1
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Anastassov S, Filo M, Khammash M. Inteins: A Swiss army knife for synthetic biology. Biotechnol Adv 2024; 73:108349. [PMID: 38552727 DOI: 10.1016/j.biotechadv.2024.108349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/13/2024]
Abstract
Inteins are proteins found in nature that execute protein splicing. Among them, split inteins stand out for their versatility and adaptability, presenting creative solutions for addressing intricate challenges in various biological applications. Their exquisite attributes, including compactness, reliability, orthogonality, low toxicity, and irreversibility, make them of interest to various fields including synthetic biology, biotechnology and biomedicine. In this review, we delve into the inherent challenges of using inteins, present approaches for overcoming these challenges, and detail their reliable use for specific cellular tasks. We will discuss the use of conditional inteins in areas like cancer therapy, drug screening, patterning, infection treatment, diagnostics and biocontainment. Additionally, we will underscore the potential of inteins in executing basic logical operations with practical implications. We conclude by showcasing their potential in crafting complex genetic circuits for performing computations and feedback control that achieves robust perfect adaptation.
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Affiliation(s)
- Stanislav Anastassov
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland
| | - Maurice Filo
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland.
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2
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Galvan S, Teixeira AP, Fussenegger M. Enhancing cell-based therapies with synthetic gene circuits responsive to molecular stimuli. Biotechnol Bioeng 2024. [PMID: 38867466 DOI: 10.1002/bit.28770] [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: 10/13/2023] [Revised: 04/21/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024]
Abstract
Synthetic biology aims to contribute to the development of next-generation patient-specific cell-based therapies for chronic diseases especially through the construction of sophisticated synthetic gene switches to enhance the safety and spatiotemporal controllability of engineered cells. Indeed, switches that sense and process specific cues, which may be either externally administered triggers or endogenous disease-associated molecules, have emerged as powerful tools for programming and fine-tuning therapeutic outputs. Living engineered cells, often referred to as designer cells, incorporating such switches are delivered to patients either as encapsulated cell implants or by infusion, as in the case of the clinically approved CAR-T cell therapies. Here, we review recent developments in synthetic gene switches responsive to molecular stimuli, spanning regulatory mechanisms acting at the transcriptional, translational, and posttranslational levels. We also discuss current challenges facing clinical translation of cell-based therapies employing these devices.
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Affiliation(s)
- Silvia Galvan
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ana P Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
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3
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Chakravarty S, Zhang R, Tian XJ. Noise Reduction in Resource-Coupled Multi-Module Gene Circuits through Antithetic Feedback Control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595570. [PMID: 38826454 PMCID: PMC11142251 DOI: 10.1101/2024.05.24.595570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Gene circuits within the same host cell often experience coupling, stemming from the competition for limited resources during transcriptional and translational processes. This resource competition introduces an additional layer of noise to gene expression. Here we present three multi-module antithetic control strategies: negatively competitive regulation (NCR) controller, alongside local and global controllers, aimed at reducing the gene expression noise within the context of resource competition. Through stochastic simulations and fluctuation-dissipation theorem (FDT) analysis, our findings highlight the superior performance of the NCR antithetic controller in reducing noise levels. Our research provides an effective control strategy for attenuating resource-driven noise and offers insight into the development of robust gene circuits.
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Affiliation(s)
- Suchana Chakravarty
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Rong Zhang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Xiao-Jun Tian
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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4
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Stone A, Rijal S, Zhang R, Tian XJ. Enhancing circuit stability under growth feedback with supplementary repressive regulation. Nucleic Acids Res 2024; 52:1512-1521. [PMID: 38164993 PMCID: PMC10853785 DOI: 10.1093/nar/gkad1233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/20/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024] Open
Abstract
The field of synthetic biology and biosystems engineering increasingly acknowledges the need for a holistic design approach that incorporates circuit-host interactions into the design process. Engineered circuits are not isolated entities but inherently entwined with the dynamic host environment. One such circuit-host interaction, 'growth feedback', results when modifications in host growth patterns influence the operation of gene circuits. The growth-mediated effects can range from growth-dependent elevation in protein/mRNA dilution rate to changes in resource reallocation within the cell, which can lead to complete functional collapse in complex circuits. To achieve robust circuit performance, synthetic biologists employ a variety of control mechanisms to stabilize and insulate circuit behavior against growth changes. Here we propose a simple strategy by incorporating one repressive edge in a growth-sensitive bistable circuit. Through both simulation and in vitro experimentation, we demonstrate how this additional repressive node stabilizes protein levels and increases the robustness of a bistable circuit in response to growth feedback. We propose the incorporation of repressive links in gene circuits as a control strategy for desensitizing gene circuits against growth fluctuations.
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Affiliation(s)
- Austin Stone
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Sadikshya Rijal
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Rong Zhang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Xiao-Jun Tian
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
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5
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Stone A, Youssef A, Rijal S, Zhang R, Tian XJ. Context-dependent redesign of robust synthetic gene circuits. Trends Biotechnol 2024:S0167-7799(24)00003-9. [PMID: 38320912 DOI: 10.1016/j.tibtech.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 02/08/2024]
Abstract
Cells provide dynamic platforms for executing exogenous genetic programs in synthetic biology, resulting in highly context-dependent circuit performance. Recent years have seen an increasing interest in understanding the intricacies of circuit-host relationships, their influence on the synthetic bioengineering workflow, and in devising strategies to alleviate undesired effects. We provide an overview of how emerging circuit-host interactions, such as growth feedback and resource competition, impact both deterministic and stochastic circuit behaviors. We also emphasize control strategies for mitigating these unwanted effects. This review summarizes the latest advances and the current state of host-aware and resource-aware design of synthetic gene circuits.
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Affiliation(s)
- Austin Stone
- School of Biological and Health System Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Abdelrahaman Youssef
- School of Biological and Health System Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Sadikshya Rijal
- School of Biological and Health System Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Rong Zhang
- School of Biological and Health System Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Xiao-Jun Tian
- School of Biological and Health System Engineering, Arizona State University, Tempe, AZ 85281, USA.
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6
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Frei T, Khammash M. Realizing Antithetic Integral Feedback Control in Mammalian Cells. Methods Mol Biol 2024; 2774:85-98. [PMID: 38441760 DOI: 10.1007/978-1-0716-3718-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Genetic circuit engineering has emerged as a powerful methodology to program the behavior of mammalian cells to respond to internal and external cues. This approach is now used to develop new therapeutics and improve production processes. However, genetic interaction networks are complex and hard to engineer rationally. Moreover, a design may fail, and it may not be possible to identify the root cause of its breakdown. Introducing designated regulatory circuitry in the form of integral feedback can introduce performance guarantees by ensuring robust and precise operation.
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Affiliation(s)
- Timothy Frei
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Basel, Switzerland.
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7
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Gao Y, Wang L, Wang B. Customizing cellular signal processing by synthetic multi-level regulatory circuits. Nat Commun 2023; 14:8415. [PMID: 38110405 PMCID: PMC10728147 DOI: 10.1038/s41467-023-44256-1] [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: 09/13/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
As synthetic biology permeates society, the signal processing circuits in engineered living systems must be customized to meet practical demands. Towards this mission, novel regulatory mechanisms and genetic circuits with unprecedented complexity have been implemented over the past decade. These regulatory mechanisms, such as transcription and translation control, could be integrated into hybrid circuits termed "multi-level circuits". The multi-level circuit design will tremendously benefit the current genetic circuit design paradigm, from modifying basic circuit dynamics to facilitating real-world applications, unleashing our capabilities to customize cellular signal processing and address global challenges through synthetic biology.
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Affiliation(s)
- Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Lei Wang
- Center of Synthetic Biology and Integrated Bioengineering & School of Engineering, Westlake University, Hangzhou, 310030, China.
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058, China.
- Research Center for Biological Computation, Zhejiang Lab, Hangzhou, 311100, China.
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8
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Gyorgy A. Competition and evolutionary selection among core regulatory motifs in gene expression control. Nat Commun 2023; 14:8266. [PMID: 38092759 PMCID: PMC10719253 DOI: 10.1038/s41467-023-43327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
Gene products that are beneficial in one environment may become burdensome in another, prompting the emergence of diverse regulatory schemes that carry their own bioenergetic cost. By ensuring that regulators are only expressed when needed, we demonstrate that autoregulation generally offers an advantage in an environment combining mutation and time-varying selection. Whether positive or negative feedback emerges as dominant depends primarily on the demand for the target gene product, typically to ensure that the detrimental impact of inevitable mutations is minimized. While self-repression of the regulator curbs the spread of these loss-of-function mutations, self-activation instead facilitates their propagation. By analyzing the transcription network of multiple model organisms, we reveal that reduced bioenergetic cost may contribute to the preferential selection of autoregulation among transcription factors. Our results not only uncover how seemingly equivalent regulatory motifs have fundamentally different impact on population structure, growth dynamics, and evolutionary outcomes, but they can also be leveraged to promote the design of evolutionarily robust synthetic gene circuits.
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Affiliation(s)
- Andras Gyorgy
- Division of Engineering, New York University Abu Dhabi, Abu Dhabi, UAE.
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9
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Araujo RP, Liotta LA. Only a topological method can identify all possible network structures capable of Robust Perfect Adaptation. PLoS Comput Biol 2023; 19:e1011638. [PMID: 37992051 PMCID: PMC10664938 DOI: 10.1371/journal.pcbi.1011638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/27/2023] [Indexed: 11/24/2023] Open
Affiliation(s)
- Robyn P. Araujo
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Lance A. Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, United States of America
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10
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Kumar S, Anastassov S, Aoki SK, Falkenstein J, Chang CH, Frei T, Buchmann P, Argast P, Khammash M. Diya - A universal light illumination platform for multiwell plate cultures. iScience 2023; 26:107862. [PMID: 37810238 PMCID: PMC10551653 DOI: 10.1016/j.isci.2023.107862] [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] [Received: 03/28/2023] [Revised: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Recent progress in protein engineering has established optogenetics as one of the leading external non-invasive stimulation strategies, with many optogenetic tools being designed for in vivo operation. Characterization and optimization of these tools require a high-throughput and versatile light delivery system targeting micro-titer culture volumes. Here, we present a universal light illumination platform - Diya, compatible with a wide range of cell culture plates and dishes. Diya hosts specially designed features ensuring active thermal management, homogeneous illumination, and minimal light bleedthrough. It offers light induction programming via a user-friendly custom-designed GUI. Through extensive characterization experiments with multiple optogenetic tools in diverse model organisms (bacteria, yeast, and human cell lines), we show that Diya maintains viable conditions for cell cultures undergoing light induction. Finally, we demonstrate an optogenetic strategy for in vivo biomolecular controller operation. With a custom-designed antithetic integral feedback circuit, we exhibit robust perfect adaptation and light-controlled set-point variation using Diya.
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Affiliation(s)
- Sant Kumar
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Stanislav Anastassov
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Stephanie K. Aoki
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Johannes Falkenstein
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Ching-Hsiang Chang
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Timothy Frei
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Peter Buchmann
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Paul Argast
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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11
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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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12
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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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13
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Haus ES, Drengstig T, Thorsen K. Structural identifiability of biomolecular controller motifs with and without flow measurements as model output. PLoS Comput Biol 2023; 19:e1011398. [PMID: 37639454 PMCID: PMC10491402 DOI: 10.1371/journal.pcbi.1011398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 09/08/2023] [Accepted: 07/28/2023] [Indexed: 08/31/2023] Open
Abstract
Controller motifs are simple biomolecular reaction networks with negative feedback. They can explain how regulatory function is achieved and are often used as building blocks in mathematical models of biological systems. In this paper we perform an extensive investigation into structural identifiability of controller motifs, specifically the so-called basic and antithetic controller motifs. Structural identifiability analysis is a useful tool in the creation and evaluation of mathematical models: it can be used to ensure that model parameters can be determined uniquely and to examine which measurements are necessary for this purpose. This is especially useful for biological models where parameter estimation can be difficult due to limited availability of measureable outputs. Our aim with this work is to investigate how structural identifiability is affected by controller motif complexity and choice of measurements. To increase the number of potential outputs we propose two methods for including flow measurements and show how this affects structural identifiability in combination with, or in the absence of, concentration measurements. In our investigation, we analyze 128 different controller motif structures using a combination of flow and/or concentration measurements, giving a total of 3648 instances. Among all instances, 34% of the measurement combinations provided structural identifiability. Our main findings for the controller motifs include: i) a single measurement is insufficient for structural identifiability, ii) measurements related to different chemical species are necessary for structural identifiability. Applying these findings result in a reduced subset of 1568 instances, where 80% are structurally identifiable, and more complex/interconnected motifs appear easier to structurally identify. The model structures we have investigated are commonly used in models of biological systems, and our results demonstrate how different model structures and measurement combinations affect structural identifiability of controller motifs.
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Affiliation(s)
- Eivind S. Haus
- Department of Electrical Engineering and Computer Science, University of Stavanger, Stavanger, Norway
| | - Tormod Drengstig
- Department of Electrical Engineering and Computer Science, University of Stavanger, Stavanger, Norway
| | - Kristian Thorsen
- Department of Electrical Engineering and Computer Science, University of Stavanger, Stavanger, Norway
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14
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Caringella G, Bandiera L, Menolascina F. Recent advances, opportunities and challenges in cybergenetic identification and control of biomolecular networks. Curr Opin Biotechnol 2023; 80:102893. [PMID: 36706519 DOI: 10.1016/j.copbio.2023.102893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 01/26/2023]
Abstract
Cybergenetics is a new area of research aimed at developing digital and biological controllers for living systems. Synthetic biologists have begun exploiting cybergenetic tools and platforms to both accelerate the development of mathematical models and develop control strategies for complex biological phenomena. Here, we review the state of the art in cybergenetic identification and control. Our aim is to lower the entry barrier to this field and foster the adoption of methods and technologies that will accelerate the pace at which Synthetic Biology progresses toward applications.
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Affiliation(s)
- Gianpio Caringella
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3DW, UK
| | - Lucia Bandiera
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3DW, UK; Centre for Engineering Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Filippo Menolascina
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3DW, UK; Centre for Engineering Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK.
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15
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Anastassov S, Filo M, Chang CH, Khammash M. A cybergenetic framework for engineering intein-mediated integral feedback control systems. Nat Commun 2023; 14:1337. [PMID: 36906662 PMCID: PMC10008564 DOI: 10.1038/s41467-023-36863-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/21/2023] [Indexed: 03/13/2023] Open
Abstract
The ability of biological systems to tightly regulate targeted variables, despite external and internal disturbances, is known as Robust Perfect Adaptation (RPA). Achieved frequently through biomolecular integral feedback controllers at the cellular level, RPA has important implications for biotechnology and its various applications. In this study, we identify inteins as a versatile class of genetic components suitable for implementing these controllers and present a systematic approach for their design. We develop a theoretical foundation for screening intein-based RPA-achieving controllers and a simplified approach for modeling them. We then genetically engineer and test intein-based controllers using commonly used transcription factors in mammalian cells and demonstrate their exceptional adaptation properties over a wide dynamic range. The small size, flexibility, and applicability of inteins across life forms allow us to create a diversity of genetic RPA-achieving integral feedback control systems that can be used in various applications, including metabolic engineering and cell-based therapy.
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Affiliation(s)
- Stanislav Anastassov
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Maurice Filo
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Ching-Hsiang Chang
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland.
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16
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Gotovtsev P. Microbial Cells as a Microrobots: From Drug Delivery to Advanced Biosensors. Biomimetics (Basel) 2023; 8:biomimetics8010109. [PMID: 36975339 PMCID: PMC10046805 DOI: 10.3390/biomimetics8010109] [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: 01/31/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
The presented review focused on the microbial cell based system. This approach is based on the application of microorganisms as the main part of a robot that is responsible for the motility, cargo shipping, and in some cases, the production of useful chemicals. Living cells in such microrobots have both advantages and disadvantages. Regarding the advantages, it is necessary to mention the motility of cells, which can be natural chemotaxis or phototaxis, depending on the organism. There are approaches to make cells magnetotactic by adding nanoparticles to their surface. Today, the results of the development of such microrobots have been widely discussed. It has been shown that there is a possibility of combining different types of taxis to enhance the control level of the microrobots based on the microorganisms' cells and the efficiency of the solving task. Another advantage is the possibility of applying the whole potential of synthetic biology to make the behavior of the cells more controllable and complex. Biosynthesis of the cargo, advanced sensing, on/off switches, and other promising approaches are discussed within the context of the application for the microrobots. Thus, a synthetic biology application offers significant perspectives on microbial cell based microrobot development. Disadvantages that follow from the nature of microbial cells such as the number of external factors influence the cells, potential immune reaction, etc. They provide several limitations in the application, but do not decrease the bright perspectives of microrobots based on the cells of the microorganisms.
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Affiliation(s)
- Pavel Gotovtsev
- National Research Center "Kurchatov Institute", Biotechnology and Bioenergy Department, Akademika Kurchatova pl. 1, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 9 Institutskiy per., 141701 Moscow, Russia
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Stability, robustness, and containment: preparing synthetic biology for real-world deployment. Curr Opin Biotechnol 2023; 79:102880. [PMID: 36621221 DOI: 10.1016/j.copbio.2022.102880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/23/2022] [Accepted: 12/07/2022] [Indexed: 01/07/2023]
Abstract
As engineered microbes are used in increasingly diverse applications across human health and bioproduction, the field of synthetic biology will need to focus on strategies that stabilize and contain the function of these populations within target environments. To this end, recent advancements have created layered sensing circuits that can compute cell survival, genetic contexts that are less susceptible to mutation, burden, and resource control circuits, and methods for population variability reduction. These tools expand the potential for real-world deployment of complex microbial systems by enhancing their environmental robustness and functional stability in the face of unpredictable host response and evolutionary pressure.
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Biomolecular feedback controllers: from theory to applications. Curr Opin Biotechnol 2023; 79:102882. [PMID: 36638743 DOI: 10.1016/j.copbio.2022.102882] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/07/2022] [Indexed: 01/13/2023]
Abstract
Billions of years of evolution have led to the creation of sophisticated genetic regulatory mechanisms that control various biological processes in a timely and precise fashion, despite their uncertain and noisy environments. Understanding such naturally existing mechanisms and even designing novel ones will have direct implications in various fields such as biotechnology, medicine, and synthetic biology. In particular, many studies have revealed that feedback-based control mechanisms inside the living cells endow the overall system with multiple attractive features, including homeostasis, noise reduction, and high dynamic performance. The remarkable interdisciplinary nature of these studies has brought together disparate disciplines such as systems/synthetic biology and control theory in an effort to design and build more powerful and reliable biomolecular control systems. Here, we review various biomolecular feedback controllers, highlight their characteristics, and point out their promising impact.
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Jeynes-Smith C, Araujo RP. Protein-protein complexes can undermine ultrasensitivity-dependent biological adaptation. J R Soc Interface 2023; 20:20220553. [PMID: 36596458 PMCID: PMC9810431 DOI: 10.1098/rsif.2022.0553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Robust perfect adaptation (RPA) is a ubiquitously observed signalling response across all scales of biological organization. A major class of network architectures that drive RPA in complex networks is the Opposer module-a feedback-regulated network into which specialized integral-computing 'opposer node(s)' are embedded. Although ultrasensitivity-generating chemical reactions have long been considered a possible mechanism for such adaptation-conferring opposer nodes, this hypothesis has relied on simplified Michaelian models, which neglect the presence of protein-protein complexes. Here we develop complex-complete models of interlinked covalent-modification cycles with embedded ultrasensitivity, explicitly capturing all molecular interactions and protein complexes. Strikingly, we demonstrate that the presence of protein-protein complexes thwarts the network's capacity for RPA in any 'free' active protein form, conferring RPA capacity instead on the concentration of a larger protein pool consisting of two distinct forms of a single protein. We further show that the presence of enzyme-substrate complexes, even at comparatively low concentrations, play a crucial and previously unrecognized role in controlling the RPA response-significantly reducing the range of network inputs for which RPA can obtain, and imposing greater parametric requirements on the RPA response. These surprising results raise fundamental new questions as to the biochemical requirements for adaptation-conferring Opposer modules within complex cellular networks.
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Affiliation(s)
- C. Jeynes-Smith
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
| | - R. P. Araujo
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
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20
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Li Y, Arce A, Lucci T, Rasmussen RA, Lucks JB. Dynamic RNA synthetic biology: new principles, practices and potential. RNA Biol 2023; 20:817-829. [PMID: 38044595 PMCID: PMC10730207 DOI: 10.1080/15476286.2023.2269508] [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: 10/28/2023] [Accepted: 08/23/2023] [Indexed: 12/05/2023] Open
Abstract
An increased appreciation of the role of RNA dynamics in governing RNA function is ushering in a new wave of dynamic RNA synthetic biology. Here, we review recent advances in engineering dynamic RNA systems across the molecular, circuit and cellular scales for important societal-scale applications in environmental and human health, and bioproduction. For each scale, we introduce the core concepts of dynamic RNA folding and function at that scale, and then discuss technologies incorporating these concepts, covering new approaches to engineering riboswitches, ribozymes, RNA origami, RNA strand displacement circuits, biomaterials, biomolecular condensates, extracellular vesicles and synthetic cells. Considering the dynamic nature of RNA within the engineering design process promises to spark the next wave of innovation that will expand the scope and impact of RNA biotechnologies.
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Affiliation(s)
- Yueyi Li
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Anibal Arce
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Tyler Lucci
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Rebecca A. Rasmussen
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, 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
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
- Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, IL, USA
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Gupta A, Khammash M. Universal structural requirements for maximal robust perfect adaptation in biomolecular networks. Proc Natl Acad Sci U S A 2022; 119:e2207802119. [PMID: 36256812 PMCID: PMC9618122 DOI: 10.1073/pnas.2207802119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/21/2022] [Indexed: 12/31/2022] Open
Abstract
Adaptation is a running theme in biology. It allows a living system to survive and thrive in the face of unpredictable environments by maintaining key physiological variables at their desired levels through tight regulation. When one such variable is maintained at a certain value at the steady state despite perturbations to a single input, this property is called robust perfect adaptation (RPA). Here we address and solve the fundamental problem of maximal RPA (maxRPA), whereby, for a designated output variable, RPA is achieved with respect to perturbations in virtually all network parameters. In particular, we show that the maxRPA property imposes certain structural constraints on the network. We then prove that these constraints are fully characterized by simple linear algebraic stoichiometric conditions which differ between deterministic and stochastic descriptions of the dynamics. We use our results to derive a new internal model principle (IMP) for biomolecular maxRPA networks, akin to the celebrated IMP in control theory. We exemplify our results through several known biological examples of robustly adapting networks and construct examples of such networks with the aid of our linear algebraic characterization. Our results reveal the universal requirements for maxRPA in all biological systems, and establish a foundation for studying adaptation in general biomolecular networks, with important implications for both systems and synthetic biology.
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Affiliation(s)
- Ankit Gupta
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, 4058 Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, 4058 Basel, Switzerland
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