Synthetic Gene Circuits

Jusiak, Barbara; Daniel, Ramiz; Farzadfard, Fahim; Nissim, Lior; Purcell, Oliver; Rubens, Jacob R.; Lu, Timothy K.

doi:10.1002/3527600906.mcb.20120068

Cited by 8 publications

(4 citation statements)

References 246 publications

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“…Many important biological processes, such as cell cycle control, use negative feedback to ensure highly robust and reliable operation. Negative feedback is employed extensively in engineered systems that need regulation: by using measurements of a system’s output to influence its input (known as closing the loop ) it is possible to reduce a system’s response time, its input–output gain, and the dependence of its response on certain system parameters and external disturbances, which makes its overall performance more robust to fluctuations in both the system’s properties and its environment. − The advantages of negative feedback in natural biological systems and in engineering have motivated researchers to implement similar features in synthetic biological systems. − The use of transcription factors to regulate expression dynamics is a long-established approach to implementing feedback; − however, this approach has potential limitations: the reliance of a closed-loop system on endogenous host proteins can result in problems with cross-talk, which arise from interference between its constituent regulators and other cellular processes . Furthermore, the resulting closed-loop system may have very low gain (depending on the repression strength of the regulating transcription factor), which is in some systems undesirable and can make tuning of downstream processes challenging.…”

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confidence: 99%

A Synthetic Recombinase-Based Feedback Loop Results in Robust Expression

et al. 2017

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Accurate control of a biological process is essential for many critical functions in biology, from the cell cycle to proteome regulation. To achieve this, negative feedback is frequently employed to provide a highly robust and reliable output. Feedback is found throughout biology and technology, but due to challenges posed by its implementation, it is yet to be widely adopted in synthetic biology. In this paper we design a synthetic feedback network using a class of recombinase proteins called integrases, which can be re-engineered to flip the orientation of DNA segments in a digital manner. This system is highly orthogonal, and demonstrates a strong capability for regulating and reducing the expression variability of genes being transcribed under its control. An excisionase protein provides the negative feedback signal to close the loop in this system, by flipping DNA segments in the reverse direction. Our integrase/excisionase negative feedback system thus provides a modular architecture that can be tuned to suit applications throughout synthetic biology and biomanufacturing that require a highly robust and orthogonally controlled output.

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confidence: 99%

A Synthetic Recombinase-Based Feedback Loop Results in Robust Expression

et al. 2017

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“…Metabolic Burden. One of the advantages of recombinase-based genetic circuits is its low metabolic burden imposed on the host cell 30 . Unlike a classic genetic circuit requiring continuous production of and action by activators or repressors to maintain the output gene expression, the output gene expression in a recombinase-based genetic circuit is determined by its DNA configuration, which is changed by DNA inversion or excision by recombinases; no further continuous recombinase supply and action is needed afterwards.…”

Section: Discussionmentioning

confidence: 99%

Logic Synthesis of Recombinase-Based Genetic Circuits

Chiu

Jiang

2016

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A synthetic approach to biology is a promising technique for various applications. Recent advancements have demonstrated the feasibility of constructing synthetic two-input logic gates in Escherichia coli cells with long-term memory based on DNA inversion induced by recombinases. Moreover, recent evidences indicate that DNA inversion mediated by genome editing tools is possible. Powerful genome editing technologies, such as CRISPR-Cas9 systems, have great potential to be exploited to implement largescale recombinase-based circuits. What remains unclear is how to construct arbitrary Boolean functions based on these emerging technologies. In this paper, we lay the theoretical foundation formalizing the connection between recombinase-based genetic circuits and Boolean functions. It enables systematic construction of any given Boolean function using recombinase-based logic gates. We further develop a methodology leveraging existing electronic design automation (EDA) tools to automate the synthesis of complex recombinase-based genetic circuits with respect to area and delay optimization. In silico experimental results demonstrate the applicability of our proposed methods as a useful tool for recombinase-based genetic circuit synthesis and optimization.The development of synthetic biology shows the feasibility to implement computing devices with DNA genetic circuits in living cells. Synthetic cellular designs often intended to implement certain functions that make cells respond to specific environmental stimuli or even change their growth and cellular development. For instance, synthetic toggle switches 1 and genetic oscillators 2-5 can be used to control cell metabolism, synthetic counters 6 can be potentially applied to the regulation of telomere length and cell aggregation, and genetic logic gates [7][8][9][10] can achieve digital computation in response to stimulus input signals. In addition to these transcription-based DNA circuits, new emerging translational mRNA circuits 11 are likely to have impact on mammalian regenerative medicine and gene therapy. Through the genetic engineering, synthetic cellular circuits are potentially useful to perform therapeutic and diagnostic functions.For some situations where noxious chemical stimuli exist for many cell generations, the computational results from the synthetic circuits in parent cells are required to be propagated to their daughter cells so that the daughter cells can save time to respond to the environmental stimuli. To achieve this transgenerational memory, one possible method is to store the computational results in separate synthetic memory devices which can be duplicated in cell divisions. In the recent work of Siuti et al.12 , a more efficient scheme for constructing synthetic cellular circuits with integrated logic and memory was proposed, where the computational result was automatically stored in the computing circuit configuration and the changes of configuration can be propagated to its descendant cells. The so-implemented circuits were built based on re...

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“…Digital computation in living cells have been widely used in synthetic biology and have been reviewed in several articles [7,8,33]. In this article, we briefly reviewed and discussed two key synthetic digital devices that were implemented in living cells.…”

Section: Noise Margin Of Digital Systems In Living Cellsmentioning

confidence: 99%

“…An outcome of these advancements is an extraordinary set of design rules and engineering tools that enable massive reprogramming of the DNA code in living organisms, including humans. This new technology, known as "synthetic biology" [6][7][8], attempts to translate engineering design principles to rational biological design [9,10], to achieve multi-signal integration and processing in living cells for diagnostic, therapeutic and biotechnological applications [11][12][13][14]. For example, living cells can be programmed to produce pharmaceutical compounds that are extremely challenging to synthesize using existing methods [11], microbiome bacteria can be programmed to detect and respond to changes in clinical homeostatis [12], and gene circuits can be engineered to identify and eliminate cancer cells [15].…”

Section: Introductionmentioning

confidence: 99%