Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli

Abstract

Analysis of the system design principles of signaling systems requires model systems where all components and regulatory interactions are known. Components of the Lac and Ntr systems were used to construct genetic circuits that display toggle switch or oscillatory behavior. Both devices contain an "activator module" consisting of a modified glnA promoter with lac operators, driving the expression of the activator, NRI. Since NRI activates the glnA promoter, this creates an autoactivated circuit repressible by LacI. The oscillator contains a "repressor module" consisting of the NRI-activated glnK promoter driving LacI expression. This circuitry produced synchronous damped oscillations in turbidostat cultures, with periods much longer than the cell cycle. For the toggle switch, LacI was provided constitutively; the level of active repressor was controlled by using a lacY mutant and varying the concentration of IPTG. This circuitry provided nearly discontinuous expression of activator.

A statistical approach reveals designs for the most robust stochastic gene oscillators

“…Interestingly the topology represented by M1 and M2 formed the basis for the robust oscillator constructed by Stricker et al 17,42 We also note the absence of the delayed negative feedback oscillator with no negative autoregulation on the repressor, which is consistent with the observation that it cannot produce sustained oscillations. 15,20,43 The last oscillator system, denoted here by M5, has also been constructed and shown to produce more stochastic behavior than the amplified negative feedback topology of M1 and M2. 17 These findings demonstrate that the modeling framework can reconstitute empirical findings in real synthetic oscillators.…”

Structure and evolution of gene regulatory networks in microbial genomes

“…Progress in sequencing technologies, high throughput experimental techniques like chromatin immunoprecipitation, and advances such as noise filters [6] and oscillators that can combine repressor functionality with that of a two-component system [3], together with improvements in measuring cellular quantities at high resolution [69], should not only enable us to design synthetic circuits for maneuvering bacterial systems [11], but also enable us to address several fundamentally unanswered questions in the years to come. Network view of transcription regulation.…”

Self-regulation in a minimal model of chemical self-replication

“…Like others, i.e., [12,19] and [38,39], we consider a simple functional form to model either repression or activation of gene transcription characterized by the values (m,n). Since genetic repression is more often observed in biochemical systems, the repression case (0,2) has been widely studied in the literature [40][41][42][43][44][45], while the activation case has been seldom used [9][10][11][12][13]. Although repression tends to stabilize a dynamical system, activation coupled with degradation can show oscillatory behavior or even complex oscillations.…”

“…In general, repression, characterized by a negative feedback, is more common in biological systems because of its tendency to stabilize the concentration of relevant metabolites [7,8]. Nevertheless, activation characterized by a positive feedback is also observed in biological systems [9][10][11][12][13], and it is considered necessary for multistability [8][9][10][11][12][13][14].…”