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Xu Z, Chang CC, Coyle SM. Synthetic Forms Most Beautiful: Engineering Insights into Self-Organization. Physiology (Bethesda) 2025; 40:0. [PMID: 39938118 DOI: 10.1152/physiol.00064.2024] [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: 12/02/2024] [Revised: 12/04/2024] [Accepted: 12/04/2024] [Indexed: 02/14/2025] Open
Abstract
Reflecting on the diversity of the natural world, Darwin famously observed that "from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved." However, the examples that we are able to observe in nature are a consequence of chance, constrained by selection, drift, and epistasis. Here we explore how the efforts of synthetic biology to build new living systems can expand our understanding of the fundamental design principles that allow life to self-organize biological form, from cellular to organismal levels. We suggest that the ability to impose a length or timescale onto a biological activity is an essential strategy for self-organization in evolved systems and a key design target that is now being realized synthetically at all scales. By learning to integrate these strategies together, we are poised to expand on evolution's success and realize a space of synthetic forms not only beautiful but with diverse applications and transformative potential.
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Affiliation(s)
- Zhejing Xu
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin, United States
- Integrated Program in Biochemistry Graduate Program, University of Wisconsin-Madison, Wisconsin, United States
| | - Chih-Chia Chang
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin, United States
- Biophysics Graduate Program, University of Wisconsin-Madison, Wisconsin, United States
| | - Scott M Coyle
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin, United States
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2
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Kong C, Huang L, Yang M, Yue N, Zhang Y, Tian C, Wei D, Shi R, Liang Y, Yao J, Wang L, Li D. Engineering the microbiome: A novel frontier in inflammatory bowel disease treatment. Chin Med J (Engl) 2025:00029330-990000000-01541. [PMID: 40364490 DOI: 10.1097/cm9.0000000000003563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Indexed: 05/15/2025] Open
Affiliation(s)
- Chen Kong
- The Second Clinical Medical College of Jinan University, Department of Gastroenterology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, China
| | - Longbin Huang
- The Second Clinical Medical College of Jinan University, Department of Gastroenterology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, China
| | - Meifeng Yang
- Department of General Medicine, Yantian District People's Hospital, Shenzhen, Guangdong 518020, China
| | - Ningning Yue
- The Second Clinical Medical College of Jinan University, Department of Gastroenterology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, China
| | - Yuan Zhang
- Department of Medical Administration, Huizhou Institute of Occupational Diseases Control and Prevention, Huizhou, Guangdong 516000, China
| | - Chengmei Tian
- Department of Emergency, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 518020, China
| | - Daoru Wei
- Department of Rehabilitation, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 518020, China
| | - Ruiyue Shi
- The Second Clinical Medical College of Jinan University, Department of Gastroenterology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, China
| | - Yujie Liang
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong 518020, China
| | - Jun Yao
- The Second Clinical Medical College of Jinan University, Department of Gastroenterology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, China
| | - Lisheng Wang
- The Second Clinical Medical College of Jinan University, Department of Gastroenterology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, China
| | - Defeng Li
- The Second Clinical Medical College of Jinan University, Department of Gastroenterology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, China
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3
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Demissie EA, Park SY, Moon JH, Lee DY. Comparative Analysis of Codon Optimization Tools: Advancing toward a Multi-Criteria Framework for Synthetic Gene Design. J Microbiol Biotechnol 2025; 35:e2411066. [PMID: 40223268 PMCID: PMC12010093 DOI: 10.4014/jmb.2411.11066] [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: 11/27/2024] [Revised: 02/13/2025] [Accepted: 02/24/2025] [Indexed: 04/15/2025]
Abstract
Codon optimization is an essential technique in synthetic biology and biopharmaceutical production, enhancing recombinant protein expression by fine-tuning genetic sequences to match the translational machinery and codon usage preferences of specific host organisms. This study presents a comprehensive comparative analysis of widely used codon optimization tools, focusing on their capacity to reflect host-specific codon biases, design principles, and parameters. Industrially relevant target proteins were evaluated in Escherichia coli, Saccharomyces cerevisiae, and CHO cells, uncovering significant variability in sequence design and clustering patterns across tools. Tools such as JCat, OPTIMIZER, ATGme, and GeneOptimizer demonstrated strong alignment with genome-wide and highly expressed gene-level codon usage, achieving high codon adaptation index (CAI) values and efficient codon-pair utilization. Conversely, tools like TISIGNER and IDT employed different optimization strategies that frequently produced divergent results. Other key parameters, including GC content, mRNA secondary structure stability (ΔG), and codon-pair bias (CPB), were analyzed to elucidate their influence on translational efficiency. While increased GC content enhanced mRNA stability in E. coli, A/T-rich codons in S. cerevisiae minimized secondary structure formation, and moderate GC content in CHO cells balanced mRNA stability and translation efficiency. Our findings highlight the limitations of single-metric approaches and advocate for a multi-criteria framework that integrates CAI, GC content, mRNA folding energy, and codon-pair considerations. This integrative strategy enables the design of tailored genetic sequences that meet host-specific requirements, advancing synthetic gene design for biotechnological innovation and precision biopharmaceutical applications.
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Affiliation(s)
- Eden A. Demissie
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seo-Young Park
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Je Hun Moon
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
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4
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Palacios S, Collins JJ, Del Vecchio D. Machine learning for synthetic gene circuit engineering. Curr Opin Biotechnol 2025; 92:103263. [PMID: 39874719 DOI: 10.1016/j.copbio.2025.103263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 01/07/2025] [Accepted: 01/08/2025] [Indexed: 01/30/2025]
Abstract
Synthetic biology leverages engineering principles to program biology with new functions for applications in medicine, energy, food, and the environment. A central aspect of synthetic biology is the creation of synthetic gene circuits - engineered biological circuits capable of performing operations, detecting signals, and regulating cellular functions. Their development involves large design spaces with intricate interactions among circuit components and the host cellular machinery. Here, we discuss the emerging role of machine learning in addressing these challenges. We articulate how machine learning may enhance synthetic gene circuit engineering, from individual components to circuit-level aspects, while highlighting associated challenges. We discuss potential hybrid approaches that combine machine learning with mechanistic modeling to leverage the advantages of data-driven models with the prescriptive ability of mechanism-based models. Machine learning and its integration with mechanistic modeling are poised to advance synthetic biology, but challenges need to be overcome for such efforts to realize their potential.
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Affiliation(s)
- Sebastian Palacios
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - James J Collins
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Domitilla Del Vecchio
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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5
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Rajasekaran R, Galateo TM, Xu Z, Bolshakov DT, Weix EWZ, Coyle SM. Genetically encoded protein oscillators for FM streaming of single-cell data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.28.640587. [PMID: 40060462 PMCID: PMC11888400 DOI: 10.1101/2025.02.28.640587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/15/2025]
Abstract
Radios and cellphones use frequency modulation (FM) of an oscillating carrier signal to reliably transmit multiplexed data while rejecting noise. Here, we establish a biochemical analogue of this paradigm using genetically encoded protein oscillators (GEOs) as carrier signals in circuits that enable continuous, real-time FM streaming of single-cell data. GEOs are constructed from evolutionarily diverse MinDE-family ATPase and activator modules that generate fast synthetic protein oscillations when co-expressed in human cells. These oscillations serve as a single-cell carrier signal, with frequency and amplitude controlled by GEO component levels and activity. We systematically characterize 169 ATPase/activator GEO pairs and engineer composite GEOs with multiple competing activators to develop a comprehensive platform for waveform programming. Using these principles, we design circuits that modulate GEO frequency in response to cellular activity and decode their responses using a calibrated machine-learning model to demonstrate sensitive, real-time FM streaming of transcription and proteasomal degradation dynamics in single cells. GEOs establish a dynamically controllable biochemical carrier signal, unlocking noise-resistant FM data-encoding paradigms that open new avenues for dynamic single-cell analysis.
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Affiliation(s)
- Rohith Rajasekaran
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Integrated Program in Biochemistry Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Thomas M Galateo
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Zhejing Xu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Integrated Program in Biochemistry Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Dennis T Bolshakov
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Elliott W Z Weix
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Scott M Coyle
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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6
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Wu CQ, Feng HY, Liu Y, Xu L. Genetically Expressed RNA Strand Displacement for Cellular Manipulation. Chembiochem 2024; 25:e202400669. [PMID: 39304987 DOI: 10.1002/cbic.202400669] [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: 08/13/2024] [Revised: 09/14/2024] [Accepted: 09/20/2024] [Indexed: 11/06/2024]
Abstract
Nucleic acid strand displacement is a pivotal concept in dynamic nucleic acid nanotechnologies, which has been extensively investigated and applied across various fields. Compared with DNA systems, the genetically expressed RNA strand displacement technology offers unique advantages for construction of genetic circuits in living cells, where RNA expression and modulation may be seamlessly integrated into the genomic network for long-term and stable regulations of diversified biological functionalities. This Concept paper provides an overview of previous efforts on developments of synthetic gene circuits through utilization of RNA strand displacement, including our endeavors in this field. Moreover, future prospects, potential applications and challenges of the genetically expressed RNA strand displacement technology are also discussed.
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Affiliation(s)
- Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Hui-Ye Feng
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yan Liu
- Department of Biochemistry and Molecular Biology, Guangdong Medical University, Zhanjiang, 524002, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
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7
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Fan S, Ma L, Song C, Han X, Zhong B, Lin Y. Promoter DNA methylation and transcription factor condensation are linked to transcriptional memory in mammalian cells. Cell Syst 2024; 15:808-823.e6. [PMID: 39243757 DOI: 10.1016/j.cels.2024.08.007] [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: 05/01/2023] [Revised: 06/08/2024] [Accepted: 08/15/2024] [Indexed: 09/09/2024]
Abstract
The regulation of genes can be mathematically described by input-output functions that are typically assumed to be time invariant. This fundamental assumption underpins the design of synthetic gene circuits and the quantitative understanding of natural gene regulatory networks. Here, we found that this assumption is challenged in mammalian cells. We observed that a synthetic reporter gene can exhibit unexpected transcriptional memory, leading to a shift in the dose-response curve upon a second induction. Mechanistically, we investigated the cis-dependency of transcriptional memory, revealing the necessity of promoter DNA methylation in establishing memory. Furthermore, we showed that the synthetic transcription factor's effective DNA binding affinity underlies trans-dependency, which is associated with its capacity to undergo biomolecular condensation. These principles enabled modulating memory by perturbing either cis- or trans-regulation of genes. Together, our findings suggest the potential pervasiveness of transcriptional memory and implicate the need to model mammalian gene regulation with time-varying input-output functions. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Shenqi Fan
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Liang Ma
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China.
| | - Chengzhi Song
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xu Han
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Bijunyao Zhong
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yihan Lin
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu 610213, Sichuan, China.
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8
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Wu RY, Wu CQ, Xie F, Xing X, Xu L. Building RNA-Mediated Artificial Signaling Pathways between Endogenous Genes. Acc Chem Res 2024; 57:1777-1789. [PMID: 38872074 DOI: 10.1021/acs.accounts.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Sophisticated genetic networks play a pivotal role in orchestrating cellular responses through intricate signaling pathways across diverse environmental conditions. Beyond the inherent complexity of natural cellular signaling networks, the construction of artificial signaling pathways (ASPs) introduces a vast array of possibilities for reshaping cellular responses, enabling programmable control of living organisms. ASPs can be integrated with existing cellular networks and redirect output responses as desired, allowing seamless communication and coordination with other cellular processes, thereby achieving designable transduction within cells. Among diversified ASPs, establishing connections between originally independent endogenous genes is of particular significance in modifying the genetic networks, so that cells can be endowed with new capabilities to sense and deal with abnormal factors related to differentiated gene expression (i.e., solve the issues of the aberrant gene expression induced by either external or internal stimuli). In a typical scenario, the two genes X and Y in the cell are originally expressed independently. After the introduction of an ASP, changes in the expression of gene X may exert a designed impact on gene Y, subsequently inducing the cellular response related to gene Y. If X represents a disease signal and Y serves as a therapeutic module, the introduction of the ASP empowers cells with a new spontaneous defense system to handle potential risks, which holds great potential for both fundamental and translational studies.In this Account, we primarily review our endeavors in the construction of RNA-mediated ASPs between endogenous genes that can respond to differentiated RNA expression. In contrast to other molecules that may be restricted to specific pathways, synthetic RNA circuits can be easily utilized and expanded as a general platform for constructing ASPs with a high degree of programmability and tunability for diversified functionalities through predictable Watson-Crick base pairing. We first provide an overview of recent advancements in RNA-based genetic circuits, encompassing but not limited to utilization of RNA toehold switches, siRNA and CRISPR systems. Despite notable progress, most reported RNA circuits have to contain at least one exogenous RNA X as input or one engineered RNA Y as a target, which is not suitable for establishing endogenous gene connections. While exogenous RNAs can be engineered and controlled as desired, constructing a general and efficient platform for manipulation of naturally occurring RNAs poses a formidable challenge, especially for the mammalian system. With a focus on this goal, we are devoted to developing efficient strategies to manipulate cell responses by establishing RNA-mediated ASPs between endogenous genes, particularly in mammalian cells. Our step-by-step progress in engineering customized cell signaling circuits, from bacterial cells to mammalian cells, from gene expression regulation to phenotype control, and from small RNA to long mRNA of low abundance and more complex secondary structures, is systematically described. Finally, future perspectives and potential applications of these RNA-mediated ASPs between endogenous genes are also discussed.
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Affiliation(s)
- Ruo-Yue Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Fan Xie
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiwen Xing
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
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Sun J, Yang R, Li Q, Zhu R, Jiang Y, Zang L, Zhang Z, Tong W, Zhao H, Li T, Li H, Qi D, Li G, Chen X, Dai Z, Liu Z. Living Synthelectronics: A New Era for Bioelectronics Powered by Synthetic Biology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2400110. [PMID: 38494761 DOI: 10.1002/adma.202400110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/23/2024] [Indexed: 03/19/2024]
Abstract
Bioelectronics, which converges biology and electronics, has attracted great attention due to their vital applications in human-machine interfaces. While traditional bioelectronic devices utilize nonliving organic and/or inorganic materials to achieve flexibility and stretchability, a biological mismatch is often encountered because human tissues are characterized not only by softness and stretchability but also by biodynamic and adaptive properties. Recently, a notable paradigm shift has emerged in bioelectronics, where living cells, and even viruses, modified via gene editing within synthetic biology, are used as core components in a new hybrid electronics paradigm. These devices are defined as "living synthelectronics," and they offer enhanced potential for interfacing with human tissues at informational and substance exchange levels. In this Perspective, the recent advances in living synthelectronics are summarized. First, opportunities brought to electronics by synthetic biology are briefly introduced. Then, strategic approaches to designing and making electronic devices using living cells/viruses as the building blocks, sensing components, or power sources are reviewed. Finally, the challenges faced by living synthelectronics are raised. It is believed that this paradigm shift will significantly contribute to the real integration of bioelectronics with human tissues.
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Affiliation(s)
- Jing Sun
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Ruofan Yang
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qingsong Li
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Runtao Zhu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ying Jiang
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Lei Zang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhibo Zhang
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Wei Tong
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Hang Zhao
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Tengfei Li
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Hanfei Li
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Dianpeng Qi
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Guanglin Li
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaodong Chen
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Zhuojun Dai
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhiyuan Liu
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Standard Robots Co.,Ltd,Room 405, Building D, Huafeng International Robot Fusen Industrial Park, Hangcheng Avenue, Guxing Community, Xixiang Street, Baoan District, Shenzhen, 518055, China
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10
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Wu CQ, Wu RY, Zhang QL, Wang LL, Wang Y, Dai C, Zhang CX, Xu L. Harnessing Catalytic RNA Circuits for Construction of Artificial Signaling Pathways in Mammalian Cells. Angew Chem Int Ed Engl 2024; 63:e202319309. [PMID: 38298112 DOI: 10.1002/anie.202319309] [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: 12/14/2023] [Revised: 01/21/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024]
Abstract
Engineering of genetic networks with artificial signaling pathways (ASPs) can reprogram cellular responses and phenotypes under different circumstances for a variety of diagnostic and therapeutic purposes. However, construction of ASPs between originally independent endogenous genes in mammalian cells is highly challenging. Here we report an amplifiable RNA circuit that can theoretically build regulatory connections between any endogenous genes in mammalian cells. We harness the system of catalytic hairpin assembly with combination of controllable CRISPR-Cas9 function to transduce the signals from distinct messenger RNA expression of trigger genes into manipulation of target genes. Through introduction of these RNA-based genetic circuits, mammalian cells are endowed with autonomous capabilities to sense the changes of RNA expression either induced by ligand stimuli or from various cell types and control the cellular responses and fates via apoptosis-related ASPs. Our design provides a generalized platform for construction of ASPs inside the genetic networks of mammalian cells based on differentiated RNA expression.
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Affiliation(s)
- Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ruo-Yue Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiu-Long Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
- School of Pharmacy and Medical Technology, Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine of Fujian Province, Putian University, Putian, 351100, China
| | - Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Chu Dai
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Chen-Xi Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
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Bacsa B, Hopl V, Derler I. Synthetic Biology Meets Ca 2+ Release-Activated Ca 2+ Channel-Dependent Immunomodulation. Cells 2024; 13:468. [PMID: 38534312 PMCID: PMC10968988 DOI: 10.3390/cells13060468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
Many essential biological processes are triggered by the proximity of molecules. Meanwhile, diverse approaches in synthetic biology, such as new biological parts or engineered cells, have opened up avenues to precisely control the proximity of molecules and eventually downstream signaling processes. This also applies to a main Ca2+ entry pathway into the cell, the so-called Ca2+ release-activated Ca2+ (CRAC) channel. CRAC channels are among other channels are essential in the immune response and are activated by receptor-ligand binding at the cell membrane. The latter initiates a signaling cascade within the cell, which finally triggers the coupling of the two key molecular components of the CRAC channel, namely the stromal interaction molecule, STIM, in the ER membrane and the plasma membrane Ca2+ ion channel, Orai. Ca2+ entry, established via STIM/Orai coupling, is essential for various immune cell functions, including cytokine release, proliferation, and cytotoxicity. In this review, we summarize the tools of synthetic biology that have been used so far to achieve precise control over the CRAC channel pathway and thus over downstream signaling events related to the immune response.
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Affiliation(s)
- Bernadett Bacsa
- Division of Medical Physics und Biophysics, Medical University of Graz, A-8010 Graz, Austria;
| | - Valentina Hopl
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria;
| | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria;
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12
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Hahn J, Ding S, Im J, Harimoto T, Leong KW, Danino T. Bacterial therapies at the interface of synthetic biology and nanomedicine. NATURE REVIEWS BIOENGINEERING 2024; 2:120-135. [PMID: 38962719 PMCID: PMC11218715 DOI: 10.1038/s44222-023-00119-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 07/05/2024]
Abstract
Bacteria are emerging as living drugs to treat a broad range of disease indications. However, the inherent advantages of these replicating and immunostimulatory therapies also carry the potential for toxicity. Advances in synthetic biology and the integration of nanomedicine can address this challenge through the engineering of controllable systems that regulate spatial and temporal activation for improved safety and efficacy. Here, we review recent progress in nanobiotechnology-driven engineering of bacteria-based therapies, highlighting limitations and opportunities that will facilitate clinical translation.
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Affiliation(s)
- Jaeseung Hahn
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Suwan Ding
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jongwon Im
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Tetsuhiro Harimoto
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - 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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13
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Hoces D, Miguens Blanco J, Hernández-López RA. A synthetic biology approach to engineering circuits in immune cells. Immunol Rev 2023; 320:120-137. [PMID: 37464881 DOI: 10.1111/imr.13244] [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: 05/23/2023] [Accepted: 06/08/2023] [Indexed: 07/20/2023]
Abstract
A synthetic circuit in a biological system involves the designed assembly of genetic elements, biomolecules, or cells to create a defined function. These circuits are central in synthetic biology, enabling the reprogramming of cellular behavior and the engineering of cells with customized responses. In cancer therapeutics, engineering T cells with circuits have the potential to overcome the challenges of current approaches, for example, by allowing specific recognition and killing of cancer cells. Recent advances also facilitate engineering integrated circuits for the controlled release of therapeutic molecules at specified locations, for example, in a solid tumor. In this review, we discuss recent strategies and applications of synthetic receptor circuits aimed at enhancing immune cell functions for cancer immunotherapy. We begin by introducing the concept of circuits in networks at the molecular and cellular scales and provide an analysis of the development and implementation of several synthetic circuits in T cells that have the goal to overcome current challenges in cancer immunotherapy. These include specific targeting of cancer cells, increased T-cell proliferation, and persistence in the tumor microenvironment. By harnessing the power of synthetic biology, and the characteristics of certain circuit architectures, it is now possible to engineer a new generation of immune cells that recognize cancer cells, while minimizing off-target toxicities. We specifically discuss T-cell circuits for antigen density sensing. These circuits allow targeting of solid tumors that share antigens with normal tissues. Additionally, we explore designs for synthetic circuits that could control T-cell differentiation or T-cell fate as well as the concept of synthetic multicellular circuits that leverage cellular communication and division of labor to achieve improved therapeutic efficacy. As our understanding of cell biology expands and novel tools for genome, protein, and cell engineering are developed, we anticipate further innovative approaches to emerge in the design and engineering of circuits in immune cells.
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Affiliation(s)
- Daniel Hoces
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Jesús Miguens Blanco
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Rogelio A Hernández-López
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Stanford Cancer Institute, Stanford, California, USA
- Chan-Zuckerberg Biohub-San Francisco, San Francisco, California, USA
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14
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Bragdon MDJ, Patel N, Chuang J, Levien E, Bashor CJ, Khalil AS. Cooperative assembly confers regulatory specificity and long-term genetic circuit stability. Cell 2023; 186:3810-3825.e18. [PMID: 37552983 PMCID: PMC10528910 DOI: 10.1016/j.cell.2023.07.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/17/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023]
Abstract
A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc-finger-based TFs. We show that circuits "wired" using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-term continuous culture. Our naturally inspired approach offers a simple, generalizable means for building high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.
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Affiliation(s)
- Meghan D J Bragdon
- Biological Design Center, Boston University, Boston, MA 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA
| | - Nikit Patel
- Biological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James Chuang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ethan Levien
- Department of Mathematics, Dartmouth College, Hanover, NH 03755, USA
| | - Caleb J Bashor
- Department of Bioengineering, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77030, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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15
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Using CIVT-SELEX to Select Aptamers as Genetic Parts to Regulate Gene Circuits in a Cell-Free System. Int J Mol Sci 2023; 24:ijms24032833. [PMID: 36769156 PMCID: PMC9917220 DOI: 10.3390/ijms24032833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
The complexity of genetic circuits has not seen a significant increase over the last decades, even with the rapid development of synthetic biology tools. One of the bottlenecks is the limited number of orthogonal transcription factor-operator pairs. Researchers have tried to use aptamer-ligand pairs as genetic parts to regulate transcription. However, most aptamers selected using traditional methods cannot be directly applied in gene circuits for transcriptional regulation. To that end, we report a new method called CIVT-SELEX to select DNA aptamers that can not only bind to macromolecule ligands but also undergo significant conformational changes, thus affecting transcription. The single-stranded DNA library with affinity to our example ligand human thrombin protein is first selected and enriched. Then, these ssDNAs are inserted into a genetic circuit and tested in the in vitro transcription screening to obtain the ones with significant inhibitory effects on downstream gene transcription when thrombins are present. These aptamer-thrombin pairs can inhibit the transcription of downstream genes, demonstrating the feasibility and robustness of their use as genetic parts in both linear DNAs and plasmids. We believe that this method can be applied to select aptamers of any target ligands and vastly expand the genetic part library for transcriptional regulation.
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16
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Zong W, Shao X, Li J, Chai Y, Hu X, Zhang X. Synthetic Intracellular Environments: From Basic Science to Applications. Anal Chem 2023; 95:535-549. [PMID: 36625127 DOI: 10.1021/acs.analchem.2c04199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Wei Zong
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
| | - Xiaotong Shao
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
| | - Jinlong Li
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China.,Heilongjiang Provincial Key Laboratory of Catalytic Synthesis for Fine Chemicals, Qiqihar University, Qiqihar161006, China
| | - Yunhe Chai
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
| | - Xinyu Hu
- Key Laboratory of Micro-Nano Optoelectronic Devices (Wenzhou), College of Electrical and Electronic Engineering, Wenzhou University, Wenzhou325035, China
| | - Xunan Zhang
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
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17
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De novo engineering of a bacterial lifestyle program. Nat Chem Biol 2022; 19:488-497. [PMID: 36522463 DOI: 10.1038/s41589-022-01194-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/30/2022] [Indexed: 12/23/2022]
Abstract
Synthetic biology has shown remarkable potential to program living microorganisms for applications. However, a notable discrepancy exists between the current engineering practice-which focuses predominantly on planktonic cells-and the ubiquitous observation of microbes in nature that constantly alternate their lifestyles on environmental variations. Here we present the de novo construction of a synthetic genetic program that regulates bacterial life cycle and enables phase-specific gene expression. The program is orthogonal, harnessing an engineered protein from 45 candidates as the biofilm matrix building block. It is also highly controllable, allowing directed biofilm assembly and decomposition as well as responsive autonomous planktonic-biofilm phase transition. Coupling to synthesis modules, it is further programmable for various functional realizations that conjugate phase-specific biomolecular production with lifestyle alteration. This work establishes a versatile platform for microbial engineering across physiological regimes, thereby shedding light on a promising path for gene circuit applications in complex contexts.
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18
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Balakrishnan R, Mori M, Segota I, Zhang Z, Aebersold R, Ludwig C, Hwa T. Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria. Science 2022; 378:eabk2066. [PMID: 36480614 PMCID: PMC9804519 DOI: 10.1126/science.abk2066] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein concentrations are set by a complex interplay between gene-specific regulatory processes and systemic factors, including cell volume and shared gene expression machineries. Elucidating this interplay is crucial for discerning and designing gene regulatory systems. We quantitatively characterized gene-specific and systemic factors that affect transcription and translation genome-wide for Escherichia coli across many conditions. The results revealed two design principles that make regulation of gene expression insulated from concentrations of shared machineries: RNA polymerase activity is fine-tuned to match translational output, and translational characteristics are similar across most messenger RNAs (mRNAs). Consequently, in bacteria, protein concentration is set primarily at the promoter level. A simple mathematical formula relates promoter activities and protein concentrations across growth conditions, enabling quantitative inference of gene regulation from omics data.
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Affiliation(s)
- Rohan Balakrishnan
- Department of Physics, University of California at San Diego, La Jolla, California 92093-0374
| | - Matteo Mori
- Department of Physics, University of California at San Diego, La Jolla, California 92093-0374
| | - Igor Segota
- Departments of Medicine and Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Zhongge Zhang
- Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093
| | - Ruedi Aebersold
- Faculty of Science, University of Zurich, Zurich, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, California 92093-0374
- Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093
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19
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Wu J, Chen B, Liu Y, Ma L, Huang W, Lin Y. Modulating gene regulation function by chemically controlled transcription factor clustering. Nat Commun 2022; 13:2663. [PMID: 35562359 PMCID: PMC9106659 DOI: 10.1038/s41467-022-30397-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/29/2022] [Indexed: 12/21/2022] Open
Abstract
Recent studies have suggested that transcriptional protein condensates (or clusters) may play key roles in gene regulation and cell fate determination. However, it remains largely unclear how the gene regulation function is quantitatively tuned by transcription factor (TF) clustering and whether TF clustering may confer emergent behaviors as in cell fate control systems. Here, to address this, we construct synthetic TFs whose clustering behavior can be chemically controlled. Through single-parameter tuning of the system (i.e., TF clustering propensity), we provide lines of evidence supporting the direct transcriptional activation and amplification of target genes by TF clustering. Single-gene imaging suggests that such amplification results from the modulation of transcriptional dynamics. Importantly, TF clustering propensity modulates the gene regulation function by significantly tuning the effective TF binding affinity and to a lesser extent the ultrasensitivity, contributing to bimodality and sustained response behavior that are reminiscent of canonical cell fate control systems. Collectively, these results demonstrate that TF clustering can modulate the gene regulation function to enable emergent behaviors, and highlight the potential applications of chemically controlled protein clustering. Transcription factor (TF) condensates appear to be pervasive, yet their roles remain debated. Here, the authors use a synthetic biology approach to show that TF clusters causally amplify transcription and can confer bimodality and “memory”.
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Affiliation(s)
- Jiegen Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Baoqiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Yadi Liu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Liang Ma
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Wen Huang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Yihan Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China. .,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.
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20
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Garcia-Perez E, Diego-Martin B, Quijano-Rubio A, Moreno-Giménez E, Selma S, Orzaez D, Vazquez-Vilar M. A copper switch for inducing CRISPR/Cas9-based transcriptional activation tightly regulates gene expression in Nicotiana benthamiana. BMC Biotechnol 2022; 22:12. [PMID: 35331211 PMCID: PMC8943966 DOI: 10.1186/s12896-022-00741-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/11/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND CRISPR-based programmable transcriptional activators (PTAs) are used in plants for rewiring gene networks. Better tuning of their activity in a time and dose-dependent manner should allow precise control of gene expression. Here, we report the optimization of a Copper Inducible system called CI-switch for conditional gene activation in Nicotiana benthamiana. In the presence of copper, the copper-responsive factor CUP2 undergoes a conformational change and binds a DNA motif named copper-binding site (CBS). RESULTS In this study, we tested several activation domains fused to CUP2 and found that the non-viral Gal4 domain results in strong activation of a reporter gene equipped with a minimal promoter, offering advantages over previous designs. To connect copper regulation with downstream programmable elements, several copper-dependent configurations of the strong dCasEV2.1 PTA were assayed, aiming at maximizing activation range, while minimizing undesired background expression. The best configuration involved a dual copper regulation of the two protein components of the PTA, namely dCas9:EDLL and MS2:VPR, and a constitutive RNA pol III-driven expression of the third component, a guide RNA with anchoring sites for the MS2 RNA-binding domain. With these optimizations, the CI/dCasEV2.1 system resulted in copper-dependent activation rates of 2,600-fold and 245-fold for the endogenous N. benthamiana DFR and PAL2 genes, respectively, with negligible expression in the absence of the trigger. CONCLUSIONS The tight regulation of copper over CI/dCasEV2.1 makes this system ideal for the conditional production of plant-derived metabolites and recombinant proteins in the field.
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Affiliation(s)
| | | | | | | | - Sara Selma
- Instituto Biología Molecular de Plantas, CSIC-UPV, Valencia, Spain
| | - Diego Orzaez
- Instituto Biología Molecular de Plantas, CSIC-UPV, Valencia, Spain
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21
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Zhan Y, Li A, Cao C, Liu Y. CRISPR signal conductor 2.0 for redirecting cellular information flow. Cell Discov 2022; 8:26. [PMID: 35288535 PMCID: PMC8921274 DOI: 10.1038/s41421-021-00371-1] [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: 09/29/2021] [Accepted: 12/28/2021] [Indexed: 12/29/2022] Open
Abstract
A key challenge in designing intelligent artificial gene circuits is generating flexible connections between arbitrary components and directly coupling them with endogenous signaling pathways. The CRISPR signal conductor based on conditionally inducible artificial transcriptional regulators can link classic cellular protein signals with targeted gene expression, but there are still problems with multiple signal processing and gene delivery. With the discovery and characterization of new Cas systems and long noncoding RNA (lncRNA) functional motifs, and because of the compatibility of guide RNA with noncoding RNA elements at multiple sites, it is increasingly possible to solve these problems. In this study, we developed CRISPR signal conductor version 2.0 by integrating various lncRNA functional motifs into different parts of the crRNA in the CRISPR-dCasΦ system. This system can directly regulate the expression of target genes by recruiting cellular endogenous transcription factors and efficiently sense a variety of protein signals that are not detected by a classical synthetic system. The new system solved the problems of background leakage and insensitive signaling responses and enabled the construction of logic gates with as many as six input signals, which can be used to specifically target cancer cells. By rewiring endogenous signaling networks, we further demonstrated the effectiveness and biosafety of this system for in vivo cancer gene therapy.
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Affiliation(s)
- Yonghao Zhan
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China.,Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Aolin Li
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Congcong Cao
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China
| | - Yuchen Liu
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China. .,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, Guangdong, China.
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22
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Pillay CS, John N. Can thiol-based redox systems be utilized as parts for synthetic biology applications? Redox Rep 2021; 26:147-159. [PMID: 34378494 PMCID: PMC8366655 DOI: 10.1080/13510002.2021.1966183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES Synthetic biology has emerged from molecular biology and engineering approaches and aims to develop novel, biologically-inspired systems for industrial and basic research applications ranging from biocomputing to drug production. Surprisingly, redoxin (thioredoxin, glutaredoxin, peroxiredoxin) and other thiol-based redox systems have not been widely utilized in many of these synthetic biology applications. METHODS We reviewed thiol-based redox systems and the development of synthetic biology applications that have used thiol-dependent parts. RESULTS The development of circuits to facilitate cytoplasmic disulfide bonding, biocomputing and the treatment of intestinal bowel disease are amongst the applications that have used thiol-based parts. We propose that genetically encoded redox sensors, thiol-based biomaterials and intracellular hydrogen peroxide generators may also be valuable components for synthetic biology applications. DISCUSSION Thiol-based systems play multiple roles in cellular redox metabolism, antioxidant defense and signaling and could therefore offer a vast and diverse portfolio of components, parts and devices for synthetic biology applications. However, factors limiting the adoption of redoxin systems for synthetic biology applications include the orthogonality of thiol-based components, limitations in the methods to characterize thiol-based systems and an incomplete understanding of the design principles of these systems.
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Affiliation(s)
- Ché S. Pillay
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Nolyn John
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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23
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Abstract
The steadfast advance of the synthetic biology field has enabled scientists to use genetically engineered cells, instead of small molecules or biologics, as the basis for the development of novel therapeutics. Cells endowed with synthetic gene circuits can control the localization, timing and dosage of therapeutic activities in response to specific disease biomarkers and thus represent a powerful new weapon in the fight against disease. Here, we conceptualize how synthetic biology approaches can be applied to programme living cells with therapeutic functions and discuss the advantages that they offer over conventional therapies in terms of flexibility, specificity and predictability, as well as challenges for their development. We present notable advances in the creation of engineered cells that harbour synthetic gene circuits capable of biological sensing and computation of signals derived from intracellular or extracellular biomarkers. We categorize and describe these developments based on the cell scaffold (human or microbial) and the site at which the engineered cell exerts its therapeutic function within its human host. The design of cell-based therapeutics with synthetic biology is a rapidly growing strategy in medicine that holds great promise for the development of effective treatments for a wide variety of human diseases.
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24
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Ellery A. Are There Biomimetic Lessons from Genetic Regulatory Networks for Developing a Lunar Industrial Ecology? Biomimetics (Basel) 2021; 6:biomimetics6030050. [PMID: 34449537 PMCID: PMC8395472 DOI: 10.3390/biomimetics6030050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 11/21/2022] Open
Abstract
We examine the prospect for employing a bio-inspired architecture for a lunar industrial ecology based on genetic regulatory networks. The lunar industrial ecology resembles a metabolic system in that it comprises multiple chemical processes interlinked through waste recycling. Initially, we examine lessons from factory organisation which have evolved into a bio-inspired concept, the reconfigurable holonic architecture. We then examine genetic regulatory networks and their application in the biological cell cycle. There are numerous subtleties that would be challenging to implement in a lunar industrial ecology but much of the essence of biological circuitry (as implemented in synthetic biology, for example) is captured by traditional electrical engineering design with emphasis on feedforward and feedback loops to implement robustness.
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Affiliation(s)
- Alex Ellery
- Department of Mechanical & Aerospace Engineering, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
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25
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Haellman V, Saxena P, Jiang Y, Fussenegger M. Rational design and optimization of synthetic gene switches for controlling cell-fate decisions in pluripotent stem cells. Metab Eng 2021; 65:99-110. [PMID: 33744461 DOI: 10.1016/j.ymben.2021.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 11/26/2022]
Abstract
Advances in synthetic biology have enabled robust control of cell behavior by using tunable genetic circuits to regulate gene expression in a ligand-dependent manner. Such circuits can be used to direct the differentiation of pluripotent stem cells (PSCs) towards desired cell types, but rational design of synthetic gene circuits in PSCs is challenging due to the variable intracellular environment. Here, we provide a framework for implementing synthetic gene switches in PSCs based on combinations of tunable transcriptional, structural, and posttranslational elements that can be engineered as required, using the vanillic acid-controlled transcriptional activator (VanA) as a model system. We further show that the VanA system can be multiplexed with the well-established reverse tetracycline-controlled transcriptional activator (rtTA) system to enable independent control of the expression of different transcription factors in human induced PSCs in order to enhance lineage specification towards early pancreatic progenitors. This work represents a first step towards standardizing the design and construction of synthetic gene switches for building robust gene-regulatory networks to guide stem cell differentiation towards a desired cell fate.
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Affiliation(s)
- Viktor Haellman
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH, 4058, Basel, Switzerland
| | - Pratik Saxena
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH, 4058, Basel, Switzerland
| | - Yanrui Jiang
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH, 4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH, 4058, Basel, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, CH, 4058, Basel, Switzerland.
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26
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Gaut NJ, Adamala KP. Reconstituting Natural Cell Elements in Synthetic Cells. Adv Biol (Weinh) 2021; 5:e2000188. [DOI: 10.1002/adbi.202000188] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/05/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Nathaniel J. Gaut
- Department of Genetics Cell Biology and Development University of Minnesota 420 Washington Ave SE Minneapolis MN 55455 USA
| | - Katarzyna P. Adamala
- Department of Genetics Cell Biology and Development University of Minnesota 420 Washington Ave SE Minneapolis MN 55455 USA
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27
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Zhang X, Shao X, Cai Z, Yan X, Zong W. The fabrication of phospholipid vesicle-based artificial cells and their functions. NEW J CHEM 2021. [DOI: 10.1039/d0nj05538g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phospholipid vesicles as artificial cells are used to simulate the cellular structure and function.
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Affiliation(s)
- Xunan Zhang
- College of Chemistry and Chemical Engineering
- Qiqihar University
- Qiqihar
- China
| | - Xiaotong Shao
- College of Chemistry and Chemical Engineering
- Qiqihar University
- Qiqihar
- China
| | - Zhenzhen Cai
- College of Chemistry and Chemical Engineering
- Qiqihar University
- Qiqihar
- China
| | - Xinyu Yan
- College of Chemistry and Chemical Engineering
- Qiqihar University
- Qiqihar
- China
| | - Wei Zong
- College of Chemistry and Chemical Engineering
- Qiqihar University
- Qiqihar
- China
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28
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Agrawal DK, Schulman R. Modular protein-oligonucleotide signal exchange. Nucleic Acids Res 2020; 48:6431-6444. [PMID: 32442276 PMCID: PMC7337525 DOI: 10.1093/nar/gkaa405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/02/2020] [Accepted: 05/14/2020] [Indexed: 12/18/2022] Open
Abstract
While many methods are available to measure the concentrations of proteins in solution, the development of a method to quantitatively report both increases and decreases in different protein concentrations in real-time using changes in the concentrations of other molecules, such as DNA outputs, has remained a challenge. Here, we present a biomolecular reaction process that reports the concentration of an input protein in situ as the concentration of an output DNA oligonucleotide strand. This method uses DNA oligonucleotide aptamers that bind either to a specific protein selectively or to a complementary DNA oligonucleotide reversibly using toehold-mediated DNA strand-displacement. It is possible to choose the sequence of output strand almost independent of the sensing protein. Using this strategy, we implemented four different exchange processes to report the concentrations of clinically relevant human α-thrombin and vascular endothelial growth factor using changes in concentrations of DNA oligonucleotide outputs. These exchange processes can operate in tandem such that the same or different output signals can indicate changes in concentration of distinct or identical input proteins. The simplicity of our approach suggests a pathway to build devices that can direct diverse output responses in response to changes in concentrations of specific proteins.
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Affiliation(s)
- Deepak K Agrawal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA.,Department of Bioengineering, University of Colorado Medicine, Aurora, CO 80045, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA.,Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, USA.,Department of Computer Science, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, USA
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29
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Safaei M, Mobini GR, Abiri A, Shojaeian A. Synthetic biology in various cellular and molecular fields: applications, limitations, and perspective. Mol Biol Rep 2020; 47:6207-6216. [PMID: 32507922 DOI: 10.1007/s11033-020-05565-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 05/28/2020] [Indexed: 01/10/2023]
Abstract
Synthetic biology breakthroughs have facilitated genetic circuit engineering to program cells through novel biological functions, dynamic gene expressions, as well as logic controls. SynBio can also participate in the rapid development of new treatments required for the human lifestyle. Moreover, these technologies are applied in the development of innovative therapeutic, diagnostic, as well as discovery-related methods within a wide range of cellular and molecular applications. In the present review study, SynBio applications in various cellular and molecular fields such as novel strategies for cancer therapy, biosensing, metabolic engineering, protein engineering, and tissue engineering were highlighted and summarized. The major safety and regulatory concerns about synthetic biology will be the environmental release, legal concerns, and risks of the engineered organisms. The final sections focused on limitations to SynBio.
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Affiliation(s)
- Mohsen Safaei
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Gholam-Reza Mobini
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Shojaeian
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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30
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Orive G, Taebnia N, Erezuma I, Andresen TL, Dolatshahi-Pirouz A. Hacking Human Beings with Machine Biology to Increase Lifespan. Trends Biotechnol 2020; 38:1312-1315. [PMID: 32499063 DOI: 10.1016/j.tibtech.2020.05.007] [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: 12/31/2019] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 11/30/2022]
Abstract
Imagine a world where machines can program cells to deliver therapeutics in a remote-controlled, time-specific, and targeted manner. Or, what if physicians could collect data continuously to establish intimate links between therapy and disease progression? Such machine biology systems could empower physicians beyond imagination and give rise to personalized treatments.
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Affiliation(s)
- Gorka Orive
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Biomedical Research Networking Centre in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain; University Institute for Regenerative Medicine and Oral Implantology - UIRMI (UPV/EHU-Fundación Eduardo Anitua), Vitoria, Spain; Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, Singapore.
| | - Nayere Taebnia
- Department of Health Technology, Center for Intestinal Absorption and Transport of Biopharmaceuticals, Technical University of Denmark, 2800 Kgs, Denmark
| | - Itsasne Erezuma
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Thomas L Andresen
- Department of Health Technology, Center for Intestinal Absorption and Transport of Biopharmaceuticals, Technical University of Denmark, 2800 Kgs, Denmark
| | - Alireza Dolatshahi-Pirouz
- Department of Health Technology, Center for Intestinal Absorption and Transport of Biopharmaceuticals, Technical University of Denmark, 2800 Kgs, Denmark; Department of Dentistry - Regenerative Biomaterials, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Philips van Leydenlaan 25, 6525, EX, Nijmegen, The Netherlands.
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31
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Wen J, Tian L, Xu M, Zhou X, Zhang Y, Cai M. A Synthetic Malonyl-CoA Metabolic Oscillator in Komagataella phaffii. ACS Synth Biol 2020; 9:1059-1068. [PMID: 32227991 DOI: 10.1021/acssynbio.9b00378] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Malonyl-CoA is a key metabolic molecule that participates in a diverse range of physiological responses and can act as a building block for a variety of value-added pharmaceuticals and chemicals. The cytosolic malonyl-CoA concentration is usually very low, and thus dynamic metabolic control of malonyl-CoA variation will aid its stable formation and efficient consumption. We developed a synthetic malonyl-CoA metabolic oscillator in yeast. A synthetic regulatory protein, Prm1-FapR, was constructed by fusing a yeast transcriptional activator, Prm1, with a bacterial malonyl-CoA-sensitive transcription repressor, FapR. Two oppositely regulated biosensors were then engineered. A total of 18 hybrid promoter variants were designed, each carrying the operator sequence (fapO) of FapR and the core promoter of PAOX1 (cPAOX1), which is naturally regulated by Prm1. The promoter activities of these variants, regulated by Prm1-FapR, were tested. Through this process, a sensor for Prm1-FapR/(-52)fapO-PAOX1 carrying an activation/deactivation regulation module was built. Meanwhile, 24 promoter variants of PGAP with fapO inserted were designed and tested using the fusion regulator, giving a sensor for Prm1-FapR/PGAP-(+22) fapO that contained a repression/derepression regulation module. Both sensors were subsequently integrated into a single cell, which exhibited correct metabolic switching of eGFP and mCherry reporters following manipulation of cytosolic malonyl-CoA levels. The Prm1-FapR/(-52)fapO-PAOX1 and the Prm1-FapR/PGAP-(+22)fapO were also used to control the malonyl-CoA source and sink pathways, respectively, for the synthesis of 6-methylsalicylic acid. This finally led to an oscillatory metabolic mode of cytosolic malonyl-CoA. Such a metabolator is useful in exploring potential industrial and biomedical applications not limited by natural cellular behavior.
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Affiliation(s)
- Jiao Wen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Lin Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Mingqiang Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, China
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32
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Shi J, Clayton C, Tian B. Nano-enabled cellular engineering for bioelectric studies. NANO RESEARCH 2020; 13:1214-1227. [PMID: 34295455 PMCID: PMC8294124 DOI: 10.1007/s12274-019-2580-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 11/24/2019] [Indexed: 06/13/2023]
Abstract
Engineered cells have opened up a new avenue for scientists and engineers to achieve specialized biological functions. Nanomaterials, such as silicon nanowires and quantum dots, can establish tight interfaces with cells either extra- or intracellularly, and they have already been widely used to control cellular functions. The future exploration of nanomaterials in cellular engineering may reveal numerous opportunities in both fundamental bioelectric studies and clinic applications. In this review, we highlight several nanomaterials-enabled non-genetic approaches to fabricating engineered cells. First, we briefly review the latest progress in engineered or synthetic cells, such as protocells that create cell-like behaviors from nonliving building blocks, and cells made by genetic or chemical modifications. Next, we illustrate the need for non-genetic cellular engineering with semiconductors and present some examples where chemical synthesis yields complex morphology or functions needed for biointerfaces. We then provide discussions in detail about the semiconductor nanostructure-enabled neural, cardiac, and microbial modulations. We also suggest the need to integrate tissue engineering with semiconductor devices to carry out more complex functions. We end this review by providing our perspectives for future development in non-genetic cellular engineering.
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Affiliation(s)
- Jiuyun Shi
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | | | - Bozhi Tian
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- The James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- The Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
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33
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Imran M, Siddiqui MK, Baig AQ, Shaker H. Molecular topological description of bacterial hypertrees. JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2020. [DOI: 10.3233/jifs-191714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Muhammad Imran
- Department of Mathematical Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | | | - Abdul Qudair Baig
- Department of Mathematics & Statistics, Institute of Southern Punjab (ISP), Multan, Pakistan
| | - Hani Shaker
- Department of Mathematics, COMSATS University Islamabad, Lahore Campus, Pakistan
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34
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Wu S, Liu J, Liu C, Yang A, Qiao J. Quorum sensing for population-level control of bacteria and potential therapeutic applications. Cell Mol Life Sci 2020; 77:1319-1343. [PMID: 31612240 PMCID: PMC11104945 DOI: 10.1007/s00018-019-03326-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/13/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023]
Abstract
Quorum sensing (QS), a microbial cell-to-cell communication process, dynamically regulates a variety of metabolism and physiological activities. In this review, we provide an update on QS applications based on autoinducer molecules including acyl-homoserine lactones (AHLs), auto-inducing peptides (AIPs), autoinducer 2 (AI-2) and indole in population-level control of bacteria, and highlight the potential in developing novel clinical therapies. We summarize the development in the combination of various genetic circuits such as genetic oscillators, toggle switches and logic gates with AHL-based QS devices in Gram-negative bacteria. An overview is then offered to the state-of-the-art of much less researched applications of AIP-based QS devices with Gram-positive bacteria, followed by a review of the applications of AI-2 and indole based QS for interspecies communication among microbial communities. Building on these general-purpose QS applications, we highlight the disruptions and manipulations of QS devices as potential clinical therapies for diseases caused by biofilm formation, antibiotic resistance and the phage invasion. The last part of reviewed literature is dedicated to mathematical modelling for QS applications. Finally, the key challenges and future perspectives of QS applications in monoclonal synthetic biology and synthetic ecology are discussed.
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Affiliation(s)
- Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Jiaheng Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China
| | - Chunjiang Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Aidong Yang
- Department of Engineering Science, University of Oxford, Oxford, OX1 3PJ, UK.
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China.
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China.
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35
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Abstract
The traditional view of protein aggregation as being strictly disease-related has been challenged by many examples of cellular aggregates that regulate beneficial biological functions. When coupled with the emerging view that many regulatory proteins undergo phase separation to form dynamic cellular compartments, it has become clear that supramolecular assembly plays wide-ranging and critical roles in cellular regulation. This presents opportunities to develop new tools to probe and illuminate this biology, and to harness the unique properties of these self-assembling systems for synthetic biology for the purposeful manipulation of biological function.
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Affiliation(s)
- Giulio Chiesa
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Szilvia Kiriakov
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, 02215, USA. .,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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36
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Chen B, Dai Z. Combination of versatile platforms for the development of synthetic biology. QUANTITATIVE BIOLOGY 2020. [DOI: 10.1007/s40484-020-0197-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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37
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Agrawal DK, Dolan EM, Hernandez NE, Blacklock KM, Khare SD, Sontag ED. Mathematical Models of Protease-Based Enzymatic Biosensors. ACS Synth Biol 2020; 9:198-208. [PMID: 32017536 DOI: 10.1021/acssynbio.9b00279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An important goal of synthetic biology is to build biosensors and circuits with well-defined input-output relationships that operate at speeds found in natural biological systems. However, for molecular computation, most commonly used genetic circuit elements typically involve several steps from input detection to output signal production: transcription, translation, and post-translational modifications. These multiple steps together require up to several hours to respond to a single stimulus, and this limits the overall speed and complexity of genetic circuits. To address this gap, molecular frameworks that rely exclusively on post-translational steps to realize reaction networks that can process inputs at a time scale of seconds to minutes have been proposed. Here, we build mathematical models of fast biosensors capable of producing Boolean logic functionality. We employ protease-based chemical and light-induced switches, investigate their operation, and provide selection guidelines for their use as on-off switches. As a proof of concept, we implement a rapamycin-induced switch in vitro and demonstrate that its response qualitatively agrees with the predictions from our models. We then use these switches as elementary blocks, developing models for biosensors that can perform OR and XOR Boolean logic computation while using reaction conditions as tuning parameters. We use sensitivity analysis to determine the time-dependent sensitivity of the output to proteolytic and protein-protein binding reaction parameters. These fast protease-based biosensors can be used to implement complex molecular circuits with a capability of processing multiple inputs controllably and algorithmically. Our framework for evaluating and optimizing circuit performance can be applied to other molecular logic circuits.
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Affiliation(s)
- Deepak K. Agrawal
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02120, United States
- Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Elliott M. Dolan
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Nancy E. Hernandez
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Kristin M. Blacklock
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Eduardo D. Sontag
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02120, United States
- Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts 02115, United States
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts 02115, United States
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38
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DeNies MS, Liu AP, Schnell S. Are the biomedical sciences ready for synthetic biology? Biomol Concepts 2020; 11:23-31. [PMID: 31982863 DOI: 10.1515/bmc-2020-0003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/02/2020] [Indexed: 11/15/2022] Open
Abstract
The ability to construct a functional system from its individual components is foundational to understanding how it works. Synthetic biology is a broad field that draws from principles of engineering and computer science to create new biological systems or parts with novel function. While this has drawn well-deserved acclaim within the biotechnology community, application of synthetic biology methodologies to study biological systems has potential to fundamentally change how biomedical research is conducted by providing researchers with improved experimental control. While the concepts behind synthetic biology are not new, we present evidence supporting why the current research environment is conducive for integration of synthetic biology approaches within biomedical research. In this perspective we explore the idea of synthetic biology as a discovery science research tool and provide examples of both top-down and bottom-up approaches that have already been used to answer important physiology questions at both the organismal and molecular level.
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Affiliation(s)
- Maxwell S DeNies
- Cellular and Molecular Biology Graduate Program, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Allen P Liu
- Cellular and Molecular Biology Graduate Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Santiago Schnell
- Cellular and Molecular Biology Graduate Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
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39
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Thavarajah W, Verosloff MS, Jung JK, Alam KK, Miller JD, Jewett MC, Young SL, Lucks JB. A Primer on Emerging Field-Deployable Synthetic Biology Tools for Global Water Quality Monitoring. NPJ CLEAN WATER 2020; 3:18. [PMID: 34267944 PMCID: PMC8279131 DOI: 10.1038/s41545-020-0064-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/09/2020] [Indexed: 05/22/2023]
Abstract
Tracking progress towards Target 6.1 of the United Nations Sustainable Development Goals, "achieving universal and equitable access to safe and affordable drinking water for all", necessitates the development of simple, inexpensive tools to monitor water quality. The rapidly growing field of synthetic biology has the potential to address this need by taking DNA-encoded sensing elements from nature and reassembling them to create field-deployable 'biosensors' that can detect pathogenic or chemical water contaminants. Here we describe water quality monitoring strategies enabled by synthetic biology and compare them to previous approaches used to detect three priority water contaminants: fecal pathogens, arsenic, and fluoride in order to explain the potential for engineered biosensors to simplify and decentralize water quality monitoring. We also briefly discuss expanding biosensors to detect emerging contaminants including metals and pharmaceuticals. We conclude with an outlook on the future of biosensor development, in which we discuss adaptability to emerging contaminants, outline current limitations, and propose steps to overcome the field's outstanding challenges to facilitate global water quality monitoring.
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Affiliation(s)
- Walter Thavarajah
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Matthew S. Verosloff
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, 2204 Tech Drive, Evanston, IL, 60208, USA
| | - Jaeyoung K. Jung
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Khalid K. Alam
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Joshua D. Miller
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Department of Anthropology, Northwestern University, 1810 Hinman Ave., Evanston, IL, 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Sera L. Young
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Department of Anthropology, Northwestern University, 1810 Hinman Ave., Evanston, IL, 60208, USA
- Institute for Policy Research, Northwestern University, 2040 Sheridan Rd, Evanston, IL, 60208 USA
- To whom correspondence should be addressed, ,
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- To whom correspondence should be addressed, ,
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40
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Rech EL. Engineering biodiversity as a model for the species conservation. AN ACAD BRAS CIENC 2019; 91:e20190568. [PMID: 31576934 DOI: 10.1590/0001-3765201920190568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/25/2019] [Indexed: 11/22/2022] Open
Abstract
Early humans have domesticated plant and animal species based on ancient empirical concepts (Darwin 1868, 1876). In 1886, Mendel established a new paradigm of hereditary laws (Mendel 1866, 1870, 1950) based on genotypic and phenotypic traits of cross-compatible species, establishing a complex breeding technology that is currently utilized for the development of most food and livestock-derived products. Recently, studies on deciphering the double-helical structure (Watson and Crick 1953a, b) and how to restrict DNA (Arber 2012) have established the foundation of recombinant DNA technology. A new era is paving the way for genetic manipulation of important traits among all the kingdom's organisms, allowing for the development of innovative and widely utilized products for the agricultural, industrial and pharmaceutical production sectors (Mc Elroy 2003, 2004, ISAAA 2016).
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Affiliation(s)
- Elibio L Rech
- EMBRAPA Genetic Resources and Biotechnology, Laboratory of Synthetic Biology and National Institute of Science and Technology on Synthetic Biology, Parque Estação Biológica, W-5 Norte, 70770-917 Brasília, DF, Brazil
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41
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Gene networks that compensate for crosstalk with crosstalk. Nat Commun 2019; 10:4028. [PMID: 31492904 PMCID: PMC6731275 DOI: 10.1038/s41467-019-12021-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 08/12/2019] [Indexed: 12/18/2022] Open
Abstract
Crosstalk is a major challenge to engineering sophisticated synthetic gene networks. A common approach is to insulate signal-transduction pathways by minimizing molecular-level crosstalk between endogenous and synthetic genetic components, but this strategy can be difficult to apply in the context of complex, natural gene networks and unknown interactions. Here, we show that synthetic gene networks can be engineered to compensate for crosstalk by integrating pathway signals, rather than by pathway insulation. We demonstrate this principle using reactive oxygen species (ROS)-responsive gene circuits in Escherichia coli that exhibit concentration-dependent crosstalk with non-cognate ROS. We quantitatively map the degree of crosstalk and design gene circuits that introduce compensatory crosstalk at the gene network level. The resulting gene network exhibits reduced crosstalk in the sensing of the two different ROS. Our results suggest that simple network motifs that compensate for pathway crosstalk can be used by biological networks to accurately interpret environmental signals. Crosstalk between genetic circuits is a major challenge for engineering sophisticated networks. Here the authors design networks that compensate for crosstalk by integrating, not insulating, pathways.
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42
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Abstract
Biological systems have evolved biochemical, electrical, mechanical, and genetic networks to perform essential functions across various length and time scales. High-aspect-ratio biological nanowires, such as bacterial pili and neurites, mediate many of the interactions and homeostasis in and between these networks. Synthetic materials designed to mimic the structure of biological nanowires could also incorporate similar functional properties, and exploiting this structure-function relationship has already proved fruitful in designing biointerfaces. Semiconductor nanowires are a particularly promising class of synthetic nanowires for biointerfaces, given (1) their unique optical and electronic properties and (2) their high degree of synthetic control and versatility. These characteristics enable fabrication of a variety of electronic and photonic nanowire devices, allowing for the formation of well-defined, functional bioelectric interfaces at the biomolecular level to the whole-organ level. In this Focus Review, we first discuss the history of bioelectric interfaces with semiconductor nanowires. We next highlight several important, endogenous biological nanowires and use these as a framework to categorize semiconductor nanowire-based biointerfaces. Within this framework we then review the fundamentals of bioelectric interfaces with semiconductor nanowires and comment on both material choice and device design to form biointerfaces spanning multiple length scales. We conclude with a discussion of areas with the potential for greatest impact using semiconductor nanowire-enabled biointerfaces in the future.
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Affiliation(s)
- Bozhi Tian
- Department of Chemistry, the University of Chicago, Chicago, IL USA
- The James Franck Institute, the University of Chicago, Chicago, IL USA
- The Institute for Biophysical Dynamics, Chicago, IL USA
| | - Charles M. Lieber
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
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43
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Rabinowitch I. What would a synthetic connectome look like? Phys Life Rev 2019; 33:1-15. [PMID: 31296448 DOI: 10.1016/j.plrev.2019.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023]
Abstract
A major challenge of contemporary neuroscience is to unravel the structure of the connectome, the ensemble of neural connections that link between different functional units of the brain, and to reveal how this structure relates to brain function. This thriving area of research largely follows the general tradition in biology of reverse-engineering, which consists of first observing and characterizing a biological system or process, and then deconstructing it into its fundamental building blocks in order to infer its modes of operation. However, a complementary form of biology has emerged, synthetic biology, which emphasizes construction-based forward-engineering. The synthetic biology approach comprises the assembly of new biological systems out of elementary biological parts. The rationale is that the act of building a system can be a powerful method for gaining deep understanding of how that system works. As the fields of connectomics and synthetic biology are independently growing, I propose to consider the benefits of combining the two, to create synthetic connectomics, a new form of neuroscience and a new form of synthetic biology. The goal of synthetic connectomics would be to artificially design and construct the connectomes of live behaving organisms. Synthetic connectomics could serve as a unifying platform for unraveling the complexities of brain operation and perhaps also for generating new forms of artificial life, and, in general, could provide a valuable opportunity for empirically exploring theoretical predictions about network function. What would a synthetic connectome look like? What purposes would it serve? How could it be constructed? This review delineates the novel notion of a synthetic connectome and aims to lay out the initial steps towards its implementation, contemplating its impact on science and society.
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Affiliation(s)
- Ithai Rabinowitch
- Department of Medical Neurobiology, IMRIC - Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem Campus, Jerusalem, 9112002, Israel.
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44
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Abstract
Cells are the basic units of life, and can be mimicked to create artificial analogs enabling the investigation of cellular mechanisms under controlled conditions. Building biomimetic systems ranging from proto-cells to cell-like objects such as compartment membranes can be achieved by collecting biobricks that self-assemble to build simplified models performing specific functions. Hence, scientists can develop and optimize new synthetic cells with biological functions by taking inspiration from nature and exploiting the advantages of synthetic biology. However, the bottom-down approach is not restricted to the basic principles of biological cells, and new mimicry systems can be designed starting with a combination of living and non-living simple molecules to focus on a cellular machinery function. In recent years, microfluidic devices have been well established to engineer bioarchitecture models resembling cell-like structures involving vesicles, compartmentalization, synthetic membranes, and the chip itself as a synthetic cell. This review aims to highlight the role of biological cells and their impact on inspiring the development of biomimetic models. The combination of the principles of synthetic biology with microfluidic technology represents the newly-introduced field of synthetic cells and synthetic membranes that can be further exploited in diagnostic and therapeutic applications.
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45
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Yue K, Zhu Y, Kai L. Cell-Free Protein Synthesis: Chassis toward the Minimal Cell. Cells 2019; 8:cells8040315. [PMID: 30959805 PMCID: PMC6523147 DOI: 10.3390/cells8040315] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 11/16/2022] Open
Abstract
The quest for a minimal cell not only sheds light on the fundamental principles of life but also brings great advances in related applied fields such as general biotechnology. Minimal cell projects came from the study of a plausible route to the origin of life. Later on, research extended and also referred to the construction of artificial cells, or even more broadly, as in vitro synthetic biology. The cell-free protein synthesis (CFPS) techniques harness the central cellular activity of transcription/translation in an open environment, providing the framework for multiple cellular processes assembling. Therefore, CFPS systems have become the first choice in the construction of the minimal cell. In this review, we focus on the recent advances in the quantitative analysis of CFPS and on its advantage for addressing the bottom-up assembly of a minimal cell and illustrate the importance of systemic chassis behavior, such as stochasticity under a compartmentalized micro-environment.
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Affiliation(s)
- Ke Yue
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Shanghai Road 101, Xuzhou 221116, China.
| | - Yiyong Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Lei Kai
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Shanghai Road 101, Xuzhou 221116, China.
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany.
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46
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Zhao Q, Wang L, Luo Y. Recent advances in natural products exploitation in Streptomyces via synthetic biology. Eng Life Sci 2019; 19:452-462. [PMID: 32625022 DOI: 10.1002/elsc.201800137] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 02/08/2019] [Accepted: 03/01/2019] [Indexed: 02/05/2023] Open
Abstract
Natural products of microbial origin have proven to be the wellspring of clinically useful compounds for human therapeutics. Streptomyces species are predominant sources of bioactive compounds, most of which serve as potential drug candidates. While the exploitation of natural products has been severely reduced over the past two decades, the growing crisis of evolution and dissemination of drug resistant pathogens have again attracted great interest in this field. The emerging synthetic biology has been heralded as a new bioengineering platform to discover novel bioactive compounds and expand bioactive natural products diversity and production. Herein, we review recent advances in the natural products exploitation of Streptomyces with the applications of synthetic biology from three major aspects, including recently developed synthetic biology tools, natural products biosynthetic pathway engineering strategies as well as chassis host modifications.
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Affiliation(s)
- Qiyuan Zhao
- Department of Gastroenterology Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center of Biotherapy Chengdu P. R. China
| | - Liping Wang
- Department of Gastroenterology Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center of Biotherapy Chengdu P. R. China
| | - Yunzi Luo
- Department of Gastroenterology Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center of Biotherapy Chengdu P. R. China
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47
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Trump BD, Cegan J, Wells E, Poinsatte-Jones K, Rycroft T, Warner C, Martin D, Perkins E, Wood MD, Linkov I. Co-evolution of physical and social sciences in synthetic biology. Crit Rev Biotechnol 2019; 39:351-365. [PMID: 30727764 DOI: 10.1080/07388551.2019.1566203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Emerging technologies research often covers various perspectives in disciplines and research areas ranging from hard sciences, engineering, policymaking, and sociology. However, the interrelationship between these different disciplinary domains, particularly the physical and social sciences, often occurs many years after a technology has matured and moved towards commercialization. Synthetic biology may serve an exception to this idea, where, since 2000, the physical and the social sciences communities have increasingly framed their research in response to various perspectives in biological engineering, risk assessment needs, governance challenges, and the social implications that the technology may incur. This paper reviews a broad collection of synthetic biology literature from 2000-2016, and demonstrates how the co-development of physical and social science communities has grown throughout synthetic biology's earliest stages of development. Further, this paper indicates that future co-development of synthetic biology scholarship will assist with significant challenges of the technology's risk assessment, governance, and public engagement needs, where an interdisciplinary approach is necessary to foster sustainable, risk-informed, and societally beneficial technological advances moving forward.
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Affiliation(s)
- Benjamin D Trump
- a Oak Ridge Institute for Science and Education , US Army Corps of Engineers, Oak Ridge , TN , USA.,b US Army Engineer Research and Development Center , Vicksburg , MS , USA
| | - Jeffrey Cegan
- c SOL Engineering Services, LLC , Vicksburg , MS , USA
| | - Emily Wells
- c SOL Engineering Services, LLC , Vicksburg , MS , USA
| | | | - Taylor Rycroft
- b US Army Engineer Research and Development Center , Vicksburg , MS , USA
| | - Christopher Warner
- b US Army Engineer Research and Development Center , Vicksburg , MS , USA
| | - David Martin
- b US Army Engineer Research and Development Center , Vicksburg , MS , USA
| | - Edward Perkins
- b US Army Engineer Research and Development Center , Vicksburg , MS , USA
| | - Matthew D Wood
- b US Army Engineer Research and Development Center , Vicksburg , MS , USA
| | - Igor Linkov
- b US Army Engineer Research and Development Center , Vicksburg , MS , USA
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48
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Fink T, Lonzarić J, Praznik A, Plaper T, Merljak E, Leben K, Jerala N, Lebar T, Strmšek Ž, Lapenta F, Benčina M, Jerala R. Design of fast proteolysis-based signaling and logic circuits in mammalian cells. Nat Chem Biol 2019; 15:115-122. [PMID: 30531965 PMCID: PMC7069760 DOI: 10.1038/s41589-018-0181-6] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/05/2018] [Indexed: 01/05/2023]
Abstract
Cellular signal transduction is predominantly based on protein interactions and their post-translational modifications, which enable a fast response to input signals. Owing to difficulties in designing new unique protein-protein interactions, designed cellular logic has focused on transcriptional regulation; however, that process has a substantially slower response, because it requires transcription and translation. Here, we present de novo design of modular, scalable signaling pathways based on proteolysis and designed coiled coils (CC) and implemented in mammalian cells. A set of split proteases with highly specific orthogonal cleavage motifs was constructed and combined with strategically positioned cleavage sites and designed orthogonal CC dimerizing domains with tunable affinity for competitive displacement after proteolytic cleavage. This framework enabled the implementation of Boolean logic functions and signaling cascades in mammalian cells. The designed split-protease-cleavable orthogonal-CC-based (SPOC) logic circuits enable response to chemical or biological signals within minutes rather than hours and should be useful for diverse medical and nonmedical applications.
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Affiliation(s)
- Tina Fink
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jan Lonzarić
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Leben
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- ENFIST Centre of Excellence, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
- ENFIST Centre of Excellence, Ljubljana, Slovenia.
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49
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Cao X, Hamilton JJ, Venturelli OS. Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities. Biochemistry 2019; 58:94-107. [PMID: 30457843 PMCID: PMC6733022 DOI: 10.1021/acs.biochem.8b01006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Microbiomes impact nearly every environment on Earth by modulating the molecular composition of the environment. Temporally changing environmental stimuli and spatial organization are major variables shaping the structure and function of microbiomes. The web of interactions among members of these communities and between the organisms and the environment dictates microbiome functions. Microbial interactions are major drivers of microbiomes and are modulated by spatiotemporal parameters. A mechanistic and quantitative understanding of ecological, molecular, and environmental forces shaping microbiomes could inform strategies to control microbiome dynamics and functions. Major challenges for harnessing the potential of microbiomes for diverse applications include the development of predictive modeling frameworks and tools for precise manipulation of microbiome behaviors.
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Affiliation(s)
| | | | - Ophelia S. Venturelli
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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50
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Nakamura M, Srinivasan P, Chavez M, Carter MA, Dominguez AA, La Russa M, Lau MB, Abbott TR, Xu X, Zhao D, Gao Y, Kipniss NH, Smolke CD, Bondy-Denomy J, Qi LS. Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells. Nat Commun 2019; 10:194. [PMID: 30643127 PMCID: PMC6331597 DOI: 10.1038/s41467-018-08158-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 12/20/2018] [Indexed: 11/24/2022] Open
Abstract
Repurposed CRISPR-Cas molecules provide a useful tool set for broad applications of genomic editing and regulation of gene expression in prokaryotes and eukaryotes. Recent discovery of phage-derived proteins, anti-CRISPRs, which serve to abrogate natural CRISPR anti-phage activity, potentially expands the ability to build synthetic CRISPR-mediated circuits. Here, we characterize a panel of anti-CRISPR molecules for expanded applications to counteract CRISPR-mediated gene activation and repression of reporter and endogenous genes in various cell types. We demonstrate that cells pre-engineered with anti-CRISPR molecules become resistant to gene editing, thus providing a means to generate "write-protected" cells that prevent future gene editing. We further show that anti-CRISPRs can be used to control CRISPR-based gene regulation circuits, including implementation of a pulse generator circuit in mammalian cells. Our work suggests that anti-CRISPR proteins should serve as widely applicable tools for synthetic systems regulating the behavior of eukaryotic cells.
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Affiliation(s)
- Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | | | - Michael Chavez
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Matthew A Carter
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Antonia A Dominguez
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Marie La Russa
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Matthew B Lau
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- International Christian School, 1 On Muk Ln, Sha Tin, 999077, Hong Kong SAR, China
| | - Timothy R Abbott
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Xiaoshu Xu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Dehua Zhao
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Yuchen Gao
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Cancer Biology Program, Stanford University, Stanford, CA, 94305, USA
| | - Nathan H Kipniss
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, CA, 94158, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA.
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA.
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