Gene rgulation in the pi clculus: Simulating cooperativity at the lambda switch

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4230 LNBI, Issue , 2006, Pages 24-55

  Kuttler, Céline ^a,c   Niehren, Joachim ^b,c,d  

^a CNRS   (France)

^b INRIA   (France)

^c UNIV LILLE   (France)

^d ECOLE CENTRALE DE LILLE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; MATHEMATICAL MODELS; PARAMETER ESTIMATION; RANDOM PROCESSES;

CONCURRENT PROGRAMMING; GENE RGULATION; TRANSCRIPTION INITIATION;

COMPUTATION THEORY;

EID: 38149103597     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11905455_2     Document Type: Conference Paper

References (47)

1. Gary K. Ackers, Alexander D. Johnson, and Madeline A. Shea. Quantitative model for gene regulation by A phage repressor. Proceedings of the National Academy of Sciences USA, 79(4):1129-1133, February 1982.
2. Adam Arkin, John Ross, and Harley H. McAdams. Stochastic kinetic analysis of developmental pathway bifurcation in phage A-infected Escherichia coli cells. Genetics, 149:1633-1648, 1998.
3. Erik Aurell, Stanley Brown, Johan Johanson, and Kim Sneppen. Stability puzzles in phage λ. Physical Review E, 65:051914, 2002.
4. Kristoffer Baek, Sine Svenningsen, Harvey Eisen, Kim Sneppen, and Stanley Brown. Single-cell analysis of A immunity regulation. Journal of Molecular Biology, 334(3) :363-372, 2003.
5. Audun Bakk. Transcriptional activation mechanisms of the PRM promoter of A phage. Biophysical Chemistry, 114(2-3) :229-234, 2005.
6. Otto G. Berg, Robert B. Winter, and Peter H. von Hippel. Diffusion-driven mechanisms of protein translocation on nucleic acids: 1 - models and theory. Biochemistry, 20:6929-6948, 1981.
7. J. M. Bower and H. Bolouri, editors. Computational Modeling of Genetic and Biochemical Networks. MIT Press, 2001.
8. Ralf Bundschuh, F. Hayot, and C. Jayaprakash. The role of dimerization in noise reduction of simple genetic networks. Journal of Theoretical Biology, 220:261-269, 2003.
9. Ian B. Dodd, A.J. Perkins, D. Tsemitsidis, and J.B. Egan. Octamerization of CI repressor is needed for effective repression of PRM and efficient switching from lysogeny. Genes & Development, 15:3013-3022, 2001.
10. Ian B Dodd, Keith E Shearwin, and J Barry Egan. Revisited gene regulation in bacteriophage A. Current Opinion in Genetics & Development, 15(2): 145-152, 2005.
11. Ian B. Dodd, Keith E. Shearwin, Alison J. Perkins, Tom Burr, Ann Hochschild, and J. Barry Egan. Cooperativity in long-range gene regulation by the lambda CI repressor. Genes Dev., 18(3):344-354, 2004.
12. Johan Elf and Mans Ehrenberg. What makes ribosome-mediated trascriptional attenuation sensitive to amino acid limitation? PLoS Computational Biology, 1(1):14-23, 2005.
13. Harley Lodish et al. Molecular Cell Biology. Freeman, 2003.
14. Daniel T. Gillespie. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics, 22:403-434, 1976.
15. Jeff Hasty, David McMillen, Farren Isaacs, and James J. Collins. Computational studies of gene regulatory networks: In numero molecular biology. Nature Reviews Genetics, 2:268-279, 2001.
16. DK Hawley, AD Johnson, and WR McClure. Functional and physical characterization of transcription initiation complexes in the bacteriophage lambda OR region. J. Biol. Chem., 260(14):8618-8626, 1985.
17. D.K. Hawley and W.R. McClure. The effect of a lambda repressor mutation on the activation of transcription initiation from the lambda PRM promoter. Cell, 32:327-333, 1983.
18. Jane Hillston. A Compositional Approach to Performance Modelling. PhD thesis, University of Edinburgh, 1995. Distinguished Dissertations Series. Cambridge University Press, 1996.
19. T. Ideker, T. Galitski, and L. Hood. A new approach to decoding life: systems biology. Annual Review of Genomics and Human Genetics, 2(343), 2001.
20. A D Johnson, A R Poteete, G Lauer, R T Sauer, G K Ackers, and M Ptashne. λ repressor and Cro - components of an efficient molecular switch. Nature, 294(5838):217-223, 1981.
21. Andrzej M. Kierzek, Jolanta Zaim, and P. Zielenkiewicz. The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression. Journal of Biological Chemistry, 276:8165-8172, 2001.
22. R. Biochemistry, 31:57-65, 1992.
23. Céline Kuttler. Bacterial transcription in the pi calculus. In 3rd International Workshop on Computational Methods in Systems Biology, 2005.
24. Mei Li, W.R. McClure, and M. M. Susskind. Changing the mechanism of transcriptional activation by phage A repressor. Proceedings of the National Academy of Sciences USA, 94:3691-3696, 1997.
25. William R. McClure. Mechanism and control of transcription initiation in prokaryotes. Annual Review Biochemistry, 54:171-204, 1985.
26. R3 and autegeneous negative control by repressor. J. Mol. Biol., pages 19-205, 1980.
27. Christine B. Michalowski and John W. Little. Postitive autoregulation of ci is a dispensable feature of the phage λ gene regulatory circuitry. J. Bacteriol., 187(18):64, 2005.
28. Robin Milner. Communicating and Mobile Systems: the π-calculus. Cambridge University Press, 1999.
29. Robin Milner, Joachim Parrow, and David Walker. A calculus of mobile processes (I and II). Information and Computation, 100:1-77, 1992.
30. Isabella Moll, Go Hirokawa, Michael C. Kiel, Akira Kaji, and Udo Bläsi. Translation initiation with 70S ribosomes: an alternative pathway for leaderless mRNAs. Nucl. Acids Res., 32(11):3354-3363, 2004.
31. Amos B. Oppenheim, Oren Kobiler, Joel Stavans, Donald L. Court, and Sankar Adhya. Switches in bacteriophage lambda development. Annual Reviews Genetics, 39:409-429, 2005.
32. Andrew Phillips and Luca Cardelli. A correct abstract machine for the stochastic pi-calculus. Transactions on Computational Systems Biology, 2005. to appear.
33. Corrado Priami. Stochastic π-calculus. Computer Journal, 6:578-589, 1995.
34. Corrado Priami, Aviv Regev, Ehud Shapiro, and William Silverman. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters, 80:25-31, 2001.
35. Mark Ptashne. A Genetic Switch: Phage Lambda Revisited. Cold Spring Harbor Laboratory Press, 3rd edition, 2004.
36. Mark Ptashne and Alexander Gann. Genes and Signals. Cold Spring Harbor Laboratory Press, 2002.
37. Aviv Regev. Computational Systems Biology: A Calculus for Biomolecular Knowledge. Tel Aviv University, 2002. PhD thesis.
38. Aviv Regev and Ehud Shapiro. Cells as computation. Nature, 419:343, 2002.
39. Aviv Regev and Ehud Shapiro. The π-calculus as an abstraction for biomolecular systems. In Gabriel Ciobanu and Grzegorz Rozenberg, editors, Modelling in Molecular Biology. Springer, 2004.
40. Bernard Révet, Brigitte von Wilcken-Bergmann, Heike Bessert, Andrew Barker, and Benno Müller-Hill. Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances. Current Biology, 9(3):151-154, 1999.
41. R control system of bacteriophage lambda: A physical-chemical model for gene regulation. Molecular Biology, 181:211-230, 1985.
42. C. S. Shean and M. E. Gottesman. Translation of the prophage λ cI transcript. Cell, 70(3):513-522, 1992.
43. Michael Slutsky and Leonid A. Mirny. Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential. Biophys. J., 87(6):4021-4035, 2004.
44. Kim Sneppen and Giovanni Zocchi. Physics in Molecular Biology. Cambridge University Press, 2005.
45. Sine L. Svenningsen, Nina Costantino, Donald L. Court, and Sankar Adhya. On the role of Cro in A prophage induction. Proceedings of the National Academy of Sciences USA, 102(12):4465-4469, 2005.
46. Jose MG Vilar and Leonor Saiz. DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise. Current Opinion in Genetics & Development, 15:1-9, 2005.
47. Rolf Wagner, Transcription Regulation in Prokaryotes. Oxford University Press, 2000.