Selection and the cell cycle: Positive darwinian selection in a well-Known DNA damage response pathway

Journal of Molecular Evolution

Volumn 71, Issue 5-6, 2010, Pages 444-457

  O'Connell, Mary J ^a  

^a DUBLIN CITY UNIVERSITY   (Ireland)

Author keywords

Adaptive evolution; Breast cancer; Cancer evolution; Cancer selection; Cell cycle; DNA repair; Positive selection; Tumor suppressor; Vertebrate evolution

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CELL CYCLE; COMPUTER PROGRAM; DNA DAMAGE; FANCONI ANEMIA; GENETIC SELECTION; GENETICS; HAPLOTYPE; HUMAN; MOUSE; PHYLOGENY; SIGNAL TRANSDUCTION; SPECIES DIFFERENCE;

ANIMALS; BRCA1 PROTEIN; BRCA2 PROTEIN; CELL CYCLE; DNA DAMAGE; FANCONI ANEMIA; HAPLOTYPES; HUMANS; MICE; MODELS, GENETIC; PHYLOGENY; SELECTION, GENETIC; SIGNAL TRANSDUCTION; SOFTWARE; SPECIES SPECIFICITY;

MAMMALIA; VERTEBRATA;

EID: 78650030468     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-010-9399-y     Document Type: Article

References (57)

1. M Anisimova Z Yang 2007 Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites Mol Biol Evol 24 1219 1228 1:CAS:528:DC%2BD2sXmtVOisL8%3D 10.1093/molbev/msm042 17339634 (Pubitemid 47343648)
2. H Ardawatia DA Liberles 2007 A systematic analysis of lineage-specific evolution in metabolic pathways Gene 387 67 74 1:CAS:528:DC%2BD28XhtlCmtL%2FL 10.1016/j.gene.2006.08.013 17034962 (Pubitemid 44959563)
3. GC Bagby Jr 2003 Genetic basis of Fanconi anemia Curr Opin Hematol 10 68 76 1:CAS:528:DC%2BD3sXnsFChtbo%3D 10.1097/00062752-200301000-00011 12483114 (Pubitemid 36020720)
4. AC Berglund B Wallner A Elofsson DA Liberles 2005 Tertiary windowing to detect positive diversifying selection J Mol Evol 60 499 504 1:CAS:528:DC%2BD2MXjvF2msrc%3D 10.1007/s00239-004-0223-4 15883884 (Pubitemid 40754790)
5. E Blom HJ van de Vrugt Y de Vries JP de Winter F Arwert H Joenje 2004 Multiple TPR motifs characterize the Fanconi anemia FANCG protein DNA Repair (Amst) 3 77 84 1:CAS:528:DC%2BD3sXpvFygsbk%3D 10.1016/j.dnarep.2003.09.007 (Pubitemid 38021998)
6. L Bromham A Rambaut PH Harvey 1996 Determinants of rate variation in mammalian DNA sequence evolution J Mol Evol 43 610 621 1:CAS:528: DyaK2sXislKjtg%3D%3D 10.1007/BF02202109 8995058 (Pubitemid 27024016)
7. A Burk-Herrick M Scally H Amrine-Madsen MJ Stanhope MS Springer 2006 Natural selection and mammalian BRCA1 sequences: elucidating functionally important sites relevant to breast cancer susceptibility in humans Mamm Genome 17 257 270 1:CAS:528:DC%2BD28XivFKitr0%3D 10.1007/s00335-005-0067-2 16518693 (Pubitemid 43327657)
8. F Cheng W Chen E Richards L Deng C Zeng 2009 SNP@Evolution: a hierarchical database of positive selection on the human genome BMC Evol Biol 9 221 10.1186/1471-2148-9-221 19732458
9. B Crespi K Summers 2005 Evolutionary biology of cancer Trends Ecol Evol 20 545 552 10.1016/j.tree.2005.07.007 16701433 (Pubitemid 41323711)
10. BJ Crespi K Summers 2006 Positive selection in the evolution of cancer Biol Rev Camb Philos Soc 81 407 424 10.1017/S1464793106007056 16762098 (Pubitemid 44092345)
11. AD D'Andrea M Grompe 2003 The Fanconi anaemia/BRCA pathway Nat Rev Cancer 3 23 34 10.1038/nrc970 12509764 (Pubitemid 37328884)
12. RR da Fonseca C Kosiol T Vinar A Siepel R Nielsen 2010 Positive selection on apoptosis related genes FEBS Lett 584 469 476 1:CAS:528:DC%2BC3cXhtVGnsr0%3D 10.1016/j.febslet.2009.12.022 20026333
13. W Davids J Gamieldien DA Liberles W Hide 2002 Positive selection scanning reveals decoupling of enzymatic activities of carbamoyl phosphate synthetase in Helicobacter pylori J Mol Evol 54 458 464 1:CAS:528:DC%2BD38Xjt1Gguro%3D 10.1007/s00239-001-0029-6 11956684 (Pubitemid 34271126)
14. Demetrius L (2005) Of mice and men. When it comes to studying ageing and the means to slow it down, mice are not just small humans. EMBO Rep 6 Spec No: S39-S44
15. MA Fleming JD Potter CJ Ramirez GK Ostrander EA Ostrander 2003 Understanding missense mutations in the BRCA1 gene: an evolutionary approach Proc Natl Acad Sci USA 100 1151 1156 1:CAS:528:DC%2BD3sXhtF2gt7c%3D 10.1073/pnas.0237285100 12531920 (Pubitemid 36183971)
16. BW Freie SL Ciccone X Li PA Plett CM Orschell EF Srour H Hanenberg D Schindler SH Lee DW Clapp 2004 A role for the Fanconi anemia C protein in maintaining the DNA damage-induced G2 checkpoint J Biol Chem 279 50986 50993 1:CAS:528:DC%2BD2cXhtVaqsr%2FN 10.1074/jbc.M407160200 15377654 (Pubitemid 40017839)
17. I Garcia-Higuera T Taniguchi S Ganesan MS Meyn C Timmers J Hejna M Grompe AD D'Andrea 2001 Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway Mol Cell 7 249 262 1:CAS:528:DC%2BD3MXis1Kitrk%3D 10.1016/S1097-2765(01)00173-3 11239454 (Pubitemid 32206493)
18. H Gavish CC dos Santos M Buchwald 1993 A Leu554-to-Pro substitution completely abolishes the functional complementing activity of the Fanconi anemia (FACC) protein Hum Mol Genet 2 123 126 1:CAS:528:DyaK3sXisFanu70%3D 10.1093/hmg/2.2.123 8499901
19. N Goldman Z Yang 1994 A codon-based model of nucleotide substitution for protein-coding DNA sequences Mol Biol Evol 11 725 1:CAS:528:DyaK2cXmt1eit70%3D 7968486
20. Graham J (1992) Cancer Selection: The NEW Theory of Evolution. Aculeus Press, Lexington, Virginia
21. S Hussain E Witt PA Huber AL Medhurst A Ashworth CG Mathew 2003 Direct interaction of the Fanconi anaemia protein FANCG with BRCA2/FANCD1 Hum Mol Genet 12 2503 2510 1:CAS:528:DC%2BD3sXnsVekt7Y%3D 10.1093/hmg/ddg266 12915460 (Pubitemid 37220414)
22. S Hussain, et al. 2004 Direct interaction of FANCD2 with BRCA2 in DNA damage response pathways Hum Mol Genet 13 1241 1248 1:CAS:528: DC%2BD2cXktF2qtL8%3D 10.1093/hmg/ddh135 15115758 (Pubitemid 38877877)
23. GA Huttley S Easteal MC Southey A Tesoriero GG Giles MR McCredie JL Hopper DJ Venter 2000 Adaptive evolution of the tumour suppressor BRCA1 in humans and chimpanzees. Australian Breast Cancer Family Study Nat Genet 25 410 413 1:CAS:528:DC%2BD3cXlvVerur0%3D 10.1038/78092 10932184 (Pubitemid 32983432)
24. AM Leroi V Koufopanou A Burt 2003 Cancer selection Nat Rev Cancer 3 226 231 1:CAS:528:DC%2BD3sXhsFGhtrs%3D 10.1038/nrc1016 12612657 (Pubitemid 37328874)
25. AP Martin SR Palumbi 1993 Body size, metabolic rate, generation time, and the molecular clock Proc Natl Acad Sci USA 90 4087 4091 1:CAS:528: DyaK3sXkt1ehs7o%3D 10.1073/pnas.90.9.4087 8483925
26. WJ Murphy, et al. 2001 Resolution of the early placental mammal radiation using Bayesian phylogenetics Science 294 2348 2351 1:CAS:528: DC%2BD3MXptFGrtrg%3D 10.1126/science.1067179 11743200 (Pubitemid 33140557)
27. K Nakanishi YG Yang AJ Pierce T Taniguchi M Digweed AD D'Andrea ZQ Wang M Jasin 2005 Human Fanconi anemia monoubiquitination pathway promotes homologous DNA repair Proc Natl Acad Sci USA 102 1110 1115 1:CAS:528:DC%2BD2MXhtFCitrw%3D 10.1073/pnas.0407796102 15650050 (Pubitemid 40170734)
28. MJ O'Connell JO McInerney 2005 Adaptive evolution of the human fatty acid synthase gene: support for the cancer selection and fat utilization hypotheses? Gene 360 151 159 10.1016/j.gene.2005.06.020 16154299 (Pubitemid 41446889)
29. M O'Driscoll PA Jeggo 2006 The role of double-strand break repair-insights from human genetics Nat Rev Genet 7 45 54 10.1038/nrg1746 16369571 (Pubitemid 41828947)
30. K Offit, et al. 2003 Shared genetic susceptibility to breast cancer, brain tumors, and Fanconi anemia J Natl Cancer Inst 95 1548 1551 1:CAS:528:DC%2BD3sXosVertbk%3D 14559878
31. S Pavard CJ Metcalf 2007 Negative selection on BRCA1 susceptibility alleles sheds light on the population genetics of late-onset diseases and aging theory PLoS One 2 e1206 10.1371/journal.pone.0001206 18030340 (Pubitemid 351638150)
32. A Pavlicek VN Noskov N Kouprina JC Barrett J Jurka V Larionov 2004 Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition Hum Mol Genet 13 2737 2751 1:CAS:528:DC%2BD2cXhtVSkt7nP 10.1093/hmg/ddh301 15385441 (Pubitemid 39567284)
33. A Rangarajan RA Weinberg 2003 Opinion: Comparative biology of mouse versus human cells: modelling human cancer in mice Nat Rev Cancer 3 952 959 1:CAS:528:DC%2BD3sXpvFahtrk%3D 10.1038/nrc1235 14737125
34. K Schmid Z Yang 2008 The trouble with sliding windows and the selective pressure in BRCA1 PLoS One 3 e3746 10.1371/journal.pone.0003746 19015730
35. RC Woodruff JJJ Thompson MA Seeger WE Spivey 1984 Variation in spontaneous mutation and repair in natural population lines of Drosophila melanogaster Heredity 53 223 234 10.1038/hdy.1984.78
36. D Shen JV Vadgama 1999 BRCA1 and BRCA2 gene mutation analysis: visit to the Breast Cancer Information Core (BIC) Oncol Res 11 63 69 1:CAS:528: DyaK1MXmtFKmurw%3D 10489161
37. CA Strathdee H Gavish WR Shannon M Buchwald 1992 Cloning of cDNAs for Fanconi's anaemia by functional complementation Nature 358 434 1:CAS:528:DyaK3sXkt1Gqu74%3D 1641028
38. Y Suzuki M Nei 2002 Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites Mol Biol Evol 19 1865 1869 1:CAS:528:DC%2BD38XovFOntLk%3D 12411595
39. C Szabo A Masiello JF Ryan LC Brody 2000 The breast cancer information core: database design, structure, and scope Hum Mutat 16 123 131 1:CAS:528:DC%2BD3cXlvFKgt7k%3D 10.1002/1098-1004(200008)16:2<123::AID- HUMU4>3.0.CO;2-Y 10923033
40. T Taniguchi I Garcia-Higuera B Xu PR Andreassen RC Gregory ST Kim WS Lane MB Kastan AD D'Andrea 2002 Convergence of the Fanconi anemia and ataxia telangiectasia signaling pathways Cell 109 459 472 1:CAS:528: DC%2BD38XjvFKgtLs%3D 10.1016/S0092-8674(02)00747-X 12086603 (Pubitemid 34564473)
41. T Taniguchi M Tischkowitz N Ameziane SV Hodgson CG Mathew H Joenje SC Mok AD D'Andrea 2003 Disruption of the Fanconi anemia-BRCA pathway in cisplatin-sensitive ovarian tumors Nat Med 9 568 574 1:CAS:528: DC%2BD3sXjtlamtLo%3D 10.1038/nm852 12692539 (Pubitemid 36597103)
42. JD Thompson DG Higgins TJ Gibson 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 22 4673 4680 1:CAS:528:DyaK2MXitlSgu74%3D 10.1093/nar/22.22.4673 7984417
43. PC Verlander JD Lin MU Udono Q Zhang RA Gibson CG Mathew AD Auerbach 1994 Mutation analysis of the Fanconi anemia gene FACC Am J Hum Genet 54 595 601 1:CAS:528:DyaK2cXktlagsbc%3D 8128956
44. BF Voight S Kudaravalli X Wen JK Pritchard 2006 A map of recent positive selection in the human genome PLoS Biol 4 e72 10.1371/journal.pbio.0040072 16494531
45. MJ Wakefield P Maxwell GA Huttley 2005 Vestige: maximum likelihood phylogenetic footprinting BMC Bioinformatics 6 130 10.1186/1471-2105-6-130 15921531 (Pubitemid 41357889)
46. W Wang 2007 Emergence of a DNA-damage response network consisting of Fanconi anaemia and BRCA proteins Nat Rev Genet 8 735 748 1:CAS:528: DC%2BD2sXhtVCrsb3J 10.1038/nrg2159 17768402 (Pubitemid 47429206)
47. ET Wang RK Moyzis 2007 Genetic evidence for ongoing balanced selection at human DNA repair genes ERCC8, FANCC, and RAD51C Mutat Res 616 165 174 1:CAS:528:DC%2BD2sXhs1Cltbs%3D 17257630
48. X Wang PR Andreassen AD D'Andrea 2004 Functional interaction of monoubiquitinated FANCD2 and BRCA2/FANCD1 in chromatin Mol Cell Biol 24 5850 5862 1:CAS:528:DC%2BD2cXls1aqt78%3D 10.1128/MCB.24.13.5850-5862.2004 15199141 (Pubitemid 38787970)
49. MA Whitney, et al. 1996 Germ cell defects and hematopoietic hypersensitivity to gamma-interferon in mice with a targeted disruption of the Fanconi anemia C gene Blood 88 49 58 1:CAS:528:DyaK28XjvFSnsLg%3D 8704201
50. B Xia, et al. 2007 Fanconi anemia is associated with a defect in the BRCA2 partner PALB2 Nat Genet 39 159 161 1:CAS:528:DC%2BD2sXpvFekug%3D%3D 10.1038/ng1942 17200672 (Pubitemid 46184344)
51. Z Yang 1998 Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution Mol Biol Evol 15 568 573 1:CAS:528:DyaK1cXislensL4%3D 9580986
52. Z Yang R Nielsen 2002 Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages Mol Biol Evol 19 908 917 1:CAS:528:DC%2BD38Xks1Ojtbk%3D 12032247
53. Z Yang R Nielsen N Goldman AM Pedersen 2000 Codon-substitution models for heterogeneous selection pressure at amino acid sites Genetics 155 431 449 1:CAS:528:DC%2BD3cXjslKhtb4%3D 10790415
54. Z Yang WS Wong R Nielsen 2005 Bayes empirical Bayes inference of amino acid sites under positive selection Mol Biol Evol 22 1107 1118 1:CAS:528:DC%2BD2MXjtFaisbk%3D 10.1093/molbev/msi097 15689528 (Pubitemid 40471423)
55. J Zhang 2004 Frequent false detection of positive selection by the likelihood method with branch-site models Mol Biol Evol 21 1332 1339 1:CAS:528:DC%2BD2cXltlKls7c%3D 10.1093/molbev/msh117 15014150 (Pubitemid 38823736)
56. J Zhang R Nielsen Z Yang 2005 Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level Mol Biol Evol 22 2472 2479 1:CAS:528:DC%2BD2MXht1KgtLbM 10.1093/molbev/msi237 16107592 (Pubitemid 41661383)
57. Zimmer C (2007) Evolved for cancer? Sci Am 296:68-74, 75A