Geodesic
Toward a General Model for the Evolution of DNA Replication in Three Domains of Life
R. Retkute1
1 School of Biosciences, Sutton Bonington Campus, University of Nottingham, LE12 5RD, UK School of Mathematics, University Park, Nottingham, University of Nottingham, NG7 2RD, UK
Mathematical modelling of natural phenomena, Tome 9 (2014) no. 3, pp. 96-106.

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Nothing is more fundamental to life than the ability to reproduce and duplicate the information cells store in their genomes. The mechanism of duplication of DNA has been conserved from prokaryotes to eukaryotes. The aim of the study was to quantify which evolutionary forces could produce the pattern of genome replication architecture observed in present-day organisms. This was achieved using an evolutionary simulation, combining random genome sequence shuffling, mutation, selection and the mathematical modeling of DNA replication. We have found parameter values which explained evolutionary pressures of DNA replication in E.coli, P.calidifontis and S. cerevisae. Surprisingly, the results of the evolutionary simulation suggests that for a fixed cost per replication origin it is more advantageous for genomes to reduce the number of replication origins under increasing uncertainty in origin activation timing.
DOI : 10.1051/mmnp/20149306

R. Retkute 1

1 School of Biosciences, Sutton Bonington Campus, University of Nottingham, LE12 5RD, UK School of Mathematics, University Park, Nottingham, University of Nottingham, NG7 2RD, UK 
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R. Retkute. Toward a General Model for the Evolution of DNA Replication in Three Domains of Life. Mathematical modelling of natural phenomena, Tome 9 (2014) no. 3, pp. 96-106. doi : 10.1051/mmnp/20149306. http://geodesic.mathdoc.fr/articles/10.1051/mmnp/20149306/

[1] A. Baker, B. Audit, S. C. H. Yang, J. Bechhoefer, A. Arneodo Phys. Rev. Let. 2012 1 5

[2] A. Baker, C. L. Chen, H. Julienne, B. Audit, Y. Dõaubenton-Carafa, C. Thermes, A. Arneodo Europ. Phys. J. E 2012 1 25

[3] A. Baker, H. Julienne, C. L. Chen, B. Audit, Y. Dõaubenton-Carafa, C. Thermes, A. Arneodo Europ. Phys. J. E 2012 1 12

[4] J. Bechhoefer, N. Rhind Tren. in Gen. 2012 374 381

[5] E. Besnard, A. Babied, L. Lapasset, O. Milhavet, H. Parrinello, C. Dantec, J. M. Marin, J.M. Lemaitre Nat. Struct. & Mol. Biol. 2012 837 844

[6] E.B. Brodie Of Brodie, S. Nicolay, M. Touchon, B. Audit, Y. D’Aubenton-Carafa, C. Thermes, A. Arneodo Phys. Rev. Let. 2005 1 4

[7] C. Cayrou, P. Coulombe, A. Vigneron, S. Stanojcic, O. Ganier, I. Peiffer, A. Puy, S. Laurent-Chabalier, R. Desprat, M. Mechali Gen. Res. 2011 1438 1449

[8] C. Cayrou, P. Coulombe, A. Puy, S. Rialle, N. Kaplan, E. Segal, M. Mechali Cell Cycl. 2012 658 667

[9] Y. Clement, P. F. Arndt Mol. Biol. & Evol. 2013 2612 2618

[10] C. Costas, M. D. Sanchez, H. Stroud, Y. Yu, J. C. Oliveros, S. Feng, A. Benguria, I. Lopez-Vidriero, X. Zhang, R. Solano, S. E. Jacobsen, C. Gutierrez Nat. Struct. & Mol. Biol. 2011 395 U190

[11] N. Donley, M. J. Thayer Sem. in Canc. Biol. 2013 80 89

[12] A. P. S. De Moura, R. Retkute, M. Hawkins, C. A. Nieduszynski NAR 2010 5623 5633

[13] M. Dos Reis, L. Wernisch Mol. Biol. & Evol. 2009 451 461

[14] F. Gao, H. Luo, C. T. Zhang Bioinformatics 2012 1551 1552

[15] F. Gao, H. Luo, C. T. Zhang NAR 2013 90 93

[16] M. G. Gauthier, P. Norio, J. Bechhoefer PLoS one 2012 1

[17] A. Gierlik, M. Kowalczuk, P. Mackiewicz, M. R. Dudek, S. Cebrat J. Theor. Biol. 2000 305 314

[18] P. Green, B. Ewing, W. Miller, P. Thomas, E. Green Nat. Gen. 2003 14 517

[19] M. Hayashi, Y. Katou, T. Itoh, M. Tazumi, Y. Yamada, T. Takahashi, T. Nakagawa, K. Shirahige, H. Masukata EMBO J. 2007 1327 1339

[20] O. Hyrien, A. Rappailles, G. Guilbaud, A. Baker, C. L. Chen, A. Goldar, N. Petryk, M. Kahli, E. Ma, Y. D’Aubenton-Carafa, B. Audit, C. Thermes, A. Arneodo J. Mol. Biol. 2013 4673 89

[21] M. Kellis, B. W. Birren, E. S. Lander Nature 2008 617 624

[22] M. L. DePamphilis. DNA replication and human disease. Cold Spring Harbor monograph series.

[23] G. I. Lang, A. W. Murray Gen. Biol. & Evol. 2011 799 811

[24] A. C. Leonard, M. Mechali Cold Spring Harbor Persp. Biol. 2013 1 18

[25] I. Liachko, A. Bhaskar, C. Lee, S. C. C. Chung, B. K. Tye, U. Keich PLoS Gen. 2010 1 12

[26] L. Liu, S. De, F. Michor Nat. Comm. 2013 1 10

[27] M. Lundgren, A. Andersson, L. M. Chen, P. Nilsson, R. Bernander PNAS 2004 7046 7051

[28] H. E. Luo, J. T. Li, M. Eshaghi, J. H. Liu, R. K. M. Karuturi BMC Bioinf. 2010 1 15

[29] J. Lygeros, K. Koutroumpas, S. Dimopoulos, I. Legouras, P. Kouretas, C. Heichinger, P. Nurse, Z. Lygerou PNAS 2008 12295 12300

[30] M. Lynch. The origins of the genome architecture. Sinauer Associates Inc Publishers, Massachusetts.

[31] M. Lynch Tr. Gen. 2010 345 52

[32] A. T. Mcgeoch, S.D. Bell Nat. Rev. Mol. Cell Biol. 2008 569 574

[33] M. Mechali, K. Yoshida, P. Coulombe, P. Pasero Curr. Op. Gen., & Dev. 2013 124 31

[34] C. A. Muller, C. A. Nieduszynski Gen. Res. 2012 1953 1962

[35] M. A. Nowak, H. Ohtsuki PNAS 2008 14924 14927

[36] S.Ohno. Evolution by Gene Duplication. Springer-Verlag, London.

[37] E. A. Pelve, A. C. Lindas, A. Knoppel, A. Mira, R. Bernander Mol. Microbiol. 2012 986 995

[38] T. J. Pohl, K. Kolor, W. L. Fangman, B. J. Brewer, M. K. Raghuraman G3 2013 1955 1963

[39] B. D. Pope, D. M. Gilbert J. Mol. Biol. 2013 4690 4695

[40] J. G. D. Prendergast, H. Campbell, N. Gilbert, M. G. Dunlop, W. A. Bickmore, C. A. M. Semple BMC Evol. Biol. 2007 1 12

[41] E. P. C. Rocha Ann. Rev. Gen. 2008 211 233

[42] N. P. Robinson, S. D. Bell FEBS J. 2005 3757 3766

[43] C. C. Siow, S. R. Nieduszynska, C. A. Muller, C. A. Nieduszynski NAR 2012 D682 D686

[44] K. Skarstad, H. B. Steen, E. Boye J. Bacteriol. 1983 656 662

[45] O. Skovgaard, M. Bak, A. Lobner-Olesen, N. Tommerup Gen. Res. 2011 1388 1393

[46] A. Srivatsan, A. Tehranchi, D. M. Macalpine, J. D. Wang PLoS Gen. 2010 1 14

[47] J. A. Stamatoyannopoulos, I. Adzhubei, R. E. Thurman, G. V. Kryukov, S. M. Mirkin, S. R. Sunyaev Nat. Gen. 2009 393 395

[48] T. Tatarinova, E. Elhaik, M. Pellegrini Gen. Biol. & Evol. 2013 1443 1456

[49] E. Yaffe, S. Farkash-Amar, A. Polten, Z. Yakhini, A. Tanay, I. Simon PLoS Gen. 2010 1 12

[50] S. C. H. Yang, N. Rhind, J. Bechhoefer Mol. Syst. Biol. 2012 1 13

[51] C. C. Weber, C. J. Pink, L. D. Hurst Mol. Biol. & Evol. 2012 873 882

[52] P. Worning, L. J. Jensen, P. H. Hallin, H. H. Staerfeldt, D. W. Ussery Env. Biol. 2006 353 361

[53] Z. Wu, H. Liu, Hailong, J. Liu, X. Q. Liu, H. Xiang BMC Gen. 2012 1 16

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