Complexification of Gene Networks by Co-evolution of Genomes and Genomic Parasites

David M. Holloway, Alexander B. Kazansky, Alexander V. Spirov

2012

Abstract

The co-evolution of species with their genomic parasites (transposons) is thought to be one of the primary ways of rewiring gene regulatory networks (GRNs). In this communication, we computationally explore some of the essential co-evolution aspects of hosts (GRNs) with their transposons. We implemented an evolutionary search of an appropriate GRN model design on the example of the Drosophila gap-gene network. Simple artificial transposons capable of spreading and transposition were implemented. With the model, we explored the hypothesis that targeting destruction of some of the regulatory connections in the GRN via the action of transposons can produce negative selection pressure. Functionally external genes can be recruited (co-opted) into the GRN under this selection pressure following transposon rewiring of the GRN. Over evolutionary time, transposition events are able to disrupt these new regulatory connections, leading to repeated cycles of recruitment, rewiring and optimization. This process can produce increasingly large GRNs with the same basic functions.

References

  1. Wilkins, A. S., 2002. The Evolution of Pathways, Sinauer Associates, Sunderland, MA.
  2. True, J. R., Carroll, S. B., 2002. Gene co-option in physiological and morphological evolution. Annu. Rev. Cell Dev. Biol., 18:53-80.
  3. Carroll, S. B., Grenier, J. K., Weatherbee, S. D., 2001. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, Malden, MA: Blackwell Science.
  4. Reinitz, J., Sharp, D. H., 1995. Mechanism of formation of eve stripes. Mechanisms of Development, 49:133-158.
  5. Jaeger, J., Surkova, S., Blagov, M. et al., 2004. Dynamic control of positional information in the early Drosophila blastoderm. Nature, 430:368-371.
  6. Sánchez, L., Thieffry, D., 2001. A logical analysis of the Drosophila gapgene system. J. Theor. Biol., 211:115- 141.
  7. Manu, Surkova, S., Spirov, A. V. et al., 2009a. Canalization of Gene Expression in the Drosophila Blastoderm by Gap Gene Cross Regulation. PLoS Biol., 73: e1000049.
  8. Manu, Surkova, S., Spirov, A. V. et al., 2009b. Canalization of Gene Expressionand Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors. PLoS Computational Biology, 53.e1000303
  9. Azevedo, R. B. R., Lohaus, R., Srinivasan, S., Dang, K. K., Burch, C. L. 2006. Sexual reproduction selects for robustness and negative epistasis in artificial gene networks. Nature, 440:87-90.
  10. Umulis, D. M., O'Connor, M. B., Othmer, H. G., 2008. Robustness of embryonic spatial patterning in Drosophila melanogaster. Current Topics in Developmental Biology, 81:65-111.
  11. Bieler, J., Pozzorini, C., Naef, F., 2011. Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains. Biophysical J., 101:287-296.
  12. Gursky, V. V., Panok, L., Myasnikova, E. M. et al., 2011. Mechanisms of gap gene expression canalization in the Drosophila blastoderm. BMC Syst. Biol., 5:118.
  13. Spirov, A., Holloway, D., 2012. Evolution in silico of genes with multiple regulatory modules on the example of the Drosophila segmentation gene hunchback. In 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2012, San Diego, pp 244-251.
  14. Spirov, A. V., Holloway, D. M., 2009. The Effects of Gene Recruitment on the Evolvability and Robustness of Pattern-Forming Gene Networks. In Advances in Computational Algorithms and Data Analysis, Lecture Notes in Electrical Engineering, Springer, pp. 29-49.
  15. Spirov, A. V., Holloway, D. M., 2010. Design of a dynamic model of genes with multiple autonomous regulatory modules by evolutionary computations. Procedia Computer Science, 1:1005-1014
  16. François, P., Hakim, V., Siggia, E. D., 2007. Deriving structure from evolution: metazoan segmentation. Mol. Syst. Biol., 3:12.
  17. Patel, N. H., 1994. Developmental evolution: insights from studies of insect segmentation. Science, 266:581- 590
  18. Sommer, R. J., Tautz, D., 1993. Involvement of an orthologue of the Drosophila pair-rule gene hairy in segment formation of the short germ-band embryo of Tribolium Coleoptera. Nature, 361:448-450.
  19. Makalowski, W., 1995. SINEs as a Genomic Scrap Yard. Chap. 5, In The Impact of Short Interspersed Elements SINEs on the Host Genome, Austin: R.G. Landes Company, pp. 81-104.
  20. Lozovskaya, E. R., Hartl, D. L., Petrov, D. A., 1995. Genomic regulation of transposable elements in Drosophila. Curr. Opin. Genet. Dev., 5:768-73.
  21. King, C. C., 1992. Modular Transposition and the Dynamical Structure of Eukaryote Regulatory Evolution. Genetica, 86:127-142.
  22. Wallace, M. R., Anderson, L. B., Saulino, A. M. et al., 1991. A de novo Alu insertion results in neurofibromatosis type 1. Nature, 353:864-866.
  23. Girard, L., Freeling, M., 1999. Regulatory changes as a consequence of transposon insertion. Dev. Genet., 25:291-296.
  24. Spirov, A. V., 1996. Self-assemblage of gene networks in evolution via recruiting of new netters. In PPSN 1996, Lecture Notes in Computer Science, 1141, pp 91-100.
  25. Spirov, A. V., Samsonova, M. G., 1997. Strategy of Coevolution of Transposons and Host Genome: Application to Evolutionary Computations. In Proc. of the Third Nordic Workshop on Genetic Algorithms and their Applications, Helsinki University, pp 71-82.
  26. Spirov, A. V., Kadyrov, A. S., 1998. Transposon element technique applied to GA-based John Muir's trail test. In High-Performance Computing and Networking, pp 925-928.
  27. Spirov, A. V., Kazansky, A. B., 2002a. Jumping genesmutators can raise efficacy of evolutionary search. In Proc. Genetic and Evolutionary Computation Conference, GECCO2002, Morgan Kaufmann Publishers, San Francisco, pp 561-568.
  28. Spirov, A. V., Kazansky, A. B., 2002b. The usage of artificial transposons for the protection of already found building blocks: the tests with royal road functions. In Proc. The 6th World Multiconference on Systemics, Cybernetics and Informatics, SCI2002, Orlando, Florida, Int. Inst. Informatics and Systemics, pp 75-80.
  29. Spirov, A. V., Kazansky, A. B., Zamdborg, L., et al., 2009. Forced Evolution in Silico by Artificial Transposons and their Genetic Operators: The John Muir Ant Problem. arXiv:0910.5542v1.
  30. Nawaz Ripon, K. S., Kwong, S., Man, K. F., 2007. A realcoding jumping gene genetic algorithm RJGGA for multiobjective optimization. Information Sciences, 177:632-654.
  31. Tang, W. K. S., Kwong, S. T. W., Man, K. F., 2008. A Jumping Genes Paradigm: Theory, Verification and Applications. IEEE Circuits and Systems Magazine, 8:18-36.
  32. Chan, T. M., Man, K. F., Kwong, S., Tang, K. S., 2008. A Jumping Gene paradigm for Evolutionary Multiobjective Optimization. IEEE Tran. On Evolutionary Computation, 12:143-159.
  33. Simões, A., Costa, E., 1999a. Transposition: A Biologically Inspired Mechanism to Use with Genetic Algorithms. In the Proceedings of the Fourth International Conference on Neural Networks and Genetic Algorithms ICANNGA'99, Springer-Verlag, pp 612-619.
  34. Simões, A., Costa, E., 1999b. Transposition versus Crossover: An Empirical Study. In Proceedings of the Genetic and Evolutionary Computation Conference GECCO'99, Orlando, Florida USA, CA: Morgan Kaufmann, pp 612-619.
  35. Simões, A., Costa, E., 2000. Using Genetic Algorithms with Asexual Transposition. In Proc. of the Genetic and Evolutionary Computation Conference GECCO'00, Las Vegas, USA, CA: Morgan Kaufmann, pp. 323-330.
  36. Simões, A., Costa, E., 2001. An Evolutionary Approach to the Zero/One Knapsack Problem: Testing Ideas from Biology. In International Conference on Neural Networks and Genetic Algorithms ICANNGA'01, Prague, Czech Republic, Springer, pp. 236-239.
  37. Liu, R., Sheng, Z., Jiao, L., 2009. Gene transposon based clonal selection algorithm for clustering. In Proc. Genetic and Evolutionary Computation Conference, GECCO 2009, pp 1251-1258
  38. Siegal, M. L., Bergman, A., 2002. Waddington's canalization revisited: developmental stability and evolution. Proc Natl Acad Sci USA, 99:10528-10532
  39. Press, W. H., Flannery, B. P., Teukolsky, S. A., Vetterling, W. T., 1988. Numerical Recipes, Cambridge University Press, Cambridge.
Download


Paper Citation


in Harvard Style

M. Holloway D., B. Kazansky A. and V. Spirov A. (2012). Complexification of Gene Networks by Co-evolution of Genomes and Genomic Parasites . In Proceedings of the 4th International Joint Conference on Computational Intelligence - Volume 1: ECTA, (IJCCI 2012) ISBN 978-989-8565-33-4, pages 238-244. DOI: 10.5220/0004170802380244


in Bibtex Style

@conference{ecta12,
author={David M. Holloway and Alexander B. Kazansky and Alexander V. Spirov},
title={Complexification of Gene Networks by Co-evolution of Genomes and Genomic Parasites },
booktitle={Proceedings of the 4th International Joint Conference on Computational Intelligence - Volume 1: ECTA, (IJCCI 2012)},
year={2012},
pages={238-244},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004170802380244},
isbn={978-989-8565-33-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the 4th International Joint Conference on Computational Intelligence - Volume 1: ECTA, (IJCCI 2012)
TI - Complexification of Gene Networks by Co-evolution of Genomes and Genomic Parasites
SN - 978-989-8565-33-4
AU - M. Holloway D.
AU - B. Kazansky A.
AU - V. Spirov A.
PY - 2012
SP - 238
EP - 244
DO - 10.5220/0004170802380244