1
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Burbano DA, Kiattisewee C, Karanjia AV, Cardiff RAL, Faulkner ID, Sugianto W, Carothers JM. CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications. Annu Rev Chem Biomol Eng 2024; 15:389-430. [PMID: 38598861 DOI: 10.1146/annurev-chembioeng-100522-114706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.
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Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Cholpisit Kiattisewee
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ava V Karanjia
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ian D Faulkner
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - James M Carothers
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
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2
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Sun Y, Zhang F, Ouyang Q, Luo C. The dynamic-process characterization and prediction of synthetic gene circuits by dynamic delay model. iScience 2024; 27:109142. [PMID: 38384832 PMCID: PMC10879701 DOI: 10.1016/j.isci.2024.109142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
Differential equation models are widely used to describe genetic regulations, predict multicomponent regulatory circuits, and provide quantitative insights. However, it is still challenging to quantitatively link the dynamic behaviors with measured parameters in synthetic circuits. Here, we propose a dynamic delay model (DDM) which includes two simple parts: the dynamic determining part and the doses-related steady-state-determining part. The dynamic determining part is usually supposed as the delay time but without a clear formula. For the first time, we give the detail formula of the dynamic determining function and provide a method for measuring all parameters of synthetic elements (include 8 activators and 5 repressors) by microfluidic system. Three synthetic circuits were built to show that the DDM can notably improve the prediction accuracy and can be used in various synthetic biology applications.
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Affiliation(s)
- Yanhong Sun
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Fengyu Zhang
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Qi Ouyang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
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3
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Buson F, Gao Y, Wang B. Genetic Parts and Enabling Tools for Biocircuit Design. ACS Synth Biol 2024; 13:697-713. [PMID: 38427821 DOI: 10.1021/acssynbio.3c00691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Synthetic biology aims to engineer biological systems for customized tasks through the bottom-up assembly of fundamental building blocks, which requires high-quality libraries of reliable, modular, and standardized genetic parts. To establish sets of parts that work well together, synthetic biologists created standardized part libraries in which every component is analyzed in the same metrics and context. Here we present a state-of-the-art review of the currently available part libraries for designing biocircuits and their gene expression regulation paradigms at transcriptional, translational, and post-translational levels in Escherichia coli. We discuss the necessary facets to integrate these parts into complex devices and systems along with the current efforts to catalogue and standardize measurement data. To better display the range of available parts and to facilitate part selection in synthetic biology workflows, we established biopartsDB, a curated database of well-characterized and useful genetic part and device libraries with detailed quantitative data validated by the published literature.
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Affiliation(s)
- Felipe Buson
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
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4
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Gao Y, Wang L, Wang B. Customizing cellular signal processing by synthetic multi-level regulatory circuits. Nat Commun 2023; 14:8415. [PMID: 38110405 PMCID: PMC10728147 DOI: 10.1038/s41467-023-44256-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
As synthetic biology permeates society, the signal processing circuits in engineered living systems must be customized to meet practical demands. Towards this mission, novel regulatory mechanisms and genetic circuits with unprecedented complexity have been implemented over the past decade. These regulatory mechanisms, such as transcription and translation control, could be integrated into hybrid circuits termed "multi-level circuits". The multi-level circuit design will tremendously benefit the current genetic circuit design paradigm, from modifying basic circuit dynamics to facilitating real-world applications, unleashing our capabilities to customize cellular signal processing and address global challenges through synthetic biology.
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Affiliation(s)
- Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Lei Wang
- Center of Synthetic Biology and Integrated Bioengineering & School of Engineering, Westlake University, Hangzhou, 310030, China.
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058, China.
- Research Center for Biological Computation, Zhejiang Lab, Hangzhou, 311100, China.
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5
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Wang L, Zhao J, Xiong X, Li L, Zhu T, Pei H. Enzyme-Free Nucleic Acid Circuits for Fold-Change Detection. Chempluschem 2023; 88:e202300083. [PMID: 37005227 DOI: 10.1002/cplu.202300083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/04/2023]
Abstract
Fold-change detection is widespread in sensory systems of various organisms. Dynamic DNA nanotechnology provides an important toolbox for reproducing structures and responses of cellular circuits. In this work, we construct an enzyme-free nucleic acid circuit based on the incoherent feed-forward loop using toehold-mediated DNA strand displacement reactions and explore its dynamic behaviors. The mathematical model based on ordinary differential equations is used to evaluate the parameter regime required for fold-change detection. After selecting appropriate parameters, the constructed synthetic circuit exhibits approximate fold-change detection for multiple rounds of inputs with different initial concentrations. This work is anticipated to shed new light on the design of DNA dynamic circuits in the enzyme-free environment.
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Affiliation(s)
- Likun Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241 (P. R., China
| | - Jiayan Zhao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241 (P. R., China
| | - Xiewei Xiong
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241 (P. R., China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241 (P. R., China
| | - Tong Zhu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241 (P. R., China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241 (P. R., China
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6
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Alba Burbano D, Cardiff RAL, Tickman BI, Kiattisewee C, Maranas CJ, Zalatan JG, Carothers JM. Engineering activatable promoters for scalable and multi-input CRISPRa/i circuits. Proc Natl Acad Sci U S A 2023; 120:e2220358120. [PMID: 37463216 PMCID: PMC10374173 DOI: 10.1073/pnas.2220358120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/13/2023] [Indexed: 07/20/2023] Open
Abstract
Dynamic, multi-input gene regulatory networks (GRNs) are ubiquitous in nature. Multilayer CRISPR-based genetic circuits hold great promise for building GRNs akin to those found in naturally occurring biological systems. We develop an approach for creating high-performing activatable promoters that can be assembled into deep, wide, and multi-input CRISPR-activation and -interference (CRISPRa/i) GRNs. By integrating sequence-based design and in vivo screening, we engineer activatable promoters that achieve up to 1,000-fold dynamic range in an Escherichia coli-based cell-free system. These components enable CRISPRa GRNs that are six layers deep and four branches wide. We show the generalizability of the promoter engineering workflow by improving the dynamic range of the light-dependent EL222 optogenetic system from 6-fold to 34-fold. Additionally, high dynamic range promoters enable CRISPRa systems mediated by small molecules and protein-protein interactions. We apply these tools to build input-responsive CRISPRa/i GRNs, including feedback loops, logic gates, multilayer cascades, and dynamic pulse modulators. Our work provides a generalizable approach for the design of high dynamic range activatable promoters and enables classes of gene regulatory functions in cell-free systems.
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Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, WA98195
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
| | - Ryan A. L. Cardiff
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Benjamin I. Tickman
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Cholpisit Kiattisewee
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Cassandra J. Maranas
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Jesse G. Zalatan
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
- Department of Chemistry, University of Washington, Seattle, WA98195
| | - James M. Carothers
- Department of Chemical Engineering, University of Washington, Seattle, WA98195
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
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7
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Stone A, Ryan J, Tang X, Tian XJ. Negatively Competitive Incoherent Feedforward Loops Mitigate Winner-Take-All Resource Competition. ACS Synth Biol 2022; 11:3986-3995. [PMID: 36355441 DOI: 10.1021/acssynbio.2c00318] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The effects of host resource limitations on the function of synthetic gene circuits have gained significant attention over the past years. Hosts, having evolved resource capacities optimal for their own genome, have been repeatedly demonstrated to suffer from the added burden of synthetic genetic programs, which may in return pose deleterious effects on the circuit's function. Three resource controller archetypes have been proposed previously to mitigate resource distribution problems in dynamic circuits: the local controller, the global controller, and a "negatively competitive" regulatory (NCR) controller that utilizes synthetic competition to combat resource competition. The dynamics of negative feedback forms of these controllers have been previously investigated, and here we extend the analysis of these resource allocation strategies to the incoherent feedforward loop (iFFL) topology. We demonstrate that the three iFFL controllers can attenuate Winner-Take-All resource competition between two bistable switches. We uncover that the parameters associated with the synthetic competition in the NCR iFFL controller are paramount to its increased efficacy over the local controller type, while the global controllers demonstrate to be relatively ineffectual. Interestingly, unlike the negative feedback counterpart topologies, iFFL controllers exhibit a unique coupling of switch activation thresholds which we term the "coactivation threshold shift" effect. Finally, we demonstrate that a nearly fully orthogonal set of bistable switches could be achieved by pairing an NCR controller with an appropriate level of controller resource consumption.
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Affiliation(s)
- Austin Stone
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona85281, United States
| | - Jordan Ryan
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana70803, United States
| | - Xun Tang
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana70803, United States
| | - Xiao-Jun Tian
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona85281, United States
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8
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Sun Y, Zhang F, Li L, Chen K, Wang S, Ouyang Q, Luo C. Two-Layered Microfluidic Devices for High-Throughput Dynamic Analysis of Synthetic Gene Circuits in E. coli. ACS Synth Biol 2022; 11:3954-3965. [PMID: 36283074 DOI: 10.1021/acssynbio.2c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Escherichia coli is a common chassis for synthetic gene circuit studies. In addition to the dose-response of synthetic gene circuits, the analysis of dynamic responses is also an important part of the future design of more complicated synthetic systems. Recently, microfluidic-based methods have been widely used for the analysis of gene expression dynamics. Here, we established a two-layered microfluidic platform for the systematic characterization of synthetic gene circuits (eight strains in eight different culture environments could be observed simultaneously with a 5 min time resolution). With this platform, both dose responses and dynamic responses with a high temporal resolution could be easily derived for further analysis. A controlled environment ensures the stability of the bacterial growth rate, excluding changes in gene expression dynamics caused by changes of the growth dilution rate. The precise environmental switch and automatic micrograph shooting ensured that there was nearly no time lag between the inducer addition and the data recording. We studied four four-node incoherent-feedforward-loop (IFFL) networks with different operators using this device. The experimental results showed that as the effect of inhibition increased, two of the IFFL networks generated pulselike dynamic gene expressions in the range of the inducer concentrations, which was different from the dynamics of the two other circuits with only a simple pattern of rising to the platform. Through fitting the dose-response curves and the dynamic response curves, corresponding parameters were derived and introduced to a simple model that could qualitatively explain the generation of pulse dynamics.
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Affiliation(s)
- Yanhong Sun
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics School of Physics, Peking University, Beijing100871, China
| | - Fengyu Zhang
- School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Lusi Li
- Academy of Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Kaiyue Chen
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang325001, China
| | - Shujing Wang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics School of Physics, Peking University, Beijing100871, China
| | - Qi Ouyang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics School of Physics, Peking University, Beijing100871, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics School of Physics, Peking University, Beijing100871, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China.,Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang325001, China
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9
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Rhea KA, McDonald ND, Cole SD, Noireaux V, Lux MW, Buckley PE. Variability in cell-free expression reactions can impact qualitative genetic circuit characterization. Synth Biol (Oxf) 2022; 7:ysac011. [PMID: 35966404 PMCID: PMC9365049 DOI: 10.1093/synbio/ysac011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/24/2022] [Accepted: 08/01/2022] [Indexed: 09/21/2023] Open
Abstract
Cell-free expression systems provide a suite of tools that are used in applications from sensing to biomanufacturing. One of these applications is genetic circuit prototyping, where the lack of cloning is required and a high degree of control over reaction components and conditions enables rapid testing of design candidates. Many studies have shown utility in the approach for characterizing genetic regulation elements, simple genetic circuit motifs, protein variants or metabolic pathways. However, variability in cell-free expression systems is a known challenge, whether between individuals, laboratories, instruments, or batches of materials. While the issue of variability has begun to be quantified and explored, little effort has been put into understanding the implications of this variability. For genetic circuit prototyping, it is unclear when and how significantly variability in reaction activity will impact qualitative assessments of genetic components, e.g. relative activity between promoters. Here, we explore this question by assessing DNA titrations of seven genetic circuits of increasing complexity using reaction conditions that ostensibly follow the same protocol but vary by person, instrument and material batch. Although the raw activities vary widely between the conditions, by normalizing within each circuit across conditions, reasonably consistent qualitative performance emerges for the simpler circuits. For the most complex case involving expression of three proteins, we observe a departure from this qualitative consistency, offering a provisional cautionary line where normal variability may disrupt reliable reuse of prototyping results. Our results also suggest that a previously described closed loop controller circuit may help to mitigate such variability, encouraging further work to design systems that are robust to variability. Graphical Abstract.
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Affiliation(s)
- Katherine A Rhea
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Nathan D McDonald
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Stephanie D Cole
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Matthew W Lux
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Patricia E Buckley
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
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10
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Copeland CE, Kim J, Copeland PL, Heitmeier CJ, Kwon YC. Characterizing a New Fluorescent Protein for a Low Limit of Detection Sensing in the Cell-Free System. ACS Synth Biol 2022; 11:2800-2810. [PMID: 35850511 PMCID: PMC9396652 DOI: 10.1021/acssynbio.2c00180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell-free protein synthesis-based biosensors have been developed as highly accurate, low-cost biosensors. However, since most biomarkers exist at low concentrations in various types of biopsies, the biosensor's dynamic range must be increased in the system to achieve low limits of detection necessary while deciphering from higher background signals. Many attempts to increase the dynamic range have relied on amplifying the input signal from the analyte, which can lead to complications of false positives. In this study, we aimed to increase the protein synthesis capability of the cell-free protein synthesis system and the output signal of the reporter protein to achieve a lower limit of detection. We utilized a new fluorescent protein, mNeonGreen, which produces a higher output than those commonly used in cell-free biosensors. Optimizations of DNA sequence and the subsequent cell-free protein synthesis reaction conditions allowed characterizing protein expression variability by given DNA template types, reaction environment, and storage additives that cause the greatest time constraint on designing the cell-free biosensor. Finally, we characterized the fluorescence kinetics of mNeonGreen compared to the commonly used reporter protein, superfolder green fluorescent protein. We expect that this finely tuned cell-free protein synthesis platform with the new reporter protein can be used with sophisticated synthetic gene circuitry networks to increase the dynamic range of a cell-free biosensor to reach lower detection limits and reduce the false-positive proportion.
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Affiliation(s)
- Caroline E Copeland
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Jeehye Kim
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Pearce L Copeland
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Chloe J Heitmeier
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Yong-Chan Kwon
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Louisiana State University Agricultural Center, Baton Rouge, Louisiana 70803, United States
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11
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Expanding luciferase reporter systems for cell-free protein expression. Sci Rep 2022; 12:11489. [PMID: 35798760 PMCID: PMC9263134 DOI: 10.1038/s41598-022-15624-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/27/2022] [Indexed: 11/08/2022] Open
Abstract
Luciferases are often used as a sensitive, versatile reporter in cell-free transcription-translation (TXTL) systems, for research and practical applications such as engineering genetic parts, validating genetic circuits, and biosensor outputs. Currently, only two luciferases (Firefly and Renilla) are commonly used without substrate cross-talk. Here we demonstrate the expansion of the cell-free luciferase reporter system, with two orthogonal luciferase reporters: N. nambi luciferase (Luz) and LuxAB. These luciferases do not have cross-reactivity with the Firefly and Renilla substrates. We also demonstrate a substrate regeneration pathway for one of the new luciferases, enabling long-term time courses of protein expression monitoring in the cell-free system. Furthermore, we reduced the number of genes required in TXTL expression, by engineering a cell extract containing part of the luciferase enzymes. Our findings lead to an expanded platform with multiple orthogonal luminescence translation readouts for in vitro protein expression.
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12
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A microfluidic optimal experimental design platform for forward design of cell-free genetic networks. Nat Commun 2022; 13:3626. [PMID: 35750678 PMCID: PMC9232554 DOI: 10.1038/s41467-022-31306-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/14/2022] [Indexed: 12/20/2022] Open
Abstract
Cell-free protein synthesis has been widely used as a “breadboard” for design of synthetic genetic networks. However, due to a severe lack of modularity, forward engineering of genetic networks remains challenging. Here, we demonstrate how a combination of optimal experimental design and microfluidics allows us to devise dynamic cell-free gene expression experiments providing maximum information content for subsequent non-linear model identification. Importantly, we reveal that applying this methodology to a library of genetic circuits, that share common elements, further increases the information content of the data resulting in higher accuracy of model parameters. To show modularity of model parameters, we design a pulse decoder and bistable switch, and predict their behaviour both qualitatively and quantitatively. Finally, we update the parameter database and indicate that network topology affects parameter estimation accuracy. Utilizing our methodology provides us with more accurate model parameters, a necessity for forward engineering of complex genetic networks. Characterization of cell-free genetic networks is inherently difficult. Here the authors use optimal experimental design and microfluidics to improve characterization, demonstrating modularity and predictability of parts in applied test cases.
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13
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Ryan J, Hong S, Foo M, Kim J, Tang X. Model-Based Investigation of the Relationship between Regulation Level and Pulse Property of I1-FFL Gene Circuits. ACS Synth Biol 2022; 11:2417-2428. [PMID: 35729788 PMCID: PMC9295143 DOI: 10.1021/acssynbio.2c00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mathematical models are powerful tools in guiding the construction of synthetic biological circuits, given their capability of accurately capturing and predicting circuit dynamics. Recent innovations in RNA technology have enabled the development of a variety of new tools for regulating gene expression at both the transcription and translation levels. However, the effects of different regulation levels on the circuit dynamics remain largely unexplored. In this study, we focus on the type 1 incoherent feed-forward loop (I1-FFL) gene circuit with four different variations (TX, TL, HY-1, HY-2), to investigate how regulation at the transcription and translation levels affect the circuit dynamics. We develop a mechanistic model for each of the four circuits and deploy sensitivity analysis to investigate the circuits' dynamics in terms of pulse generation. Based on the analysis, we observe that the repression regulation mechanism dominates the characteristics of the pulse as compared to the activation regulation mechanism and find that the I1-FFL with transcription repression has a higher chance of generating a pulse meeting the desired criteria. The experimental results in Escherichia coli also confirm our findings from the computational analysis. We expect our findings to facilitate future experimental construction of gene circuits with insights on the selection of appropriate transcription and translation regulation tools.
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Affiliation(s)
- Jordan Ryan
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Seongho Hong
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Mathias Foo
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Xun Tang
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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14
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Liu B, Cuba Samaniego C, Bennett M, Chappell J, Franco E. RNA Compensation: A Positive Feedback Insulation Strategy for RNA-Based Transcription Networks. ACS Synth Biol 2022; 11:1240-1250. [PMID: 35244392 DOI: 10.1021/acssynbio.1c00540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The lack of signaling modularity of biomolecular systems poses major challenges toward engineering complex networks. Directional signaling between an upstream and a downstream circuit requires the presence of binding events, which result in the consumption of regulatory molecules and can compromise the operation of the upstream circuit. This issue has been previously addressed by introducing insulation strategies that include high-gain negative feedback and activation-deactivation reaction cycles. In this paper, we focus on RNA-based circuits and propose a new positive-feedback strategy to mitigate signal consumption that we propose occurs for each regulatory event due to irreversible binding of the RNA input to the RNA target. To mitigate this, an extra RNA input is added in tandem with transcription output to compensate the RNA consumption, leading to concentration robustness of the input RNA molecule regardless of the amount of downstream modules. We term this strategy RNA compensation, and it can be applied to systems that have a stringent input-output gain, such as Small Transcription Activating RNAs (STARs). Our theoretical analysis shows that RNA compensation not only eliminates the signaling consumption in individual STAR-based regulators, but also improves the composability of STAR cascades and the modularity of RNA bistable systems.
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Affiliation(s)
- Baiyang Liu
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Christian Cuba Samaniego
- Department of Mechanical and Aerospace Engineering, Bioengineering, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Matthew Bennett
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - James Chappell
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, Bioengineering, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
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15
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Tickman BI, Burbano DA, Chavali VP, Kiattisewee C, Fontana J, Khakimzhan A, Noireaux V, Zalatan JG, Carothers JM. Multi-layer CRISPRa/i circuits for dynamic genetic programs in cell-free and bacterial systems. Cell Syst 2022; 13:215-229.e8. [PMID: 34800362 DOI: 10.1016/j.cels.2021.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/24/2021] [Accepted: 10/26/2021] [Indexed: 11/29/2022]
Abstract
CRISPR-Cas transcriptional circuits hold great promise as platforms for engineering metabolic networks and information processing circuits. Historically, prokaryotic CRISPR control systems have been limited to CRISPRi. Creating approaches to integrate CRISPRa for transcriptional activation with existing CRISPRi-based systems would greatly expand CRISPR circuit design space. Here, we develop design principles for engineering prokaryotic CRISPRa/i genetic circuits with network topologies specified by guide RNAs. We demonstrate that multi-layer CRISPRa/i cascades and feedforward loops can operate through the regulated expression of guide RNAs in cell-free expression systems and E. coli. We show that CRISPRa/i circuits can program complex functions by designing type 1 incoherent feedforward loops acting as fold-change detectors and tunable pulse-generators. By investigating how component characteristics relate to network properties such as depth, width, and speed, this work establishes a framework for building scalable CRISPRa/i circuits as regulatory programs in cell-free expression systems and bacterial hosts. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Benjamin I Tickman
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, WA 98195, USA
| | - Diego Alba Burbano
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, WA 98195, USA; Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Venkata P Chavali
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, WA 98195, USA
| | - Cholpisit Kiattisewee
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, WA 98195, USA
| | - Jason Fontana
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, WA 98195, USA
| | - Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jesse G Zalatan
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, WA 98195, USA; Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - James M Carothers
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, WA 98195, USA; Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA.
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16
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Liu B, Chappell J. Computational Design of Small Transcription Activating RNAs (STARs). Methods Mol Biol 2022; 2518:87-97. [PMID: 35666440 DOI: 10.1007/978-1-0716-2421-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A major goal of synthetic biology has been to develop libraries of versatile genetic regulators that enable the precise control of gene expression. In recent years, the creation of novel RNA design motifs has allowed for the bottom-up, computational design of large libraries of high-performing and orthogonal RNA regulator systems. One example of this is Small Transcription Activating RNAs (STARs), which function through the conditional formation of terminator hairpins to activate the transcription of targeted genes. STARs have found broad utility for creating synthetic gene circuits, engineering metabolic pathways, and creating new types of diagnostics. Here we describe the method to computationally design, build, and characterize STAR regulators.
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Affiliation(s)
- Baiyang Liu
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - James Chappell
- Department of BioSciences, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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17
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Anderson DA, Voigt CA. Competitive dCas9 binding as a mechanism for transcriptional control. Mol Syst Biol 2021; 17:e10512. [PMID: 34747560 PMCID: PMC8574044 DOI: 10.15252/msb.202110512] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022] Open
Abstract
Catalytically dead Cas9 (dCas9) is a programmable transcription factor that can be targeted to promoters through the design of small guide RNAs (sgRNAs), where it can function as an activator or repressor. Natural promoters use overlapping binding sites as a mechanism for signal integration, where the binding of one can block, displace, or augment the activity of the other. Here, we implemented this strategy in Escherichia coli using pairs of sgRNAs designed to repress and then derepress transcription through competitive binding. When designed to target a promoter, this led to 27-fold repression and complete derepression. This system was also capable of ratiometric input comparison over two orders of magnitude. Additionally, we used this mechanism for promoter sequence-independent control by adopting it for elongation control, achieving 8-fold repression and 4-fold derepression. This work demonstrates a new genetic control mechanism that could be used to build analog circuit or implement cis-regulatory logic on CRISPRi-targeted native genes.
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Affiliation(s)
- Daniel A Anderson
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Christopher A Voigt
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
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18
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19
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Design and Evaluation of Synthetic RNA-Based Incoherent Feed-Forward Loop Circuits. Biomolecules 2021; 11:biom11081182. [PMID: 34439849 PMCID: PMC8391864 DOI: 10.3390/biom11081182] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/31/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022] Open
Abstract
RNA-based regulators are promising tools for building synthetic biological systems that provide a powerful platform for achieving a complex regulation of transcription and translation. Recently, de novo-designed synthetic RNA regulators, such as the small transcriptional activating RNA (STAR), toehold switch (THS), and three-way junction (3WJ) repressor, have been utilized to construct RNA-based synthetic gene circuits in living cells. In this work, we utilized these regulators to construct type 1 incoherent feed-forward loop (IFFL) circuits in vivo and explored their dynamic behaviors. A combination of a STAR and 3WJ repressor was used to construct an RNA-only IFFL circuit. However, due to the fast kinetics of RNA–RNA interactions, there was no significant timescale difference between the direct activation and the indirect inhibition, that no pulse was observed in the experiments. These findings were confirmed with mechanistic modeling and simulation results for a wider range of conditions. To increase delay in the inhibition pathway, we introduced a protein synthesis process to the circuit and designed an RNA–protein hybrid IFFL circuit using THS and TetR protein. Simulation results indicated that pulse generation could be achieved with this RNA–protein hybrid model, and this was further verified with experimental realization in E. coli. Our findings demonstrate that while RNA-based regulators excel in speed as compared to protein-based regulators, the fast reaction kinetics of RNA-based regulators could also undermine the functionality of a circuit (e.g., lack of significant timescale difference). The agreement between experiments and simulations suggests that the mechanistic modeling can help debug issues and validate the hypothesis in designing a new circuit. Moreover, the applicability of the kinetic parameters extracted from the RNA-only circuit to the RNA–protein hybrid circuit also indicates the modularity of RNA-based regulators when used in a different context. We anticipate the findings of this work to guide the future design of gene circuits that rely heavily on the dynamics of RNA-based regulators, in terms of both modeling and experimental realization.
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20
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Garenne D, Thompson S, Brisson A, Khakimzhan A, Noireaux V. The all-E. coliTXTL toolbox 3.0: new capabilities of a cell-free synthetic biology platform. Synth Biol (Oxf) 2021; 6:ysab017. [PMID: 34712841 PMCID: PMC8546610 DOI: 10.1093/synbio/ysab017] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/19/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
The new generation of cell-free gene expression systems enables the prototyping and engineering of biological systems in vitro over a remarkable scope of applications and physical scales. As the utilization of DNA-directed in vitro protein synthesis expands in scope, developing more powerful cell-free transcription-translation (TXTL) platforms remains a major goal to either execute larger DNA programs or improve cell-free biomanufacturing capabilities. In this work, we report the capabilities of the all-E. coli TXTL toolbox 3.0, a multipurpose cell-free expression system specifically developed for synthetic biology. In non-fed batch-mode reactions, the synthesis of the fluorescent reporter protein eGFP (enhanced green fluorescent protein) reaches 4 mg/ml. In synthetic cells, consisting of liposomes loaded with a TXTL reaction, eGFP is produced at concentrations of >8 mg/ml when the chemical building blocks feeding the reaction diffuse through membrane channels to facilitate exchanges with the outer solution. The bacteriophage T7, encoded by a genome of 40 kb and ∼60 genes, is produced at a concentration of 1013 PFU/ml (plaque forming unit/ml). This TXTL system extends the current cell-free expression capabilities by offering unique strength and properties, for testing regulatory elements and circuits, biomanufacturing biologics or building synthetic cells.
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Affiliation(s)
- David Garenne
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Seth Thompson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Amaury Brisson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
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21
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Collins SP, Rostain W, Liao C, Beisel CL. Sequence-independent RNA sensing and DNA targeting by a split domain CRISPR-Cas12a gRNA switch. Nucleic Acids Res 2021; 49:2985-2999. [PMID: 33619539 PMCID: PMC7968991 DOI: 10.1093/nar/gkab100] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 01/13/2021] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
CRISPR technologies increasingly require spatiotemporal and dosage control of nuclease activity. One promising strategy involves linking nuclease activity to a cell's transcriptional state by engineering guide RNAs (gRNAs) to function only after complexing with a ‘trigger’ RNA. However, standard gRNA switch designs do not allow independent selection of trigger and guide sequences, limiting gRNA switch application. Here, we demonstrate the modular design of Cas12a gRNA switches that decouples selection of these sequences. The 5′ end of the Cas12a gRNA is fused to two distinct and non-overlapping domains: one base pairs with the gRNA repeat, blocking formation of a hairpin required for Cas12a recognition; the other hybridizes to the RNA trigger, stimulating refolding of the gRNA repeat and subsequent gRNA-dependent Cas12a activity. Using a cell-free transcription-translation system and Escherichia coli, we show that designed gRNA switches can respond to different triggers and target different DNA sequences. Modulating the length and composition of the sensory domain altered gRNA switch performance. Finally, gRNA switches could be designed to sense endogenous RNAs expressed only under specific growth conditions, rendering Cas12a targeting activity dependent on cellular metabolism and stress. Our design framework thus further enables tethering of CRISPR activities to cellular states.
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Affiliation(s)
- Scott P Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - William Rostain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Évry, France
| | - Chunyu Liao
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str. 2/D15, 97080 Würzburg, Germany
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA.,Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str. 2/D15, 97080 Würzburg, Germany.,Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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22
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Cetnar DP, Salis HM. Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons. ACS Synth Biol 2021; 10:318-332. [PMID: 33464822 DOI: 10.1021/acssynbio.0c00471] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
mRNA degradation is a central process that affects all gene expression levels, and yet, the determinants that control mRNA decay rates remain poorly characterized. Here, we applied a synthetic biology, learn-by-design approach to elucidate the sequence and structural determinants that control mRNA stability in bacterial operons. We designed, constructed, and characterized 82 operons in Escherichia coli, systematically varying RNase binding site characteristics, translation initiation rates, and transcriptional terminator efficiencies in the 5' untranslated region (UTR), intergenic, and 3' UTR regions, followed by measuring their mRNA levels using reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays during exponential growth. We show that introducing long single-stranded RNA into 5' UTRs reduced mRNA levels by up to 9.4-fold and that lowering translation rates reduced mRNA levels by up to 11.8-fold. We also found that RNase binding sites in intergenic regions had much lower effects on mRNA levels. Surprisingly, changing the transcriptional termination efficiency or introducing long single-stranded RNA into 3' UTRs had no effect on upstream mRNA levels. From these measurements, we developed and validated biophysical models of ribosome protection and RNase activity with excellent quantitative agreement. We also formulated design rules to rationally control a mRNA's stability, facilitating the automated design of engineered genetic systems with desired functionalities.
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23
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24
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Santos-Moreno J, Schaerli Y. CRISPR-based gene expression control for synthetic gene circuits. Biochem Soc Trans 2020; 48:1979-1993. [PMID: 32964920 PMCID: PMC7609024 DOI: 10.1042/bst20200020] [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: 07/03/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/22/2022]
Abstract
Synthetic gene circuits allow us to govern cell behavior in a programmable manner, which is central to almost any application aiming to harness engineered living cells for user-defined tasks. Transcription factors (TFs) constitute the 'classic' tool for synthetic circuit construction but some of their inherent constraints, such as insufficient modularity, orthogonality and programmability, limit progress in such forward-engineering endeavors. Here we review how CRISPR (clustered regularly interspaced short palindromic repeats) technology offers new and powerful possibilities for synthetic circuit design. CRISPR systems offer superior characteristics over TFs in many aspects relevant to a modular, predictable and standardized circuit design. Thus, the choice of CRISPR technology as a framework for synthetic circuit design constitutes a valid alternative to complement or replace TFs in synthetic circuits and promises the realization of more ambitious designs.
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Affiliation(s)
- Javier Santos-Moreno
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Yolanda Schaerli
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
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25
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Kuo J, Yuan R, Sánchez C, Paulsson J, Silver PA. Toward a translationally independent RNA-based synthetic oscillator using deactivated CRISPR-Cas. Nucleic Acids Res 2020; 48:8165-8177. [PMID: 32609820 PMCID: PMC7430638 DOI: 10.1093/nar/gkaa557] [Citation(s) in RCA: 13] [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: 05/13/2020] [Revised: 06/16/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022] Open
Abstract
In synthetic circuits, CRISPR-Cas systems have been used effectively for endpoint changes from an initial state to a final state, such as in logic gates. Here, we use deactivated Cas9 (dCas9) and deactivated Cas12a (dCas12a) to construct dynamic RNA ring oscillators that cycle continuously between states over time in bacterial cells. While our dCas9 circuits using 103-nt guide RNAs showed irregular fluctuations with a wide distribution of peak-to-peak period lengths averaging approximately nine generations, a dCas12a oscillator design with 40-nt CRISPR RNAs performed much better, having a strongly repressed off-state, distinct autocorrelation function peaks, and an average peak-to-peak period length of ∼7.5 generations. Along with free-running oscillator circuits, we measure repression response times in open-loop systems with inducible RNA steps to compare with oscillator period times. We track thousands of cells for 24+ h at the single-cell level using a microfluidic device. In creating a circuit with nearly translationally independent behavior, as the RNAs control each others' transcription, we present the possibility for a synthetic oscillator generalizable across many organisms and readily linkable for transcriptional control.
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Affiliation(s)
- James Kuo
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Ruoshi Yuan
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Carlos Sánchez
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Johan Paulsson
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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26
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Laohakunakorn N. Cell-Free Systems: A Proving Ground for Rational Biodesign. Front Bioeng Biotechnol 2020; 8:788. [PMID: 32793570 PMCID: PMC7393481 DOI: 10.3389/fbioe.2020.00788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/22/2020] [Indexed: 11/13/2022] Open
Abstract
Cell-free gene expression systems present an alternative approach to synthetic biology, where biological gene expression is harnessed inside non-living, in vitro biochemical reactions. Taking advantage of a plethora of recent experimental innovations, they easily overcome certain challenges for computer-aided biological design. For instance, their open nature renders all their components directly accessible, greatly facilitating model construction and validation. At the same time, these systems present their own unique difficulties, such as limited reaction lifetimes and lack of homeostasis. In this Perspective, I propose that cell-free systems are an ideal proving ground to test rational biodesign strategies, as demonstrated by a small but growing number of examples of model-guided, forward engineered cell-free biosystems. It is likely that advances gained from this approach will contribute to our efforts to more reliably and systematically engineer both cell-free as well as living cellular systems for useful applications.
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Affiliation(s)
- Nadanai Laohakunakorn
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
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27
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Abstract
The cell-free molecular synthesis of biochemical systems is a rapidly growing field of research. Advances in the Human Genome Project, DNA synthesis, and other technologies have allowed the in vitro construction of biochemical systems, termed cell-free biology, to emerge as an exciting domain of bioengineering. Cell-free biology ranges from the molecular to the cell-population scales, using an ever-expanding variety of experimental platforms and toolboxes. In this review, we discuss the ongoing efforts undertaken in the three major classes of cell-free biology methodologies, namely protein-based, nucleic acids–based, and cell-free transcription–translation systems, and provide our perspectives on the current challenges as well as the major goals in each of the subfields.
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Affiliation(s)
- Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Allen P. Liu
- Departments of Mechanical Engineering, Biomedical Engineering, Biophysics, and the Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan 48109, USA
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28
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Agrawal DK, Marshall R, Noireaux V, Sontag ED. In vitro implementation of robust gene regulation in a synthetic biomolecular integral controller. Nat Commun 2019; 10:5760. [PMID: 31848346 PMCID: PMC6917713 DOI: 10.1038/s41467-019-13626-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022] Open
Abstract
Feedback mechanisms play a critical role in the maintenance of cell homeostasis in the presence of disturbances and uncertainties. Motivated by the need to tune the dynamics and improve the robustness of gene circuits, biological engineers have proposed various designs that mimic natural molecular feedback control mechanisms. However, practical and predictable implementations have proved challenging because of the complexity of synthesis and analysis of complex biomolecular networks. Here, we analyze and experimentally validate a synthetic biomolecular controller executed in vitro. The controller ensures that gene expression rate tracks an externally imposed reference level, and achieves this goal even in the presence of certain kinds of disturbances. Our design relies upon an analog of the well-known principle of integral feedback in control theory. We implement the controller in an Escherichia coli cell-free transcription-translation system, which allows rapid prototyping and implementation. Modeling and theory guide experimental implementation with well-defined operational predictability.
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Affiliation(s)
- Deepak K Agrawal
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Marshall
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Eduardo D Sontag
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA.
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston MA, USA.
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29
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Silverman AD, Karim AS, Jewett MC. Cell-free gene expression: an expanded repertoire of applications. Nat Rev Genet 2019; 21:151-170. [DOI: 10.1038/s41576-019-0186-3] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/24/2022]
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30
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Zhao J, Pokhilko A, Ebenhöh O, Rosser SJ, Colloms SD. A single-input binary counting module based on serine integrase site-specific recombination. Nucleic Acids Res 2019; 47:4896-4909. [PMID: 30957849 PMCID: PMC6511857 DOI: 10.1093/nar/gkz245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/24/2019] [Accepted: 03/26/2019] [Indexed: 01/09/2023] Open
Abstract
A device that counts and records the number of events experienced by an individual cell could have many uses in experimental biology and biotechnology. Here, we report a DNA-based 'latch' that switches between two states upon each exposure to a repeated stimulus. The key component of the latch is a DNA segment whose orientation is inverted by the actions of ϕC31 integrase and its recombination directionality factor (RDF). Integrase expression is regulated by an external input, while RDF expression is controlled by the state of the latch, such that the orientation of the invertible segment switches efficiently each time the device receives an input pulse. Recombination occurs over a time scale of minutes after initiation of integrase expression. The latch requires a delay circuit, implemented with a transcriptional repressor expressed in only one state, to ensure that each input pulse results in only one inversion of the DNA segment. Development and optimization of the latch in living cells was driven by mathematical modelling of the recombination reactions and gene expression regulated by the switch. We discuss how N latches built with orthogonal site-specific recombination systems could be chained together to form a binary ripple counter that could count to 2N - 1.
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Affiliation(s)
- Jia Zhao
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, Scotland
| | - Alexandra Pokhilko
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, Scotland
| | - Oliver Ebenhöh
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, D-40225 Düsseldorf, Germany,Institute of Quantitative and Theoretical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Susan J Rosser
- SynthSys - Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, CH Waddington Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JD, Scotland,Correspondence may also be addressed to Susan J. Rosser. Tel. +44 131 650 50 86;
| | - Sean D Colloms
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, Scotland,To whom correspondence should be addressed. Tel: +44 141 330 6236; Fax: +44 141 330 4878;
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31
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Jeong D, Klocke M, Agarwal S, Kim J, Choi S, Franco E, Kim J. Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems. Methods Protoc 2019; 2:E39. [PMID: 31164618 PMCID: PMC6632179 DOI: 10.3390/mps2020039] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/12/2019] [Accepted: 05/08/2019] [Indexed: 01/07/2023] Open
Abstract
Synthetic biology brings engineering disciplines to create novel biological systems for biomedical and technological applications. The substantial growth of the synthetic biology field in the past decade is poised to transform biotechnology and medicine. To streamline design processes and facilitate debugging of complex synthetic circuits, cell-free synthetic biology approaches has reached broad research communities both in academia and industry. By recapitulating gene expression systems in vitro, cell-free expression systems offer flexibility to explore beyond the confines of living cells and allow networking of synthetic and natural systems. Here, we review the capabilities of the current cell-free platforms, focusing on nucleic acid-based molecular programs and circuit construction. We survey the recent developments including cell-free transcription-translation platforms, DNA nanostructures and circuits, and novel classes of riboregulators. The links to mathematical models and the prospects of cell-free synthetic biology platforms will also be discussed.
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Affiliation(s)
- Dohyun Jeong
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Korea.
| | - Melissa Klocke
- Department of Mechanical Engineering, University of California at Riverside, 900 University Ave, Riverside, CA 92521, USA.
| | - Siddharth Agarwal
- Department of Mechanical Engineering, University of California at Riverside, 900 University Ave, Riverside, CA 92521, USA.
| | - Jeongwon Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Korea.
| | - Seungdo Choi
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Korea.
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Jongmin Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Korea.
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Brave new ‘RNA’ world—advances in RNA tools and their application for understanding and engineering biological systems. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.02.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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