A novel method to analyze nucleocytoplasmic transport in vivo by using short peptide tags

Synthetic circuits that process multiple light and chemical signal inputs

Background

Multi-signal processing circuits are essential for rational design of sophisticated synthetic systems with good controllability and modularity, therefore, enable construction of high-level networks. Moreover, light-inducible systems provide fast and reversible means for spatiotemporal control of gene expression.

Results

Here, in HEK 293 cells, we present combinatory genetic circuits responding to light and chemical signals, simultaneously. We first constructed a dual input circuit converting different light intensities into varying of the sensitivity of the promoter to a chemical inducer (doxycycline). Next, we generated a ternary input circuit, which responded to light, doxycycline and cumate. This circuit allowed us to use different combinations of blue light and the two chemical inducers to generate gradual output values over two orders of magnitude.

Conclusions

Overall, in this study, we devise genetic circuits sensing and processing light and chemical inducers. Our work may provide insights into bio-computation and fine-tuning expression of the transgene.

Electronic supplementary material

The online version of this article (doi:10.1186/s12918-016-0384-y) contains supplementary material, which is available to authorized users.

Elements of the cellular metabolic structure

A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell.

A novel TetR-regulating peptide turns off rtTA-mediated activation of gene expression

Conditional regulation of gene expression is a powerful and indispensable method for analyzing gene function. The “Tet-On” system is a tool widely used for that purpose. Here, the transregulator rtTA mediates expression of a gene of interest after addition of the small molecule effector doxycycline. Although very effective in rapidly turning on gene expression, the system is hampered by the long half-life of doxycycline which makes shutting down gene expression rapidly very difficult to achieve. We isolated an rtTA-binding peptide by in vivo selection that acts as a doxycycline antagonist and leads to rapid and efficient shut down of rtTA-mediated reporter gene expression in a human cell line. This peptide represents the basis for novel effector molecules which complement the “Tet-system” by enabling the investigator to rapidly turn gene expression not just on at will, but now also off.