Scaling up genetic circuit design for cellular computing: advances and prospects

Abstract

Synthetic biology aims to engineer and redesign biological systems for useful real-world applications in biomanufacturing, biosensing and biotherapy following a typical design-build-test cycle. Inspired from computer science and electronics, synthetic gene circuits have been designed to exhibit control over the flow of information in biological systems. Two types are Boolean logic inspired TRUE or FALSE digital logic and graded analog computation. Key principles for gene circuit engineering include modularity, orthogonality, predictability and reliability. Initial circuits in the field were small and hampered by a lack of modular and orthogonal components, however in recent years the library of available parts has increased vastly. New tools for high throughput DNA assembly and characterization have been developed enabling rapid prototyping, systematic in situ characterization, as well as automated design and assembly of circuits. Recently implemented computing paradigms in circuit memory and distributed computing using cell consortia will also be discussed. Finally, we will examine existing challenges in building predictable large-scale circuits including modularity, context dependency and metabolic burden as well as tools and methods used to resolve them. These new trends and techniques have the potential to accelerate design of larger gene circuits and result in an increase in our basic understanding of circuit and host behaviour.

An expanded library of orthogonal split inteins enables modular multi-peptide assemblies

“…18). Thus, the seven split inteins tested were validated to be able to implement Boolean logic computation in vivo 37 .…”

Trade-offs in Robustness to Perturbations of Bacterial Population Controllers

“…We showed that, in this controller architecture, there is a trade-off between robustness to environmental disturbances and robustness to perturbations in available resources to the genetic circuit. Placing different genetic circuit components in multiple cells has been proposed as a possible solution to relieve some resource sharing effects for larger genetic circuits [15], [21], [32]. However, our analysis shows that when fluctuations in cellular resources are considered, it is not possible to tune the population controller to be both robust to extracellular disturbances and to intracellular disturbances.…”

A Novel Eukaryote‐Like CRISPR Activation Tool in Bacteria: Features and Capabilities

“…In synthetic biology, the digital response is a property that is helpful in signal amplification and cascade control, [ 64–66 ] and is frequently achieved by the introduction of a positive feedback loop that steepens the response curve. [ 67–71 ] Construction of such loops using CRISPRa in bacteria has long been a challenge due to insufficient dynamic range and limitation of high basal expression. Since our CRISPRa overcame such issues, we were able to implement a positive feedback loop to achieve a digital response.…”