An MCM family protein promotes interhomolog recombination by preventing precocious intersister repair of meiotic DSBs

English version

Autoři: Miao Tian ^aff001; Josef Loidl ^aff001
Působiště autorů: Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria ^aff001
Vyšlo v časopise: An MCM family protein promotes interhomolog recombination by preventing precocious intersister repair of meiotic DSBs. PLoS Genet 15(12): e32767. doi:10.1371/journal.pgen.1008514
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008514

Souhrn

Recombinational repair of meiotic DNA double-strand breaks (DSBs) uses the homologous chromosome as a template, although the sister chromatid offers itself as a spatially more convenient substrate. In many organisms, this choice is reinforced by the recombination protein Dmc1. In Tetrahymena, the repair of DSBs, which are formed early in prophase, is postponed to late prophase when homologous chromosomes and sister chromatids become juxtaposed owing to tight parallel packing in the thread-shaped nucleus, and thus become equally suitable for use as repair templates. The delay in DSB repair is achieved by rejection of the invading strand by the Sgs1 helicase in early meiotic prophase. In the absence of Mcmd1, a meiosis-specific minichromosome maintenance (MCM)-like protein (and its partner Pamd1), Dmc1 is prematurely lost from chromatin and DNA synthesis (as monitored by BrdU incorporation) takes place in early prophase. In mcmd1Δ and pamd1Δ mutants, only a few crossovers are formed. In a mcmd1Δ hop2Δ double mutant, normal timing of Dmc1 loss and DNA synthesis is restored. Because Tetrahymena Hop2 is believed to enable homologous strand invasion, we conclude that Dmc1 loss in the absence of Mcmd1 affects only post-invasion recombination intermediates. Therefore, we propose that the Dmc1 nucleofilament becomes dismantled immediately after forming a heteroduplex with a template strand. As a consequence, repair synthesis and D-loop extension starts in early prophase intermediates and prevents strand rejection before the completion of homologous pairing. In this case, DSB repair may primarily use the sister chromatid. We conclude that Mcmd1‒Pamd1 protects the Dmc1 nucleofilament from premature dismantling, thereby suppressing precocious repair synthesis and excessive intersister strand exchange at the cost of homologous recombination.

Klíčová slova:

DNA recombination – DNA repair – DNA synthesis – Homologous recombination – Meiosis – Meiotic prophase – Recombinant proteins – Tetrahymena

Zdroje

1. Heyer WD, Ehmsen KT, Liu J (2010) Regulation of homologous recombination in eukaryotes. Annu Rev Genet 113–139.

2. de Massy B (2013) Initiation of meiotic recombination: how and where? Conservation and specificities among eukaryotes. Annu Rev Genet 47 : 563–599. doi: 10.1146/annurev-genet-110711-155423 24050176

3. Hunter N (2015) Meiotic recombination: the essence of heredity. CSH Perspect Biol 7: a016618.

4. Lam I, Keeney S (2014) Mechanism and regulation of meiotic recombination initiation. CSH Perspect Biol 7: a016634.

5. Daley JM, Gaines WA, Kwon Y, Sung P (2014) Regulation of DNA pairing in homologous recombination. CSH Perspect Biol a017954.

6. Li X, Heyer WD (2009) RAD54 controls access to the invading 3-OH end after RAD51-mediated DNA strand invasion in homologous recombination in Saccharomyces cerevisiae. Nucl Acids Res 37 : 638–646. doi: 10.1093/nar/gkn980 19074197

7. Ward JD, Muzzini DM, Petalcorin MIR, Martinez-Perez E, Martin JS, Plevani P, Cassata G, Marini F, Boulton SJ (2010) Overlapping mechanisms promote postsynaptic RAD-51 filament disassembly during meiotic double-strand break repair. Mol Cell 37 : 259–272. doi: 10.1016/j.molcel.2009.12.026 20122407

8. Loidl J, Lorenz A (2016) DNA double-strand break formation and repair in Tetrahymena meiosis. Sem Cell Dev Biol 54 : 126–134.

9. Cole E, Sugai T (2012) Developmental progression of Tetrahymena through the cell cycle and conjugation. In: Collins K, editors. Tetrahymena thermophila. San Diego: Academic Press. pp. 177–236.

10. Lukaszewicz A, Howard-Till RA, Novatchkova M, Mochizuki K, Loidl J (2010) MRE11 and COM1/SAE2 are required for double-strand break repair and efficient chromosome pairing during meiosis of the protist Tetrahymena. Chromosoma 119 : 505–518. doi: 10.1007/s00412-010-0274-9 20422424

11. Howard-Till RA, Lukaszewicz A, Loidl J (2011) The recombinases Rad51 and Dmc1 play distinct roles in DNA break repair and recombination partner choice in the meiosis of Tetrahymena. PLoS Genet 7: e1001359. doi: 10.1371/journal.pgen.1001359 21483758

12. Lukaszewicz A, Howard-Till RA, Loidl J (2013) Mus81 nuclease and Sgs1 helicase are essential for meiotic recombination in a protist lacking a synaptonemal complex. Nucleic Acids Res 41 : 9296–9309. doi: 10.1093/nar/gkt703 23935123

13. Loidl J, Lukaszewicz A, Howard-Till RA, Koestler T (2012) The Tetrahymena meiotic chromosome bouquet is organized by centromeres and promotes interhomolog recombination. J Cell Sci 125 : 5873–5880. doi: 10.1242/jcs.112664 22976299

14. Loidl J, Scherthan H (2004) Organization and pairing of meiotic chromosomes in the ciliate Tetrahymena thermophila. J Cell Sci 117 : 5791–5801. doi: 10.1242/jcs.01504 15522890

15. Mochizuki K, Novatchkova M, Loidl J (2008) DNA double-strand breaks, but not crossovers, are required for the reorganization of meiotic nuclei in Tetrahymena. J Cell Sci 121 : 2148–2158. doi: 10.1242/jcs.031799 18522989

16. Takara TJ, Bell SP (2009) Putting two heads together to unwind DNA. Cell 139 : 652–654. doi: 10.1016/j.cell.2009.10.037 19914158

17. Griffin WC, Trakselis MA (2019) The MCM8/9 complex: a recent recruit to the roster of helicases involved in genome maintenance. DNA Repair 76 : 1–10. doi: 10.1016/j.dnarep.2019.02.003 30743181

18. Kohl KP, Jones CD, Sekelsky J (2012) Evolution of an MCM complex in flies that promotes meiotic crossovers by blocking BLM helicase. Science 338 : 1363–1365. doi: 10.1126/science.1228190 23224558

19. Xiong J, Lu X, Zhou Z, Chang Y, Yuan D, Tian M, Zhou Z, Wang L, Fu C, Orias E, Miao W (2012) Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using deep RNA sequencing. PLoS ONE 7: e30630. doi: 10.1371/journal.pone.0030630 22347391

20. Traven A, Heierhorst J (2005) SQ/TQ cluster domains: concentrated ATM/ATR kinase phosporylation site regions in DNA-damage-response proteins. Bioessays 27 : 397–407. doi: 10.1002/bies.20204 15770685

21. Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong S-Y, Lopez R, Hunter S (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30 : 1236–1240. doi: 10.1093/bioinformatics/btu031 24451626

22. Drozdetskiy A, Cole C, Procter J, Barton GJ (2015) JPred4: a protein secondary structure prediction server. Nucl Acids Res 43: W389–W394. doi: 10.1093/nar/gkv332 25883141

23. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protoc 10 : 845–858.

24. McDonald BB (1966) The exchange of RNA and protein during conjugation in Tetrahymena. J Protozool 13 : 277–285. doi: 10.1111/j.1550-7408.1966.tb01908.x 5953847

25. Zhao W, Saro D, Hammel M, Kwon Y, Xu Y, Rambo RP, Williams GJ, Chi P, Lu L, Pezza RJ, Camerini-Otero RD, Tainer JA, Wang H-W, Sung P (2014) Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing. Nucleic Acids Res 42 : 906–917. doi: 10.1093/nar/gkt924 24150939

26. Kang H-A, Shin H-C, Kalantzi A-S, Toseland CP, Kim H-M, Gruber S, Dal Peraro M, Oh B-H (2015) Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination. Nucl Acids Res 43 : 3841–3856. doi: 10.1093/nar/gkv172 25740648

27. Crickard JB, Kwon Y, Sung P, Greene EC (2019) Dynamic interactions of the homologous pairing 2 (Hop2)-meiotic nuclear divisions 1 (Mnd1) protein complex with meiotic presynaptic filaments in budding yeast. J Biol Chem 294 : 490–501. doi: 10.1074/jbc.RA118.006146 30420424

28. Mahadevaiah SK, Turner JMA, Baudat F, Rogakou EP, De Boer P, Blanco-Rodríguez J, Jasin M, Keeney S, Bonner WM, Burgoyne PS (2001) Recombinational DNA double-strand breaks in mice precede synapsis. Nature Genetics 27 : 271–276. doi: 10.1038/85830 11242108

29. Song XY, Gjoneska E, Ren QH, Taverna SD, Allis CD, Gorovsky MA (2007) Phosphorylation of the SQ H2A.X motif is required for proper meiosis and mitosis in Tetrahymena thermophila. Mol Cell Biol 27 : 2648–2660. doi: 10.1128/MCB.01910-06 17242195

30. Xu L, Marians KJ (2002) A dynamic RecA filament permits DNA polymerase-catalyzed extension of the invading strand in recombination intermediates. J Biol Chem 277 : 14321–14328. doi: 10.1074/jbc.M112418200 11832493

31. Symington LS, Heyer WD (2006) Some disassembly required: role of DNA translocases in the disruption of recombination intermediates and dead-end complexes. Genes Dev 20 : 2479–2486. doi: 10.1101/gad.1477106 16980577

32. Solinger JA, Kiianitsa K, Heyer W-D (2002) Rad54, a Swi2/Snf2-like recombinational repair protein, disassembles Rad51:dsDNA filaments. Mol Cell 10 : 1175–1188. doi: 10.1016/s1097-2765(02)00743-8 12453424

33. Joshi N, Brown MS, Bishop DK, Börner GV (2015) Gradual implementation of the meiotic recombination program via checkpoint pathways controlled by global DSB levels. Mol Cell 57 : 1–15. doi: 10.1016/j.molcel.2014.12.022

34. Lukaszewicz A, Shodhan A, Loidl J (2015) Exo1 and Mre11 execute meiotic DSB end resection in the protist Tetrahymena. DNA Repair 35 : 137–143. doi: 10.1016/j.dnarep.2015.08.005 26519827

35. Hatkevich T, Sekelsky J (2017) Bloom syndrome helicase in meiosis: pro-crossover functions of an anti-crossover protein. Bioessays 39: doi: 10.1002/bies.201700073 28792069

36. Oh SD, Lao JP, Hwang PYH, Taylor AF, Smith GR, Hunter N (2007) BLM ortholog, Sgs1, prevents aberrant crossing-over by suppressing formation of multichromatid joint molecules. Cell 130 : 259–272. doi: 10.1016/j.cell.2007.05.035 17662941

37. Goldfarb T, Lichten M (2010) Frequent and efficient use of the sister chromatid for DNA double-strand break repair during budding yeast meiosis. PLoS Biol 8: e1000520. doi: 10.1371/journal.pbio.1000520 20976044

38. Lake CM, Teeter K, Page SL, Nielsen R, Hawley RS (2007) A genetic analysis of the Drosophila mcm5 gene defines a domain specifically required for meiotic recombination. Genetics 176 : 2151–2163. doi: 10.1534/genetics.107.073551 17565942

39. Blanton HL, Radford SJ, McMahan S, Kearney HM, Ibrahim JG, Sekelsky J (2005) REC, Drosophila MCM8, drives formation of meiotic crossovers. PLoS Genet 1 : 343–354.

40. Guilbaud G, Sale JE (2012) Unwinding to recombine. Mol Cell 47 : 493–494. doi: 10.1016/j.molcel.2012.08.006 22920289

41. Lutzmann M, Grey C, Traver S, Ganier O, Maya-Mendoza A, Ranisavljevic N, Bernex F, Nishiyama A, Montel N, Gavois E, Forichon L, de Massy B, Méchali M (2012) MCM8 -⁠ and MCM9-deficient mice reveal gametogenesis defects and genome instability due to impaired homologous recombination. Mol Cell 47 : 523–534. doi: 10.1016/j.molcel.2012.05.048 22771120

42. Crismani W, Portemer V, Froger N, Chelysheva L, Horlow C, Vrielynck N, Mercier R (2013) MCM8 is required for a pathway of meiotic double-strand break repair independent of DMC1 in Arabidopsis thaliana. PLoS Genet 9.

43. Hartmann M, Kohl KP, Sekelsky J, Hatkevich T (2019) Meiotic MCM proteins promote and inhibit crossovers during meiotic recombination. Genetics 212 : 461–468. doi: 10.1534/genetics.119.302221 31028111

44. Finsterbusch F, Ravindranathan R, Dereli I, Stanzione M, Trankner D, Tóth A (2016) Alignment of homologous chromosomes and effective repair of programmed DNA double-strand breaks during mouse meiosis require the minichromosome maintenance domain containing 2 (MCMDC2) protein. PLoS Genet 12.

45. McNairn AJ, Rinaldi VD, Schimenti JC (2017) Repair of meiotic DNA breaks and homolog pairing in mouse meiosis requires a minichromosome maintenance (MCM) paralog. Genetics 205 : 529–537. doi: 10.1534/genetics.116.196808 27986806

46. Orias E, Hamilton EP, Orias JD (2000) Tetrahymena as a laboratory organism: useful strains, cell culture, and cell line maintenance. In: Asai DJ, Forney JD, editors. Tetrahymena thermophila. San Diego: Academic Press. pp. 189–211.

47. Cassidy-Hanley D, Bowen J, Lee JH, Cole E, VerPlank LA, Gaertig J, Gorovsky MA, Bruns PJ (1997) Germline and somatic transformation of mating Tetrahymena thermophila by particle bombardment. Genetics 146 : 135–147. 9136007

48. Mochizuki K (2008) High efficiency transformation of Tetrahymena using a codon-optimized neomycin resistance gene. Gene 425 : 79–83. doi: 10.1016/j.gene.2008.08.007 18775482

49. Gao S, Xiong J, Zhang C, Berquist BR, Yang R, Zhao M, Molascon AJ, Kwiatkowski SY, Yuan D, Qin Z, Wen J, Kapler GM, Andrews PC, Miao W, Liu Y (2013) Impaired replication elongation in Tetrahymena mutants deficient in histone H3 lysine 27 mono-methylation. Genes Dev 27 : 1662–1679. doi: 10.1101/gad.218966.113 23884606

50. Loidl J, Mochizuki K (2009) Tetrahymena meiotic nuclear reorganization is induced by a checkpoint kinase-dependent response to DNA damage. Mol Biol Cell 20 : 2428–2437. doi: 10.1091/mbc.E08-10-1058 19297526

51. Bruns PJ, Brussard TEB (1981) Nullisomic Tetrahymena: eliminating germinal chromosomes. Science 213 : 549–551. doi: 10.1126/science.213.4507.549 17794842

52. Shodhan A, Lukaszewicz A, Novatchkova M, Loidl J (2014) Msh4 and Msh5 function in SC-independent chiasma formation during the streamlined meiosis of Tetrahymena. Genetics 198 : 983–993. doi: 10.1534/genetics.114.169698 25217051

53. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32 : 1792–1797. doi: 10.1093/nar/gkh340 15034147

54. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30 : 2725–2729. doi: 10.1093/molbev/mst197 24132122