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Simulating Bacterial Transcription and Translation in a Stochastic π Calculus

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Transactions on Computational Systems Biology VI

Part of the book series: Lecture Notes in Computer Science ((TCSB,volume 4220))

Abstract

Stochastic simulation of genetic networks based on models in the stochastic π-calculus is a promising recent approach. This paper contributes an extensible model of the central mechanisms of gene expression i.e. transcription and translation, at the prototypical instance of bacteria. We reach extensibility through object-oriented abstractions, that are expressible in a stochastic π-calculus with pattern guarded inputs. We illustrate our generic model by simulating the effect of translational bursting in bacterial gene expression.

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References

  1. Abbondanzieri, E.A., Greenleaf, W.J., Shaevitz, J.W., Landick, R., Block, S.M.: Direct observation of base-pair stepping by RNA polymerase. Nature 438, 460–465 (2005)

    Article  Google Scholar 

  2. Adalsteinsson, D., McMillen, D., Elston, T.: Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. BMC Bioinformatics 5(1), 24 (2004)

    Article  Google Scholar 

  3. Arkin, A., Ross, J., McAdams, H.H.: Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells. Genetics 149, 1633–1648 (1998)

    Google Scholar 

  4. Banerjee, S., Chalissery, J., Bandey, I., Sen, R.J.: Rho-dependent transcription termination: More questions than answers. Journal of Microbiology 44(1), 11–22 (2006)

    Google Scholar 

  5. Barnard, A., Wolfe, A., Busby, S.: Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes. Current Opinion in Microbiology 7, 102–108 (2004)

    Article  Google Scholar 

  6. Blossey, R., Cardelli, L., Phillips, A.: A compositional approach to the stochastic dynamics of gene networks. In: Priami, C., Cardelli, L., Emmott, S. (eds.) Transactions on Computational Systems Biology IV. LNCS (LNBI), vol. 3939, pp. 99–122. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  7. Brenner, S., Jacob, F., Meselson, M.: An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature 190, 576–581 (1961)

    Article  Google Scholar 

  8. Cardelli, L.: Abstract machines of systems biology. In: Priami, C., Merelli, E., Gonzalez, P., Omicini, A. (eds.) Transactions on Computational Systems Biology III. LNCS (LNBI), vol. 3737, pp. 145–168. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  9. Cardelli, L.: Brane calculi: interactions of biological membranes. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257–278. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  10. Carpousis, A.J.: The Escherichia coli RNA degradosome: structure, function and relationship to other ribonucleolytic multienzyme complexes. Biochemical Society Transactions 30(2), 150–154 (2002)

    Article  Google Scholar 

  11. Carrier, T.A., Keasling, J.D.: Mechanistic modeling of mRNA decay. Journal of Theoretical Biology 189, 195–209 (1997)

    Article  Google Scholar 

  12. Chabrier-Rivier, N., Chiaverini, M., Danos, V., Fages, F., Schächter, V.: Modeling and querying biomolecular interaction networks. Theoretical Computer Science 325(1), 24–44 (2004)

    Google Scholar 

  13. Chabrier-Rivier, N., Fages, F., Soliman, S.: The biochemical abstract machine BIOCHAM. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 172–191. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  14. Danos, V., Laneve, C.: Formal molecular biology. Theoretical Computer Science 325(1), 69–110 (2004)

    Article  MATH  MathSciNet  Google Scholar 

  15. Dasika, M.S., Gupta, A., Maranas, C.D.: DEMSIM: a discrete event based mechanistic simulation platform for gene expression and regulation dynamics. Journal of Theoretical Biology 232(1), 55–69 (2005)

    Article  MathSciNet  Google Scholar 

  16. Dennis, P.P., Ehrenberg, M., Bremer, H.: Control of rRNA synthesis in Escherichia coli: a systems biology approach. Microbiology and Molecular Biology Reviews 68(4), 639–668 (2004)

    Article  Google Scholar 

  17. Dijkstra, E.W.: Hierarchical ordering of sequential processes. Acta Inf. 1, 115–138 (1971)

    Article  MathSciNet  Google Scholar 

  18. Duchier, D., Kuttler, C.: Biomolecular agents as multi-behavioural concurrent objects. In: Proceedings of the First International Workshop on Methods and Tools for Coordinating Concurrent, Distributed and Mobile Systems (MTCoord 2005). Electronic Notes in Theoretical Computer Science, vol. 150, pp. 31–49 (2006)

    Google Scholar 

  19. Elf, J., Ehrenberg, M.: What makes ribosome-mediated trascriptional attenuation sensitive to amino acid limitation? PLoS Computational Biology 1(1), 14–23 (2005)

    Article  Google Scholar 

  20. Alberts, B., et al.: Molecular Biology of the Cell. Garland Science (2002)

    Google Scholar 

  21. Frank, J., Agrawal, R.K.: A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406, 318–322 (2000)

    Article  Google Scholar 

  22. Gillespie, D.T.: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics 22, 403–434 (1976)

    Article  MathSciNet  Google Scholar 

  23. Golding, I., Paulsson, J., Zawilski, S.M., Cox, E.C.: Real-time kinetics of gene activity in individual bacteria. Cell 123(6), 1025–1036 (2005)

    Article  Google Scholar 

  24. Gowrishankar, J., Harinarayanan, R.: Why is transcription coupled to translation in bacteria? Molecular Microbiology 54(3), 598–603 (2004)

    Article  Google Scholar 

  25. Gros, F., Hiatt, H., Gilbert, W., Kurland, C.G., Risebrough, R.W., Watson, J.D.: Unstable ribonucleic acid revealed by pulse labeling of Escherichia coli. Nature 190, 581–585 (1961)

    Article  Google Scholar 

  26. Grunberg-Manago, M.: Messenger RNA stability and its role in control of gene expression in bacteria and phages. Annual Reviews Genetics, 193–227 (1999)

    Google Scholar 

  27. Henkin, T.M.: Transcription termination control in bacteria. Current Opinion in Microbiology 3(2), 149–153 (2000)

    Article  MathSciNet  Google Scholar 

  28. Hsu, L.M.: Promoter clearance and escape in prokaryotes. Biochimica et Biophysica Acta 1577, 191–207 (2002)

    Google Scholar 

  29. Kaern, M., Blake, W.J., Collins, J.J.: The engineering of gene regulatory networks. Annual Review Biomedical Engineering 5, 179–206 (2003)

    Article  Google Scholar 

  30. Kaern, M., Elston, T., Blake, W., Collins, J.: Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 6(6), 451–467 (2005)

    Article  Google Scholar 

  31. Kierzek, A.M.: STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm. Bioinformatics 18(3), 470–481 (2002)

    Article  Google Scholar 

  32. Kierzek, A.M., Zaim, J., Zielenkiewicz, P.: The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression. Journal of Biological Chemistry 276, 8165–8172 (2001)

    Article  Google Scholar 

  33. Kobiler, O., Rokney, A., Friedman, N., Court, D.L., Stavans, J., Oppenheim, A.B.: Quantitative kinetic analysis of the bacteriophage λ genetic network. Proceedings of the National Academy of Sciences USA 102(12), 4470–4475 (2005)

    Article  Google Scholar 

  34. Kuttler, C., Niehren, J.: Gene regulation in the pi calculus: Simulating cooperativity at the lambda switch. In: Priami, C., Ingólfsdóttir, A., Mishra, B., Riis Nielson, H. (eds.) Transactions on Computational Systems Biology VII. LNCS (LNBI), vol. 4230, pp. 24–55. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  35. Kuttler, C., Lhoussaine, C., Niehren, J.: A stochastic pi calculus for concurrent objects. Technical report, INRIA (2006)

    Google Scholar 

  36. Maciag, K., Altschuler, S.J., Slack, M.D., Krogan, N.J., Emili, A., Greenblatt, J.F., Maniatis, T., Wu, L.F.: Systems-level analyses identify extensive coupling among gene expression machines. Molecular Systems Biology (2006)

    Google Scholar 

  37. Maniatis, T., Need, R.: An extensive network of coupling among gene expression machines. Nature 416, 499–506 (2002)

    Article  Google Scholar 

  38. McAdams, H.H., Arkin, A.: Stochastic mechanisms in gene expression. Proceedings of the National Academy of Sciences USA 94, 814–819 (1997)

    Article  Google Scholar 

  39. McClure, W.R.: Mechanism and control of transcription initiation in prokaryotes. Annual Review Biochemistry 54, 171–204 (1985)

    Article  Google Scholar 

  40. Milner, R.: Communicating and Mobile Systems: the π-calculus. Cambridge University Press, Cambridge (1999)

    Google Scholar 

  41. Milner, R.: What’s in a name? In: Computer Systems: Theory, Technology, and Applications. A tribute to Roger Needham. Monographs in Computer Science, pp. 205–211. Springer, Heidelberg (2004)

    Google Scholar 

  42. Milner, R., Parrow, J., Walker, D.: A calculus of mobile processes (I and II). Information and Computation 100, 1–77 (1992)

    Article  MATH  MathSciNet  Google Scholar 

  43. Neufing, P.J., Shearwin, K.E., Egan, J.B.: Establishing lysogenic transcription in the temperate coliphage 186. Journal of Bacteriology 183(7), 2376–2379 (2001)

    Article  Google Scholar 

  44. Orphanides, G., Reinberg, D.: A unified theory of gene expression. Cell 108, 439–451 (2002)

    Article  Google Scholar 

  45. Ozbudak, E.M., Thattai, M., Kurtser, I., Grossman, A., van Oudenaarden, A.D.: Regulation of noise in the expression of a single gene. Nature Genetics 31, 69–73 (2002)

    Article  Google Scholar 

  46. Paul, B.J., Ross, W., Gaal, T., Gourse, R.L.: rRNA transcription in E. Coli. Annual Review Genetics 38, 749–770 (2004)

    Article  Google Scholar 

  47. Paulino, H., Marques, P., Lopes, L., Vasconcelos, V.T., Silva, F.: A multi-threaded asynchronous language. In: Malyshkin, V.E. (ed.) PaCT 2003. LNCS, vol. 2763, pp. 316–323. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  48. Phillips, A., Cardelli, L.: A correct abstract machine for the stochastic pi-calculus. In: Transactions on Computational Systems Biology, Special issue of BioConcur 2004 (in press)

    Google Scholar 

  49. Prandi, D., Priami, C., Quaglia, P.: Process calculi in a biological context. Bulletin of the EATCS 85, 53–69 (2005)

    MATH  MathSciNet  Google Scholar 

  50. Priami, C.: Stochastic π-calculus. Computer Journal 6, 578–589 (1995)

    Article  Google Scholar 

  51. Priami, C., Quaglia, P.: Beta binders for biological interactions. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 20–33. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  52. Priami, C., Regev, A., Shapiro, E., Silverman, W.: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80, 25–31 (2001)

    Article  MATH  MathSciNet  Google Scholar 

  53. Ptashne, M.: A Genetic Switch: Phage Lambda Revisited, 3rd edn. Cold Spring Harbor Laboratory Press (2004)

    Google Scholar 

  54. Ptashne, M., Gann, A.: Genes and Signals. Cold Spring Harbor Laboratory Press (2002)

    Google Scholar 

  55. Ramsey, S., Orrell, D., Bolouri, H.: Dizzy: stochastic simulation of large-scale genetic regulatory networks. Journal of Bioinformatics and Computational Biology 3(2), 415–436 (2005)

    Article  Google Scholar 

  56. Raser, J.M., O’Shea, E.K.: Noise in Gene Expression: Origins, Consequences, and Control. Science 309(5743), 2010–2013 (2005)

    Article  Google Scholar 

  57. Ravara, A., Vasconcelos, V.T.: Typing non-uniform concurrent objects. In: Palamidessi, C. (ed.) CONCUR 2000. LNCS, vol. 1877, pp. 474–488. Springer, Heidelberg (2000)

    Chapter  Google Scholar 

  58. Ray, P.N., Pearson, M.L.: Evidence for post-transcriptional control of the morphogenetic genes of bacteriophage lambda. Journal Molecular Biology 85(1), 163–175 (1974)

    Article  Google Scholar 

  59. Regev, A., Shapiro, E.: Cells as computation. Nature 419, 343 (2002)

    Article  Google Scholar 

  60. Regonesi, M.E., Favero, M.D., Basilico, F., Briani, F., Benazzi, L., Tortora, P., Mauri, P., Deho, G.: Analysis of the Escherichia coli RNA degradosome composition by a proteomic approach. Biochimie 88(2), 151–161 (2006)

    Article  Google Scholar 

  61. Sarjoughian, H.S., Cellier, F.E. (eds.): Discrete Event Modeling and Simulation Technologies: A Tapestry of Systems and AI-based Theories and Methodologies. Springer, New York (2001)

    MATH  Google Scholar 

  62. Schmeissner, U., Court, D., Shimatake, H., Rosenberg, M.: Promoter for the establishment of repressor synthesis in bacteriophage lambda. Proceedings of the National Academy of Sciences USA 77(6), 3191–3195 (1980)

    Article  Google Scholar 

  63. Shea, M., Ackers, G.K.: The O R control system of bacteriophage lambda: A physical-chemical model for gene regulation. Molecular Biology 181, 211–230 (1985)

    Article  Google Scholar 

  64. Shearwin, K.W., Callen, B.P., Egan, J.B.: Transcriptional interference - a crash course. Trends in Genetics 21, 339–345 (2005)

    Article  Google Scholar 

  65. Sneppen, K., Zocchi, G.: Physics in Molecular Biology. Cambridge University Press, Cambridge (2005)

    Book  Google Scholar 

  66. Steege, D.A.: Emerging features of mRNA decay in bacteria. RNA 6(8), 1079–1090 (2000)

    Article  Google Scholar 

  67. Swain, P.S.: Efficient attenuation of stochasticity in gene expression through post-transcriptional control. Journal of Molecular Biology 344, 965–976 (2004)

    Article  Google Scholar 

  68. Vasconcelos, V.T., Tokoro, M.: A typing system for a calculus of objects. In: Veni Madhavan, C.E., Nori, K.V. (eds.) FSTTCS 1990. LNCS, vol. 472, pp. 460–474. Springer, Heidelberg (1990)

    Google Scholar 

  69. Voit, E.O.: Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists. Cambridge University Press, Cambridge (2000)

    Google Scholar 

  70. von Heijne, G., Nilsson, L., Blomberg, C.: Translation and messenger RNA secondary structure. Journal of Theoretical Biology 68, 321–329 (1977)

    Article  Google Scholar 

  71. Wagner, R.: Transcription Regulation in Prokaryotes. Oxford University Press, Oxford (2000)

    Google Scholar 

  72. Yanofsky, C.: Trancription attenuation. Journal Biological Chemistry, 609–612 (1988)

    Google Scholar 

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Authors and Affiliations

  1. Interdisciplinary Research Institute and LIFL, Lille, France

    Céline Kuttler

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  1. Céline Kuttler
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  1. Centre for Computational and Systems Biology, The Microsoft Research - University of Trento, Piazza Manci, 17, 38050, Povo, (TN), Italy

    Corrado Priami

  2. LFCS, University of Edinburgh,  

    Gordon Plotkin

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Kuttler, C. (2006). Simulating Bacterial Transcription and Translation in a Stochastic π Calculus. In: Priami, C., Plotkin, G. (eds) Transactions on Computational Systems Biology VI. Lecture Notes in Computer Science(), vol 4220. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11880646_6

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  • DOI: https://doi.org/10.1007/11880646_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-45779-4

  • Online ISBN: 978-3-540-46236-1

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