Modeling the role of cyclic AMP in catabolite repression of inducible enzyme biosynthesis in microbial cells

Structured model of genetic control via the lac promoter in Escherichia coli

A model that describes induction of protein synthesis from lac-based promoters has been developed and incorporated into the single-cell model of Escherichia coli with transcriptional and translational modifications. Unlike previous models of lac-based promoters, this model allows a priori prediction of the intracellular parameters controlling transcription from lac-based promoters with only the extracellular levels of substrate and inducer as inputs. Because of the structural detail of the model, it is possible to simulate different genetic constructions for comparison, such as Lacl(q) strains versus wild-type cells, or including lacl on a multicopy plasmid. Expression from lac to tac promoters is predicted to yield 5% and 30% of the total cellular protein, respectively, with a pBR322-type plasmid. The model predicts the experimental observation that the Lacl(q) strain is not as fully induced as the wild-type strains, even at higher inducer concentrations. Additionally, the model predicts the right order of magnitude of protein production from lac and tac promoters when mechanisms for attenuation of transcription at lower translational efficiency are considered. Finally, the model predicts that for high copy number systems ribosomes become limiting in the synthesis of plasmid-encoded proteins. (c) 1994 John Wiley & Sons, Inc.

Dynamics of induced CAT expression in E. coli

The dynamics of chemically induced chloramphenicolaceyl-transferase (CAT) expression are determined in batch cultures of Escherichia coli DH5alphaF'IQ [pKK262-1]. This article is directed towards understanding the coupling of induced cloned-protein synthesis and reduced cell growth which are balanced in the optimal system. Experimental results indicate that the best inducer (IPTG) concentration is near 1.0 mM when added during midexponential growth. Lower concentrations cause only weak induction, whereas higher concentrations cause sufficiently strong induction that cell growth is suppressed. Induction at the onset of the stationary phase results in high expression but is accompanied by stimulated protease activity. Also, cell mass yield is adversely affected by enhanced protein synthesis. A structured metabolic model is shown to predict the responses of instantaneous growth rate and productivity which result from protein overexpression. This model can be employed to predict alternative reactor strategies and operating conditions necessary for the design of efficient bioprocess.

Comparison of deterministic and stochastic models of the lac operon genetic network

The lac operon has been a paradigm for genetic regulation with positive feedback, and several modeling studies have described its dynamics at various levels of detail. However, it has not yet been analyzed how stochasticity can enrich the system's behavior, creating effects that are not observed in the deterministic case. To address this problem we use a comparative approach. We develop a reaction network for the dynamics of the lac operon genetic switch and derive corresponding deterministic and stochastic models that incorporate biological details. We then analyze the effects of key biomolecular mechanisms, such as promoter strength and binding affinities, on the behavior of the models. No assumptions or approximations are made when building the models other than those utilized in the reaction network. Thus, we are able to carry out a meaningful comparison between the predictions of the two models to demonstrate genuine effects of stochasticity. Such a comparison reveals that in the presence of stochasticity, certain biomolecular mechanisms can profoundly influence the region where the system exhibits bistability, a key characteristic of the lac operon dynamics. For these cases, the temporal asymptotic behavior of the deterministic model remains unchanged, indicating a role of stochasticity in modulating the behavior of the system.

Kinetics of product formation and plasmid segregation in recombinant microbial populations

Experimental and mathematical analysis of productivity of cultures containing recombinant plasmids is based in this work on the following paradigm: molecular controls leads to single cell kinetics leads to cell population dynamics leads to reactor productivity. Mathematical models have been developed for replication control of the lambda dv plasmid and for efficiency of the lac promoter-operator based on the molecular control mechanisms of these systems in Escherichia coli. A special and important attribute of these models is their ability to describe quantitatively a wide range of genetic effects as well as environmental influences on molecular control function. Equations describing plasmid maintenance and distribution in growing cell cultures have been determined based on the population-balance equations applicable to a segregated culture model. The washout dilution rate for continuous cultivation of plasmid-containing Saccharomyces cerevisiae in selective medium is given in terms of single-cell division-cycle parameters and plasmid copy number for one single-cell model of plasmid replication and segregation. A new experimental method based on flow cytometry for rapid characterization of heterogeneity of single-cell accumulation of a plasmid gene product is also described. Generalization of these methods and of the overall strategy should provide a useful framework for synthesis of biological and engineering principles and methods to optimize organisms and processes based on recombinant DNA technology.