More Like this

1. Engineering Genetic Circuits: Advancements in Genetic Design Automation Tools and Standards for Synthetic Biology

   https://doi.org/10.1016/j.mib.2022.102155  

   Buecherl, Lukas ; Myers, Chris J. ( May 2022 , Current opinion in microbiology)

   Takano, Eriko ; Breitling, Rainer (Ed.)

   Synthetic biology is a field at the intersection of biology and engineering. Inspired by engineering principles, researchers use defined parts to build functionally defined biological circuits. Genetic design automation allows scientists to design, model, and analyze their genetic circuits in silico before building them in the lab, saving time and resources in the process. Establishing synthetic biology’s future is dependent on genetic design automation, since the computational approach opens the field to a broad, interdisciplinary community. However, challenges with part libraries, standards, and software tools are currently stalling progress in the field. This review first covers re- cent advancements in genetic design automation, followed by an assessment of the challenges ahead, and a proposed automated genetic design workflow for the future. 

   more » « less
2. Quantitative characterization of recombinase-based digitizer circuits enables predictable amplification of biological signals

   https://doi.org/10.1038/s42003-021-02325-5  

   Kiwimagi, Katherine A. ; Letendre, Justin H. ; Weinberg, Benjamin H. ; Wang, Junmin ; Chen, Mingzhe ; Watanabe, Leandro ; Myers, Chris J. ; Beal, Jacob ; Wong, Wilson W. ; Weiss, Ron ( July 2021 , Communications Biology)

   Many synthetic gene circuits are restricted to single-use applications or require iterative refinement for incorporation into complex systems. One example is the recombinase-based digitizer circuit, which has been used to improve weak or leaky biological signals. Here we present a workflow to quantitatively define digitizer performance and predict responses to different input signals. Using a combination of signal-to-noise ratio (SNR), area under a receiver operating characteristic curve (AUC), and fold change (FC), we evaluate three small-molecule inducible digitizer designs demonstrating FC up to 508x and SNR up to 3.77 dB. To study their behavior further and improve modularity, we develop a mixed phenotypic/mechanistic model capable of predicting digitizer configurations that amplify a synNotch cell-to-cell communication signal (Δ SNR up to 2.8 dB). We hope the metrics and modeling approaches here will facilitate incorporation of these digitizers into other systems while providing an improved workflow for gene circuit characterization.

    

   more » « less
3. Genetic Circuits for Feedback Control of Gamma-Aminobutyric Acid Biosynthesis in Probiotic Escherichia coli Nissle 1917

   https://doi.org/10.3390/metabo14010044  

   Lebovich, Matthew ; Lora, Marcos A. ; Gracia-David, Jared ; Andrews, Lauren B. ( January 2024 , Metabolites)

   Engineered microorganisms such as the probiotic strain Escherichia coli Nissle 1917 (EcN) offer a strategy to sense and modulate the concentration of metabolites or therapeutics in the gastrointestinal tract. Here, we present an approach to regulate the production of the depression-associated metabolite gamma-aminobutyric acid (GABA) in EcN using genetic circuits that implement negative feedback. We engineered EcN to produce GABA by overexpressing glutamate decarboxylase and applied an intracellular GABA biosensor to identify growth conditions that improve GABA biosynthesis. We next employed characterized genetically encoded NOT gates to construct genetic circuits with layered feedback to control the rate of GABA biosynthesis and the concentration of GABA produced. Looking ahead, this approach may be utilized to design feedback control of microbial metabolite biosynthesis to achieve designable smart microbes that act as living therapeutics.

    

   more » « less
4. Robustness of networked systems to unintended interactions with application to engineered genetic circuits

   https://doi.org/10.1109/tcns.2021.3078144  

   Qian, Yili ; Del Vecchio, Domitilla ( May 2021 , IEEE Transactions on Control of Network Systems)

   null (Ed.)

   A networked dynamical system is composed of subsystems interconnected via prescribed interactions. In many engineering applications, however, one subsystem can also affect others via unintended interactions that can significantly change the intended network's behavior. Although unintended interactions can be modeled as disturbance inputs to the subsystems, these disturbances depend on the network's states. Thus, a disturbance attenuation property of each subsystem is insufficient to ensure that the network is robust to unintended interactions. Here, we provide conditions on subsystem dynamics and interaction maps, such that a network is robust to unintended interactions. These conditions require that each subsystem asymptotically attenuates constant external disturbances, is monotone or near-monotone, the unintended interactions are monotone, and the prescribed interactions do not contain feedback loops. We apply this result to guide the design of resource-limited genetic circuits composed of feedback-regulated subsystems. 

   more » « less
5. Multi-layer CRISPRa/i circuits for dynamic genetic programs in cell-free and bacterial systems

   https://doi.org/10.1016/j.cels.2021.10.008  

   Tickman, Benjamin I. ; Burbano, Diego Alba ; Chavali, Venkata P. ; Kiattisewee, Cholpisit ; Fontana, Jason ; Khakimzhan, Aset ; Noireaux, Vincent ; Zalatan, Jesse G. ; Carothers, James M. ( March 2022 , Cell Systems)