Synthetic metabolic computation in a bioluminescence-sensing system

Abstract

Bioluminescence is visible light produced and emitted by living cells using various biological systems (e.g. luxCDABE cassette). Today, this phenomenon is widely exploited in biological research, biotechnology and medical applications as a quantitative technique for the detection of biological signals. However, this technique has mostly been used to detect a single input only. In this work, we re-engineered the complex genetic structure of luxCDABE cassette to build a biological unit that can detect multi-inputs, process the cellular information and report the computation results. We first split the luxCDABE operon into several parts to create a genetic circuit that can compute a soft minimum in living cells. Then, we used the new design to implement an AND logic function with better performance as compared to AND logic functions based on protein-protein interactions. Furthermore, by controlling the reverse reaction of the luxCDABE cassette independently from the forward reaction, we built a comparator with a programmable detection threshold. Finally, we applied the redesigned cassette to build an incoherent feedforward loop that reduced the unwanted crosstalk between stress-responsive promoters (recA, katG). This work demonstrates the construction of genetic circuits that combine regulations of gene expression with metabolic pathways, for sensing and computing in living cells.

Quantifying the distribution of protein oligomerization degree reflects cellular information capacity

“…The common rules underlying protein oligomerization distribution can help better understand biological processes in nature and reveal new design principles of cellular architecture. The challenging tasks of synthetic biology include scale-up protein network generation and robust computation performance for living cells for use in diagnostic, therapeutic and biotechnological applications 58 – 60 . Expanding our knowledge of protein oligomerization in the context of single molecules, multimolecular networks and whole cells will contribute to new levels of understanding of the critical roles that cooperativity play in the function of complex biological systems.…”

Combating Infectious Diseases with Synthetic Biology

“…Lately, there has been an increased interest in developing genetic circuits with tunable detection thresholds which would tune and increase the performance and reliability of the outputs at desired levels. 15 , 16 Synthetic gene regulatory circuits that are able to improve the fold change activation of a target promoter have also been designed and can serve as a helpful tool when engineering living therapeutics. 15 − 17 In order to control bacteria growth at the specific target tissue, metabolic auxotrophy can be used.…”

“… 15 , 16 Synthetic gene regulatory circuits that are able to improve the fold change activation of a target promoter have also been designed and can serve as a helpful tool when engineering living therapeutics. 15 − 17 In order to control bacteria growth at the specific target tissue, metabolic auxotrophy can be used. Also, a recent study by Chien et al showed a design of different biosensors that can control the growth of the bacteria at a specific organ based on pH, lactate, and oxygen signatures of the organ’s microenvironment.…”

A Photocleavable Contrast Agent for Light-Responsive MRI

“…The most prominent optical imaging technique is fluorescence imaging, which relies on the detection of light emitted from fluorescent tracers after their excitation through irradiation at an appropriate wavelength [ 11 , 12 , 13 , 14 , 15 ]. Similarly, in (bio-)luminescence imaging, light from emitting moieties is recorded as a signal, but without the need to excite the respective tracer [ 16 , 17 , 18 ]. As light is inherently absent in the human body, luminescence imaging is characterized by outstanding sensitivity and specificity, as only the externally applied imaging agents generate a signal.…”