1
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Cannarsa MC, Liguori F, Pellicciotta N, Frangipane G, Di Leonardo R. Light-driven synchronization of optogenetic clocks. eLife 2024; 13:RP97754. [PMID: 39405096 PMCID: PMC11479589 DOI: 10.7554/elife.97754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2024] Open
Abstract
Synthetic genetic oscillators can serve as internal clocks within engineered cells to program periodic expression. However, cell-to-cell variability introduces a dispersion in the characteristics of these clocks that drives the population to complete desynchronization. Here, we introduce the optorepressilator, an optically controllable genetic clock that combines the repressilator, a three-node synthetic network in E. coli, with an optogenetic module enabling to reset, delay, or advance its phase using optical inputs. We demonstrate that a population of optorepressilators can be synchronized by transient green light exposure or entrained to oscillate indefinitely by a train of short pulses, through a mechanism reminiscent of natural circadian clocks. Furthermore, we investigate the system's response to detuned external stimuli observing multiple regimes of global synchronization. Integrating experiments and mathematical modeling, we show that the entrainment mechanism is robust and can be understood quantitatively from single cell to population level.
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Affiliation(s)
- Maria Cristina Cannarsa
- Department of Physics, Sapienza University of RomeRomaItaly
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of RomeRomeItaly
| | - Filippo Liguori
- Department of Physics, Sapienza University of RomeRomaItaly
- Center for Life Nano & Neuro Science, Fondazione Istituto Italiano di Tecnologia (IIT)RomaItaly
| | - Nicola Pellicciotta
- Department of Physics, Sapienza University of RomeRomaItaly
- NANOTEC-CNR, Soft and Living Matter Laboratory, Institute of NanotechnologyRomeItaly
| | - Giacomo Frangipane
- Department of Physics, Sapienza University of RomeRomaItaly
- NANOTEC-CNR, Soft and Living Matter Laboratory, Institute of NanotechnologyRomeItaly
| | - Roberto Di Leonardo
- Department of Physics, Sapienza University of RomeRomaItaly
- NANOTEC-CNR, Soft and Living Matter Laboratory, Institute of NanotechnologyRomeItaly
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2
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Liguori F, Pellicciotta N, Milanetti E, Xi Windemuth S, Ruocco G, Di Leonardo R, Danino T. Dynamic Gene Expression Mitigates Mutational Escape in Lysis-Driven Bacteria Cancer Therapy. BIODESIGN RESEARCH 2024; 6:0049. [PMID: 39301524 PMCID: PMC11411163 DOI: 10.34133/bdr.0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/09/2024] [Accepted: 08/25/2024] [Indexed: 09/22/2024] Open
Abstract
Engineered bacteria have the potential to deliver therapeutic payloads directly to tumors, with synthetic biology enabling precise control over therapeutic release in space and time. However, it remains unclear how to optimize therapeutic bacteria for durable colonization and sustained payload release. Here, we characterize nonpathogenic Escherichia coli expressing the bacterial toxin Perfringolysin O (PFO) and dynamic strategies that optimize therapeutic efficacy. While PFO is known for its potent cancer cell cytotoxicity, we present experimental evidence that expression of PFO causes lysis of bacteria in both batch culture and microfluidic systems, facilitating its efficient release. However, prolonged expression of PFO leads to the emergence of a mutant population that limits therapeutic-releasing bacteria in a PFO expression level-dependent manner. We present sequencing data revealing the mutant takeover and employ molecular dynamics to confirm that the observed mutations inhibit the lysis efficiency of PFO. To analyze this further, we developed a mathematical model describing the evolution of therapeutic-releasing and mutant bacteria populations revealing trade-offs between therapeutic load delivered and fraction of mutants that arise. We demonstrate that a dynamic strategy employing short and repeated inductions of the pfo gene better preserves the original population of therapeutic bacteria by mitigating the effects of mutational escape. Altogether, we demonstrate how dynamic modulation of gene expression can address mutant takeovers giving rise to limitations in engineered bacteria for therapeutic applications.
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Affiliation(s)
- Filippo Liguori
- Department of Physics, Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Nicola Pellicciotta
- NANOTEC-CNR, Soft and Living Matter Laboratory, Institute of Nanotechnology, Rome, Italy
- Department of Physics, Sapienza University of Rome, Rome, Italy
| | - Edoardo Milanetti
- Department of Physics, Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Sophia Xi Windemuth
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Giancarlo Ruocco
- Department of Physics, Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Roberto Di Leonardo
- Department of Physics, Sapienza University of Rome, Rome, Italy
- NANOTEC-CNR, Soft and Living Matter Laboratory, Institute of Nanotechnology, Rome, Italy
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
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3
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Joshi SHN, Jenkins C, Ulaeto D, Gorochowski TE. Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology. BIODESIGN RESEARCH 2024; 6:0037. [PMID: 38919711 PMCID: PMC11197468 DOI: 10.34133/bdr.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024] Open
Abstract
Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.
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Affiliation(s)
| | - Christopher Jenkins
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - David Ulaeto
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - Thomas E. Gorochowski
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- BrisEngBio,
School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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4
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Elahi Y, Baker MAB. Light Control in Microbial Systems. Int J Mol Sci 2024; 25:4001. [PMID: 38612810 PMCID: PMC11011852 DOI: 10.3390/ijms25074001] [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: 01/15/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Light is a key environmental component influencing many biological processes, particularly in prokaryotes such as archaea and bacteria. Light control techniques have revolutionized precise manipulation at molecular and cellular levels in recent years. Bacteria, with adaptability and genetic tractability, are promising candidates for light control studies. This review investigates the mechanisms underlying light activation in bacteria and discusses recent advancements focusing on light control methods and techniques for controlling bacteria. We delve into the mechanisms by which bacteria sense and transduce light signals, including engineered photoreceptors and light-sensitive actuators, and various strategies employed to modulate gene expression, protein function, and bacterial motility. Furthermore, we highlight recent developments in light-integrated methods of controlling microbial responses, such as upconversion nanoparticles and optical tweezers, which can enhance the spatial and temporal control of bacteria and open new horizons for biomedical applications.
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5
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Lugagne JB, Blassick CM, Dunlop MJ. Deep model predictive control of gene expression in thousands of single cells. Nat Commun 2024; 15:2148. [PMID: 38459057 PMCID: PMC10923782 DOI: 10.1038/s41467-024-46361-1] [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: 08/09/2023] [Accepted: 02/26/2024] [Indexed: 03/10/2024] Open
Abstract
Gene expression is inherently dynamic, due to complex regulation and stochastic biochemical events. However, the effects of these dynamics on cell phenotypes can be difficult to determine. Researchers have historically been limited to passive observations of natural dynamics, which can preclude studies of elusive and noisy cellular events where large amounts of data are required to reveal statistically significant effects. Here, using recent advances in the fields of machine learning and control theory, we train a deep neural network to accurately predict the response of an optogenetic system in Escherichia coli cells. We then use the network in a deep model predictive control framework to impose arbitrary and cell-specific gene expression dynamics on thousands of single cells in real time, applying the framework to generate complex time-varying patterns. We also showcase the framework's ability to link expression patterns to dynamic functional outcomes by controlling expression of the tetA antibiotic resistance gene. This study highlights how deep learning-enabled feedback control can be used to tailor distributions of gene expression dynamics with high accuracy and throughput without expert knowledge of the biological system.
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Affiliation(s)
- Jean-Baptiste Lugagne
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, USA.
- Biological Design Center, Boston University, Boston, Massachusetts, 02215, USA.
| | - Caroline M Blassick
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, USA
- Biological Design Center, Boston University, Boston, Massachusetts, 02215, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, USA.
- Biological Design Center, Boston University, Boston, Massachusetts, 02215, USA.
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6
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Tague N, Coriano-Ortiz C, Sheets MB, Dunlop MJ. Light-inducible protein degradation in E. coli with the LOVdeg tag. eLife 2024; 12:RP87303. [PMID: 38270583 PMCID: PMC10945698 DOI: 10.7554/elife.87303] [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] [Indexed: 01/26/2024] Open
Abstract
Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light-controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system and introduce a powerful new tool for bacterial optogenetics.
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Affiliation(s)
- Nathan Tague
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
| | - Cristian Coriano-Ortiz
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
| | - Michael B Sheets
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
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7
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Espinel-Ríos S, Morabito B, Pohlodek J, Bettenbrock K, Klamt S, Findeisen R. Toward a modeling, optimization, and predictive control framework for fed-batch metabolic cybergenetics. Biotechnol Bioeng 2024; 121:366-379. [PMID: 37942516 DOI: 10.1002/bit.28575] [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: 02/04/2023] [Revised: 09/22/2023] [Accepted: 10/14/2023] [Indexed: 11/10/2023]
Abstract
Biotechnology offers many opportunities for the sustainable manufacturing of valuable products. The toolbox to optimize bioprocesses includes extracellular process elements such as the bioreactor design and mode of operation, medium formulation, culture conditions, feeding rates, and so on. However, these elements are frequently insufficient for achieving optimal process performance or precise product composition. One can use metabolic and genetic engineering methods for optimization at the intracellular level. Nevertheless, those are often of static nature, failing when applied to dynamic processes or if disturbances occur. Furthermore, many bioprocesses are optimized empirically and implemented with little-to-no feedback control to counteract disturbances. The concept of cybergenetics has opened new possibilities to optimize bioprocesses by enabling online modulation of the gene expression of metabolism-relevant proteins via external inputs (e.g., light intensity in optogenetics). Here, we fuse cybergenetics with model-based optimization and predictive control for optimizing dynamic bioprocesses. To do so, we propose to use dynamic constraint-based models that integrate the dynamics of metabolic reactions, resource allocation, and inducible gene expression. We formulate a model-based optimal control problem to find the optimal process inputs. Furthermore, we propose using model predictive control to address uncertainties via online feedback. We focus on fed-batch processes, where the substrate feeding rate is an additional optimization variable. As a simulation example, we show the optogenetic control of the ATPase enzyme complex for dynamic modulation of enforced ATP wasting to adjust product yield and productivity.
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Affiliation(s)
- Sebastián Espinel-Ríos
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Bruno Morabito
- Yokogawa Insilico Biotechnology GmbH, Stuttgart, Germany
| | - Johannes Pohlodek
- Control and Cyber-Physical Systems Laboratory, Technical University of Darmstadt, Darmstadt, Germany
| | - Katja Bettenbrock
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Steffen Klamt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Rolf Findeisen
- Control and Cyber-Physical Systems Laboratory, Technical University of Darmstadt, Darmstadt, Germany
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8
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Biggs BW, de Paz AM, Bhan NJ, Cybulski TR, Church GM, Tyo KEJ. Engineering Ca 2+-Dependent DNA Polymerase Activity. ACS Synth Biol 2023; 12:3301-3311. [PMID: 37856140 DOI: 10.1021/acssynbio.3c00302] [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] [Indexed: 10/20/2023]
Abstract
Advancements in synthetic biology have provided new opportunities in biosensing, with applications ranging from genetic programming to diagnostics. Next generation biosensors aim to expand the number of accessible environments for measurements, increase the number of measurable phenomena, and improve the quality of the measurement. To this end, an emerging area in the field has been the integration of DNA as an information storage medium within biosensor outputs, leveraging nucleic acids to record the biosensor state over time. However, slow signal transduction steps, due to the time scales of transcription and translation, bottleneck many sensing-DNA recording approaches. DNA polymerases (DNAPs) have been proposed as a solution to the signal transduction problem by operating as both the sensor and responder, but there is presently a lack of DNAPs with functional sensitivity to many desirable target ligands. Here, we engineer components of the Pol δ replicative polymerase complex of Saccharomyces cerevisiae to sense and respond to Ca2+, a metal cofactor relevant to numerous biological phenomena. Through domain insertion and binding site grafting to Pol δ subunits, we demonstrate functional allosteric sensitivity to Ca2+. Together, this work provides an important foundation for future efforts in the development of DNAP-based biosensors.
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Affiliation(s)
- Bradley W Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexandra M de Paz
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Namita J Bhan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Thaddeus R Cybulski
- Interdepartmental Neuroscience Program, Northwestern University, Chicago, Illinois 60611, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
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9
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Tague N, Coriano-Ortiz C, Sheets MB, Dunlop MJ. Light inducible protein degradation in E. coli with the LOVdeg tag. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530042. [PMID: 36865169 PMCID: PMC9980293 DOI: 10.1101/2023.02.25.530042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system, and introduce a powerful new tool for bacterial optogenetics.
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10
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Lebovich M, Zeng M, Andrews LB. Algorithmic Programming of Sequential Logic and Genetic Circuits for Recording Biochemical Concentration in a Probiotic Bacterium. ACS Synth Biol 2023; 12:2632-2649. [PMID: 37581922 PMCID: PMC10510703 DOI: 10.1021/acssynbio.3c00232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Indexed: 08/16/2023]
Abstract
Through the implementation of designable genetic circuits, engineered probiotic microorganisms could be used as noninvasive diagnostic tools for the gastrointestinal tract. For these living cells to report detected biomarkers or signals after exiting the gut, the genetic circuits must be able to record these signals by using genetically encoded memory. Complex memory register circuits could enable multiplex interrogation of biomarkers and signals. A theory-based approach to create genetic circuits containing memory, known as sequential logic circuits, was previously established for a model laboratory strain of Escherichia coli, yet how circuit component performance varies for nonmodel and clinically relevant bacterial strains is poorly understood. Here, we develop a scalable computational approach to design robust sequential logic circuits in probiotic strain Escherichia coli Nissle 1917 (EcN). In this work, we used TetR-family transcriptional repressors to build genetic logic gates that can be composed into sequential logic circuits, along with a set of engineered sensors relevant for use in the gut environment. Using standard methods, 16 genetic NOT gates and nine sensors were experimentally characterized in EcN. These data were used to design and predict the performance of circuit designs. We present a set of genetic circuits encoding both combinational logic and sequential logic and show that the circuit outputs are in close agreement with our quantitative predictions from the design algorithm. Furthermore, we demonstrate an analog-like concentration recording circuit that detects and reports three input concentration ranges of a biochemical signal using sequential logic.
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Affiliation(s)
- Matthew Lebovich
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology
Training Program, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Min Zeng
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B. Andrews
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology
Training Program, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Molecular
and Cellular Biology Graduate Program, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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11
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Klumpe HE, Lugagne JB, Khalil AS, Dunlop MJ. Deep Neural Networks for Predicting Single-Cell Responses and Probability Landscapes. ACS Synth Biol 2023; 12:2367-2381. [PMID: 37467372 DOI: 10.1021/acssynbio.3c00203] [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] [Indexed: 07/21/2023]
Abstract
Engineering biology relies on the accurate prediction of cell responses. However, making these predictions is challenging for a variety of reasons, including the stochasticity of biochemical reactions, variability between cells, and incomplete information about underlying biological processes. Machine learning methods, which can model diverse input-output relationships without requiring a priori mechanistic knowledge, are an ideal tool for this task. For example, such approaches can be used to predict gene expression dynamics given time-series data of past expression history. To explore this application, we computationally simulated single-cell responses, incorporating different sources of noise and alternative genetic circuit designs. We showed that deep neural networks trained on these simulated data were able to correctly infer the underlying dynamics of a cell response even in the presence of measurement noise and stochasticity in the biochemical reactions. The training set size and the amount of past data provided as inputs both affected prediction quality, with cascaded genetic circuits that introduce delays requiring more past data. We also tested prediction performance on a bistable auto-activation circuit, finding that our initial method for predicting a single trajectory was fundamentally ill-suited for multimodal dynamics. To address this, we updated the network architecture to predict the entire distribution of future states, showing it could accurately predict bimodal expression distributions. Overall, these methods can be readily applied to the diverse prediction tasks necessary to predict and control a variety of biological circuits, a key aspect of many synthetic biology applications.
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Affiliation(s)
- Heidi E Klumpe
- Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
| | - Jean-Baptiste Lugagne
- Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
| | - Ahmad S Khalil
- Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Mary J Dunlop
- Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
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12
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Harmer ZP, McClean MN. Lustro: High-throughput optogenetic experiments enabled by automation and a yeast optogenetic toolkit. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536078. [PMID: 37066312 PMCID: PMC10104134 DOI: 10.1101/2023.04.07.536078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Optogenetic systems use genetically-encoded light-sensitive proteins to control cellular processes. This provides the potential to orthogonally control cells with light, however these systems require many design-build-test cycles to achieve a functional design and multiple illumination variables need to be laboriously tuned for optimal stimulation. We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae . We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets, incorporate these light-sensitive dimerizers into split transcription factors, and automate illumination and measurement of cultures in a 96-well microplate format for high-throughput characterization. We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression. This approach is generalizable to high-throughput characterization of optogenetic systems across a range of biological systems and applications.
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13
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Parolo C, Idili A, Heikenfeld J, Plaxco KW. Conformational-switch biosensors as novel tools to support continuous, real-time molecular monitoring in lab-on-a-chip devices. LAB ON A CHIP 2023; 23:1339-1348. [PMID: 36655710 PMCID: PMC10799767 DOI: 10.1039/d2lc00716a] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Recent years have seen continued expansion of the functionality of lab on a chip (LOC) devices. Indeed LOCs now provide scientists and developers with useful and versatile platforms across a myriad of chemical and biological applications. The field still fails, however, to integrate an often important element of bench-top analytics: real-time molecular measurements that can be used to "guide" a chemical response. Here we describe the analytical techniques that could provide LOCs with such real-time molecular monitoring capabilities. It appears to us that, among the approaches that are general (i.e., that are independent of the reactive or optical properties of their targets), sensing strategies relying on binding-induced conformational change of bioreceptors are most likely to succeed in such applications.
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Affiliation(s)
- Claudio Parolo
- Barcelona Institute for Global Health, Hospital Clínic Universitat de Barcelona, 08036, Barcelona, Spain
| | - Andrea Idili
- Department of Chemical Science and Technologies, University of Rome, Tor Vergata, 00133 Rome, Italy
| | - Jason Heikenfeld
- Novel Devices Laboratory, University of Cincinnati, Cincinnati, Ohio, USA
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA.
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California, USA
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14
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Pouzet S, Cruz-Ramón J, Le Bec M, Cordier C, Banderas A, Barral S, Castaño-Cerezo S, Lautier T, Truan G, Hersen P. Optogenetic control of beta-carotene bioproduction in yeast across multiple lab-scales. Front Bioeng Biotechnol 2023; 11:1085268. [PMID: 36814715 PMCID: PMC9939774 DOI: 10.3389/fbioe.2023.1085268] [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] [Received: 10/31/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Optogenetics arises as a valuable tool to precisely control genetic circuits in microbial cell factories. Light control holds the promise of optimizing bioproduction methods and maximizing yields, but its implementation at different steps of the strain development process and at different culture scales remains challenging. In this study, we aim to control beta-carotene bioproduction using optogenetics in Saccharomyces cerevisiae and investigate how its performance translates across culture scales. We built four lab-scale illumination devices, each handling different culture volumes, and each having specific illumination characteristics and cultivating conditions. We evaluated optogenetic activation and beta-carotene production across devices and optimized them both independently. Then, we combined optogenetic induction and beta-carotene production to make a light-inducible beta-carotene producer strain. This was achieved by placing the transcription of the bifunctional lycopene cyclase/phytoene synthase CrtYB under the control of the pC120 optogenetic promoter regulated by the EL222-VP16 light-activated transcription factor, while other carotenogenic enzymes (CrtI, CrtE, tHMG) were expressed constitutively. We show that illumination, culture volume and shaking impact differently optogenetic activation and beta-carotene production across devices. This enabled us to determine the best culture conditions to maximize light-induced beta-carotene production in each of the devices. Our study exemplifies the stakes of scaling up optogenetics in devices of different lab scales and sheds light on the interplays and potential conflicts between optogenetic control and metabolic pathway efficiency. As a general principle, we propose that it is important to first optimize both components of the system independently, before combining them into optogenetic producing strains to avoid extensive troubleshooting. We anticipate that our results can help designing both strains and devices that could eventually lead to larger scale systems in an effort to bring optogenetics to the industrial scale.
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Affiliation(s)
- Sylvain Pouzet
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Jessica Cruz-Ramón
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Matthias Le Bec
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Céline Cordier
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Alvaro Banderas
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Simon Barral
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Sara Castaño-Cerezo
- Toulouse Biotechnology Institute, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l′Agriculture, l′Alimentation et l′Environnement (INRAE), Institut National des Sciences Appliquées (INSA), Toulouse, France
| | - Thomas Lautier
- Toulouse Biotechnology Institute, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l′Agriculture, l′Alimentation et l′Environnement (INRAE), Institut National des Sciences Appliquées (INSA), Toulouse, France,CNRS@CREATE, Singapore Institute of Food and Biotechnology Innovation, Agency for Science Technology and Research, Singapore, Singapore
| | - Gilles Truan
- Toulouse Biotechnology Institute, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l′Agriculture, l′Alimentation et l′Environnement (INRAE), Institut National des Sciences Appliquées (INSA), Toulouse, France
| | - Pascal Hersen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,*Correspondence: Pascal Hersen,
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15
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Braniff N, Pearce T, Lu Z, Astwood M, Forrest WSR, Receno C, Ingalls B. NLoed: A Python Package for Nonlinear Optimal Experimental Design in Systems Biology. ACS Synth Biol 2022; 11:3921-3928. [PMID: 36473701 PMCID: PMC9765746 DOI: 10.1021/acssynbio.2c00131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Indexed: 12/12/2022]
Abstract
Modeling in systems and synthetic biology relies on accurate parameter estimates and predictions. Accurate model calibration relies, in turn, on data and on how well suited the available data are to a particular modeling task. Optimal experimental design (OED) techniques can be used to identify experiments and data collection procedures that will most efficiently contribute to a given modeling objective. However, implementation of OED is limited by currently available software tools that are not well suited for the diversity of nonlinear models and non-normal data commonly encountered in biological research. Moreover, existing OED tools do not make use of the state-of-the-art numerical tools, resulting in inefficient computation. Here, we present the NLoed software package and demonstrate its use with in vivo data from an optogenetic system in Escherichia coli. NLoed is an open-source Python library providing convenient access to OED methods, with particular emphasis on experimental design for systems biology research. NLoed supports a wide variety of nonlinear, multi-input/output, and dynamic models and facilitates modeling and design of experiments over a wide variety of data types. To support OED investigations, the NLoed package implements maximum likelihood fitting and diagnostic tools, providing a comprehensive modeling workflow. NLoed offers an accessible, modular, and flexible OED tool set suited to the wide variety of experimental scenarios encountered in systems biology research. We demonstrate NLoed's capabilities by applying it to experimental design for characterization of a bacterial optogenetic system.
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Affiliation(s)
- Nathan Braniff
- Department of Applied Mathematics, University of Waterloo, Waterloo, OntarioN2L 3G1, Canada
| | - Taylor Pearce
- Department of Applied Mathematics, University of Waterloo, Waterloo, OntarioN2L 3G1, Canada
| | - Zixuan Lu
- Department of Applied Mathematics, University of Waterloo, Waterloo, OntarioN2L 3G1, Canada
| | - Michael Astwood
- Department of Applied Mathematics, University of Waterloo, Waterloo, OntarioN2L 3G1, Canada
| | - William S. R. Forrest
- Department of Applied Mathematics, University of Waterloo, Waterloo, OntarioN2L 3G1, Canada
| | - Cody Receno
- Department of Applied Mathematics, University of Waterloo, Waterloo, OntarioN2L 3G1, Canada
| | - Brian Ingalls
- Department of Applied Mathematics, University of Waterloo, Waterloo, OntarioN2L 3G1, Canada
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16
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Multamäki E, García de Fuentes A, Sieryi O, Bykov A, Gerken U, Ranzani A, Köhler J, Meglinski I, Möglich A, Takala H. Optogenetic Control of Bacterial Expression by Red Light. ACS Synth Biol 2022; 11:3354-3367. [PMID: 35998606 PMCID: PMC9594775 DOI: 10.1021/acssynbio.2c00259] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Indexed: 01/24/2023]
Abstract
In optogenetics, as in nature, sensory photoreceptors serve to control cellular processes by light. Bacteriophytochrome (BphP) photoreceptors sense red and far-red light via a biliverdin chromophore and, in response, cycle between the spectroscopically, structurally, and functionally distinct Pr and Pfr states. BphPs commonly belong to two-component systems that control the phosphorylation of cognate response regulators and downstream gene expression through histidine kinase modules. We recently demonstrated that the paradigm BphP from Deinococcus radiodurans exclusively acts as a phosphatase but that its photosensory module can control the histidine kinase activity of homologous receptors. Here, we apply this insight to reprogram two widely used setups for bacterial gene expression from blue-light to red-light control. The resultant pREDusk and pREDawn systems allow gene expression to be regulated down and up, respectively, uniformly under red light by 100-fold or more. Both setups are realized as portable, single plasmids that encode all necessary components including the biliverdin-producing machinery. The triggering by red light affords high spatial resolution down to the single-cell level. As pREDusk and pREDawn respond sensitively to red light, they support multiplexing with optogenetic systems sensitive to other light colors. Owing to the superior tissue penetration of red light, the pREDawn system can be triggered at therapeutically safe light intensities through material layers, replicating the optical properties of the skin and skull. Given these advantages, pREDusk and pREDawn enable red-light-regulated expression for diverse use cases in bacteria.
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Affiliation(s)
- Elina Multamäki
- Department
of Anatomy, University of Helsinki, Helsinki 00014, Finland
| | | | - Oleksii Sieryi
- Optoelectronics
and Measurement Techniques, University of
Oulu, Oulu 90014, Finland
| | - Alexander Bykov
- Optoelectronics
and Measurement Techniques, University of
Oulu, Oulu 90014, Finland
| | - Uwe Gerken
- Lehrstuhl
für Spektroskopie weicher Materie, Universität Bayreuth, Bayreuth 95447, Germany
| | | | - Jürgen Köhler
- Lehrstuhl
für Spektroskopie weicher Materie, Universität Bayreuth, Bayreuth 95447, Germany
| | - Igor Meglinski
- Optoelectronics
and Measurement Techniques, University of
Oulu, Oulu 90014, Finland
- College
of Engineering and Physical Sciences, Aston
University, Birmingham B4 7ET, U.K.
| | - Andreas Möglich
- Lehrstuhl
für Biochemie, Photobiochemie, Universität
Bayreuth, Bayreuth 95447, Germany
| | - Heikki Takala
- Department
of Anatomy, University of Helsinki, Helsinki 00014, Finland
- Department
of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla 40014, Finland
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17
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Ohlendorf R, Möglich A. Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives. Front Bioeng Biotechnol 2022; 10:1029403. [PMID: 36312534 PMCID: PMC9614035 DOI: 10.3389/fbioe.2022.1029403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.
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Affiliation(s)
- Robert Ohlendorf
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center for Biochemistry and Molecular Biology, Universität Bayreuth, Bayreuth, Germany
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany
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18
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An adaptive tracking illumination system for optogenetic control of single bacterial cells. Appl Microbiol Biotechnol 2022; 106:6775-6784. [PMID: 36129484 DOI: 10.1007/s00253-022-12177-6] [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: 05/26/2022] [Revised: 08/08/2022] [Accepted: 09/07/2022] [Indexed: 11/02/2022]
Abstract
Single-cell behaviors are essential during early-stage biofilm formation. In this study, we aimed to evaluate whether single-cell behaviors could be precisely and continuously manipulated by optogenetics. We thus established adaptive tracking illumination (ATI), a novel illumination method to precisely manipulate the gene expression and bacterial behavior of Pseudomonas aeruginosa on the surface at the single-cell level by using the combination of a high-throughput bacterial tracking algorithm, optogenetic manipulation, and adaptive microscopy. ATI enables precise gene expression control by manipulating the optogenetic module gene expression and type IV pili (TFP)-mediated motility and microcolony formation during biofilm formation through bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) level modifications in single cells. Moreover, we showed that the spatial organization of single cells in mature biofilms could be controlled using ATI. Therefore, this novel method we established might markedly answer various questions or resolve problems in microbiology. KEY POINTS: • High-resolution spatial and continuous optogenetic control of individual bacteria. • Phenotype-specific optogenetic control of individual bacteria. • Capacity to control biologically relevant processes in engineered single cells.
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19
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Kumar S, Khammash M. Platforms for Optogenetic Stimulation and Feedback Control. Front Bioeng Biotechnol 2022; 10:918917. [PMID: 35757811 PMCID: PMC9213687 DOI: 10.3389/fbioe.2022.918917] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Harnessing the potential of optogenetics in biology requires methodologies from different disciplines ranging from biology, to mechatronics engineering, to control engineering. Light stimulation of a synthetic optogenetic construct in a given biological species can only be achieved via a suitable light stimulation platform. Emerging optogenetic applications entail a consistent, reproducible, and regulated delivery of light adapted to the application requirement. In this review, we explore the evolution of light-induction hardware-software platforms from simple illumination set-ups to sophisticated microscopy, microtiter plate and bioreactor designs, and discuss their respective advantages and disadvantages. Here, we examine design approaches followed in performing optogenetic experiments spanning different cell types and culture volumes, with induction capabilities ranging from single cell stimulation to entire cell culture illumination. The development of automated measurement and stimulation schemes on these platforms has enabled researchers to implement various in silico feedback control strategies to achieve computer-controlled living systems—a theme we briefly discuss in the last part of this review.
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Affiliation(s)
- Sant Kumar
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
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20
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Mazraeh D, Di Ventura B. Synthetic microbiology applications powered by light. Curr Opin Microbiol 2022; 68:102158. [PMID: 35660240 DOI: 10.1016/j.mib.2022.102158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022]
Abstract
Synthetic biology is a field of research in which molecular parts (mostly nucleic acids and proteins) are de novo created or modified and then used either alone or in combination to achieve new functions that can help solve the problems of our modern society. In synthetic microbiology, microbes are employed rather than other organisms or cell-free systems. Optogenetics, a relatively recently established technology that relies on the use of genetically encoded photosensitive proteins to control biological processes with high spatiotemporal precision, offers the possibility to empower synthetic (micro)biology applications due to the many positive features that light has as an external trigger. In this review, we describe recent synthetic microbiology applications that made use of optogenetics after briefly introducing the molecular mechanism behind some of the most employed optogenetic tools. We highlight the power and versatility of this technique, which opens up new horizons for both research and industry.
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Affiliation(s)
- Daniel Mazraeh
- Signaling Research Centres BIOSS and CIBSS, and Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Barbara Di Ventura
- Signaling Research Centres BIOSS and CIBSS, and Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
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21
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Davidović A, Chait R, Batt G, Ruess J. Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. PLoS Comput Biol 2022; 18:e1009950. [PMID: 35303737 PMCID: PMC8967023 DOI: 10.1371/journal.pcbi.1009950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/30/2022] [Accepted: 02/21/2022] [Indexed: 01/30/2023] Open
Abstract
Understanding and characterising biochemical processes inside single cells requires experimental platforms that allow one to perturb and observe the dynamics of such processes as well as computational methods to build and parameterise models from the collected data. Recent progress with experimental platforms and optogenetics has made it possible to expose each cell in an experiment to an individualised input and automatically record cellular responses over days with fine time resolution. However, methods to infer parameters of stochastic kinetic models from single-cell longitudinal data have generally been developed under the assumption that experimental data is sparse and that responses of cells to at most a few different input perturbations can be observed. Here, we investigate and compare different approaches for calculating parameter likelihoods of single-cell longitudinal data based on approximations of the chemical master equation (CME) with a particular focus on coupling the linear noise approximation (LNA) or moment closure methods to a Kalman filter. We show that, as long as cells are measured sufficiently frequently, coupling the LNA to a Kalman filter allows one to accurately approximate likelihoods and to infer model parameters from data even in cases where the LNA provides poor approximations of the CME. Furthermore, the computational cost of filtering-based iterative likelihood evaluation scales advantageously in the number of measurement times and different input perturbations and is thus ideally suited for data obtained from modern experimental platforms. To demonstrate the practical usefulness of these results, we perform an experiment in which single cells, equipped with an optogenetic gene expression system, are exposed to various different light-input sequences and measured at several hundred time points and use parameter inference based on iterative likelihood evaluation to parameterise a stochastic model of the system.
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Affiliation(s)
- Anđela Davidović
- Department of Computational Biology, Institut Pasteur, Paris, France
| | - Remy Chait
- Biosciences, Living Systems Institute, University of Exeter, Exeter, The United Kingdom
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Gregory Batt
- Department of Computational Biology, Institut Pasteur, Paris, France
- Inria Paris, Paris, France
| | - Jakob Ruess
- Department of Computational Biology, Institut Pasteur, Paris, France
- Inria Paris, Paris, France
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22
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Hoffman SM, Tang AY, Avalos JL. Optogenetics Illuminates Applications in Microbial Engineering. Annu Rev Chem Biomol Eng 2022; 13:373-403. [PMID: 35320696 DOI: 10.1146/annurev-chembioeng-092120-092340] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Optogenetics has been used in a variety of microbial engineering applications, such as chemical and protein production, studies of cell physiology, and engineered microbe-host interactions. These diverse applications benefit from the precise spatiotemporal control that light affords, as well as its tunability, reversibility, and orthogonality. This combination of unique capabilities has enabled a surge of studies in recent years investigating complex biological systems with completely new approaches. We briefly describe the optogenetic tools that have been developed for microbial engineering, emphasizing the scientific advancements that they have enabled. In particular, we focus on the unique benefits and applications of implementing optogenetic control, from bacterial therapeutics to cybergenetics. Finally, we discuss future research directions, with special attention given to the development of orthogonal multichromatic controls. With an abundance of advantages offered by optogenetics, the future is bright in microbial engineering. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Shannon M Hoffman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA; , ,
| | - Allison Y Tang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA; , ,
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA; , , .,The Andlinger Center for Energy and the Environment, Department of Molecular Biology, and High Meadows Environmental Institute, Princeton University, Princeton, New Jersey, USA
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23
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Komera I, Gao C, Guo L, Hu G, Chen X, Liu L. Bifunctional optogenetic switch for improving shikimic acid production in E. coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:13. [PMID: 35418155 PMCID: PMC8822657 DOI: 10.1186/s13068-022-02111-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/28/2022] [Indexed: 12/19/2022]
Abstract
BACKGROUND Biomass formation and product synthesis decoupling have been proven to be promising to increase the titer of desired value add products. Optogenetics provides a potential strategy to develop light-induced circuits that conditionally control metabolic flux redistribution for enhanced microbial production. However, the limited number of light-sensitive proteins available to date hinders the progress of light-controlled tools. RESULTS To address these issues, two optogenetic systems (TPRS and TPAS) were constructed by reprogramming the widely used repressor TetR and protease TEVp to expand the current optogenetic toolkit. By merging the two systems, a bifunctional optogenetic switch was constructed to enable orthogonally regulated gene transcription and protein accumulation. Application of this bifunctional switch to decouple biomass formation and shikimic acid biosynthesis allowed 35 g/L of shikimic acid production in a minimal medium from glucose, representing the highest titer reported to date by E. coli without the addition of any chemical inducers and expensive aromatic amino acids. This titer was further boosted to 76 g/L when using rich medium fermentation. CONCLUSION The cost effective and light-controlled switch reported here provides important insights into environmentally friendly tools for metabolic pathway regulation and should be applicable to the production of other value-add chemicals.
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Affiliation(s)
- Irene Komera
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China. .,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China.
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24
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Zhang C, Zhao W, Duvall SW, Kowallis KA, Childers WS. Regulation of the activity of bacterial histidine kinase PleC by the scaffolding protein PodJ. J Biol Chem 2022; 298:101683. [PMID: 35124010 PMCID: PMC8980812 DOI: 10.1016/j.jbc.2022.101683] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
Scaffolding proteins can customize the response of signaling networks to support cell development and behaviors. PleC is a bifunctional histidine kinase whose signaling activity coordinates asymmetric cell division to yield a motile swarmer cell and a stalked cell in the gram-negative bacterium Caulobacter crescentus. Past studies have shown that PleC’s switch in activity from kinase to phosphatase correlates with a change in its subcellular localization pattern from diffuse to localized at the new cell pole. Here we investigated how the bacterial scaffolding protein PodJ regulates the subcellular positioning and activity of PleC. We reconstituted the PleC-PodJ signaling complex through both heterologous expressions in Escherichia coli and in vitro studies. In vitro, PodJ phase separates as a biomolecular condensate that recruits PleC and inhibits its kinase activity. We also constructed an in vivo PleC-CcaS chimeric histidine kinase reporter assay and demonstrated using this method that PodJ leverages its intrinsically disordered region to bind to PleC’s PAS sensory domain and regulate PleC-CcaS signaling. Regulation of the PleC-CcaS was most robust when PodJ was concentrated at the cell poles and was dependent on the allosteric coupling between PleC-CcaS’s PAS sensory domain and its downstream histidine kinase domain. In conclusion, our in vitro biochemical studies suggest that PodJ phase separation may be coupled to changes in PleC enzymatic function. We propose that this coupling of phase separation and allosteric regulation may be a generalizable phenomenon among enzymes associated with biomolecular condensates.
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25
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Tang K, Beyer HM, Zurbriggen MD, Gärtner W. The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters. Chem Rev 2021; 121:14906-14956. [PMID: 34669383 PMCID: PMC8707292 DOI: 10.1021/acs.chemrev.1c00194] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/15/2022]
Abstract
This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.
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Affiliation(s)
- Kun Tang
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Hannes M. Beyer
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute
of Synthetic Biology and CEPLAS, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Wolfgang Gärtner
- Retired: Max Planck Institute
for Chemical Energy Conversion. At present: Institute for Analytical Chemistry, University
Leipzig, Linnéstrasse
3, 04103 Leipzig, Germany
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26
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Xue R, Wang Y, Wang T, Lyu M, Mo G, Fan X, Li J, Yen K, Yu S, Liu Q, Xu J. Functional Verification of Novel ELMO1 Variants by Live Imaging in Zebrafish. Front Cell Dev Biol 2021; 9:723804. [PMID: 34993193 PMCID: PMC8724260 DOI: 10.3389/fcell.2021.723804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/17/2021] [Indexed: 02/02/2023] Open
Abstract
ELMO1 (Engulfment and Cell Motility1) is a gene involved in regulating cell motility through the ELMO1-DOCK2-RAC complex. Contrary to DOCK2 (Dedicator of Cytokinesis 2) deficiency, which has been reported to be associated with immunodeficiency diseases, variants of ELMO1 have been associated with autoimmune diseases, such as diabetes and rheumatoid arthritis (RA). To explore the function of ELMO1 in immune cells and to verify the functions of novel ELMO1 variants in vivo, we established a zebrafish elmo1 mutant model. Live imaging revealed that, similar to mammals, the motility of neutrophils and T-cells was largely attenuated in zebrafish mutants. Consequently, the response of neutrophils to injury or bacterial infection was significantly reduced in the mutants. Furthermore, the reduced mobility of neutrophils could be rescued by the expression of constitutively activated Rac proteins, suggesting that zebrafish elmo1 mutant functions via a conserved mechanism. With this mutant, three novel human ELMO1 variants were transiently and specifically expressed in zebrafish neutrophils. Two variants, p.E90K (c.268G>A) and p.D194G (c.581A>G), could efficiently recover the motility defect of neutrophils in the elmo1 mutant; however, the p.R354X (c.1060C>T) variant failed to rescue the mutant. Based on those results, we identified that zebrafish elmo1 plays conserved roles in cell motility, similar to higher vertebrates. Using the transient-expression assay, zebrafish elmo1 mutants could serve as an effective model for human variant verification in vivo.
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Affiliation(s)
- Rongtao Xue
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ying Wang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | | | - Mei Lyu
- Laboratory of Immunology and Regeneration, School of Medicine, South China University of Technology, Guangzhou, China
| | - Guiling Mo
- GuangZhou KingMed Center For Clinical Laboratory Co., Ltd., International Biotech Island, Guangzhou, China
| | - Xijie Fan
- GuangZhou KingMed Center For Clinical Laboratory Co., Ltd., International Biotech Island, Guangzhou, China
| | - Jianchao Li
- Laboratory of Molecular and Structural Biology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Kuangyu Yen
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Kuangyu Yen, ; Shihui Yu, ; Qifa Liu, ; Jin Xu,
| | - Shihui Yu
- GuangZhou KingMed Center For Clinical Laboratory Co., Ltd., International Biotech Island, Guangzhou, China
- *Correspondence: Kuangyu Yen, ; Shihui Yu, ; Qifa Liu, ; Jin Xu,
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Kuangyu Yen, ; Shihui Yu, ; Qifa Liu, ; Jin Xu,
| | - Jin Xu
- Laboratory of Immunology and Regeneration, School of Medicine, South China University of Technology, Guangzhou, China
- *Correspondence: Kuangyu Yen, ; Shihui Yu, ; Qifa Liu, ; Jin Xu,
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27
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Lazar JT, Tabor JJ. Bacterial two-component systems as sensors for synthetic biology applications. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:100398. [PMID: 34917859 PMCID: PMC8670732 DOI: 10.1016/j.coisb.2021.100398] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Two-component systems (TCSs) are a ubiquitous family of signal transduction pathways that enable bacteria to sense and respond to diverse physical, chemical, and biological stimuli outside and inside the cell. Synthetic biologists have begun to repurpose TCSs for applications in optogenetics, materials science, gut microbiome engineering, and soil nutrient biosensing, among others. New engineering methods including genetic refactoring, DNA-binding domain swapping, detection threshold tuning, and phosphorylation cross-talk insulation are being used to increase the reliability of TCS sensor performance and tailor TCS signaling properties to the requirements of specific applications. There is now potential to combine these methods with large-scale gene synthesis and laboratory screening to discover the inputs sensed by many uncharacterized TCSs and develop a large new family of genetically-encoded sensors that respond to an unrivaled breadth of stimuli.
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Affiliation(s)
- John T Lazar
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, Houston, TX, USA
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
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28
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Lindner F, Diepold A. Optogenetics in bacteria - applications and opportunities. FEMS Microbiol Rev 2021; 46:6427354. [PMID: 34791201 PMCID: PMC8892541 DOI: 10.1093/femsre/fuab055] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Optogenetics holds the promise of controlling biological processes with superb temporal and spatial resolution at minimal perturbation. Although many of the light-reactive proteins used in optogenetic systems are derived from prokaryotes, applications were largely limited to eukaryotes for a long time. In recent years, however, an increasing number of microbiologists use optogenetics as a powerful new tool to study and control key aspects of bacterial biology in a fast and often reversible manner. After a brief discussion of optogenetic principles, this review provides an overview of the rapidly growing number of optogenetic applications in bacteria, with a particular focus on studies venturing beyond transcriptional control. To guide future experiments, we highlight helpful tools, provide considerations for successful application of optogenetics in bacterial systems, and identify particular opportunities and challenges that arise when applying these approaches in bacteria.
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Affiliation(s)
- Florian Lindner
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Andreas Diepold
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany.,SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
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29
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Chen JX, Lim B, Steel H, Song Y, Ji M, Huang WE. Redesign of ultrasensitive and robust RecA gene circuit to sense DNA damage. Microb Biotechnol 2021; 14:2481-2496. [PMID: 33661573 PMCID: PMC8601168 DOI: 10.1111/1751-7915.13767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 01/10/2023] Open
Abstract
SOS box of the recA promoter, PVRecA from Vibrio natriegens was characterized, cloned and expressed in a probiotic strain E. coli Nissle 1917. This promoter was then rationally engineered according to predicted interactions between LexA repressor and PVRecA . The redesigned PVRecA-AT promoter showed a sensitive and robust response to DNA damage induced by UV and genotoxic compounds. Rational design of PVRecA coupled to an amplification gene circuit increased circuit output amplitude 4.3-fold in response to a DNA damaging compound mitomycin C. A TetR-based negative feedback loop was added to the PVRecA-AT amplifier to achieve a robust SOS system, resistant to environmental fluctuations in parameters including pH, temperature, oxygen and nutrient conditions. We found that E. coli Nissle 1917 with optimized PVRecA-AT adapted to UV exposure and increased SOS response 128-fold over 40 h cultivation in turbidostat mini-reactor. We also showed the potential of this PVRecA-AT system as an optogenetic actuator, which can be controlled spatially through UV radiation. We demonstrated that the optimized SOS responding gene circuits were able to detect carcinogenic biomarker molecules with clinically relevant concentrations. The ultrasensitive SOS gene circuits in probiotic E. coli Nissle 1917 would be potentially useful for bacterial diagnosis.
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Affiliation(s)
- Jack X. Chen
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Boon Lim
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Harrison Steel
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Yizhi Song
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Mengmeng Ji
- Oxford Suzhou Centre for Advanced ResearchSuzhou215123China
| | - Wei E. Huang
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
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30
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A light tunable differentiation system for the creation and control of consortia in yeast. Nat Commun 2021; 12:5829. [PMID: 34611168 PMCID: PMC8492667 DOI: 10.1038/s41467-021-26129-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
Artificial microbial consortia seek to leverage division-of-labour to optimize function and possess immense potential for bioproduction. Co-culturing approaches, the preferred mode of generating a consortium, remain limited in their ability to give rise to stable consortia having finely tuned compositions. Here, we present an artificial differentiation system in budding yeast capable of generating stable microbial consortia with custom functionalities from a single strain at user-defined composition in space and in time based on optogenetically-driven genetic rewiring. Owing to fast, reproducible, and light-tunable dynamics, our system enables dynamic control of consortia composition in continuous cultures for extended periods. We further demonstrate that our system can be extended in a straightforward manner to give rise to consortia with multiple subpopulations. Our artificial differentiation strategy establishes a novel paradigm for the creation of complex microbial consortia that are simple to implement, precisely controllable, and versatile to use.
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31
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Kusuda M, Shimizu H, Toya Y. Reactor control system in bacterial co-culture based on fluorescent proteins using an Arduino-based home-made device. Biotechnol J 2021; 16:e2100169. [PMID: 34553835 DOI: 10.1002/biot.202100169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 11/11/2022]
Abstract
BACKGROUND Co-culture, fermentation with more than two microbial strains, is a potential flexible method for optimizing the metabolic conversion process in bio-production. However, maintaining an ideal population throughout the fermentation process remains a challenge. METHODS AND RESULTS In this study, we developed a proportional control system for controlling the population ratio of Escherichia coli strains to a set value during continuous co-culture. Two E. coli strains were distinguished by expressing different fluorescent proteins, and their population ratio was determined by culture fluorescence. Furthermore, different types of amino acid auxotrophs were provided to each strain, and among these, growth was controlled by the amino acid concentrations in the feed medium. An Arduino-based device was developed using light-emitting diodes and cadmium sulfide light sensors for the in-line monitoring of culture fluorescence. Two E. coli strains of methionine auxotroph green fluorescent protein (GFP) expressing (met-GFP) strain and arginine auxotroph red fluorescent protein (RFP) expressing (arg-RFP) strain were co-cultured using a jar-fermenter. The amounts of methionine and arginine in the feed medium were altered to guide the population ratio to a set value. During the continuous culture, the population ratio between the met-GFP and arg-RFP strains was successfully maintained at approximately the setpoint values. CONCLUSION This study demonstrated the development of a home-made device for controlling the reactor of E. coli based on fluorescent proteins using inexpensive parts.
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Affiliation(s)
- Minori Kusuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
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32
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Bat-Erdene U, Billingsley JM, Turner WC, Lichman BR, Ippoliti FM, Garg NK, O'Connor SE, Tang Y. Cell-Free Total Biosynthesis of Plant Terpene Natural Products using an Orthogonal Cofactor Regeneration System. ACS Catal 2021; 11:9898-9903. [PMID: 35355836 DOI: 10.1021/acscatal.1c02267] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here we report the one-pot, cell-free enzymatic synthesis of the plant monoterpene nepetalactol starting from the readily available geraniol. A pair of orthogonal cofactor regeneration systems permitted NAD+-dependent geraniol oxidation followed by NADPH-dependent reductive cyclization without isolation of intermediates. The orthogonal cofactor regeneration system maintained a high ratio of NAD+ to NADH and a low ratio of NADP+ to NADPH. The overall reaction contains four biosynthetic enzymes, including a soluble P450; and five accessory and cofactor regeneration enzymes. Furthermore, addition of a NAD+-dependent dehydrogenase to the one-pot mixture led to ~1 g/L of nepetalactone, the active cat- attractant in catnip.
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Affiliation(s)
- Undramaa Bat-Erdene
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - John M Billingsley
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - William C Turner
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Benjamin R Lichman
- Centre for Agricultural Products, Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Francesca M Ippoliti
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Neil K Garg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
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33
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Köksaldı İÇ, Köse S, Ahan RE, Hacıosmanoğlu N, Şahin Kehribar E, Güngen MA, Baştuğ A, Dinç B, Bodur H, Özkul A, Şeker UÖŞ. SARS-CoV-2 Detection with De Novo-Designed Synthetic Riboregulators. Anal Chem 2021; 93:9719-9727. [PMID: 34192453 PMCID: PMC8265535 DOI: 10.1021/acs.analchem.1c00886] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/17/2021] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 is a human pathogen and the main cause of COVID-19 disease, announced as a global pandemic by the World Health Organization. COVID-19 is characterized by severe conditions, and early diagnosis can make dramatic changes for both personal and public health. Low-cost, easy-to-use diagnostic capabilities can have a very critical role in controlling the transmission of the disease. Here, we are reporting a state-of-the-art diagnostic tool developed with an in vitro synthetic biology approach by employing engineered de novo riboregulators. Our design coupled with a home-made point-of-care device can detect and report the presence of SARS-CoV-2-specific genes. The presence of SARS-CoV-2-related genes triggers the translation of sfGFP mRNAs, resulting in a green fluorescence output. The approach proposed here has the potential of being a game changer in SARS-CoV-2 diagnostics by providing an easy-to-run, low-cost diagnostic capability.
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Affiliation(s)
- İlkay Çisil Köksaldı
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Sıla Köse
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Recep Erdem Ahan
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Nedim Hacıosmanoğlu
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Ebru Şahin Kehribar
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Murat Alp Güngen
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Aliye Baştuğ
- Department of Infectious Diseases and Clinical
Microbiology, Health Science University Turkey, Ankara City
Hospital, 06800 Ankara, Turkey
| | - Bedia Dinç
- Department of Infectious Diseases and Clinical
Microbiology, Health Science University Turkey, Ankara City
Hospital, 06800 Ankara, Turkey
| | - Hürrem Bodur
- Department of Infectious Diseases and Clinical
Microbiology, Health Science University Turkey, Ankara City
Hospital, 06800 Ankara, Turkey
| | - Aykut Özkul
- Faculty of Veterinary Medicine, Department of
Virology, Ankara University, 06110 Ankara,
Turkey
- Biotechnology Institute, Ankara
University, 06135 Ankara, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
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34
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Abstract
Microbially produced indole metabolites serve as a diverse family of interspecies and interkingdom signaling molecules in the context of human health, crop production, and antibiotic resistance. We mined the protein database for sensors of indole metabolites and developed a biosensor for indole-3-aldehyde (I3A). Microbially produced I3A has been associated with reducing inflammation in diseases such as ulcerative colitis by stimulating the aryl hydrocarbon receptor pathway. We engineered an E. coli strain embedded with a single plasmid carrying a chimeric two-component system that detects I3A. Our I3A receptor characterization confirmed binding site residues that contribute to the sensor's I3A detection range of 0.1-10 μM. This new I3A biosensor opens the door to sensing indole metabolites produced at various host-microbe interfaces and provides new parts for synthetic biology applications.
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Affiliation(s)
- Jiefei Wang
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Chao Zhang
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Childers
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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35
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Stephens K, Zakaria FR, VanArsdale E, Payne GF, Bentley WE. Electronic signals are electrogenetically relayed to control cell growth and co-culture composition. Metab Eng Commun 2021; 13:e00176. [PMID: 34194997 PMCID: PMC8233222 DOI: 10.1016/j.mec.2021.e00176] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/20/2021] [Accepted: 05/31/2021] [Indexed: 01/17/2023] Open
Abstract
There is much to be gained by enabling electronic interrogation and control of biological function. While the benefits of bioelectronics that rely on potential-driven ionic flows are well known (electrocardiograms, defibrillators, neural prostheses, etc) there are relatively few advances targeting nonionic molecular networks, including genetic circuits. Redox activities combine connectivity to electronics with the potential for specific genetic control in cells. Here, electrode-generated hydrogen peroxide is used to actuate an electrogenetic "relay" cell population, which interprets the redox cue and synthesizes a bacterial signaling molecule (quorum sensing autoinducer AI-1) that, in turn, signals increased growth rate in a second population. The dramatically increased growth rate of the second population is enabled by expression of a phosphotransferase system protein, HPr, which is important for glucose transport. The potential to electronically modulate cell growth via direct genetic control will enable new opportunities in the treatment of disease and manufacture of biological therapeutics and other molecules.
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Affiliation(s)
- Kristina Stephens
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| | - Fauziah Rahma Zakaria
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| | - Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
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36
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Repina NA, McClave T, Johnson HJ, Bao X, Kane RS, Schaffer DV. Engineered Illumination Devices for Optogenetic Control of Cellular Signaling Dynamics. Cell Rep 2021; 31:107737. [PMID: 32521262 PMCID: PMC9357365 DOI: 10.1016/j.celrep.2020.107737] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 03/09/2020] [Accepted: 05/14/2020] [Indexed: 10/31/2022] Open
Abstract
Spatially and temporally varying patterns of morphogen signals during development drive cell fate specification at the proper location and time. However, current in vitro methods typically do not allow for precise, dynamic spatiotemporal control of morphogen signaling and are thus insufficient to readily study how morphogen dynamics affect cell behavior. Here, we show that optogenetic Wnt/β-catenin pathway activation can be controlled at user-defined intensities, temporal sequences, and spatial patterns using engineered illumination devices for optogenetic photostimulation and light activation at variable amplitudes (LAVA). By patterning human embryonic stem cell (hESC) cultures with varying light intensities, LAVA devices enabled dose-responsive control of optoWnt activation and Brachyury expression. Furthermore, time-varying and spatially localized patterns of light revealed tissue patterning that models the embryonic presentation of Wnt signals in vitro. LAVA devices thus provide a low-cost, user-friendly method for high-throughput and spatiotemporal optogenetic control of cell signaling for applications in developmental and cell biology.
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Affiliation(s)
- Nicole A Repina
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA; Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas McClave
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hunter J Johnson
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA; Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaoping Bao
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ravi S Kane
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - David V Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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37
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Harnessing the central dogma for stringent multi-level control of gene expression. Nat Commun 2021; 12:1738. [PMID: 33741937 PMCID: PMC7979795 DOI: 10.1038/s41467-021-21995-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/18/2021] [Indexed: 11/17/2022] Open
Abstract
Strictly controlled inducible gene expression is crucial when engineering biological systems where even tiny amounts of a protein have a large impact on function or host cell viability. In these cases, leaky protein production must be avoided, but without affecting the achievable range of expression. Here, we demonstrate how the central dogma offers a simple solution to this challenge. By simultaneously regulating transcription and translation, we show how basal expression of an inducible system can be reduced, with little impact on the maximum expression rate. Using this approach, we create several stringent expression systems displaying >1000-fold change in their output after induction and show how multi-level regulation can suppress transcriptional noise and create digital-like switches between ‘on’ and ‘off’ states. These tools will aid those working with toxic genes or requiring precise regulation and propagation of cellular signals, plus illustrate the value of more diverse regulatory designs for synthetic biology. Inducible gene expression systems should minimise leaky output and offer a large achievable range of expression. Here, the authors regulate transcription and translation together to suppress noise and create digital-like responses, while maintaining a large expression range in vivo and in vitro.
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38
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Lovelett RJ, Zhao EM, Lalwani MA, Toettcher JE, Kevrekidis IG, L Avalos J. Dynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering Applications. ACS Synth Biol 2021; 10:219-227. [PMID: 33492138 PMCID: PMC10410538 DOI: 10.1021/acssynbio.0c00372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic control of engineered microbes using light via optogenetics has been demonstrated as an effective strategy for improving the yield of biofuels, chemicals, and other products. An advantage of using light to manipulate microbial metabolism is the relative simplicity of interfacing biological and computer systems, thereby enabling in silico control of the microbe. Using this strategy for control and optimization of product yield requires an understanding of how the microbe responds in real-time to the light inputs. Toward this end, we present mechanistic models of a set of yeast optogenetic circuits. We show how these models can predict short- and long-time response to varying light inputs and how they are amenable to use with model predictive control (the industry standard among advanced control algorithms). These models reveal dynamics characterized by time-scale separation of different circuit components that affect the steady and transient levels of the protein under control of the circuit. Ultimately, this work will help enable real-time control and optimization tools for improving yield and consistency in the production of biofuels and chemicals using microbial fermentations.
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Affiliation(s)
- Robert J Lovelett
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Evan M Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Makoto A Lalwani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton, New Jersey 08544, United States
| | - Ioannis G Kevrekidis
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- The Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States
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39
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Soffer G, Perry JM, Shih SCC. Real-Time Optogenetics System for Controlling Gene Expression Using a Model-Based Design. Anal Chem 2021; 93:3181-3188. [PMID: 33543619 DOI: 10.1021/acs.analchem.0c04594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Optimization of engineered biological systems requires precise control over the rates and timing of gene expression. Optogenetics is used to dynamically control gene expression as an alternative to conventional chemical-based methods since it provides a more convenient interface between digital control software and microbial culture. Here, we describe the construction of a real-time optogenetics platform, which performs closed-loop control over the CcaR-CcaS two-plasmid system in Escherichia coli. We showed the first model-based design approach by constructing a nonlinear representation of the CcaR-CcaS system, tuned the model through open-loop experimentation to capture the experimental behavior, and applied the model in silico to inform the necessary changes to build a closed-loop optogenetic control system. Our system periodically induces and represses the CcaR-CcaS system while recording optical density and fluorescence using image processing techniques. We highlight the facile nature of constructing our system and how our model-based design approach will potentially be used to model other systems requiring closed-loop optogenetic control.
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Affiliation(s)
- Guy Soffer
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd West, Montréal, Québec H3G1M8, Canada.,Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B1R6, Canada
| | - James M Perry
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B1R6, Canada.,Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B1R6, Canada
| | - Steve C C Shih
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd West, Montréal, Québec H3G1M8, Canada.,Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B1R6, Canada.,Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B1R6, Canada
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40
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Baumschlager A, Khammash M. Synthetic Biological Approaches for Optogenetics and Tools for Transcriptional Light-Control in Bacteria. Adv Biol (Weinh) 2021; 5:e2000256. [PMID: 34028214 DOI: 10.1002/adbi.202000256] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/11/2021] [Indexed: 12/22/2022]
Abstract
Light has become established as a tool not only to visualize and investigate but also to steer biological systems. This review starts by discussing the unique features that make light such an effective control input in biology. It then gives an overview of how light-control came to progress, starting with photoactivatable compounds and leading up to current genetic implementations using optogenetic approaches. The review then zooms in on optogenetics, focusing on photosensitive proteins, which form the basis for optogenetic engineering using synthetic biological approaches. As the regulation of transcription provides a highly versatile means for steering diverse biological functions, the focus of this review then shifts to transcriptional light regulators, which are presented in the biotechnologically highly relevant model organism Escherichia coli.
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Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
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41
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Zhao EM, Lalwani MA, Lovelett RJ, García-Echauri SA, Hoffman SM, Gonzalez CL, Toettcher JE, Kevrekidis IG, Avalos JL. Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering. ACS Synth Biol 2020; 9:3254-3266. [PMID: 33232598 PMCID: PMC10399620 DOI: 10.1021/acssynbio.0c00305] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The use of optogenetics in metabolic engineering for light-controlled microbial chemical production raises the prospect of utilizing control and optimization techniques routinely deployed in traditional chemical manufacturing. However, such mechanisms require well-characterized, customizable tools that respond fast enough to be used as real-time inputs during fermentations. Here, we present OptoINVRT7, a new rapid optogenetic inverter circuit to control gene expression in Saccharomyces cerevisiae. The circuit induces gene expression in only 0.6 h after switching cells from light to darkness, which is at least 6 times faster than previous OptoINVRT optogenetic circuits used for chemical production. In addition, we introduce an engineered inducible GAL1 promoter (PGAL1-S), which is stronger than any constitutive or inducible promoter commonly used in yeast. Combining OptoINVRT7 with PGAL1-S achieves strong and light-tunable levels of gene expression with as much as 132.9 ± 22.6-fold induction in darkness. The high performance of this new optogenetic circuit in controlling metabolic enzymes boosts production of lactic acid and isobutanol by more than 50% and 15%, respectively. The strength and controllability of OptoINVRT7 and PGAL1-S open the door to applying process control tools to engineered metabolisms to improve robustness and yields in microbial fermentations for chemical production.
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Affiliation(s)
- Evan M. Zhao
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Makoto A. Lalwani
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Robert J. Lovelett
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, 221 Maryland
Hall, Johns Hopkins University, 2400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Sergio A. García-Echauri
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Shannon M. Hoffman
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Christopher L. Gonzalez
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Jared E. Toettcher
- Department of Molecular Biology, 140 Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Ioannis G. Kevrekidis
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, 221 Maryland
Hall, Johns Hopkins University, 2400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - José L. Avalos
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, 140 Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
- The Andlinger Center for Energy and the Environment, Princeton University, 86 Olden Street, Princeton, New Jersey 08544, United States
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42
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Hartsough LA, Park M, Kotlajich MV, Lazar JT, Han B, Lin CCJ, Musteata E, Gambill L, Wang MC, Tabor JJ. Optogenetic control of gut bacterial metabolism to promote longevity. eLife 2020; 9:56849. [PMID: 33325823 PMCID: PMC7744093 DOI: 10.7554/elife.56849] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022] Open
Abstract
Gut microbial metabolism is associated with host longevity. However, because it requires direct manipulation of microbial metabolism in situ, establishing a causal link between these two processes remains challenging. We demonstrate an optogenetic method to control gene expression and metabolite production from bacteria residing in the host gut. We genetically engineer an Escherichia coli strain that secretes colanic acid (CA) under the quantitative control of light. Using this optogenetically-controlled strain to induce CA production directly in the Caenorhabditis elegans gut, we reveal the local effect of CA in protecting intestinal mitochondria from stress-induced hyper-fragmentation. We also demonstrate that the lifespan-extending effect of this strain is positively correlated with the intensity of green light, indicating a dose-dependent CA benefit on the host. Thus, optogenetics can be used to achieve quantitative and temporal control of gut bacterial metabolism in order to reveal its local and systemic effects on host health and aging.
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Affiliation(s)
| | | | | | - John Tyler Lazar
- Department of Chemical and Biomolecular Engineering, Houston, United States
| | - Bing Han
- Huffington Center on Aging, Houston, United States
| | - Chih-Chun J Lin
- Huffington Center on Aging, Houston, United States.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, United States
| | - Elena Musteata
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, United States
| | - Lauren Gambill
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, United States
| | - Meng C Wang
- Huffington Center on Aging, Houston, United States.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, United States.,Howard Hughes Medical Institute, Houston, United States
| | - Jeffrey J Tabor
- Department of Bioengineering, Houston, United States.,Systems, Synthetic, and Physical Biology Program, Rice University, Houston, United States.,Department of Biosciences, Houston, United States
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43
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Pouzet S, Banderas A, Le Bec M, Lautier T, Truan G, Hersen P. The Promise of Optogenetics for Bioproduction: Dynamic Control Strategies and Scale-Up Instruments. Bioengineering (Basel) 2020; 7:E151. [PMID: 33255280 PMCID: PMC7712799 DOI: 10.3390/bioengineering7040151] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/11/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Progress in metabolic engineering and synthetic and systems biology has made bioproduction an increasingly attractive and competitive strategy for synthesizing biomolecules, recombinant proteins and biofuels from renewable feedstocks. Yet, due to poor productivity, it remains difficult to make a bioproduction process economically viable at large scale. Achieving dynamic control of cellular processes could lead to even better yields by balancing the two characteristic phases of bioproduction, namely, growth versus production, which lie at the heart of a trade-off that substantially impacts productivity. The versatility and controllability offered by light will be a key element in attaining the level of control desired. The popularity of light-mediated control is increasing, with an expanding repertoire of optogenetic systems for novel applications, and many optogenetic devices have been designed to test optogenetic strains at various culture scales for bioproduction objectives. In this review, we aim to highlight the most important advances in this direction. We discuss how optogenetics is currently applied to control metabolism in the context of bioproduction, describe the optogenetic instruments and devices used at the laboratory scale for strain development, and explore how current industrial-scale bioproduction processes could be adapted for optogenetics or could benefit from existing photobioreactor designs. We then draw attention to the steps that must be undertaken to further optimize the control of biological systems in order to take full advantage of the potential offered by microbial factories.
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Affiliation(s)
- Sylvain Pouzet
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 26 rue d’Ulm, 75005 Paris, France; (A.B.); (M.L.B.)
- Sorbonne Université, 75005 Paris, France
- Laboratoire MSC, UMR7057, Université Paris Diderot-CNRS, 75013 Paris, France
| | - Alvaro Banderas
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 26 rue d’Ulm, 75005 Paris, France; (A.B.); (M.L.B.)
- Sorbonne Université, 75005 Paris, France
- Laboratoire MSC, UMR7057, Université Paris Diderot-CNRS, 75013 Paris, France
| | - Matthias Le Bec
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 26 rue d’Ulm, 75005 Paris, France; (A.B.); (M.L.B.)
- Sorbonne Université, 75005 Paris, France
- Laboratoire MSC, UMR7057, Université Paris Diderot-CNRS, 75013 Paris, France
| | - Thomas Lautier
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 31400 Toulouse, France; (T.L.); (G.T.)
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science Technology and Research, Singapore 138673, Singapore
| | - Gilles Truan
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 31400 Toulouse, France; (T.L.); (G.T.)
| | - Pascal Hersen
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 26 rue d’Ulm, 75005 Paris, France; (A.B.); (M.L.B.)
- Sorbonne Université, 75005 Paris, France
- Laboratoire MSC, UMR7057, Université Paris Diderot-CNRS, 75013 Paris, France
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44
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Hongdusit A, Liechty ET, Fox JM. Optogenetic interrogation and control of cell signaling. Curr Opin Biotechnol 2020; 66:195-206. [PMID: 33053496 DOI: 10.1016/j.copbio.2020.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 02/05/2023]
Abstract
Signaling networks control the flow of information through biological systems and coordinate the chemical processes that constitute cellular life. Optogenetic actuators - genetically encoded proteins that undergo light-induced changes in activity or conformation - are useful tools for probing signaling networks over time and space. They have permitted detailed dissections of cellular proliferation, differentiation, motility, and death, and enabled the assembly of synthetic systems with applications in areas as diverse as photography, chemical synthesis, and medicine. In this review, we provide a brief introduction to optogenetic systems and describe their application to molecular-level analyses of cell signaling. Our discussion highlights important research achievements and speculates on future opportunities to exploit optogenetic systems in the study and assembly of complex biochemical networks.
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Affiliation(s)
- Akarawin Hongdusit
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80303, USA
| | - Evan T Liechty
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80303, USA
| | - Jerome M Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80303, USA.
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45
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Toward a systematic design of smart probiotics. Curr Opin Biotechnol 2020; 64:199-209. [DOI: 10.1016/j.copbio.2020.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 04/24/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022]
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46
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Steel H, Habgood R, Kelly CL, Papachristodoulou A. In situ characterisation and manipulation of biological systems with Chi.Bio. PLoS Biol 2020; 18:e3000794. [PMID: 32730242 PMCID: PMC7419009 DOI: 10.1371/journal.pbio.3000794] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 08/11/2020] [Accepted: 07/08/2020] [Indexed: 11/18/2022] Open
Abstract
The precision and repeatability of in vivo biological studies is predicated upon methods for isolating a targeted subsystem from external sources of noise and variability. However, in many experimental frameworks, this is made challenging by nonstatic environments during host cell growth, as well as variability introduced by manual sampling and measurement protocols. To address these challenges, we developed Chi.Bio, a parallelised open-source platform that represents a new experimental paradigm in which all measurement and control actions can be applied to a bulk culture in situ. In addition to continuous-culturing capabilities, it incorporates tunable light outputs, spectrometry, and advanced automation features. We demonstrate its application to studies of cell growth and biofilm formation, automated in silico control of optogenetic systems, and readout of multiple orthogonal fluorescent proteins in situ. By integrating precise measurement and actuation hardware into a single low-cost platform, Chi.Bio facilitates novel experimental methods for synthetic, systems, and evolutionary biology and broadens access to cutting-edge research capabilities.
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Affiliation(s)
- Harrison Steel
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Robert Habgood
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Ciarán L. Kelly
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
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47
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Sexton JT, Tabor JJ. Multiplexing cell-cell communication. Mol Syst Biol 2020; 16:e9618. [PMID: 32672881 PMCID: PMC7365139 DOI: 10.15252/msb.20209618] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/02/2020] [Accepted: 06/16/2020] [Indexed: 11/09/2022] Open
Abstract
The engineering of advanced multicellular behaviors, such as the programmed growth of biofilms or tissues, requires cells to communicate multiple aspects of physiological information. Unfortunately, few cell-cell communication systems have been developed for synthetic biology. Here, we engineer a genetically encoded channel selector device that enables a single communication system to transmit two separate intercellular conversations. Our design comprises multiplexer and demultiplexer sub-circuits constructed from a total of 12 CRISPRi-based transcriptional logic gates, an acyl homoserine lactone-based communication module, and three inducible promoters that enable small molecule control over the conversations. Experimentally parameterized mathematical models of the sub-components predict the steady state and dynamical performance of the full system. Multiplexed cell-cell communication has applications in synthetic development, metabolic engineering, and other areas requiring the coordination of multiple pathways among a community of cells.
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Affiliation(s)
- John T Sexton
- Department of BioengineeringRice UniversityHoustonTXUSA
| | - Jeffrey J Tabor
- Department of BioengineeringRice UniversityHoustonTXUSA
- Department of BioSciencesRice UniversityHoustonTXUSA
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48
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Li X, Zhang C, Xu X, Miao J, Yao J, Liu R, Zhao Y, Chen X, Yang Y. A single-component light sensor system allows highly tunable and direct activation of gene expression in bacterial cells. Nucleic Acids Res 2020; 48:e33. [PMID: 31989175 PMCID: PMC7102963 DOI: 10.1093/nar/gkaa044] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 01/11/2020] [Accepted: 01/16/2020] [Indexed: 11/23/2022] Open
Abstract
Light-regulated modules offer unprecedented new ways to control cellular behaviour with precise spatial and temporal resolution. Among a variety of bacterial light-switchable gene expression systems, single-component systems consisting of single transcription factors would be more useful due to the advantages of speed, simplicity, and versatility. In the present study, we developed a single-component light-activated bacterial gene expression system (eLightOn) based on a novel LOV domain from Rhodobacter sphaeroides (RsLOV). The eLightOn system showed significant improvements over the existing single-component bacterial light-activated expression systems, with benefits including a high ON/OFF ratio of >500-fold, a high activation level, fast activation kinetics, and/or good adaptability. Additionally, the induction characteristics, including regulatory windows, activation kinetics and light sensitivities, were highly tunable by altering the expression level of LexRO. We demonstrated the usefulness of the eLightOn system in regulating cell division and swimming by controlling the expression of the FtsZ and CheZ genes, respectively, as well as constructing synthetic Boolean logic gates using light and arabinose as the two inputs. Taken together, our data indicate that the eLightOn system is a robust and highly tunable tool for quantitative and spatiotemporal control of bacterial gene expression.
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Affiliation(s)
- Xie Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Changcheng Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Xiaopei Xu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Jun Miao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Jing Yao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.,CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.,CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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49
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Heterogeneity coordinates bacterial multi-gene expression in single cells. PLoS Comput Biol 2020; 16:e1007643. [PMID: 32004314 PMCID: PMC7015429 DOI: 10.1371/journal.pcbi.1007643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 02/12/2020] [Accepted: 01/09/2020] [Indexed: 11/19/2022] Open
Abstract
For a genetically identical microbial population, multi-gene expression in various environments requires effective allocation of limited resources and precise control of heterogeneity among individual cells. However, it is unclear how resource allocation and cell-to-cell variation jointly shape the overall performance. Here we demonstrate a Simpson’s paradox during overexpression of multiple genes: two competing proteins in single cells correlated positively for every induction condition, but the overall correlation was negative. Yet this phenomenon was not observed between two competing mRNAs in single cells. Our analytical framework shows that the phenomenon arises from competition for translational resource, with the correlation modulated by both mRNA and ribosome variability. Thus, heterogeneity plays a key role in single-cell multi-gene expression and provides the population with an evolutionary advantage, as demonstrated in this study. Microbes perform multitasking for a wide range of purposes, including survival, adaptation, colonization, and evolution. Both modelling and experimental results at the ensemble level reveal trade-offs between different tasks due to resource competition, but it is unclear how single cells allocate limited intracellular resources to perform multitasking, and how does a population coordinate single cell performances during multitasking to maximize population efficiencies. In this study, we address this question by using bacterial multi-gene overexpression as the basic form of multitasking. We discovered and analyzed a statistical phenomenon called Simpson’s paradox, where competing proteins in single cells correlate positively at each constant condition, although the proteins correlate negatively when all conditions are combined. We demonstrate that the phenomenon arises from competition for translational resources, with the correlation modulated by heterogeneity of both mRNA and ribosomes. We further show that heterogeneity coordinates multiple functional modules, conferring an evolutionary advantage on the population. Our work discloses that heterogeneity in the form of Simpson’s paradox is an important phenomenon in coordinating multi-gene expression.
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50
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Venayak N, Raj K, Mahadevan R. Impact framework: A python package for writing data analysis workflows to interpret microbial physiology. Metab Eng Commun 2019; 9:e00089. [PMID: 31011536 PMCID: PMC6462781 DOI: 10.1016/j.mec.2019.e00089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 12/26/2022] Open
Abstract
Microorganisms can be genetically engineered to solve a range of challenges in diverse including health, environmental protection and sustainability. The natural complexity of biological systems makes this an iterative cycle, perturbing metabolism and making stepwise progress toward a desired phenotype through four major stages: design, build, test, and data interpretation. This cycle has been accelerated by advances in molecular biology (e.g. robust DNA synthesis and assembly techniques), liquid handling automation and scale-down characterization platforms, generating large heterogeneous data sets. Here, we present an extensible Python package for scientists and engineers working with large biological data sets to interpret, model, and visualize data: the IMPACT (Integrated Microbial Physiology: Analysis, Characterization and Translation) framework. Impact aims to ease the development of Python-based data analysis workflows for a range of stakeholders in the bioengineering process, offering open-source tools for data analysis, physiology characterization and translation to visualization. Using this framework, biologists and engineers can opt for reproducible and extensible programmatic data analysis workflows, mediating a bottleneck limiting the throughput of microbial engineering. The Impact framework is available at https://github.com/lmse/impact.
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Affiliation(s)
- Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Kaushik Raj
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
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