title: Robustness, stability and efficiency of phage lambda genetic switch: dynamical structure analysis.
abstract: Based on the dynamical structure theory for complex networks recently developed by one of us and on the physical-chemical models for gene regulation, developed by Shea and Ackers in the 1980's, we formulate a direct and concise mathematical framework for the genetic switch controlling phage lambda life cycles, which naturally includes the stochastic effect. The dynamical structure theory states that the dynamics of a complex network is determined by its four elementary components: The dissipation (analogous to degradation), the stochastic force, the driving force determined by a potential, and the transverse force. The potential may be interpreted as a landscape for the phage development in terms of attractive basins, saddle points, peaks and valleys. The dissipation gives rise to the adaptivity of the phage in the landscape defined by the potential: The phage always has the tendency to approach the bottom of the nearby attractive basin. The transverse force tends to keep the network on the equal-potential contour of the landscape. The stochastic fluctuation gives the phage the ability to search around the potential landscape by passing through saddle points. With molecular parameters in our model fixed primarily by the experimental data on wild-type phage and supplemented by data on one mutant, our calculated results on mutants agree quantitatively with the available experimental observations on other mutants for protein number, lysogenization frequency, and a lysis frequency in lysogen culture. The calculation reproduces the observed robustness of the phage lambda genetic switch. This is the first mathematical description that successfully represents such a wide variety of major experimental phenomena. Specifically, we find: (1) The explanation for both the stability and the efficiency of phage lambda genetic switch is the exponential dependence of saddle point crossing rate on potential barrier height, a result of the stochastic motion in a landscape; and (2) The positive feedback of cI repressor gene transcription, enhanced by the CI dimer cooperative binding, is the key to the robustness of the phage lambda genetic switch against mutations and fluctuations in kinetic parameter values.
authors.affiliation: GenMath, Corp. 5525 27th Ave.N.E., Seattle, WA 98105, USA.
authors.forename: X-M
authors.initials: XM
authors.lastname: Zhu
authors.forename: L
authors.initials: L
authors.lastname: Yin
authors.forename: L
authors.initials: L
authors.lastname: Hood
authors.forename: P
authors.initials: P
authors.lastname: Ao
mesh_terms: D010582:Bacteriophage lambda / Q000235:genetics*; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000235:genetics*; D015967:Gene Expression Regulation, Viral / Q000235:genetics*; D005812:Genes, Switch / Q000235:genetics*; D042822:Genomic Instability / Q000235:genetics; D008242:Lysogeny / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical; D012097:Repressor Proteins / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D014764:Viral Proteins