an Exonuclease 1-Independent Mismatch Repair Pathway
- Eleven Candidate Susceptibility Genes for Common Familial Colorectal Cancer
- The Histone H3 K27 Methyltransferase KMT6 Regulates Development and Expression of Secondary Metabolite Gene Clusters
- A Mutation in the Gene in Labrador Retrievers with Hereditary Nasal Parakeratosis (HNPK) Provides Insights into the Epigenetics of Keratinocyte Differentiation