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Jung JK, Dreyer KS, Dray KE, Muldoon JJ, George J, Shirman S, Cabezas MD, D’Aquino AE, Verosloff MS, Seki K, Rybnicky GA, Alam KK, Bagheri N, Jewett MC, Leonard JN, Mangan NM, Lucks JB. Developing, characterizing and modeling CRISPR-based point-of-use pathogen diagnostics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601853. [PMID: 39005318 PMCID: PMC11244977 DOI: 10.1101/2024.07.03.601853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Recent years have seen intense interest in the development of point-of-care nucleic acid diagnostic technologies to address the scaling limitations of laboratory-based approaches. Chief among these are combinations of isothermal amplification approaches with CRISPR-based detection and readouts of target products. Here, we contribute to the growing body of rapid, programmable point-of-care pathogen tests by developing and optimizing a one-pot NASBA-Cas13a nucleic acid detection assay. This test uses the isothermal amplification technique NASBA to amplify target viral nucleic acids, followed by Cas13a-based detection of amplified sequences. We first demonstrate an in-house formulation of NASBA that enables optimization of individual NASBA components. We then present design rules for NASBA primer sets and LbuCas13a guide RNAs for fast and sensitive detection of SARS-CoV-2 viral RNA fragments, resulting in 20 - 200 aM sensitivity without any specialized equipment. Finally, we explore the combination of high-throughput assay condition screening with mechanistic ordinary differential equation modeling of the reaction scheme to gain a deeper understanding of the NASBA-Cas13a system. This work presents a framework for developing a mechanistic understanding of reaction performance and optimization that uses both experiments and modeling, which we anticipate will be useful in developing future nucleic acid detection technologies.
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Affiliation(s)
- Jaeyoung K. Jung
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Center for Water Research, Northwestern University (Evanston, IL, USA)
| | - Kathleen S. Dreyer
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
| | - Kate E. Dray
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
| | - Joseph J. Muldoon
- Department of Medicine, University of California, San Francisco (San Francisco, CA, USA)
- Gladstone-UCSF Institute of Genomic Immunology (San Francisco, CA, USA)
| | - Jithin George
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Department of Engineering Sciences and Applied Mathematics, Northwestern University (Evanston, IL, USA)
- NSF-Simons Center for Quantitative Biology, Northwestern University (Evanston, IL, USA)
| | - Sasha Shirman
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- NSF-Simons Center for Quantitative Biology, Northwestern University (Evanston, IL, USA)
| | - Maria D. Cabezas
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Department of Biomedical Engineering, Northwestern University (Evanston, IL, USA)
| | - Anne E. D’Aquino
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Stemloop, Inc. (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
| | - Matthew S. Verosloff
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
| | - Kosuke Seki
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
| | - Grant A. Rybnicky
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
- Chemistry of Life Processes Institute, Northwestern University (Evanston, IL, USA)
| | | | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
- Departments of Biology and Chemical Engineering, University of Washington (Seattle, WA, USA)
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Department of Bioengineering, Stanford University (Stanford, CA)
| | - Joshua N. Leonard
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
| | - Niall M. Mangan
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Department of Engineering Sciences and Applied Mathematics, Northwestern University (Evanston, IL, USA)
- NSF-Simons Center for Quantitative Biology, Northwestern University (Evanston, IL, USA)
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Center for Water Research, Northwestern University (Evanston, IL, USA)
- Chemistry of Life Processes Institute, Northwestern University (Evanston, IL, USA)
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2
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Kell B, Ripsman R, Hilfinger A. Noise properties of adaptation-conferring biochemical control modules. Proc Natl Acad Sci U S A 2023; 120:e2302016120. [PMID: 37695915 PMCID: PMC10515136 DOI: 10.1073/pnas.2302016120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/12/2023] [Indexed: 09/13/2023] Open
Abstract
A key goal of synthetic biology is to develop functional biochemical modules with network-independent properties. Antithetic integral feedback (AIF) is a recently developed control module in which two control species perfectly annihilate each other's biological activity. The AIF module confers robust perfect adaptation to the steady-state average level of a controlled intracellular component when subjected to sustained perturbations. Recent work has suggested that such robustness comes at the unavoidable price of increased stochastic fluctuations around average levels. We present theoretical results that support and quantify this trade-off for the commonly analyzed AIF variant in the idealized limit with perfect annihilation. However, we also show that this trade-off is a singular limit of the control module: Even minute deviations from perfect adaptation allow systems to achieve effective noise suppression as long as cells can pay the corresponding energetic cost. We further show that a variant of the AIF control module can achieve significant noise suppression even in the idealized limit with perfect adaptation. This atypical configuration may thus be preferable in synthetic biology applications.
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Affiliation(s)
- Brayden Kell
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ONL5L 1C6, Canada
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
- National Science Foundation-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL60208
| | - Ryan Ripsman
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Andreas Hilfinger
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ONL5L 1C6, Canada
- Department of Mathematics, University of Toronto, Toronto, ONM5S 2E4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ONM5S 3G5, Canada
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3
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Alexis E, Schulte CCM, Cardelli L, Papachristodoulou A. Regulation strategies for two-output biomolecular networks. J R Soc Interface 2023; 20:20230174. [PMID: 37528680 PMCID: PMC10394417 DOI: 10.1098/rsif.2023.0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/06/2023] [Indexed: 08/03/2023] Open
Abstract
Feedback control theory facilitates the development of self-regulating systems with desired performance which are predictable and insensitive to disturbances. Feedback regulatory topologies are found in many natural systems and have been of key importance in the design of reliable synthetic bio-devices operating in complex biological environments. Here, we study control schemes for biomolecular processes with two outputs of interest, expanding previously described concepts based on single-output systems. Regulation of such processes may unlock new design possibilities but can be challenging due to coupling interactions; also potential disturbances applied on one of the outputs may affect both. We therefore propose architectures for robustly manipulating the ratio/product and linear combinations of the outputs as well as each of the outputs independently. To demonstrate their characteristics, we apply these architectures to a simple process of two mutually activated biomolecular species. We also highlight the potential for experimental implementation by exploring synthetic realizations both in vivo and in vitro. This work presents an important step forward in building bio-devices capable of sophisticated functions.
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Affiliation(s)
- Emmanouil Alexis
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Carolin C. M. Schulte
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Luca Cardelli
- Department of Computer Science, University of Oxford, Oxford OX1 3QD, UK
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4
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Rhea KA, McDonald ND, Cole SD, Noireaux V, Lux MW, Buckley PE. Variability in cell-free expression reactions can impact qualitative genetic circuit characterization. Synth Biol (Oxf) 2022; 7:ysac011. [PMID: 35966404 PMCID: PMC9365049 DOI: 10.1093/synbio/ysac011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/24/2022] [Accepted: 08/01/2022] [Indexed: 09/21/2023] Open
Abstract
Cell-free expression systems provide a suite of tools that are used in applications from sensing to biomanufacturing. One of these applications is genetic circuit prototyping, where the lack of cloning is required and a high degree of control over reaction components and conditions enables rapid testing of design candidates. Many studies have shown utility in the approach for characterizing genetic regulation elements, simple genetic circuit motifs, protein variants or metabolic pathways. However, variability in cell-free expression systems is a known challenge, whether between individuals, laboratories, instruments, or batches of materials. While the issue of variability has begun to be quantified and explored, little effort has been put into understanding the implications of this variability. For genetic circuit prototyping, it is unclear when and how significantly variability in reaction activity will impact qualitative assessments of genetic components, e.g. relative activity between promoters. Here, we explore this question by assessing DNA titrations of seven genetic circuits of increasing complexity using reaction conditions that ostensibly follow the same protocol but vary by person, instrument and material batch. Although the raw activities vary widely between the conditions, by normalizing within each circuit across conditions, reasonably consistent qualitative performance emerges for the simpler circuits. For the most complex case involving expression of three proteins, we observe a departure from this qualitative consistency, offering a provisional cautionary line where normal variability may disrupt reliable reuse of prototyping results. Our results also suggest that a previously described closed loop controller circuit may help to mitigate such variability, encouraging further work to design systems that are robust to variability. Graphical Abstract.
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Affiliation(s)
- Katherine A Rhea
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Nathan D McDonald
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Stephanie D Cole
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Matthew W Lux
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Patricia E Buckley
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
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5
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Ryan J, Hong S, Foo M, Kim J, Tang X. Model-Based Investigation of the Relationship between Regulation Level and Pulse Property of I1-FFL Gene Circuits. ACS Synth Biol 2022; 11:2417-2428. [PMID: 35729788 PMCID: PMC9295143 DOI: 10.1021/acssynbio.2c00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mathematical models are powerful tools in guiding the construction of synthetic biological circuits, given their capability of accurately capturing and predicting circuit dynamics. Recent innovations in RNA technology have enabled the development of a variety of new tools for regulating gene expression at both the transcription and translation levels. However, the effects of different regulation levels on the circuit dynamics remain largely unexplored. In this study, we focus on the type 1 incoherent feed-forward loop (I1-FFL) gene circuit with four different variations (TX, TL, HY-1, HY-2), to investigate how regulation at the transcription and translation levels affect the circuit dynamics. We develop a mechanistic model for each of the four circuits and deploy sensitivity analysis to investigate the circuits' dynamics in terms of pulse generation. Based on the analysis, we observe that the repression regulation mechanism dominates the characteristics of the pulse as compared to the activation regulation mechanism and find that the I1-FFL with transcription repression has a higher chance of generating a pulse meeting the desired criteria. The experimental results in Escherichia coli also confirm our findings from the computational analysis. We expect our findings to facilitate future experimental construction of gene circuits with insights on the selection of appropriate transcription and translation regulation tools.
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Affiliation(s)
- Jordan Ryan
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Seongho Hong
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Mathias Foo
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Xun Tang
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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6
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Khan A, Saha G, Pal RK. Controlling the Effects of External Perturbations on a Gene Regulatory Network Using Proportional-Integral-Derivative Controller. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1531-1544. [PMID: 33206608 DOI: 10.1109/tcbb.2020.3039038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Gene regulatory networks are biologically robust, which imparts resilience to living systems against most external perturbations affecting them. However, there is a limit to this and disturbances beyond this limit can impart unwanted signalling on one or more master regulators in a network. Certain disturbances may affect the functioning of other constituent genes of the same network. In most cases, this phenomenon can have some effect on the functioning of the living organism. In this investigation, we have proposed a methodology to mitigate the effects of external perturbations on a genetic network using a proportional-integral-derivative controller. The proposed controller has been used to perturb one or more of the other unaffected master regulators such that the most affected gene/s of the network revert to their normal state. The only required condition of such type of manoeuvring is that there should be multiple master regulators in a network. The proposed technique has been experimented on a 10-gene DREAM4 benchmark network and also on a larger 20-gene network, where only downregulation has been considered due to data constraints. Simulation results indicate that the most vulnerable genes can be reverted to their normal expression levels in 10 out of the 16 simulations performed.
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7
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Sootla A, Delalez N, Alexis E, Norman A, Steel H, Wadhams GH, Papachristodoulou A. Dichotomous feedback: a signal sequestration-based feedback mechanism for biocontroller design. J R Soc Interface 2022; 19:20210737. [PMID: 35440202 PMCID: PMC9019519 DOI: 10.1098/rsif.2021.0737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We introduce a new design framework for implementing negative feedback regulation in synthetic biology, which we term ‘dichotomous feedback’. Our approach is different from current methods, in that it sequesters existing fluxes in the process to be controlled, and in this way takes advantage of the process’s architecture to design the control law. This signal sequestration mechanism appears in many natural biological systems and can potentially be easier to realize than ‘molecular sequestration’ and other comparison motifs that are nowadays common in biomolecular feedback control design. The loop is closed by linking the strength of signal sequestration to the process output. Our feedback regulation mechanism is motivated by two-component signalling systems, where a second response regulator could be competing with the natural response regulator thus sequestering kinase activity. Here, dichotomous feedback is established by increasing the concentration of the second response regulator as the level of the output of the natural process increases. Extensive analysis demonstrates how this type of feedback shapes the signal response, attenuates intrinsic noise while increasing robustness and reducing crosstalk.
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Affiliation(s)
- Aivar Sootla
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Nicolas Delalez
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Emmanouil Alexis
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Arthur Norman
- Department of Biochemistry, University of Oxford, Oxford OX1 3PJ, UK
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - George H Wadhams
- Department of Biochemistry, University of Oxford, Oxford OX1 3PJ, UK
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8
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Dray KE, Muldoon JJ, Mangan NM, Bagheri N, Leonard JN. GAMES: A Dynamic Model Development Workflow for Rigorous Characterization of Synthetic Genetic Systems. ACS Synth Biol 2022; 11:1009-1029. [PMID: 35023730 PMCID: PMC9097825 DOI: 10.1021/acssynbio.1c00528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mathematical modeling is invaluable for advancing understanding and design of synthetic biological systems. However, the model development process is complicated and often unintuitive, requiring iteration on various computational tasks and comparisons with experimental data. Ad hoc model development can pose a barrier to reproduction and critical analysis of the development process itself, reducing the potential impact and inhibiting further model development and collaboration. To help practitioners manage these challenges, we introduce the Generation and Analysis of Models for Exploring Synthetic Systems (GAMES) workflow, which includes both automated and human-in-the-loop processes. We systematically consider the process of developing dynamic models, including model formulation, parameter estimation, parameter identifiability, experimental design, model reduction, model refinement, and model selection. We demonstrate the workflow with a case study on a chemically responsive transcription factor. The generalizable workflow presented in this tutorial can enable biologists to more readily build and analyze models for various applications.
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Affiliation(s)
- Kate E. Dray
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Joseph J. Muldoon
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Niall M. Mangan
- Engineering Sciences and Applied Mathematics Program, Northwestern University, Evanston, IL 60208, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA.,Departments of Biology and Chemical Engineering, University of Washington, Seattle, WA 98195, USA.,Co-corresponding authors: Joshua N. Leonard, , Neda Bagheri,
| | - Joshua N. Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA.,Chemistry of Life Processes Institute, and Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA.,Co-corresponding authors: Joshua N. Leonard, , Neda Bagheri,
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9
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Abstract
Synthetic biology increasingly enables the construction of sophisticated functions in mammalian cells. A particularly promising frontier combines concepts drawn from industrial process control engineering-which is used to confer and balance properties such as stability and efficiency-with understanding as to how living systems have evolved to perform similar tasks with biological components. In this review, we first survey the state-of-the-art for both technologies and strategies available for genetic programming in mammalian cells. We then discuss recent progress in implementing programming objectives inspired by engineered and natural control mechanisms. Finally, we consider the transformative role of model-guided design in the present and future construction of customized mammalian cell functions for applications in biotechnology, medicine, and fundamental research.
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10
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Cetnar DP, Salis HM. Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons. ACS Synth Biol 2021; 10:318-332. [PMID: 33464822 DOI: 10.1021/acssynbio.0c00471] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
mRNA degradation is a central process that affects all gene expression levels, and yet, the determinants that control mRNA decay rates remain poorly characterized. Here, we applied a synthetic biology, learn-by-design approach to elucidate the sequence and structural determinants that control mRNA stability in bacterial operons. We designed, constructed, and characterized 82 operons in Escherichia coli, systematically varying RNase binding site characteristics, translation initiation rates, and transcriptional terminator efficiencies in the 5' untranslated region (UTR), intergenic, and 3' UTR regions, followed by measuring their mRNA levels using reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays during exponential growth. We show that introducing long single-stranded RNA into 5' UTRs reduced mRNA levels by up to 9.4-fold and that lowering translation rates reduced mRNA levels by up to 11.8-fold. We also found that RNase binding sites in intergenic regions had much lower effects on mRNA levels. Surprisingly, changing the transcriptional termination efficiency or introducing long single-stranded RNA into 3' UTRs had no effect on upstream mRNA levels. From these measurements, we developed and validated biophysical models of ribosome protection and RNase activity with excellent quantitative agreement. We also formulated design rules to rationally control a mRNA's stability, facilitating the automated design of engineered genetic systems with desired functionalities.
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11
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Cuba Samaniego C, Franco E. Ultrasensitive molecular controllers for quasi-integral feedback. Cell Syst 2021; 12:272-288.e3. [PMID: 33539724 DOI: 10.1016/j.cels.2021.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 09/22/2020] [Accepted: 01/11/2021] [Indexed: 12/24/2022]
Abstract
Feedback control has enabled the success of automated technologies by mitigating the effects of variability, unknown disturbances, and noise. While it is known that biological feedback loops reduce the impact of noise and help shape kinetic responses, many questions remain about how to design molecular integral controllers. Here, we propose a modular strategy to build molecular quasi-integral feedback controllers, which involves following two design principles. The first principle is to utilize an ultrasensitive response, which determines the gain of the controller and influences the steady-state error. The second is to use a tunable threshold of the ultrasensitive response, which determines the equilibrium point of the system. We describe a reaction network, named brink controller, that satisfies these conditions by combining molecular sequestration and an activation/deactivation cycle. With computational models, we examine potential biological implementations of brink controllers, and we illustrate different example applications.
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Affiliation(s)
- Christian Cuba Samaniego
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Elisa Franco
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA; Bioengineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; Mechanical Engineering, University of California at Riverside, Riverside, CA 92521, USA.
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12
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Gómez-Schiavon M, Dods G, El-Samad H, Ng AH. Multidimensional Characterization of Parts Enhances Modeling Accuracy in Genetic Circuits. ACS Synth Biol 2020; 9:2917-2926. [PMID: 33166452 DOI: 10.1021/acssynbio.0c00288] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mathematical models can aid the design of genetic circuits, but may yield inaccurate results if individual parts are not modeled at the appropriate resolution. To illustrate the importance of this concept, we study transcriptional cascades consisting of two inducible synthetic transcription factors connected in series. Despite the simplicity of this design, we find that accurate prediction of circuit behavior requires mapping the dose responses of each circuit component along the dimensions of both its expression level and its inducer concentration. Using this multidimensional characterization, we were able to computationally explore the behavior of 16 different circuit designs. We experimentally verified a subset of these predictions and found substantial agreement. This method of biological part characterization enables the use of models to identify (un)desired circuit behaviors prior to experimental implementation, thus shortening the design-build-test cycle for more complex circuits.
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Affiliation(s)
- Mariana Gómez-Schiavon
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, United States
| | - Galen Dods
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, United States
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, United States
- Chan−Zuckerberg Biohub, San Francisco, California 94158, United States
- Cell Design Institute, University of California, San Francisco, San Francisco, California 94158, United States
| | - Andrew H. Ng
- Cell Design Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94158, United States
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13
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Müller J, Siemann-Herzberg M, Takors R. Modeling Cell-Free Protein Synthesis Systems-Approaches and Applications. Front Bioeng Biotechnol 2020; 8:584178. [PMID: 33195146 PMCID: PMC7655533 DOI: 10.3389/fbioe.2020.584178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/29/2020] [Indexed: 01/03/2023] Open
Abstract
In vitro systems are ideal setups to investigate the basic principles of biochemical reactions and subsequently the bricks of life. Cell-free protein synthesis (CFPS) systems mimic the transcription and translation processes of whole cells in a controlled environment and allow the detailed study of single components and reaction networks. In silico studies of CFPS systems help us to understand interactions and to identify limitations and bottlenecks in those systems. Black-box models laid the foundation for understanding the production and degradation dynamics of macromolecule components such as mRNA, ribosomes, and proteins. Subsequently, more sophisticated models revealed shortages in steps such as translation initiation and tRNA supply and helped to partially overcome these limitations. Currently, the scope of CFPS modeling has broadened to various applications, ranging from the screening of kinetic parameters to the stochastic analysis of liposome-encapsulated CFPS systems and the assessment of energy supply properties in combination with flux balance analysis (FBA).
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Affiliation(s)
| | | | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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14
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Abstract
Integral feedback control is commonly used in mechanical and electrical systems to achieve zero steady-state error following an external disturbance. Equivalently, in biological systems, a property known as robust perfect adaptation guarantees robustness to environmental perturbations and return to the pre-disturbance state. Previously, Briat et al proposed a biomolecular design for integral feedback control (robust perfect adaptation) called the antithetic feedback motif. The antithetic feedback controller uses the sequestration binding reaction of two biochemical species to record the integral of the error between the current and the desired output of the network it controls. The antithetic feedback motif has been successfully built using synthetic components in vivo in Escherichia coli and Saccharomyces cerevisiae cells. However, these previous synthetic implementations of antithetic feedback have not produced perfect integral feedback control due to the degradation and dilution of the two controller species. Furthermore, previous theoretical results have cautioned that integral control can only be achieved under stability conditions that not all antithetic feedback motifs necessarily fulfill. In this paper, we study how to design antithetic feedback motifs that simultaneously achieve good stability and small steady-state error properties, even as the controller species are degraded and diluted. We provide simple tuning guidelines to achieve flexible and practical synthetic biological implementations of antithetic feedback control. We use several tools and metrics from control theory to design antithetic feedback networks, paving the path for the systematic design of synthetic biological controllers.
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Affiliation(s)
- Ania-Ariadna Baetica
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, Box 2542, San Francisco, CA 94158, United States of America
| | - Yoke Peng Leong
- Department of Control and Dynamical Systems, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, United States of America
| | - Richard M Murray
- Department of Control and Dynamical Systems, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, United States of America.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States of America
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15
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Laohakunakorn N. Cell-Free Systems: A Proving Ground for Rational Biodesign. Front Bioeng Biotechnol 2020; 8:788. [PMID: 32793570 PMCID: PMC7393481 DOI: 10.3389/fbioe.2020.00788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/22/2020] [Indexed: 11/13/2022] Open
Abstract
Cell-free gene expression systems present an alternative approach to synthetic biology, where biological gene expression is harnessed inside non-living, in vitro biochemical reactions. Taking advantage of a plethora of recent experimental innovations, they easily overcome certain challenges for computer-aided biological design. For instance, their open nature renders all their components directly accessible, greatly facilitating model construction and validation. At the same time, these systems present their own unique difficulties, such as limited reaction lifetimes and lack of homeostasis. In this Perspective, I propose that cell-free systems are an ideal proving ground to test rational biodesign strategies, as demonstrated by a small but growing number of examples of model-guided, forward engineered cell-free biosystems. It is likely that advances gained from this approach will contribute to our efforts to more reliably and systematically engineer both cell-free as well as living cellular systems for useful applications.
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Affiliation(s)
- Nadanai Laohakunakorn
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
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16
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Agrawal DK, Dolan EM, Hernandez NE, Blacklock KM, Khare SD, Sontag ED. Mathematical Models of Protease-Based Enzymatic Biosensors. ACS Synth Biol 2020; 9:198-208. [PMID: 32017536 DOI: 10.1021/acssynbio.9b00279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An important goal of synthetic biology is to build biosensors and circuits with well-defined input-output relationships that operate at speeds found in natural biological systems. However, for molecular computation, most commonly used genetic circuit elements typically involve several steps from input detection to output signal production: transcription, translation, and post-translational modifications. These multiple steps together require up to several hours to respond to a single stimulus, and this limits the overall speed and complexity of genetic circuits. To address this gap, molecular frameworks that rely exclusively on post-translational steps to realize reaction networks that can process inputs at a time scale of seconds to minutes have been proposed. Here, we build mathematical models of fast biosensors capable of producing Boolean logic functionality. We employ protease-based chemical and light-induced switches, investigate their operation, and provide selection guidelines for their use as on-off switches. As a proof of concept, we implement a rapamycin-induced switch in vitro and demonstrate that its response qualitatively agrees with the predictions from our models. We then use these switches as elementary blocks, developing models for biosensors that can perform OR and XOR Boolean logic computation while using reaction conditions as tuning parameters. We use sensitivity analysis to determine the time-dependent sensitivity of the output to proteolytic and protein-protein binding reaction parameters. These fast protease-based biosensors can be used to implement complex molecular circuits with a capability of processing multiple inputs controllably and algorithmically. Our framework for evaluating and optimizing circuit performance can be applied to other molecular logic circuits.
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Affiliation(s)
- Deepak K. Agrawal
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02120, United States
- Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Elliott M. Dolan
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Nancy E. Hernandez
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Kristin M. Blacklock
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Eduardo D. Sontag
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02120, United States
- Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts 02115, United States
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts 02115, United States
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17
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Agrawal DK, Marshall R, Noireaux V, Sontag ED. In vitro implementation of robust gene regulation in a synthetic biomolecular integral controller. Nat Commun 2019; 10:5760. [PMID: 31848346 PMCID: PMC6917713 DOI: 10.1038/s41467-019-13626-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022] Open
Abstract
Feedback mechanisms play a critical role in the maintenance of cell homeostasis in the presence of disturbances and uncertainties. Motivated by the need to tune the dynamics and improve the robustness of gene circuits, biological engineers have proposed various designs that mimic natural molecular feedback control mechanisms. However, practical and predictable implementations have proved challenging because of the complexity of synthesis and analysis of complex biomolecular networks. Here, we analyze and experimentally validate a synthetic biomolecular controller executed in vitro. The controller ensures that gene expression rate tracks an externally imposed reference level, and achieves this goal even in the presence of certain kinds of disturbances. Our design relies upon an analog of the well-known principle of integral feedback in control theory. We implement the controller in an Escherichia coli cell-free transcription-translation system, which allows rapid prototyping and implementation. Modeling and theory guide experimental implementation with well-defined operational predictability.
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Affiliation(s)
- Deepak K Agrawal
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Marshall
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Eduardo D Sontag
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA.
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston MA, USA.
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18
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Steel H, Papachristodoulou A. Low-Burden Biological Feedback Controllers for Near-Perfect Adaptation. ACS Synth Biol 2019; 8:2212-2219. [PMID: 31500408 DOI: 10.1021/acssynbio.9b00125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The robustness and reliability of synthetic biological systems can be substantially improved by the introduction of feedback control architectures that parallel those employed in traditional engineering disciplines. One common control goal is adaptation (or disturbance rejection), which refers to a system's ability to maintain a constant output despite variation in some of its constituent processes (as frequently occurs in noisy cellular environments) or external perturbations. In this paper, we propose and analyze a control architecture that employs integrase and excisionase proteins to invert regions of DNA and an mRNA-mRNA annihilation reaction. Combined, these components approximate the functionality of a switching controller (as employed in classical control engineering) with three distinct operational modes. We demonstrate that this system is capable of near-perfect adaptation to variation in rates of both transcription and translation and can also operate without excessive consumption of cellular resources. The system's steady-state behavior is analyzed, and limits on its operating range are derived. Deterministic simulations of its dynamics are presented and are then extended to the stochastic case, which treats biochemical reactions as discrete events.
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Affiliation(s)
- Harrison Steel
- Dept of Engineering Science, University of Oxford, Oxford OX1 3PJ, U.K
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19
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Kelly CL, Harris AWK, Steel H, Hancock EJ, Heap JT, Papachristodoulou A. Synthetic negative feedback circuits using engineered small RNAs. Nucleic Acids Res 2019; 46:9875-9889. [PMID: 30212900 PMCID: PMC6182179 DOI: 10.1093/nar/gky828] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 09/06/2018] [Indexed: 12/13/2022] Open
Abstract
Negative feedback is known to enable biological and man-made systems to perform reliably in the face of uncertainties and disturbances. To date, synthetic biological feedback circuits have primarily relied upon protein-based, transcriptional regulation to control circuit output. Small RNAs (sRNAs) are non-coding RNA molecules that can inhibit translation of target messenger RNAs (mRNAs). In this work, we modelled, built and validated two synthetic negative feedback circuits that use rationally-designed sRNAs for the first time. The first circuit builds upon the well characterised tet-based autorepressor, incorporating an externally-inducible sRNA to tune the effective feedback strength. This allows more precise fine-tuning of the circuit output in contrast to the sigmoidal, steep input–output response of the autorepressor alone. In the second circuit, the output is a transcription factor that induces expression of an sRNA, which inhibits translation of the mRNA encoding the output, creating direct, closed-loop, negative feedback. Analysis of the noise profiles of both circuits showed that the use of sRNAs did not result in large increases in noise. Stochastic and deterministic modelling of both circuits agreed well with experimental data. Finally, simulations using fitted parameters allowed dynamic attributes of each circuit such as response time and disturbance rejection to be investigated.
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Affiliation(s)
- Ciarán L Kelly
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK.,Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Andreas W K Harris
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Edward J Hancock
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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20
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Hard Limits and Performance Tradeoffs in a Class of Antithetic Integral Feedback Networks. Cell Syst 2019; 9:49-63.e16. [PMID: 31279505 DOI: 10.1016/j.cels.2019.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/28/2019] [Accepted: 05/30/2019] [Indexed: 12/18/2022]
Abstract
Feedback regulation is pervasive in biology at both the organismal and cellular level. In this article, we explore the properties of a particular biomolecular feedback mechanism called antithetic integral feedback, which can be implemented using the binding of two molecules. Our work develops an analytic framework for understanding the hard limits, performance tradeoffs, and architectural properties of this simple model of biological feedback control. Using tools from control theory, we show that there are simple parametric relationships that determine both the stability and the performance of these systems in terms of speed, robustness, steady-state error, and leakiness. These findings yield a holistic understanding of the behavior of antithetic integral feedback and contribute to a more general theory of biological control systems.
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21
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Olsman N, Xiao F, Doyle JC. Architectural Principles for Characterizing the Performance of Antithetic Integral Feedback Networks. iScience 2019; 14:277-291. [PMID: 31015073 PMCID: PMC6479019 DOI: 10.1016/j.isci.2019.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/14/2019] [Accepted: 04/01/2019] [Indexed: 02/06/2023] Open
Abstract
As we begin to design increasingly complex synthetic biomolecular systems, it is essential to develop rational design methodologies that yield predictable circuit performance. Here we apply mathematical tools from the theory of control and dynamical systems to yield practical insights into the architecture and function of a particular class of biological feedback circuit. Specifically, we show that it is possible to analytically characterize both the operating regime and performance tradeoffs of an antithetic integral feedback circuit architecture. Furthermore, we demonstrate how these principles can be applied to inform the design process of a particular synthetic feedback circuit.
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Affiliation(s)
- Noah Olsman
- Department of Control and Dynamical Systems, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02215, USA.
| | - Fangzhou Xiao
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - John C Doyle
- Department of Control and Dynamical Systems, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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22
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Baetica AA, Westbrook A, El-Samad H. Control theoretical concepts for synthetic and systems biology. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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23
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Westbrook A, Tang X, Marshall R, Maxwell CS, Chappell J, Agrawal DK, Dunlop MJ, Noireaux V, Beisel CL, Lucks J, Franco E. Distinct timescales of RNA regulators enable the construction of a genetic pulse generator. Biotechnol Bioeng 2019; 116:1139-1151. [DOI: 10.1002/bit.26918] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/25/2018] [Accepted: 01/06/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Alexandra Westbrook
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University Ithaca New York
| | - Xun Tang
- Department of Mechanical Engineering University of California at Riverside Riverside California
| | - Ryan Marshall
- School of Physics and Astronomy, University of Minnesota Minneapolis Minnesota
| | - Colin S. Maxwell
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina
| | | | - Deepak K. Agrawal
- Biomedical Engineering Department Boston University Boston Massachusetts
| | - Mary J. Dunlop
- Biomedical Engineering Department Boston University Boston Massachusetts
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota Minneapolis Minnesota
| | - Chase L. Beisel
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina
- Helmholtz Institute for RNA‐based Infection Research (HIRI) Helmholtz‐Centre for Infection Research (HZI), Würzburg Germany
- Faculty of Medicine, University of Würzburg Würzburg Germany
| | - Julius Lucks
- Department of Chemical and Biological Engineering Northwestern University Evanston Illinois
| | - Elisa Franco
- Department of Mechanical Engineering University of California at Riverside Riverside California
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24
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Lugagne JB, Dunlop MJ. Cell-machine interfaces for characterizing gene regulatory network dynamics. ACTA ACUST UNITED AC 2019; 14:1-8. [PMID: 31579842 DOI: 10.1016/j.coisb.2019.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Gene regulatory networks and the dynamic responses they produce offer a wealth of information about how biological systems process information about their environment. Recently, researchers interested in dissecting these networks have been outsourcing various parts of their experimental workflow to computers. Here we review how, using microfluidic or optogenetic tools coupled with fluorescence imaging, it is now possible to interface cells and computers. These platforms enable scientists to perform informative dynamic stimulations of genetic pathways and monitor their reaction. It is also possible to close the loop and regulate genes in real time, providing an unprecedented view of how signals propagate through the network. Finally, we outline new tools that can be used within the framework of cell-machine interfaces.
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Affiliation(s)
- Jean-Baptiste Lugagne
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.,Biological Design Center, Boston University, Boston, MA, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.,Biological Design Center, Boston University, Boston, MA, USA
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25
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A quasi-integral controller for adaptation of genetic modules to variable ribosome demand. Nat Commun 2018; 9:5415. [PMID: 30575748 PMCID: PMC6303309 DOI: 10.1038/s41467-018-07899-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 12/03/2018] [Indexed: 01/25/2023] Open
Abstract
The behavior of genetic circuits is often poorly predictable. A gene’s expression level is not only determined by the intended regulators, but also affected by changes in ribosome availability imparted by expression of other genes. Here we design a quasi-integral biomolecular feedback controller that enables the expression level of any gene of interest (GOI) to adapt to changes in available ribosomes. The feedback is implemented through a synthetic small RNA (sRNA) that silences the GOI’s mRNA, and uses orthogonal extracytoplasmic function (ECF) sigma factor to sense the GOI’s translation and to actuate sRNA transcription. Without the controller, the expression level of the GOI is reduced by 50% when a resource competitor is activated. With the controller, by contrast, gene expression level is practically unaffected by the competitor. This feedback controller allows adaptation of genetic modules to variable ribosome demand and thus aids modular construction of complicated circuits. Competition for shared cellular resources often renders genetic circuits poorly predictable. Here the authors design a biomolecular quasi-integral controller that allows gene expression to adapt to variable demand in translation resources.
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