Qualitatively distinct phenotypes in the design space of biochemical systems

FEBS Letters

Volumn 583, Issue 24, 2009, Pages 3914-3922

  Savageau, Michael A ^a   Fasani, Rick A ^a  

^a University of California   (United States)

Author keywords

Biochemical systems theory; Fitness; Phage lambda gene circuitry; Robustness; System design principle; Tolerance

Indexed keywords

MESSENGER RNA; PROTEIN DERIVATIVE;

BIOCHEMISTRY; CELL FATE; DIMERIZATION; DNA DAMAGE; GENE MUTATION; GENE SEQUENCE; GENOTYPE PHENOTYPE CORRELATION; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; MOLECULAR DYNAMICS; MOLECULAR MODEL; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN STABILITY; QUALITATIVE ANALYSIS; REVIEW; STANDARDIZATION; SYSTEMS BIOLOGY;

BACTERIOPHAGE LAMBDA; GENE REGULATORY NETWORKS; GENOTYPE; LYSOGENY; MODELS, GENETIC; PHENOTYPE;

ENTEROBACTERIA PHAGE LAMBDA;

EID: 71149094663     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2009.10.073     Document Type: Review

References (46)

1. Homer (800-600 BC) The Odyssey, "Never, anywhere, have I seen so great a likeness in man or woman - But it is truly strange! This boy must be the son of Odysseus, Telémakhos, the child he left at home that year the Akhaian host made war on Troy" 4, 152-156.
2. Sturtevant A.H. A History of Genetics (1965), Harper and Row, New York
3. Brenner S. Genomics: The end of the beginning. Science 287 (2000) 2173-2174
4. Hlavacek W.S. How to deal with large models?. Mol. Syst. Biol. 5 (2009) 240-242
5. Daun S., Rubin J., Vodovotz Y., Roy A., Parker R., and Clermont G. An ensemble of models of the acute inflammatory response to bacterial lipopolysaccharide in rats: Results from parameter space reduction. J. Theor. Biol. 253 (2008) 843-853
6. Gutenkunst R.N., Waterfall J.J., Casey F.P., Brown K.S., Myers C.R., et al. Universally sloppy parameter sensitivities in systems biology models. PLoS Comput. Biol. 3 (2007) 1871-1878
7. Oppenheim A.B., Kobiler O., Stavans J., Court D.L., and Adhya S. Switches in bacteriophage lambda development. Annu. Rev. Genet. 39 (2005) 409-429
8. Tian T., and Burrage K. Bistability and switching in the lysis/lysogeny genetic regulatory network of bacteriophage lambda. J. Theor. Biol. 227 (2004) 229-237
9. Court D.L., Oppenheim A.B., and Adhya S. A new look at bacteriophage λ genetic networks. J. Bacteriol. 189 (2007) 298-304
10. Ptashne M. A Genetic Switch (1992), Blackwell Scientific Publications, Cambridge, UK
11. Svenningsen S.L., Costantino N., Court D.L., and Adhya S. On the role of Cro in lambda prophage induction. Proc. Natl. Acad. Sci. USA 102 (2005) 4465-4469
12. Atsumi S., and Little J.W. Role of the lytic repressor in prophage induction of phage λ as analyzed by a module-replacement approach. Proc. Natl. Acad. Sci. USA 103 (2006) 4558-4563
13. Schubert R.A., Dodd I.B., Egan J.B., and Shearwin K.E. CRO's role in the CI-CRO bistable switch is critical for λ's transition from lysogeny to lytic development. Genes Dev. 21 (2009) 2461-2472
14. Santillan M., and Mackey M.C. Why the lysogenic state of phage lambda is so stable: A mathematical modeling approach. Biophys. J. 86 (2004) 75-84
15. Vilar J.M., and Saiz L. DNA looping in gene regulation: From the assembly of macromolecular complexes to the control of transcriptional noise. Curr. Opin. Genet. Dev. 15 (2005) 136-144
16. Lou C., Yang X., Liu X., He B., and Ouyang Q. A quantitative study of λ-phage switch and its components. Biophys. J. 92 (2007) 2685-2693
17. Anderson L.M., and Yang H. DNA looping can enhance lysogenic CI transcription in phage lambda. Proc. Natl. Acad. Sci. USA 105 (2008) 5827-5832
18. Anderson, L.M. and Yang, H. (2008). A simplified model for lysogenic regulation through DNA looping. In: 30th Annual International IEEE EMBS Conference, Vancouver, British Columbia, Canada, August 20-24, pp. 607-610.
19. Aurell E., Brown S., Johanson J., and Sneppen K. Stability puzzles in phage lambda. Phys. Rev. E 65 (2002) 051914-051919
20. Aurell E., and Sneppen K. Epigenetics as a first exit problem. Phys. Rev. Lett. 88 (2002) 048101
21. Zhu X.M., Yin L., Hood L., and Ao P. Calculating biological behaviors of epigenetic states in the phage lambda life cycle. Funct. Integr. Genomics 4 (2004) 188-195
22. Dodd I.B., Perkins A.J., Tsemitsidis D., and Egan J.B. Octamerization of λ CI repressor is needed for effective repression of pRM and efficient switching from lysogeny. Genes Dev. 15 (2001) 3013-3022
23. Little J.W. The SOS regulatory system: Control of its state by the level of RecA protease. J. Mol. Biol. 167 (1983) 791-808
24. Powell M.J.D. A fast algorithm for nonlinearly constrained optimization calculations, numerical analysis. In: Watson G.A. (Ed). Lecture Notes in Mathematics vol. 630 (1978), Springer-Verlag 144-157
25. Han S.P. A globally convergent method for nonlinear programming. J. Optimiz. Theory Appl. 22 (1977) 297-309
26. Burz D., Becket D., Benson N., and Ackers G.K. Self-assembly of bacteriophage λ CI repressor: Effects of single-site mutations on the monomer-dimer equilibrium. Biochemistry 33 (1994) 8399-8405
27. Court D.L., Crombrugghe B., Adhya S., and Gottesman M. Bacteriophage lambda Hin function II. Enhanced stability of lambda messenger RNA. J. Mol. Biol. 138 (1980) 731-743
28. Sezonov G., Joseleau-Petit D., and D'Ari R. Escherichia coli Physiology in Luria-Bertani Broth. J. Bacteriol. 189 (2007) 8746-8749
29. Savageau M.A. Design principles for elementary gene circuits: Elements, methods, and examples. Chaos 11 (2001) 142-159
30. Savageau M.A., Coelho P.M.B.M., Fasani R.A., Tolla D.A., and Salvador A. Phenotypes and tolerances in the design space of biochemical systems. Proc. Natl. Acad. Sci. USA 106 (2009) 6435-6440
31. Coelho P.M.B.M., Salvador A., and Savageau M.A. Global tolerance of biochemical systems and the design of moiety-transfer cycles. PLoS Comput. Biol. 5 3 (2009) e1000319
32. Savageau M.A., and Voit E.O. Recasting nonlinear differential equations as S-systems: A canonical nonlinear form. Math. Biosci. 87 (1987) 83-115
33. Savageau M.A. Biochemical systems analysis II. The steady state solutions for an n-pool system using a power-law approximation. J. Theor. Biol. 25 (1969) 370-379
34. Savageau M.A. Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology (1976), Addison-Wesley, Reading, Mass
35. Savageau M.A. Concepts relating the behavior of biochemical systems to their underlying molecular properties. Arch. Biochem. Biophys. 145 (1971) 612-621
36. Savageau M.A. Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems. Nature 229 (1971) 542-544
37. Savageau M.A. Optimal design of feedback control by inhibition: Dynamic considerations. J. Mol. Evol. 5 (1975) 199-222
38. Salvador A. Synergism analysis of metabolic processes: II. Tensor formulation and treatment of stoichiometric constraints. Math. Biosci. 163 (2000) 131-158
39. Little J.W., Shepley D.P., and Wert D.W. Robustness of a gene regulatory circuit. EMBO J. 18 (1999) 4299-4307
40. Goebel R., Sanfelice R.G., and Teel A.R. Hybrid dynamical systems. IEEE Control Syst. Mag. 29 (2009) 28-93
41. Reichardt L., and Kaiser A.D. Control of lambda repressor synthesis. Proc. Natl. Acad. Sci. USA 68 (1971) 2185-2189
42. Kobiler O., Rokney A., Friedman N., Court D.L., Stavans J., and Oppenheim A.B. Quantitative kinetic analysis of the bacteriophage λ genetic network. Proc. Natl. Acad. Sci. USA 102 (2005) 5310-5311
43. Kourilsky P., and Knapp A. Lysogenization by bacteriophage λ. III. Multiplicity dependent phenomena occurring upon infection by λ. Biochimie 56 (1974) 1517-1523
44. Osterhout R.E., Figueroa I.A., Keasling J.D., and Arkin A.P. Global analysis of host response to induction of a latent bacteriophage. BMC Microbiol. 7 (2007) 82-93
45. Michalowski C.B., Short M.D., and Little J.W. Sequence tolerance of the phage lambda PRM promoter: Implications for evolution of gene regulatory circuitry. J. Bacteriol. 186 (2004) 7988-7999
46. Atsumi S., and Little J.W. A synthetic phage λ regulatory circuit. Proc. Natl. Acad. Sci. USA 103 (2006) 19045-19050