Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics

Stochastic fluctuations affect the dynamics of biological systems. Typically, such noise causes perturbations that can permit genetic circuits to escape stable states, triggering, for example, phenotypic switching. In contrast, studies have shown that noise can surprisingly also generate new states, which exist solely in the presence of fluctuations. In those instances noise is supplied externally to the dynamical system. Here, we present a mechanism in which noise intrinsic to a simple genetic circuit effectively stabilizes a deterministically unstable state. Furthermore, this noise-induced stabilization represents a unique mechanism for a genetic timer. Specifically, we analyzed the effect of noise intrinsic to a prototypical two-component gene-circuit architecture composed of interacting positive and negative feedback loops. Genetic circuits with this topology are common in biology and typically regulate cell cycles and circadian clocks. These systems can undergo a variety of bifurcations in response to parameter changes. Simulations show that near one such bifurcation, noise induces oscillations around an unstable spiral point and thus effectively stabilizes this unstable fixed point. Because of the periodicity of these oscillations, the lifetime of the noise-dependent stabilization exhibits a polymodal distribution with multiple, well defined, and regularly spaced peaks. Therefore, the noise-induced stabilization presented here constitutes a minimal mechanism for a genetic circuit to function as a timer that could be used in the engineering of synthetic circuits.bifurcation ͉ dynamics ͉ circuit ͉ stochastic ͉ quantized cycle S tochastic fluctuations in gene expression and protein concentrations are a natural by-product of biochemical reactions in cells. Properties of this biochemical noise within genetic circuits, such as their amplitude, distribution, and propagation, have been extensively characterized (1-9). Additionally, theoretical and experimental studies have established that such noise can induce stochastic switching between distinct and stable phenotypic states (5, 10-23). Noise within genetic circuits is therefore thought to contribute to phenotypic heterogeneity in genetically identical cellular populations. It has also recently been shown experimentally that noise can trigger cellular differentiation in fruit flies and bacteria (14,17,18,24). Together, these studies establish that noise can play an active functional role in cellular processes by effectively destabilizing and thus inducing escape from stable phenotypic states.Besides its common role in destabilizing stable states, noise can also have the more counterintuitive effect of generating new stable states that do not exist in the absence of fluctuations (25). In particular, noise-induced bistability has been reported theoretically (26, 27) and experimentally (2). In those situations, one of the two stable solution branches is usually present irrespective of fluctuations, whereas the second one is purely induced by noise (28). The appeara...

Section: Effect Of Noise On Activator-repressor Circuit Dynamics Near Amentioning

confidence: 98%

A genetic timer through noise-induced stabilization of an unstable state

Turcotte

García-Ojalvo

Süel

2008

“…Synthetic gene networks, on the other hand, are rationally designed and constructed to realize core topological modules of GRN in vivo without interference from auxiliary connections. They can therefore be studied in isolation to greater detail and reveal novel insights into the design and working of biological systems and processes (15), such as gene expression noise (4,(16)(17)(18)(19)(20)(21), multistability (8,10,22), oscillations (23)(24)(25)(26), intracellular signaling (27,28), intercellular communications (29,30), and multicellular pattern formation (31,32).…”

mentioning

confidence: 99%

Engineering of regulated stochastic cell fate determination

Wu¹,

Li³

et al. 2013

157

Both microbes and multicellular organisms actively regulate their cell fate determination to cope with changing environments or to ensure proper development. Here, we use synthetic biology approaches to engineer bistable gene networks to demonstrate that stochastic and permanent cell fate determination can be achieved through initializing gene regulatory networks (GRNs) at the boundary between dynamic attractors. We realize this experimentally by linking a synthetic GRN to a natural output of galactose metabolism regulation in yeast. Combining mathematical modeling and flow cytometry, we show that our engineered systems are bistable and that inherent gene expression stochasticity does not induce spontaneous state transitioning at steady state. Mathematical analysis predicts that stochastic cell fate determination in this case can only be realized when gene expression fluctuation occurs on or near attractor basin boundaries (the points of instability). Guided by numerical simulations, experiments are designed and performed with quantitatively diverse gene networks to test model predictions, which are verified by both flow cytometry and singlecell microscopy. By interfacing rationally designed synthetic GRNs with background gene regulation mechanisms, this work investigates intricate properties of networks that illuminate possible regulatory mechanisms for cell differentiation and development that can be initiated from points of instability.

“…In the context of synthetic biology (8)(9)(10)(11)(12)(13)(14)(15), signaling represents a challenging case because pathway modification requires protein reengineering or de novo design. Both are hard tasks, but progress has been steady (1,(16)(17)(18)(19).…”

mentioning

confidence: 99%

Transplantation of prokaryotic two-component signaling pathways into mammalian cells

Hansen

Mailand

Swaminathan

et al. 2014

Significance Synthetic biology and genetic engineering would greatly benefit from engineered genetic elements that are orthogonal to the host in which they operate. Two-component signaling pathways are the prevalent signal processing modality in prokaryotes that is also found in low eukaryotes and plants but absent from vertebrate cells. Here we investigate whether the elements of prokaryotic two-component pathways are operational in mammalian cells. We find that the core biochemical processes are maintained, whereas the capacity to sense chemical ligands is diminished or obscured. We use the pathways for multiinput gene regulation and show that they can serve as a rich source of orthogonal building blocks for gene expression control in mammalian cells. Our findings open new avenues in synthetic circuit design.