101
|
Xie M, Fussenegger M. Designing cell function: assembly of synthetic gene circuits for cell biology applications. Nat Rev Mol Cell Biol 2019; 19:507-525. [PMID: 29858606 DOI: 10.1038/s41580-018-0024-z] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Synthetic biology is the discipline of engineering application-driven biological functionalities that were not evolved by nature. Early breakthroughs of cell engineering, which were based on ectopic (over)expression of single sets of transgenes, have already had a revolutionary impact on the biotechnology industry, regenerative medicine and blood transfusion therapies. Now, we require larger-scale, rationally assembled genetic circuits engineered to programme and control various human cell functions with high spatiotemporal precision in order to solve more complex problems in applied life sciences, biomedicine and environmental sciences. This will open new possibilities for employing synthetic biology to advance personalized medicine by converting cells into living therapeutics to combat hitherto intractable diseases.
Collapse
Affiliation(s)
- Mingqi Xie
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,University of Basel, Faculty of Science, Basel, Switzerland.
| |
Collapse
|
102
|
Pandi A, Koch M, Voyvodic PL, Soudier P, Bonnet J, Kushwaha M, Faulon JL. Metabolic perceptrons for neural computing in biological systems. Nat Commun 2019; 10:3880. [PMID: 31462649 PMCID: PMC6713752 DOI: 10.1038/s41467-019-11889-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/08/2019] [Indexed: 12/30/2022] Open
Abstract
Synthetic biological circuits are promising tools for developing sophisticated systems for medical, industrial, and environmental applications. So far, circuit implementations commonly rely on gene expression regulation for information processing using digital logic. Here, we present a different approach for biological computation through metabolic circuits designed by computer-aided tools, implemented in both whole-cell and cell-free systems. We first combine metabolic transducers to build an analog adder, a device that sums up the concentrations of multiple input metabolites. Next, we build a weighted adder where the contributions of the different metabolites to the sum can be adjusted. Using a computational model fitted on experimental data, we finally implement two four-input perceptrons for desired binary classification of metabolite combinations by applying model-predicted weights to the metabolic perceptron. The perceptron-mediated neural computing introduced here lays the groundwork for more advanced metabolic circuits for rapid and scalable multiplex sensing. So far, synthetic genetic circuits have relied on digital logic for information processing. Here the authors present metabolic perceptrons that use analog weighted adders to vary the contributions of multiple inputs, resulting in different classification functions.
Collapse
Affiliation(s)
- Amir Pandi
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Mathilde Koch
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Peter L Voyvodic
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, University of Montpellier, Montpellier, France
| | - Paul Soudier
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jerome Bonnet
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, University of Montpellier, Montpellier, France
| | - Manish Kushwaha
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France. .,iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France. .,SYNBIOCHEM Center, School of Chemistry, University of Manchester, Manchester, UK.
| |
Collapse
|
103
|
Mohammadniaei M, Park C, Min J, Sohn H, Lee T. Fabrication of Electrochemical-Based Bioelectronic Device and Biosensor Composed of Biomaterial-Nanomaterial Hybrid. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1064:263-296. [PMID: 30471039 PMCID: PMC7120487 DOI: 10.1007/978-981-13-0445-3_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of bioelectronics has paved the way for the development of biochips, biomedical devices, biosensors and biocomputation devices. Various biosensors and biomedical devices have been developed to commercialize laboratory products and transform them into industry products in the clinical, pharmaceutical, environmental fields. Recently, the electrochemical bioelectronic devices that mimicked the functionality of living organisms in nature were applied to the use of bioelectronics device and biosensors. In particular, the electrochemical-based bioelectronic devices and biosensors composed of biomolecule-nanoparticle hybrids have been proposed to generate new functionality as alternatives to silicon-based electronic computation devices, such as information storage, process, computations and detection. In this chapter, we described the recent progress of bioelectronic devices and biosensors based on biomaterial-nanomaterial hybrid.
Collapse
Affiliation(s)
- Mohsen Mohammadniaei
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, South Korea
| | - Chulhwan Park
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea
| | - Junhong Min
- School of Integrative Engineering Chung-Ang University, Seoul, South Korea
| | - Hiesang Sohn
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea.
| | - Taek Lee
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea.
| |
Collapse
|
104
|
Abstract
Large-scale sequencing of human tumours has uncovered a vast array of genomic alterations. Genetically engineered mouse models recapitulate many features of human cancer and have been instrumental in assigning biological meaning to specific cancer-associated alterations. However, their time, cost and labour-intensive nature limits their broad utility; thus, the functional importance of the majority of genomic aberrations in cancer remains unknown. Recent advances have accelerated the functional interrogation of cancer-associated alterations within in vivo models. Specifically, the past few years have seen the emergence of CRISPR-Cas9-based strategies to rapidly generate increasingly complex somatic alterations and the development of multiplexed and quantitative approaches to ascertain gene function in vivo.
Collapse
|
105
|
Gao T, Chen T, Feng C, He X, Mu C, Anzai JI, Li G. Design and fabrication of flexible DNA polymer cocoons to encapsulate live cells. Nat Commun 2019; 10:2946. [PMID: 31270421 PMCID: PMC6610073 DOI: 10.1038/s41467-019-10845-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 05/31/2019] [Indexed: 12/20/2022] Open
Abstract
The capability to encapsulate designated live cells into a biologically and mechanically tunable polymer layer is in high demand. Here, an approach to weave functional DNA polymer cocoons has been proposed as an encapsulation method. By developing in situ DNA-oriented polymerization (isDOP), we demonstrate a localized, programmable, and biocompatible encapsulation approach to graft DNA polymers onto live cells. Further guided by two mutually aided enzymatic reactions, the grafted DNA polymers are assembled into DNA polymer cocoons at the cell surface. Therefore, the coating of bacteria, yeast, and mammalian cells has been achieved. The capabilities of this approach may offer significant opportunities to engineer cell surfaces and enable the precise manipulation of the encapsulated cells, such as encoding, handling, and sorting, for many biomedical applications.
Collapse
Affiliation(s)
- Tao Gao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, Shanghai, P.R. China
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, P.R. China
| | - Tianshu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, Shanghai, P.R. China
| | - Chang Feng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, P.R. China
| | - Xiang He
- School of Biomedical Engineering, Shanghai Jiao Tong University, 200240, Shanghai, P.R. China
| | - Chaoli Mu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, P.R. China
| | - Jun-Ichi Anzai
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Genxi Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, Shanghai, P.R. China.
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, P.R. China.
| |
Collapse
|
106
|
Abstract
DNA outperforms most conventional storage media in terms of information retention time, physical density, and volumetric coding capacity. Advances in synthesis and sequencing technologies have enabled implementations of large synthetic DNA databases with impressive storage capacity and reliable data recovery. Several robust DNA storage architectures featuring random access, error correction, and content rewritability have been constructed with the potential for scalability and cost reduction. We survey these recent achievements and discuss alternative routes for overcoming the hurdles of engineering practical DNA storage systems. We also review recent exciting work on in vivo DNA memory including intracellular recorders constructed by programmable genome editing tools. Besides information storage, DNA could serve as a versatile molecular computing substrate. We highlight several state-of-the-art DNA computing techniques such as strand displacement, localized hybridization chain reactions, and enzymatic reaction networks. We summarize how these simple primitives have facilitated rational designs and implementations of in vitro DNA reaction networks that emulate digital/analog circuits, artificial neural networks, or nonlinear dynamic systems. We envision these modular primitives could be strategically adapted for sophisticated database operations and massively parallel computations on DNA databases. We also highlight in vivo DNA computing modules such as CRISPR logic gates for building scalable genetic circuits in living cells. To conclude, we discuss various implications and challenges of DNA-based storage and computing, and we particularly encourage innovative work on bridging these two areas of research to further explore molecular parallelism and near-data processing. Such integrated molecular systems could lead to far-reaching applications in biocomputing, security, and medicine.
Collapse
|
107
|
Abstract
The combination of modern biotechnologies such as DNA synthesis, λ red recombineering, CRISPR-based editing and next-generation high-throughput sequencing increasingly enables precise manipulation of genes and genomes. Beyond rational design, these technologies also enable the targeted, and potentially continuous, introduction of multiple mutations. While this might seem to be merely a return to natural selection, the ability to target evolution greatly reduces fitness burdens and focuses mutation and selection on those genes and traits that best contribute to a desired phenotype, ultimately throwing evolution into fast forward.
Collapse
|
108
|
Ishiguro S, Mori H, Yachie N. DNA event recorders send past information of cells to the time of observation. Curr Opin Chem Biol 2019; 52:54-62. [PMID: 31200335 DOI: 10.1016/j.cbpa.2019.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/26/2019] [Accepted: 05/10/2019] [Indexed: 11/17/2022]
Abstract
While current omics and single cell technologies have enabled measurements of high-resolution molecular snapshots of cells at a large scale, these technologies all require destruction of samples and prevent us from analyzing dynamic changes in molecular profiles, phenotypes, and behaviors of individual cells in a complex system. One possible direction to overcome this issue is the development of a cell-embedded 'event recorder' system, whereby molecular and phenotypic information of a cell(s) can be obtained at the time of observation with their past event information stored in 'heritable polymers' of the same cell. This concept has been demonstrated by many synthetic cellular circuits that monitor and transmit a certain set of environmental and intracellular signals into DNA, and have now been further accelerated by recent CRISPR-related technologies. Notably, the discovery of the RT-Cas1-Cas2 system, which acquires sequences of cellular transcripts into a specific host genomic region, has enabled recording of a broader range of molecular profile histories in the DNA tapes of cells, to understand the dynamics of complex biological processes that cannot be addressed by current technologies.
Collapse
Affiliation(s)
- Soh Ishiguro
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan; Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Hideto Mori
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan; Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Nozomu Yachie
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan; Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan; Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo 113-0033, Japan; PRESTO, Japan Science and Technology Agency (JST), Tokyo 153-8904, Japan.
| |
Collapse
|
109
|
Tan ZL, Zheng X, Wu Y, Jian X, Xing X, Zhang C. In vivo continuous evolution of metabolic pathways for chemical production. Microb Cell Fact 2019; 18:82. [PMID: 31088458 PMCID: PMC6518619 DOI: 10.1186/s12934-019-1132-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/04/2019] [Indexed: 01/07/2023] Open
Abstract
Microorganisms have long been used as chemical plant to convert simple substrates into complex molecules. Various metabolic pathways have been optimised over the past few decades, but the progresses were limited due to our finite knowledge on metabolism. Evolution is a knowledge-free genetic randomisation approach, employed to improve the chemical production in microbial cell factories. However, evolution of large, complex pathway was a great challenge. The invention of continuous culturing systems and in vivo genetic diversification technologies have changed the way how laboratory evolution is conducted, render optimisation of large, complex pathway possible. In vivo genetic diversification, phenotypic selection, and continuous cultivation are the key elements in in vivo continuous evolution, where any human intervention in the process is prohibited. This approach is crucial in highly efficient evolution strategy of metabolic pathway evolution.
Collapse
Affiliation(s)
- Zheng Lin Tan
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama City, Kanagawa Prefecture, 226-8503 Japan
- Laboratory of Future Interdisciplinary Research and Science Technology, Tokyo Institute of Technology, Yokohama City, Kanagawa Prefecture, 226-8503 Japan
| | - Xiang Zheng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Yinan Wu
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Xingjin Jian
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Xinhui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
| |
Collapse
|
110
|
Healy CP, Deans TL. Genetic circuits to engineer tissues with alternative functions. J Biol Eng 2019; 13:39. [PMID: 31073328 PMCID: PMC6500048 DOI: 10.1186/s13036-019-0170-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/17/2019] [Indexed: 12/23/2022] Open
Abstract
Persistent and complex problems arising with respect to human physiology and pathology have led to intense investigation into therapies and tools that permit more targeted outcomes and biomimetic responses to pathological conditions. A primary goal in mammalian synthetic biology is to build genetic circuits that exert fine control over cell behavior for next-generation biomedical applications. In pursuit of this, synthetic biologists have engineered cells endowed with genetic circuits with sensor that are capable of reacting to a variety of stimuli and responding with targeted behavior. Here, we highlight how synthetic biology approaches are being used to program cells with novel functions for therapeutic applications, and how they can be used in stem cells to improve differentiation outcomes. These approaches open the possibilities for engineering synthetic tissues for employing personalized medicine and to develop next-generation biomedical therapies.
Collapse
Affiliation(s)
- C P Healy
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112 USA
| | - T L Deans
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112 USA
| |
Collapse
|
111
|
Ahan RE, Kırpat BM, Saltepe B, Şeker UÖŞ. A Self-Actuated Cellular Protein Delivery Machine. ACS Synth Biol 2019; 8:686-696. [PMID: 30811932 DOI: 10.1021/acssynbio.9b00062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Engineered bacterial cells have great promise to solve global problems, yet they are hampered by a lack of convenient strategy for controlled protein release. A well-controlled protein translocation through cellular membranes is essential for cell-based protein delivery. Here we have developed a controlled protein release system by programming a bacterial autotransporter system named Ag43. Ag43 protein is engineered by adding a protease digestion site between its translocation and cargo domains. Once it is displayed on the cell surface, we managed to release the cargo proteins in defined conditions by processing environmental signals. The protein release in terms of time and quantity can be controlled through changing the inducer conditions. We thought that the release system can be adopted for complex genetic circuitries due to its simplicity. We implemented the protein release system to develop a cellular device that is able to release proteins in a sequence response to ordered chemical signals. We envision that development of genetically controlled protein release systems will improve the applications of synthetic organisms in cell based therapies, especially for cases with a need for controlled protein release using the cues from the biological environment.
Collapse
Affiliation(s)
- Recep Erdem Ahan
- UNAM−National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Büşra Merve Kırpat
- UNAM−National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Behide Saltepe
- UNAM−National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM−National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
- Neuroscience Graduate Program, Bilkent University, 06800 Ankara, Turkey
| |
Collapse
|
112
|
Zañudo JGT, Guinn MT, Farquhar K, Szenk M, Steinway SN, Balázsi G, Albert R. Towards control of cellular decision-making networks in the epithelial-to-mesenchymal transition. Phys Biol 2019; 16:031002. [PMID: 30654341 PMCID: PMC6405305 DOI: 10.1088/1478-3975/aaffa1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We present the epithelial-to-mesenchymal transition (EMT) from two perspectives: experimental/technological and theoretical. We review the state of the current understanding of the regulatory networks that underlie EMT in three physiological contexts: embryonic development, wound healing, and metastasis. We describe the existing experimental systems and manipulations used to better understand the molecular participants and factors that influence EMT and metastasis. We review the mathematical models of the regulatory networks involved in EMT, with a particular emphasis on the network motifs (such as coupled feedback loops) that can generate intermediate hybrid states between the epithelial and mesenchymal states. Ultimately, the understanding gained about these networks should be translated into methods to control phenotypic outcomes, especially in the context of cancer therapeutic strategies. We present emerging theories of how to drive the dynamics of a network toward a desired dynamical attractor (e.g. an epithelial cell state) and emerging synthetic biology technologies to monitor and control the state of cells.
Collapse
Affiliation(s)
- Jorge Gómez Tejeda Zañudo
- Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
- Department of Medical Oncology, Dana-Farber Cancer Center, Boston, MA 02215, USA
- Cancer Program, Eli and Edythe L. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - M. Tyler Guinn
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11794 USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Medical Scientist Training Program, 101 Nicolls Road, Stony Brook, NY 11794, USA
| | - Kevin Farquhar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mariola Szenk
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11794 USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Steven N. Steinway
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Gábor Balázsi
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11794 USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Réka Albert
- Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
113
|
Goñi-Moreno A, de la Cruz F, Rodríguez-Patón A, Amos M. Dynamical Task Switching in Cellular Computers. Life (Basel) 2019; 9:E14. [PMID: 30691149 PMCID: PMC6463194 DOI: 10.3390/life9010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/23/2018] [Accepted: 01/23/2019] [Indexed: 01/24/2023] Open
Abstract
We present a scheme for implementing a version of task switching in engineered bacteria, based on the manipulation of plasmid copy numbers. Our method allows for the embedding of multiple computations in a cellular population, whilst minimising resource usage inefficiency. We describe the results of computational simulations of our model, and discuss the potential for future work in this area.
Collapse
Affiliation(s)
- Angel Goñi-Moreno
- School of Computing, Newcastle University, Newcastle Upon Tyne NE4 5TG, UK.
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria, 39011 Santander, Spain.
| | - Alfonso Rodríguez-Patón
- Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, 28660 Madrid, Spain.
| | - Martyn Amos
- Department of Computer and Information Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
| |
Collapse
|
114
|
Zhou Q, Zhan H, Liao X, Fang L, Liu Y, Xie H, Yang K, Gao Q, Ding M, Cai Z, Huang W, Liu Y. A revolutionary tool: CRISPR technology plays an important role in construction of intelligentized gene circuits. Cell Prolif 2018; 52:e12552. [PMID: 30520167 PMCID: PMC6496519 DOI: 10.1111/cpr.12552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/28/2018] [Accepted: 08/30/2018] [Indexed: 12/11/2022] Open
Abstract
With the development of synthetic biology, synthetic gene circuits have shown great applied potential in medicine, biology, and as commodity chemicals. An ultimate challenge in the construction of gene circuits is the lack of effective, programmable, secure and sequence-specific gene editing tools. The clustered regularly interspaced short palindromic repeat (CRISPR) system, a CRISPR-associated RNA-guided endonuclease Cas9 (CRISPR-associated protein 9)-targeted genome editing tool, has recently been applied in engineering gene circuits for its unique properties-operability, high efficiency and programmability. The traditional single-targeted therapy cannot effectively distinguish tumour cells from normal cells, and gene therapy for single targets has poor anti-tumour effects, which severely limits the application of gene therapy. Currently, the design of gene circuits using tumour-specific targets based on CRISPR/Cas systems provides a new way for precision cancer therapy. Hence, the application of intelligentized gene circuits based on CRISPR technology effectively guarantees the safety, efficiency and specificity of cancer therapy. Here, we assessed the use of synthetic gene circuits and if the CRISPR system could be used, especially artificial switch-inducible Cas9, to more effectively target and treat tumour cells. Moreover, we also discussed recent advances, prospectives and underlying challenges in CRISPR-based gene circuit development.
Collapse
Affiliation(s)
- Qun Zhou
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, China.,Department of Urology, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Hengji Zhan
- Department of Urology, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xinhui Liao
- Department of Urology, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Lan Fang
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, China
| | - Yuhan Liu
- Department of Urology, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Haibiao Xie
- Department of Urology, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Kang Yang
- Department of Urology, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qunjun Gao
- Department of Urology, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Mengting Ding
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, China.,Department of Urology, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhiming Cai
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, China.,Department of Urology, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Weiren Huang
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, China.,Department of Urology, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yuchen Liu
- Department of Urology, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| |
Collapse
|
115
|
Abstract
While several genome editing methods exist, few are suitable for the continuous evolution of targeted sequences. Here we develop bacterial retroelements known as "retrons" for the dynamic, in vivo editing and mutagenesis of targeted genes. We first optimized retrons' ability to introduce preprogrammed mutations, optimizing both their expression and the host machinery that interacts with them to increase the incorporation frequency of mutations 78-fold over rates previously reported in synthetic systems. The optimized system is capable of simultaneously overwriting 13 separate positions spanning a 31-base length, and is for the first time shown to yield targeted deletions and insertions. To engineer retrons as a tool to introduce novel, unprogrammed mutations in specific targeted regions, we expressed them under a mutagenic T7 RNA polymerase. This coupled mutagenic T7 RNA polymerase-retron system enabled the evolution of diverse variants of environmentally selected antibiotic resistance genes, producing mutation rates in the targeted region 190-fold higher than background cellular mutation rates, potentially enabling the dynamic, continuous self-evolution of selected phenotypes.
Collapse
|
116
|
Liu Z, Zhang J, Jin J, Geng Z, Qi Q, Liang Q. Programming Bacteria With Light-Sensors and Applications in Synthetic Biology. Front Microbiol 2018; 9:2692. [PMID: 30467500 PMCID: PMC6236058 DOI: 10.3389/fmicb.2018.02692] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/22/2018] [Indexed: 12/11/2022] Open
Abstract
Photo-receptors are widely present in both prokaryotic and eukaryotic cells, which serves as the foundation of tuning cell behaviors with light. While practices in eukaryotic cells have been relatively established, trials in bacterial cells have only been emerging in the past few years. A number of light sensors have been engineered in bacteria cells and most of them fall into the categories of two-component and one-component systems. Such a sensor toolbox has enabled practices in controlling synthetic circuits at the level of transcription and protein activity which is a major topic in synthetic biology, according to the central dogma. Additionally, engineered light sensors and practices of tuning synthetic circuits have served as a foundation for achieving light based real-time feedback control. Here, we review programming bacteria cells with light, introducing engineered light sensors in bacteria and their applications, including tuning synthetic circuits and achieving feedback controls over microbial cell culture.
Collapse
Affiliation(s)
- Zedao Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Jizhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Jiao Jin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Zilong Geng
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| |
Collapse
|
117
|
Abstract
Measuring biological data across time and space is critical for understanding complex biological processes and for various biosurveillance applications. However, such data are often inaccessible or difficult to directly obtain. Less invasive, more robust and higher-throughput biological recording tools are needed to profile cells and their environments. DNA-based cellular recording is an emerging and powerful framework for tracking intracellular and extracellular biological events over time across living cells and populations. Here, we review and assess DNA recorders that utilize CRISPR nucleases, integrases and base-editing strategies, as well as recombinase and polymerase-based methods. Quantitative characterization, modelling and evaluation of these DNA-recording modalities can guide their design and implementation for specific application areas.
Collapse
Affiliation(s)
- Ravi U Sheth
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.
| |
Collapse
|
118
|
|
119
|
Xiang Y, Dalchau N, Wang B. Scaling up genetic circuit design for cellular computing: advances and prospects. NATURAL COMPUTING 2018; 17:833-853. [PMID: 30524216 PMCID: PMC6244767 DOI: 10.1007/s11047-018-9715-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Synthetic biology aims to engineer and redesign biological systems for useful real-world applications in biomanufacturing, biosensing and biotherapy following a typical design-build-test cycle. Inspired from computer science and electronics, synthetic gene circuits have been designed to exhibit control over the flow of information in biological systems. Two types are Boolean logic inspired TRUE or FALSE digital logic and graded analog computation. Key principles for gene circuit engineering include modularity, orthogonality, predictability and reliability. Initial circuits in the field were small and hampered by a lack of modular and orthogonal components, however in recent years the library of available parts has increased vastly. New tools for high throughput DNA assembly and characterization have been developed enabling rapid prototyping, systematic in situ characterization, as well as automated design and assembly of circuits. Recently implemented computing paradigms in circuit memory and distributed computing using cell consortia will also be discussed. Finally, we will examine existing challenges in building predictable large-scale circuits including modularity, context dependency and metabolic burden as well as tools and methods used to resolve them. These new trends and techniques have the potential to accelerate design of larger gene circuits and result in an increase in our basic understanding of circuit and host behaviour.
Collapse
Affiliation(s)
- Yiyu Xiang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR UK
| | | | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR UK
| |
Collapse
|
120
|
Schmidt F, Cherepkova MY, Platt RJ. Transcriptional recording by CRISPR spacer acquisition from RNA. Nature 2018; 562:380-385. [DOI: 10.1038/s41586-018-0569-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/21/2018] [Indexed: 12/11/2022]
|
121
|
Wu F, Bethke JH, Wang M, You L. Quantitative and synthetic biology approaches to combat bacterial pathogens. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018; 4:116-126. [PMID: 30263975 DOI: 10.1016/j.cobme.2017.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antibiotic resistance is one of the biggest threats to public health. The rapid emergence of resistant bacterial pathogens endangers the efficacy of current antibiotics and has led to increasing mortality and economic burden. This crisis calls for more rapid and accurate diagnosis to detect and identify pathogens, as well as to characterize their response to antibiotics. Building on this foundation, treatment options also need to be improved to use current antibiotics more effectively and develop alternative strategies that complement the use of antibiotics. We here review recent developments in diagnosis and treatment of bacterial pathogens with a focus on quantitative biology and synthetic biology approaches.
Collapse
Affiliation(s)
- Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Jonathan H Bethke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA
| | - Meidi Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, 27708, USA
| |
Collapse
|
122
|
Abstract
Natural life is encoded by evolvable, DNA-based memory. Recent advances in dynamic genome-engineering technologies, which we collectively refer to as in vivo DNA writing, have opened new avenues for investigating and engineering biology. This Review surveys these technological advances, outlines their prospects and emerging applications, and discusses the features and current limitations of these technologies for building various genetic circuits for processing and recording information in living cells.
Collapse
Affiliation(s)
- Fahim Farzadfard
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Timothy K Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| |
Collapse
|
123
|
Abstract
Bacteriophage research has been instrumental to advancing many fields of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been adapted for building gene circuits to program biological systems. Phages also exhibit significant medical potential as antibacterial agents and bacterial diagnostics due to their extreme specificity for their host, and our growing ability to engineer them further enhances this potential. Phages have also been used as scaffolds for genetically programmable biomaterials that have highly tunable properties. Furthermore, phages are central to powerful directed evolution platforms, which are being leveraged to enhance existing biological functions and even produce new ones. In this review, we discuss recent examples of how phage research is influencing these next-generation biotechnologies.
Collapse
Affiliation(s)
- Sebastien Lemire
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Kevin M Yehl
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Timothy K Lu
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; .,Synthetic Biology Group, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
124
|
Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
Collapse
Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
| |
Collapse
|
125
|
Ozdemir T, Fedorec AJ, Danino T, Barnes CP. Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity. Cell Syst 2018; 7:5-16. [DOI: 10.1016/j.cels.2018.06.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/31/2018] [Accepted: 06/15/2018] [Indexed: 12/31/2022]
|
126
|
Li M, Zheng M, Wu S, Tian C, Liu D, Weizmann Y, Jiang W, Wang G, Mao C. In vivo production of RNA nanostructures via programmed folding of single-stranded RNAs. Nat Commun 2018; 9:2196. [PMID: 29875441 PMCID: PMC5989258 DOI: 10.1038/s41467-018-04652-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/14/2018] [Indexed: 11/12/2022] Open
Abstract
Programmed self-assembly of nucleic acids is a powerful approach for nano-constructions. The assembled nanostructures have been explored for various applications. However, nucleic acid assembly often requires chemical or in vitro enzymatical synthesis of DNA or RNA, which is not a cost-effective production method on a large scale. In addition, the difficulty of cellular delivery limits the in vivo applications. Herein we report a strategy that mimics protein production. Gene-encoded DNA duplexes are transcribed into single-stranded RNAs, which self-fold into well-defined RNA nanostructures in the same way as polypeptide chains fold into proteins. The resulting nanostructure contains only one component RNA molecule. This approach allows both in vitro and in vivo production of RNA nanostructures. In vivo synthesized RNA strands can fold into designed nanostructures inside cells. This work not only suggests a way to synthesize RNA nanostructures on a large scale and at a low cost but also facilitates the in vivo applications. RNA nanostructures have been demonstrated in a range of biological applications, but their assembly and delivery to cells is difficult. Here the authors demonstrate the in vivo assembly of a RNA nanostructure from a single transcript inside the cellular environment.
Collapse
Affiliation(s)
- Mo Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Mengxi Zheng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Siyu Wu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Cheng Tian
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Di Liu
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
| | - Yossi Weizmann
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
| | - Wen Jiang
- Markey Center for Structural Biology and Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Guansong Wang
- The Institute of Respiratory Diseases, Xinqiao Hospital, 400037, Chongqing, China.
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
| |
Collapse
|
127
|
Abstract
Genetically engineered bacteria have the potential to diagnose and treat a wide range of diseases linked to the gastrointestinal tract, or gut. Such engineered microbes will be less expensive and invasive than current diagnostics and more effective and safe than current therapeutics. Recent advances in synthetic biology have dramatically improved the reliability with which bacteria can be engineered with the sensors, genetic circuits, and output (actuator) genes necessary for diagnostic and therapeutic functions. However, to deploy such bacteria in vivo, researchers must identify appropriate gut-adapted strains and consider performance metrics such as sensor detection thresholds, circuit computation speed, growth rate effects, and the evolutionary stability of engineered genetic systems. Other recent reviews have focused on engineering bacteria to target cancer or genetically modifying the endogenous gut microbiota in situ. Here, we develop a standard approach for engineering "smart probiotics," which both diagnose and treat disease, as well as "diagnostic gut bacteria" and "drug factory probiotics," which perform only the former and latter function, respectively. We focus on the use of cutting-edge synthetic biology tools, gut-specific design considerations, and current and future engineering challenges.
Collapse
|
128
|
Abstract
Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry—biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function.
Collapse
Affiliation(s)
- Caleb J. Bashor
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;,
| | - James J. Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;,
- Harvard–MIT Program in Health Sciences and Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
| |
Collapse
|
129
|
Verechshagina N, Nikitchina N, Yamada Y, Harashima Н, Tanaka M, Orishchenko K, Mazunin I. Future of human mitochondrial DNA editing technologies. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:214-221. [PMID: 29764251 DOI: 10.1080/24701394.2018.1472773] [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: 12/11/2022]
Abstract
ATP and other metabolites, which are necessary for the development, maintenance, and functioning of bodily cells are all synthesized in the mitochondria. Multiple copies of the genome, present within the mitochondria, together with its maternal inheritance, determine the clinical manifestation and spreading of mutations in mitochondrial DNA (mtDNA). The main obstacle in the way of thorough understanding of mitochondrial biology and the development of gene therapy methods for mitochondrial diseases is the absence of systems that allow to directly change mtDNA sequence. Here, we discuss existing methods of manipulating the level of mtDNA heteroplasmy, as well as the latest systems, that could be used in the future as tools for human mitochondrial genome editing.
Collapse
Affiliation(s)
- N Verechshagina
- a Laboratory of Molecular Genetics Technologies , Immanuel Kant Baltic Federal University , Kaliningrad , Russia
| | - N Nikitchina
- a Laboratory of Molecular Genetics Technologies , Immanuel Kant Baltic Federal University , Kaliningrad , Russia
| | - Y Yamada
- b Faculty of Pharmaceutical Sciences, Laboratory for Molecular Design of Pharmaceutics , Hokkaido University , Sapporo , Japan
| | - Н Harashima
- b Faculty of Pharmaceutical Sciences, Laboratory for Molecular Design of Pharmaceutics , Hokkaido University , Sapporo , Japan
| | - M Tanaka
- c Department for Health and Longevity Research , National Institutes of Biomedical Innovation, Health and Nutrition , Ibaraki City, Osaka , Japan.,d Department of Neurology , Juntendo University Graduate School of Medicine , Tokyo , Japan
| | - K Orishchenko
- a Laboratory of Molecular Genetics Technologies , Immanuel Kant Baltic Federal University , Kaliningrad , Russia.,e Laboratory of Cell Technologies , Institute of Cytology and Genetics SB RAS , Novosibirsk , Russia
| | - I Mazunin
- a Laboratory of Molecular Genetics Technologies , Immanuel Kant Baltic Federal University , Kaliningrad , Russia
| |
Collapse
|
130
|
Affiliation(s)
- Joanne M L Ho
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA. .,Department of Bioengineering, Rice University, Houston, TX, USA
| |
Collapse
|
131
|
Tang W, Liu DR. Rewritable multi-event analog recording in bacterial and mammalian cells. Science 2018; 360:eaap8992. [PMID: 29449507 PMCID: PMC5898985 DOI: 10.1126/science.aap8992] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/22/2017] [Accepted: 02/08/2018] [Indexed: 12/26/2022]
Abstract
We present two CRISPR-mediated analog multi-event recording apparatus (CAMERA) systems that use base editors and Cas9 nucleases to record cellular events in bacteria and mammalian cells. The devices record signal amplitude or duration as changes in the ratio of mutually exclusive DNA sequences (CAMERA 1) or as single-base modifications (CAMERA 2). We achieved recording of multiple stimuli in bacteria or mammalian cells, including exposure to antibiotics, nutrients, viruses, light, and changes in Wnt signaling. When recording to multicopy plasmids, reliable readout requires as few as 10 to 100 cells. The order of stimuli can be recorded through an overlapping guide RNA design, and memories can be erased and re-recorded over multiple cycles. CAMERA systems serve as "cell data recorders" that write a history of endogenous or exogenous signaling events into permanent DNA sequence modifications in living cells.
Collapse
Affiliation(s)
- Weixin Tang
- Merkin Institute for Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, and Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - David R Liu
- Merkin Institute for Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, and Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
132
|
Bober JR, Beisel CL, Nair NU. Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications. Annu Rev Biomed Eng 2018. [PMID: 29528686 DOI: 10.1146/annurev-bioeng-062117-121019] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An increasing number of studies have strongly correlated the composition of the human microbiota with many human health conditions and, in several cases, have shown that manipulating the microbiota directly affects health. These insights have generated significant interest in engineering indigenous microbiota community members and nonresident probiotic bacteria as biotic diagnostics and therapeutics that can probe and improve human health. In this review, we discuss recent advances in synthetic biology to engineer commensal and probiotic lactic acid bacteria, bifidobacteria, and Bacteroides for these purposes, and we provide our perspective on the future potential of these technologies.
Collapse
Affiliation(s)
- Josef R Bober
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, USA;
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Nikhil U Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, USA;
| |
Collapse
|
133
|
Tian B, Xu S, Rogers JA, Cestellos-Blanco S, Yang P, Carvalho-de-Souza JL, Bezanilla F, Liu J, Bao Z, Hjort M, Cao Y, Melosh N, Lanzani G, Benfenati F, Galli G, Gygi F, Kautz R, Gorodetsky AA, Kim SS, Lu TK, Anikeeva P, Cifra M, Krivosudský O, Havelka D, Jiang Y. Roadmap on semiconductor-cell biointerfaces. Phys Biol 2018; 15:031002. [PMID: 29205173 PMCID: PMC6599646 DOI: 10.1088/1478-3975/aa9f34] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world.
Collapse
Affiliation(s)
- Bozhi Tian
- Department of Chemistry, University of Chicago, Chicago, IL 60637, United States of America
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
134
|
|
135
|
Abstract
Our ability to generate bacterial strains with unique and increasingly complex functions has rapidly expanded in recent times. The capacity for DNA synthesis is increasing and costing less; new tools are being developed for fast, large-scale genetic manipulation; and more tested genetic parts are available for use, as is the knowledge of how to use them effectively. These advances promise to unlock an exciting array of 'smart' bacteria for clinical use but will also challenge scientists to better optimize preclinical testing regimes for early identification and validation of promising strains and strategies. Here, we review recent advances in the development and testing of engineered bacterial diagnostics and therapeutics. We highlight new technologies that will assist the development of more complex, robust and reliable engineered bacteria for future clinical applications, and we discuss approaches to more efficiently evaluate engineered strains throughout their preclinical development.
Collapse
|
136
|
Saltepe B, Kehribar EŞ, Su Yirmibeşoğlu SS, Şafak Şeker UÖ. Cellular Biosensors with Engineered Genetic Circuits. ACS Sens 2018; 3:13-26. [PMID: 29168381 DOI: 10.1021/acssensors.7b00728] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An increasing interest in building novel biological devices with designed cellular functionalities has triggered the search of innovative tools for biocomputation. Utilizing the tools of synthetic biology, numerous genetic circuits have been implemented such as engineered logic operation in analog and digital circuits. Whole cell biosensors are widely used biological devices that employ several biocomputation tools to program cells for desired functions. Up to the present date, a wide range of whole-cell biosensors have been designed and implemented for disease theranostics, biomedical applications, and environmental monitoring. In this review, we investigated the recent developments in biocomputation tools such as analog, digital, and mix circuits, logic gates, switches, and state machines. Additionally, we stated the novel applications of biological devices with computing functionalities for diagnosis and therapy of various diseases such as infections, cancer, or metabolic diseases, as well as the detection of environmental pollutants such as heavy metals or organic toxic compounds. Current whole-cell biosensors are innovative alternatives to classical biosensors; however, there is still a need to advance decision making capabilities by developing novel biocomputing devices.
Collapse
Affiliation(s)
- Behide Saltepe
- UNAM-Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Ebru Şahin Kehribar
- UNAM-Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | | | - Urartu Özgür Şafak Şeker
- UNAM-Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| |
Collapse
|
137
|
Abstract
Optogenetics is a technology wherein researchers combine light and genetically engineered photoreceptors to control biological processes with unrivaled precision. Near-infrared (NIR) wavelengths (>700 nm) are desirable optogenetic inputs due to their low phototoxicity and spectral isolation from most photoproteins. The bacteriophytochrome photoreceptor 1 (BphP1), found in several purple photosynthetic bacteria, senses NIR light and activates transcription of photosystem promoters by binding to and inhibiting the transcriptional repressor PpsR2. Here, we examine the response of a library of output promoters to increasing levels of Rhodopseudomonas palustris PpsR2 expression, and we identify that of Bradyrhizobium sp. BTAi1 crtE as the most strongly repressed in Escherichia coli. Next, we optimize Rps. palustris bphP1 and ppsR2 expression in a strain engineered to produce the required chromophore biliverdin IXα in order to demonstrate NIR-activated transcription. Unlike a previously engineered bacterial NIR photoreceptor, our system does not require production of a second messenger, and it exhibits rapid response dynamics. It is also the most red-shifted bacterial optogenetic tool yet reported by approximately 50 nm. Accordingly, our BphP1-PpsR2 system has numerous applications in bacterial optogenetics.
Collapse
Affiliation(s)
- Nicholas T. Ong
- Department of Bioengineering, ‡Department of Biosciences, Rice University, 6100
Main Street, Houston, Texas 77005, United States
| | - Evan J. Olson
- Department of Bioengineering, ‡Department of Biosciences, Rice University, 6100
Main Street, Houston, Texas 77005, United States
| | - Jeffrey J. Tabor
- Department of Bioengineering, ‡Department of Biosciences, Rice University, 6100
Main Street, Houston, Texas 77005, United States
| |
Collapse
|
138
|
Sheth RU, Yim SS, Wu FL, Wang HH. Multiplex recording of cellular events over time on CRISPR biological tape. Science 2017; 358:1457-1461. [PMID: 29170279 PMCID: PMC7869111 DOI: 10.1126/science.aao0958] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/29/2017] [Accepted: 11/13/2017] [Indexed: 12/12/2022]
Abstract
Although dynamics underlie many biological processes, our ability to robustly and accurately profile time-varying biological signals and regulatory programs remains limited. Here we describe a framework for storing temporal biological information directly in the genomes of a cell population. We developed a "biological tape recorder" in which biological signals trigger intracellular DNA production that is then recorded by the CRISPR-Cas adaptation system. This approach enables stable recording over multiple days and accurate reconstruction of temporal and lineage information by sequencing CRISPR arrays. We further demonstrate a multiplexing strategy to simultaneously record the temporal availability of three metabolites (copper, trehalose, and fucose) in the environment of a cell population over time. This work enables the temporal measurement of dynamic cellular states and environmental changes and suggests new applications for chronicling biological events on a large scale.
Collapse
Affiliation(s)
- Ravi U. Sheth
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Sung Sun Yim
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Felix L. Wu
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Harris H. Wang
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| |
Collapse
|
139
|
|
140
|
Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation. Nat Chem 2017; 9:1056-1067. [DOI: 10.1038/nchem.2852] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/11/2017] [Indexed: 12/12/2022]
|
141
|
Folliard T, Steel H, Prescott TP, Wadhams G, Rothschild LJ, Papachristodoulou A. A Synthetic Recombinase-Based Feedback Loop Results in Robust Expression. ACS Synth Biol 2017; 6:1663-1671. [PMID: 28602075 DOI: 10.1021/acssynbio.7b00131] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accurate control of a biological process is essential for many critical functions in biology, from the cell cycle to proteome regulation. To achieve this, negative feedback is frequently employed to provide a highly robust and reliable output. Feedback is found throughout biology and technology, but due to challenges posed by its implementation, it is yet to be widely adopted in synthetic biology. In this paper we design a synthetic feedback network using a class of recombinase proteins called integrases, which can be re-engineered to flip the orientation of DNA segments in a digital manner. This system is highly orthogonal, and demonstrates a strong capability for regulating and reducing the expression variability of genes being transcribed under its control. An excisionase protein provides the negative feedback signal to close the loop in this system, by flipping DNA segments in the reverse direction. Our integrase/excisionase negative feedback system thus provides a modular architecture that can be tuned to suit applications throughout synthetic biology and biomanufacturing that require a highly robust and orthogonally controlled output.
Collapse
Affiliation(s)
- Thomas Folliard
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Harrison Steel
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, U.K
| | - Thomas P. Prescott
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, U.K
| | - George Wadhams
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Lynn J. Rothschild
- National
Aeronautics
and Space Administration Ames Research Center, Moffett Field, California 94035, United States
| | | |
Collapse
|
142
|
Engstrom MD, Pfleger BF. Transcription control engineering and applications in synthetic biology. Synth Syst Biotechnol 2017; 2:176-191. [PMID: 29318198 PMCID: PMC5655343 DOI: 10.1016/j.synbio.2017.09.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/26/2017] [Accepted: 09/26/2017] [Indexed: 12/18/2022] Open
Abstract
In synthetic biology, researchers assemble biological components in new ways to produce systems with practical applications. One of these practical applications is control of the flow of genetic information (from nucleic acid to protein), a.k.a. gene regulation. Regulation is critical for optimizing protein (and therefore activity) levels and the subsequent levels of metabolites and other cellular properties. The central dogma of molecular biology posits that information flow commences with transcription, and accordingly, regulatory tools targeting transcription have received the most attention in synthetic biology. In this mini-review, we highlight many past successes and summarize the lessons learned in developing tools for controlling transcription. In particular, we focus on engineering studies where promoters and transcription terminators (cis-factors) were directly engineered and/or isolated from DNA libraries. We also review several well-characterized transcription regulators (trans-factors), giving examples of how cis- and trans-acting factors have been combined to create digital and analogue switches for regulating transcription in response to various signals. Last, we provide examples of how engineered transcription control systems have been used in metabolic engineering and more complicated genetic circuits. While most of our mini-review focuses on the well-characterized bacterium Escherichia coli, we also provide several examples of the use of transcription control engineering in non-model organisms. Similar approaches have been applied outside the bacterial kingdom indicating that the lessons learned from bacterial studies may be generalized for other organisms.
Collapse
Affiliation(s)
- Michael D. Engstrom
- Genetics-Biotechnology Center, University of Wisconsin-Madison School of Medicine and Public Health, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison College of Engineering, USA
| | - Brian F. Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison College of Engineering, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, USA
| |
Collapse
|
143
|
Pu J, Dewey JA, Hadji A, LaBelle JL, Dickinson BC. RNA Polymerase Tags To Monitor Multidimensional Protein-Protein Interactions Reveal Pharmacological Engagement of Bcl-2 Proteins. J Am Chem Soc 2017; 139:11964-11972. [PMID: 28767232 PMCID: PMC5828006 DOI: 10.1021/jacs.7b06152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We report the development of a new technology for monitoring multidimensional protein-protein interactions (PPIs) inside live mammalian cells using split RNA polymerase (RNAP) tags. In this new system, a protein-of-interest is tagged with an N-terminal split RNAP (RNAPN), and multiple potential binding partners are each fused to orthogonal C-terminal RNAPs (RNAPC). Assembly of RNAPN with each RNAPC is highly dependent on interactions between the tagged proteins. Each PPI-mediated RNAPN-RNAPC assembly transcribes from a separate promoter on a supplied DNA substrate, thereby generating a unique RNA output signal for each PPI. We develop and validate this new approach in the context of the Bcl-2 family of proteins. These key regulators of apoptosis are important cancer mediators, but are challenging to therapeutically target due to imperfect selectivity that leads to either off-target toxicity or tumor resistance. We demonstrate binary (1 × 1) and ternary (1 × 2) Bcl-2 PPI analyses by imaging fluorescent protein translation from mRNA outputs. Next, we perform a 1 × 4 PPI network analysis by direct measurement of four unique RNA signals via RT-qPCR. Finally, we use these new tools to monitor pharmacological engagement of Bcl-2 protein inhibitors, and uncover inhibitor-dependent competitive PPIs. The split RNAP tags improve upon other protein fragment complementation (PFC) approaches by offering both multidimensionality and sensitive detection using nucleic acid amplification and analysis techniques. Furthermore, this technology opens new opportunities for synthetic biology applications due to the versatility of RNA outputs for cellular engineering applications.
Collapse
Affiliation(s)
- Jinyue Pu
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Jeffrey A. Dewey
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Abbas Hadji
- Section of Hematology, Oncology, Stem Cell Transplantation, Department of Pediatrics, The University of Chicago, Comer Children’s Hospital, Chicago, IL, 60637
| | - James L. LaBelle
- Section of Hematology, Oncology, Stem Cell Transplantation, Department of Pediatrics, The University of Chicago, Comer Children’s Hospital, Chicago, IL, 60637
| | | |
Collapse
|
144
|
Qu X, Wang S, Ge Z, Wang J, Yao G, Li J, Zuo X, Shi J, Song S, Wang L, Li L, Pei H, Fan C. Programming Cell Adhesion for On-Chip Sequential Boolean Logic Functions. J Am Chem Soc 2017; 139:10176-10179. [DOI: 10.1021/jacs.7b04040] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiangmeng Qu
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Shaopeng Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Zhilei Ge
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Jianbang Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Guangbao Yao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Jiye Shi
- Kellogg
College, University of Oxford, Oxford, OX2 6PN, U.K
| | - Shiping Song
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Li Li
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Hao Pei
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| |
Collapse
|
145
|
Fernandez-Rodriguez J, Moser F, Song M, Voigt CA. Engineering RGB color vision into Escherichia coli. Nat Chem Biol 2017; 13:706-708. [PMID: 28530708 DOI: 10.1038/nchembio.2390] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 03/03/2017] [Indexed: 11/09/2022]
Abstract
Optogenetic tools use colored light to rapidly control gene expression in space and time. We designed a genetically encoded system that gives Escherichia coli the ability to distinguish between red, green, and blue (RGB) light and respond by changing gene expression. We use this system to produce 'color photographs' on bacterial culture plates by controlling pigment production and to redirect metabolic flux by expressing CRISPRi guide RNAs.
Collapse
Affiliation(s)
- Jesus Fernandez-Rodriguez
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Felix Moser
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Miryoung Song
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
146
|
Agent-based modelling in synthetic biology. Essays Biochem 2017; 60:325-336. [PMID: 27903820 PMCID: PMC5264505 DOI: 10.1042/ebc20160037] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/31/2016] [Accepted: 09/08/2016] [Indexed: 11/17/2022]
Abstract
Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions.
Collapse
|
147
|
Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| |
Collapse
|
148
|
Zheng X, Xing XH, Zhang C. Targeted mutagenesis: A sniper-like diversity generator in microbial engineering. Synth Syst Biotechnol 2017; 2:75-86. [PMID: 29062964 PMCID: PMC5636951 DOI: 10.1016/j.synbio.2017.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/26/2022] Open
Abstract
Mutations, serving as the raw materials of evolution, have been extensively utilized to increase the chances of engineering molecules or microbes with tailor-made functions. Global and targeted mutagenesis are two main methods of obtaining various mutations, distinguished by the range of action they can cover. While the former one stresses the mining of novel genetic loci within the whole genomic background, targeted mutagenesis performs in a more straightforward manner, bringing evolutionary escape and error catastrophe under control. In this review, we classify the existing techniques of targeted mutagenesis into two categories in terms of whether the diversity is generated in vitro or in vivo, and briefly introduce the mechanisms and applications of them separately. The inherent connections and development trends of the two classes are also discussed to provide an insight into the next generation evolution research.
Collapse
Key Words
- 3′-LTR, 3’-long terminal repeat
- 5-FOA, 5-fluoro-orotic acid
- CRISPR/Cas9, clustered regularly interspaced short palindromic repeats and associated protein 9
- DNA Pol III, DNA polymerase III
- DNA PolI, DNA polymerase I
- DSB, double strand break
- Evolution
- FLASH, fast ligation-based automatable solid-phase high-throughput
- HDR, homology-directed repair
- HIV, human immunodeficiency virus
- ICE, in vivo continuous evolution
- LIC, ligation-independent cloning
- MAGE, multiplex automated genome engineering
- MMEJ, microhomology-mediated end-joining
- Mutations
- NHEJ, error-prone non-homologous end-joining
- ORF, open reading frame
- PAM, protospacer-adjacent motif
- RVD, repeat variable di-residue
- Synthetic biology
- TALE, transcription activator-like effector
- TALEN, transcription activator-like effector nuclease
- TP, terminal protein
- TP-DNAP, TP-DNA polymerase fusion
- TaGTEAM, targeting glycosylase to embedded arrays for mutagenesis
- Targeted mutagenesis
- YOGE, yeast oligo-mediated genome engineering
- ZF, zinc-finger protein
- ZFN, zinc-finger nuclease
- dCas9, catalytically dead Cas9
- dNTP, deoxy-ribonucleoside triphosphate
- dsDNA, double-stranded DNA
- error-prone PCR, error-prone polymerase chain reaction
- non-GMO, non-genetically modified organism
- pre-crRNA, pre-CRISPR RNA
- sctetR, single chain tetR
- sgRNA, single-guide RNA
- ssDNA, single-stranded DNA
- tracrRNA, trans-encoded RNA
Collapse
Affiliation(s)
| | | | - Chong Zhang
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Institute of Biochemical Engineering, Department of Chemical Engineering, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
| |
Collapse
|
149
|
Riglar DT, Giessen TW, Baym M, Kerns SJ, Niederhuber MJ, Bronson RT, Kotula JW, Gerber GK, Way JC, Silver PA. Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation. Nat Biotechnol 2017; 35:653-658. [PMID: 28553941 DOI: 10.1038/nbt.3879] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/07/2017] [Indexed: 02/07/2023]
Abstract
Bacteria can be engineered to function as diagnostics or therapeutics in the mammalian gut but commercial translation of technologies to accomplish this has been hindered by the susceptibility of synthetic genetic circuits to mutation and unpredictable function during extended gut colonization. Here, we report stable, engineered bacterial strains that maintain their function for 6 months in the mouse gut. We engineered a commensal murine Escherichia coli strain to detect tetrathionate, which is produced during inflammation. Using our engineered diagnostic strain, which retains memory of exposure in the gut for analysis by fecal testing, we detected tetrathionate in both infection-induced and genetic mouse models of inflammation over 6 months. The synthetic genetic circuits in the engineered strain were genetically stable and functioned as intended over time. The durable performance of these strains confirms the potential of engineered bacteria as living diagnostics.
Collapse
Affiliation(s)
- David T Riglar
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Michael Baym
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - S Jordan Kerns
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Matthew J Niederhuber
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Roderick T Bronson
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan W Kotula
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Georg K Gerber
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey C Way
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| |
Collapse
|
150
|
Satomura A, Nishioka R, Mori H, Sato K, Kuroda K, Ueda M. Precise genome-wide base editing by the CRISPR Nickase system in yeast. Sci Rep 2017; 7:2095. [PMID: 28522803 PMCID: PMC5437071 DOI: 10.1038/s41598-017-02013-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/03/2017] [Indexed: 11/09/2022] Open
Abstract
The CRISPR/Cas9 system has been applied to efficient genome editing in many eukaryotic cells. However, the bases that can be edited by this system have been limited to those within the protospacer adjacent motif (PAM) and guide RNA-targeting sequences. In this study, we developed a genome-wide base editing technology, "CRISPR Nickase system" that utilizes a single Cas9 nickase. This system was free from the limitation of editable bases that was observed in the CRISPR/Cas9 system, and was able to precisely edit bases up to 53 bp from the nicking site. In addition, this system showed no off-target editing, in contrast to the CRISPR/Cas9 system. Coupling the CRISPR Nickase system with yeast gap repair cloning enabled the construction of yeast mutants within only five days. The CRISPR Nickase system provides a versatile and powerful technology for rapid, site-specific, and precise base editing in yeast.
Collapse
Affiliation(s)
- Atsushi Satomura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan.,Japan Society for the Promotion of Science, Sakyo-ku, Kyoto, Japan
| | - Ryosuke Nishioka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hitoshi Mori
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kosuke Sato
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan.
| |
Collapse
|