51
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Csörgő B, León LM, Chau-Ly IJ, Vasquez-Rifo A, Berry JD, Mahendra C, Crawford ED, Lewis JD, Bondy-Denomy J. A compact Cascade–Cas3 system for targeted genome engineering. Nat Methods 2020; 17:1183-1190. [DOI: 10.1038/s41592-020-00980-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 09/15/2020] [Indexed: 12/26/2022]
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52
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Abstract
Preventing the escape of hazardous genes from genetically modified organisms (GMOs) into the environment is one of the most important issues in biotechnology research. Various strategies were developed to create "genetic firewalls" that prevent the leakage of GMOs; however, they were not specially designed to prevent the escape of genes. To address this issue, we developed amino acid (AA)-swapped genetic codes orthogonal to the standard genetic code, namely SL (Ser and Leu were swapped) and SLA genetic codes (Ser, Leu, and Ala were swapped). From mRNAs encoded by the AA-swapped genetic codes, functional proteins were only synthesized in translation systems featuring the corresponding genetic codes. These results clearly demonstrated the orthogonality of the AA-swapped genetic codes against the standard genetic code and their potential to function as "genetic firewalls for genes". Furthermore, we propose "a codon-bypass strategy" to develop a GMO with an AA-swapped genetic code.
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Affiliation(s)
- Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Masahiro Tozaki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, 464-8603, Japan
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53
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Cooper RM, Hasty J. One-Day Construction of Multiplex Arrays to Harness Natural CRISPR-Cas Systems. ACS Synth Biol 2020; 9:1129-1137. [PMID: 32271547 DOI: 10.1021/acssynbio.9b00489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems are prokaryotic immune systems that have proliferated widely not only in bacteria and archaea, but also much more recently, in human biological research and applications. Much work to date has utilized synthetic sgRNAs along with the CRISPR nuclease Cas9, but the discovery of array-processing nucleases now allows the use of more compact, natural CRISPR arrays in heterologous hosts, in addition to organisms with endogenous systems. Unfortunately, the construction of multiplex natural CRISPR arrays remains technically challenging, expensive, and/or time-consuming. This limitation hampers research involving natural CRISPR arrays in both native and heterologous hosts. To address this problem, we present a method to assemble CRISPR arrays that is simple, rapid, affordable, and highly scalable-we assembled 9-spacer arrays with 1 day's worth of work. We used this method to harness the endogenous CRISPR-Cas system of the highly competent bacterium Acinetobacter baylyi, showing that while single spacers are not always completely effective at blocking DNA acquisition through natural competence, multiplex natural CRISPR arrays enable both nearly complete DNA exclusion and genome editing, including with multiple targets for both. In addition to demonstrating a CRISPR array assembly method that will benefit a variety of applications, we also find a potential bet-hedging strategy for balancing CRISPR defense versus DNA acquisition in naturally competent A. baylyi.
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Affiliation(s)
- Robert M. Cooper
- BioCircuits Institute, University of California, San Diego, La Jolla, California 92093, United States
- San Diego Center for Systems Biology, La Jolla, California 92093, United States
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, California 92093, United States
- San Diego Center for Systems Biology, La Jolla, California 92093, United States
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
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54
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Stirling F, Naydich A, Bramante J, Barocio R, Certo M, Wellington H, Redfield E, O’Keefe S, Gao S, Cusolito A, Way J, Silver P. Synthetic Cassettes for pH-Mediated Sensing, Counting, and Containment. Cell Rep 2020; 30:3139-3148.e4. [DOI: 10.1016/j.celrep.2020.02.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/15/2019] [Accepted: 02/07/2020] [Indexed: 12/18/2022] Open
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55
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Rottinghaus AG, Amrofell MB, Moon TS. Biosensing in Smart Engineered Probiotics. Biotechnol J 2020; 15:e1900319. [PMID: 31860168 DOI: 10.1002/biot.201900319] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/05/2019] [Indexed: 01/01/2023]
Abstract
Engineered microbes are exciting alternatives to current diagnostics and therapeutics. Researchers have developed a wide range of genetic tools and parts to engineer probiotic and commensal microbes. Among these tools and parts, biosensors allow the microbes to sense and record or to sense and respond to chemical and environmental signals in the body, enabling them to report on health conditions of the animal host and/or deliver therapeutics in a controlled manner. This review focuses on how biosensing is applied to engineer "smart" microbes for in vivo diagnostic, therapeutic, and biocontainment goals. Hurdles that need to be overcome when transitioning from high-throughput in vitro systems to low-throughput in vivo animal models, new technologies that can be implemented to alleviate this experimental gap, and areas where future advancements can be made to maximize the utility of biosensing for medical applications are also discussed. As technologies for engineering microbes continue to be developed, these engineered organisms will be used to address many medical challenges.
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Affiliation(s)
- Austin G Rottinghaus
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Matthew B Amrofell
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, 63130, USA
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56
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Clark M, Maselko M. Transgene Biocontainment Strategies for Molecular Farming. FRONTIERS IN PLANT SCIENCE 2020; 11:210. [PMID: 32194598 PMCID: PMC7063990 DOI: 10.3389/fpls.2020.00210] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/11/2020] [Indexed: 05/21/2023]
Abstract
Advances in plant synthetic biology promise to introduce novel agricultural products in the near future. 'Molecular farms' will include crops engineered to produce medications, vaccines, biofuels, industrial enzymes, and other high value compounds. These crops have the potential to reduce costs while dramatically increasing scales of synthesis and provide new economic opportunities to farmers. Current transgenic crops may be considered safe given their long-standing use, however, some applications of molecular farming may pose risks to human health and the environment. Unwanted gene flow from engineered crops could potentially contaminate the food supply, and affect wildlife. There is also potential for unwanted gene flow into engineered crops which may alter their ability to produce compounds of interest. Here, we briefly discuss the applications of molecular farming and explore the various genetic and physical methods that can be used for transgene biocontainment. As yet, no technology can be applied to all crop species, such that a combination of approaches may be necessary. Effective biocontainment is needed to enable large scale molecular farming.
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Affiliation(s)
- Michael Clark
- Applied Biosciences, Macquarie University, North Ryde, NSW, Australia
| | - Maciej Maselko
- Applied Biosciences, Macquarie University, North Ryde, NSW, Australia
- CSIRO Health and Biosecurity, Canberra, ACT, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD, Australia
- *Correspondence: Maciej Maselko,
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57
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Genome Maintenance Proteins Modulate Autoimmunity Mediated Primed Adaptation by the Escherichia coli Type I-E CRISPR-Cas System. Genes (Basel) 2019; 10:genes10110872. [PMID: 31683605 PMCID: PMC6896009 DOI: 10.3390/genes10110872] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/22/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Bacteria and archaea use CRISPR-Cas adaptive immunity systems to interfere with viruses, plasmids, and other mobile genetic elements. During the process of adaptation, CRISPR-Cas systems acquire immunity by incorporating short fragments of invaders’ genomes into CRISPR arrays. The acquisition of fragments of host genomes leads to autoimmunity and may drive chromosomal rearrangements, negative cell selection, and influence bacterial evolution. In this study, we investigated the role of proteins involved in genome stability maintenance in spacer acquisition by the Escherichia coli type I-E CRISPR-Cas system targeting its own genome. We show here, that the deletion of recJ decreases adaptation efficiency and affects accuracy of spacers incorporation into CRISPR array. Primed adaptation efficiency is also dramatically inhibited in double mutants lacking recB and sbcD but not in single mutants suggesting independent involvement and redundancy of RecBCD and SbcCD pathways in spacer acquisition. While the presence of at least one of two complexes is crucial for efficient primed adaptation, RecBCD and SbcCD affect the pattern of acquired spacers. Overall, our data suggest distinct roles of the RecBCD and SbcCD complexes and of RecJ in spacer precursor selection and insertion into CRISPR array and highlight the functional interplay between CRISPR-Cas systems and host genome maintenance mechanisms.
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58
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Dolan AE, Hou Z, Xiao Y, Gramelspacher MJ, Heo J, Howden SE, Freddolino PL, Ke A, Zhang Y. Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas. Mol Cell 2019; 74:936-950.e5. [PMID: 30975459 PMCID: PMC6555677 DOI: 10.1016/j.molcel.2019.03.014] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/04/2019] [Accepted: 03/13/2019] [Indexed: 01/08/2023]
Abstract
CRISPR-Cas systems enable microbial adaptive immunity and provide eukaryotic genome editing tools. These tools employ a single effector enzyme of type II or V CRISPR to generate RNA-guided, precise genome breaks. Here we demonstrate the feasibility of using type I CRISPR-Cas to effectively introduce a spectrum of long-range chromosomal deletions with a single RNA guide in human embryonic stem cells and HAP1 cells. Type I CRISPR systems rely on the multi-subunit ribonucleoprotein (RNP) complex Cascade to identify DNA targets and on the helicase-nuclease enzyme Cas3 to degrade DNA processively. With RNP delivery of T. fusca Cascade and Cas3, we obtained 13%-60% editing efficiency. Long-range PCR-based and high-throughput-sequencing-based lesion analyses reveal that a variety of deletions, ranging from a few hundred base pairs to 100 kilobases, are created upstream of the target site. These results highlight the potential utility of type I CRISPR-Cas for long-range genome manipulations and deletion screens in eukaryotes.
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Affiliation(s)
- Adam E Dolan
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Zhonggang Hou
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA; State Key Laboratory of Natural Medicines, Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China
| | - Max J Gramelspacher
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jaewon Heo
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Sara E Howden
- Murdoch Children's Research Institute, Flemington Rd., Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.
| | - Yan Zhang
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA.
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59
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Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas. Mol Cell 2019. [PMID: 30975459 DOI: 10.1016/j.molcel.2019.03.014.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
CRISPR-Cas systems enable microbial adaptive immunity and provide eukaryotic genome editing tools. These tools employ a single effector enzyme of type II or V CRISPR to generate RNA-guided, precise genome breaks. Here we demonstrate the feasibility of using type I CRISPR-Cas to effectively introduce a spectrum of long-range chromosomal deletions with a single RNA guide in human embryonic stem cells and HAP1 cells. Type I CRISPR systems rely on the multi-subunit ribonucleoprotein (RNP) complex Cascade to identify DNA targets and on the helicase-nuclease enzyme Cas3 to degrade DNA processively. With RNP delivery of T. fusca Cascade and Cas3, we obtained 13%-60% editing efficiency. Long-range PCR-based and high-throughput-sequencing-based lesion analyses reveal that a variety of deletions, ranging from a few hundred base pairs to 100 kilobases, are created upstream of the target site. These results highlight the potential utility of type I CRISPR-Cas for long-range genome manipulations and deletion screens in eukaryotes.
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60
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Development of bacteria as diagnostics and therapeutics by genetic engineering. J Microbiol 2019; 57:637-643. [DOI: 10.1007/s12275-019-9105-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/08/2019] [Accepted: 04/11/2019] [Indexed: 12/11/2022]
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61
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Xia PF, Ling H, Foo JL, Chang MW. Synthetic genetic circuits for programmable biological functionalities. Biotechnol Adv 2019; 37:107393. [PMID: 31051208 DOI: 10.1016/j.biotechadv.2019.04.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/09/2019] [Accepted: 04/28/2019] [Indexed: 02/06/2023]
Abstract
Living organisms evolve complex genetic networks to interact with the environment. Due to the rapid development of synthetic biology, various modularized genetic parts and units have been identified from these networks. They have been employed to construct synthetic genetic circuits, including toggle switches, oscillators, feedback loops and Boolean logic gates. Building on these circuits, complex genetic machines with capabilities in programmable decision-making could be created. Consequently, these accomplishments have led to novel applications, such as dynamic and autonomous modulation of metabolic networks, directed evolution of biological units, remote and targeted diagnostics and therapies, as well as biological containment methods to prevent release of engineered microorganisms and genetic materials. Herein, we outline the principles in genetic circuit design that have initiated a new chapter in transforming concepts to realistic applications. The features of modularized building blocks and circuit architecture that facilitate realization of circuits for a variety of novel applications are discussed. Furthermore, recent advances and challenges in employing genetic circuits to impart microorganisms with distinct and programmable functionalities are highlighted. We envision that this review gives new insights into the design of synthetic genetic circuits and offers a guideline for the implementation of different circuits in various aspects of biotechnology and bioengineering.
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Affiliation(s)
- Peng-Fei Xia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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62
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Uribe RV, van der Helm E, Misiakou MA, Lee SW, Kol S, Sommer MOA. Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla. Cell Host Microbe 2019; 25:233-241.e5. [PMID: 30737174 DOI: 10.1016/j.chom.2019.01.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/24/2018] [Accepted: 01/02/2019] [Indexed: 01/07/2023]
Abstract
CRISPR-Cas systems in bacteria and archaea provide immunity against bacteriophages and plasmids. To overcome CRISPR immunity, phages have acquired anti-CRISPR genes that reduce CRISPR-Cas activity. Using a synthetic genetic circuit, we developed a high-throughput approach to discover anti-CRISPR genes from metagenomic libraries based on their functional activity rather than sequence homology or genetic context. We identified 11 DNA fragments from soil, animal, and human metagenomes that circumvent Streptococcus pyogenes Cas9 activity in our selection strain. Further in vivo and in vitro characterization of a subset of these hits validated the activity of four anti-CRISPRs. Notably, homologs of some of these anti-CRISPRs were detected in seven different phyla, namely Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Spirochaetes, and Balneolaeota, and have high sequence identity suggesting recent horizontal gene transfer. Thus, anti-CRISPRs against type II-A CRISPR-Cas systems are widely distributed across bacterial phyla, suggesting a more complex ecological role than previously appreciated.
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Affiliation(s)
- Ruben V Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Eric van der Helm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Maria-Anna Misiakou
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Sang-Woo Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Stefan Kol
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark.
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63
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Xue C, Sashital DG. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in Enterobacteriaceae. EcoSal Plus 2019; 8:10.1128/ecosalplus.ESP-0008-2018. [PMID: 30724156 PMCID: PMC6368399 DOI: 10.1128/ecosalplus.esp-0008-2018] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 12/17/2022]
Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against invasion by bacteriophages and other mobile genetic elements. Short fragments of invader DNA are stored as immunological memories within CRISPR (clustered regularly interspaced short palindromic repeat) arrays in the host chromosome. These arrays provide a template for RNA molecules that can guide CRISPR-associated (Cas) proteins to specifically neutralize viruses upon subsequent infection. Over the past 10 years, our understanding of CRISPR-Cas systems has benefited greatly from a number of model organisms. In particular, the study of several members of the Gram-negative Enterobacteriaceae family, especially Escherichia coli and Pectobacterium atrosepticum, have provided significant insights into the mechanisms of CRISPR-Cas immunity. In this review, we provide an overview of CRISPR-Cas systems present in members of the Enterobacteriaceae. We also detail the current mechanistic understanding of the type I-E and type I-F CRISPR-Cas systems that are commonly found in enterobacteria. Finally, we discuss how phages can escape or inactivate CRISPR-Cas systems and the measures bacteria can enact to counter these types of events.
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Affiliation(s)
- Chaoyou Xue
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA
- Present address: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA
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64
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Lau CH. Applications of CRISPR-Cas in Bioengineering, Biotechnology, and Translational Research. CRISPR J 2018; 1:379-404. [PMID: 31021245 DOI: 10.1089/crispr.2018.0026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CRISPR technology is rapidly evolving, and the scope of CRISPR applications is constantly expanding. CRISPR was originally employed for genome editing. Its application was then extended to epigenome editing, karyotype engineering, chromatin imaging, transcriptome, and metabolic pathway engineering. Now, CRISPR technology is being harnessed for genetic circuits engineering, cell signaling sensing, cellular events recording, lineage information reconstruction, gene drive, DNA genotyping, miRNA quantification, in vivo cloning, site-directed mutagenesis, genomic diversification, and proteomic analysis in situ. It has also been implemented in the translational research of human diseases such as cancer immunotherapy, antiviral therapy, bacteriophage therapy, cancer diagnosis, pathogen screening, microbiota remodeling, stem-cell reprogramming, immunogenomic engineering, vaccine development, and antibody production. This review aims to summarize the key concepts of these CRISPR applications in order to capture the current state of play in this fast-moving field. The key mechanisms, strategies, and design principles for each technological advance are also highlighted.
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Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, City University of Hong Kong , Hong Kong, SAR, China
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65
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Zhu Y, Huang Z. Recent advances in structural studies of the CRISPR-Cas-mediated genome editing tools. Natl Sci Rev 2018; 6:438-451. [PMID: 34691893 PMCID: PMC8291651 DOI: 10.1093/nsr/nwy150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and accompanying CRISPR-associated (Cas) proteins provide RNA-guided adaptive immunity for prokaryotes to defend themselves against viruses. The CRISPR-Cas systems have attracted much attention in recent years for their power in aiding the development of genome editing tools. Based on the composition of the CRISPR RNA-effector complex, the CRISPR-Cas systems can be divided into two classes and six types. In this review, we summarize recent advances in the structural biology of the CRISPR-Cas-mediated genome editing tools, which helps us to understand the mechanism of how the guide RNAs assemble with diverse Cas proteins to cleave target nucleic acids.
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Affiliation(s)
- Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
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66
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Moser F, Espah Borujeni A, Ghodasara AN, Cameron E, Park Y, Voigt CA. Dynamic control of endogenous metabolism with combinatorial logic circuits. Mol Syst Biol 2018; 14:e8605. [PMID: 30482789 PMCID: PMC6263354 DOI: 10.15252/msb.20188605] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 11/09/2022] Open
Abstract
Controlling gene expression during a bioprocess enables real-time metabolic control, coordinated cellular responses, and staging order-of-operations. Achieving this with small molecule inducers is impractical at scale and dynamic circuits are difficult to design. Here, we show that the same set of sensors can be integrated by different combinatorial logic circuits to vary when genes are turned on and off during growth. Three Escherichia coli sensors that respond to the consumption of feedstock (glucose), dissolved oxygen, and by-product accumulation (acetate) are constructed and optimized. By integrating these sensors, logic circuits implement temporal control over an 18-h period. The circuit outputs are used to regulate endogenous enzymes at the transcriptional and post-translational level using CRISPRi and targeted proteolysis, respectively. As a demonstration, two circuits are designed to control acetate production by matching their dynamics to when endogenous genes are expressed (pta or poxB) and respond by turning off the corresponding gene. This work demonstrates how simple circuits can be implemented to enable customizable dynamic gene regulation.
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Affiliation(s)
- Felix Moser
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amin Espah Borujeni
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amar N Ghodasara
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ewen Cameron
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yongjin Park
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
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67
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Meyer AJ, Segall-Shapiro TH, Glassey E, Zhang J, Voigt CA. Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors. Nat Chem Biol 2018; 15:196-204. [DOI: 10.1038/s41589-018-0168-3] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/05/2018] [Indexed: 11/09/2022]
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68
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Purcell O, Wang J, Siuti P, Lu TK. Encryption and steganography of synthetic gene circuits. Nat Commun 2018; 9:4942. [PMID: 30467337 PMCID: PMC6250736 DOI: 10.1038/s41467-018-07144-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/10/2018] [Indexed: 12/29/2022] Open
Abstract
Synthetic biologists use artificial gene circuits to control and engineer living cells. As engineered cells become increasingly commercialized, it will be desirable to protect the intellectual property contained in these circuits. Here, we introduce strategies to hide the design of synthetic gene circuits, making it more difficult for an unauthorized third party to determine circuit structure and function. We present two different approaches: the first uses encryption by overlapping uni-directional recombinase sites to scramble circuit topology and the second uses steganography by adding genes and interconnections to obscure circuit topology. We also discuss a third approach: to use synthetic genetic codes to mask the function of synthetic circuits. For each approach, we discuss relative strengths, weaknesses, and practicality of implementation, with the goal to inspire further research into this important and emerging area.
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Affiliation(s)
- Oliver Purcell
- Synthetic Biology Center, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA, 02139, USA
| | - Jerry Wang
- Synthetic Biology Center, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA, 02139, USA
| | - Piro Siuti
- Synthetic Biology Center, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA, 02139, USA
| | - Timothy K Lu
- Synthetic Biology Center, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA, 02139, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA. .,Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
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69
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Escherichia coli as a host for metabolic engineering. Metab Eng 2018; 50:16-46. [DOI: 10.1016/j.ymben.2018.04.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/21/2022]
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70
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Pedrolli DB, Ribeiro NV, Squizato PN, de Jesus VN, Cozetto DA. Engineering Microbial Living Therapeutics: The Synthetic Biology Toolbox. Trends Biotechnol 2018; 37:100-115. [PMID: 30318171 DOI: 10.1016/j.tibtech.2018.09.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 12/31/2022]
Abstract
Microbes can be engineered to act like living therapeutics designed to perform specific actions in the human body. From fighting and preventing infections to eliminating tumors and treating metabolic disorders, engineered living systems are the next generation of therapeutics. In recent years, synthetic biologists have greatly expanded the genetic toolbox for microbial living therapeutics, adding sensors, regulators, memory circuits, delivery devices, and kill switches. These advances have paved the way for successful engineering of fully functional living therapeutics, with sensing, production, and biocontainment devices. However, some important tools are still missing from the box. In this review, we cover the most recent biological parts and approaches developed and describe the missing tools needed to build robust living therapeutics.
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Affiliation(s)
- Danielle B Pedrolli
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017.
| | - Nathan V Ribeiro
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017
| | - Patrick N Squizato
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017
| | - Victor N de Jesus
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017
| | - Daniel A Cozetto
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017
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71
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Motomura K, Sano K, Watanabe S, Kanbara A, Gamal Nasser AH, Ikeda T, Ishida T, Funabashi H, Kuroda A, Hirota R. Synthetic Phosphorus Metabolic Pathway for Biosafety and Contamination Management of Cyanobacterial Cultivation. ACS Synth Biol 2018; 7:2189-2198. [PMID: 30203964 DOI: 10.1021/acssynbio.8b00199] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recent progress in genetic engineering and synthetic biology have greatly expanded the production capabilities of cyanobacteria, but concerns regarding biosafety issues and the risk of contamination of cultures in outdoor culture conditions remain to be resolved. With this dual goal in mind, we applied the recently established biological containment strategy based on phosphite (H3PO3, Pt) dependency to the model cyanobacterium Synechococcus elongatus PCC 7942 ( Syn 7942). Pt assimilation capability was conferred on Syn 7942 by the introduction of Pt dehydrogenase (PtxD) and hypophosphite transporter (HtxBCDE) genes that allow the uptake of Pt, but not phosphate (H3PO4, Pi). We then identified and disrupted the two indigenous Pi transporters, pst (Synpcc7942_2441 to 2445) and pit (Synpcc7942_0184). The resultant strain failed to grow on any media containing various types of P compounds other than Pt. The strain did not yield any escape mutants for at least 28 days with a detection limit of 3.6 × 10-11 per colony forming unit, and rapidly lost viability in the absence of Pt. Moreover, growth competition of the Pt-dependent strain with wild-type cyanobacteria revealed that the Pt-dependent strain could dominate in cultures containing Pt as the sole P source. Because Pt is rarely available in aquatic environments this strategy can contribute to both biosafety and contamination management of genetically engineered cyanobacteria.
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Affiliation(s)
- Kei Motomura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency (JST-ALCA), Chiyoda-ku, Tokyo 102-0076, Japan
| | - Kosuke Sano
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Satoru Watanabe
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency (JST-ALCA), Chiyoda-ku, Tokyo 102-0076, Japan
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Akihiro Kanbara
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Abdel-Hady Gamal Nasser
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takenori Ishida
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency (JST-ALCA), Chiyoda-ku, Tokyo 102-0076, Japan
| | - Ryuichi Hirota
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency (JST-ALCA), Chiyoda-ku, Tokyo 102-0076, Japan
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Whitford CM, Dymek S, Kerkhoff D, März C, Schmidt O, Edich M, Droste J, Pucker B, Rückert C, Kalinowski J. Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications. J Biol Eng 2018; 12:13. [PMID: 30123321 PMCID: PMC6090650 DOI: 10.1186/s13036-018-0105-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/25/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Biosafety is a key aspect in the international Genetically Engineered Machine (iGEM) competition, which offers student teams an amazing opportunity to pursue their own research projects in the field of Synthetic Biology. iGEM projects often involve the creation of genetically engineered bacterial strains. To minimize the risks associated with bacterial release, a variety of biosafety systems were constructed, either to prevent survival of bacteria outside the lab or to hinder horizontal or vertical gene transfer. MAIN BODY Physical containment methods such as bioreactors or microencapsulation are considered the first safety level. Additionally, various systems involving auxotrophies for both natural and synthetic compounds have been utilized by iGEM teams in recent years. Combinatorial systems comprising multiple auxotrophies have been shown to reduced escape frequencies below the detection limit. Furthermore, a number of natural toxin-antitoxin systems can be deployed to kill cells under certain conditions. Additionally, parts of naturally occurring toxin-antitoxin systems can be used for the construction of 'kill switches' controlled by synthetic regulatory modules, allowing control of cell survival. Kill switches prevent cell survival but do not completely degrade nucleic acids. To avoid horizontal gene transfer, multiple mechanisms to cleave nucleic acids can be employed, resulting in 'self-destruction' of cells. Changes in light or temperature conditions are powerful regulators of gene expression and could serve as triggers for kill switches or self-destruction systems. Xenobiology-based containment uses applications of Xeno-DNA, recoded codons and non-canonical amino acids to nullify the genetic information of constructed cells for wild type organisms. A 'minimal genome' approach brings the opportunity to reduce the genome of a cell to only genes necessary for survival under lab conditions. Such cells are unlikely to survive in the natural environment and are thus considered safe hosts. If suitable for the desired application, a shift to cell-free systems based on Xeno-DNA may represent the ultimate biosafety system. CONCLUSION Here we describe different containment approaches in synthetic biology, ranging from auxotrophies to minimal genomes, which can be combined to significantly improve reliability. Since the iGEM competition greatly increases the number of people involved in synthetic biology, we will focus especially on biosafety systems developed and applied in the context of the iGEM competition.
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Affiliation(s)
| | - Saskia Dymek
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Denise Kerkhoff
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Camilla März
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Olga Schmidt
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Maximilian Edich
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Julian Droste
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Boas Pucker
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Present address: Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Christian Rückert
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
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Tarasava K, Oh EJ, Eckert CA, Gill RT. CRISPR-Enabled Tools for Engineering Microbial Genomes and Phenotypes. Biotechnol J 2018; 13:e1700586. [DOI: 10.1002/biot.201700586] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 05/09/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Katia Tarasava
- Chemical and Biological Engineering, University of Colorado; Boulder CO USA
- Renewable and Sustainable Energy Institute, University of Colorado; Boulder CO USA
| | - Eun Joong Oh
- Renewable and Sustainable Energy Institute, University of Colorado; Boulder CO USA
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado; Boulder CO USA
- Biosciences Center, National Renewable Energy Laboratory; Golden CO USA
| | - Ryan T. Gill
- Chemical and Biological Engineering, University of Colorado; Boulder CO USA
- Renewable and Sustainable Energy Institute, University of Colorado; Boulder CO USA
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74
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Sedlmayer F, Aubel D, Fussenegger M. Synthetic gene circuits for the detection, elimination and prevention of disease. Nat Biomed Eng 2018; 2:399-415. [PMID: 31011195 DOI: 10.1038/s41551-018-0215-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/05/2018] [Indexed: 12/13/2022]
Abstract
In living organisms, naturally evolved sensors that constantly monitor and process environmental cues trigger corrective actions that enable the organisms to cope with changing conditions. Such natural processes have inspired biologists to construct synthetic living sensors and signalling pathways, by repurposing naturally occurring proteins and by designing molecular building blocks de novo, for customized diagnostics and therapeutics. In particular, designer cells that employ user-defined synthetic gene circuits to survey disease biomarkers and to autonomously re-adjust unbalanced pathological states can coordinate the production of therapeutics, with controlled timing and dosage. Furthermore, tailored genetic networks operating in bacterial or human cells have led to cancer remission in experimental animal models, owing to the network's unprecedented specificity. Other applications of designer cells in infectious, metabolic and autoimmune diseases are also being explored. In this Review, we describe the biomedical applications of synthetic gene circuits in major disease areas, and discuss how the first genetically engineered devices developed on the basis of synthetic-biology principles made the leap from the laboratory to the clinic.
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Affiliation(s)
- Ferdinand Sedlmayer
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Dominique Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Lyon, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. .,Faculty of Science, University of Basel, Basel, Switzerland.
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75
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Next-generation biocontainment systems for engineered organisms. Nat Chem Biol 2018; 14:530-537. [PMID: 29769737 DOI: 10.1038/s41589-018-0056-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 03/09/2018] [Indexed: 12/14/2022]
Abstract
The increasing use of engineered organisms for industrial, clinical, and environmental applications poses a growing risk of spreading hazardous biological entities into the environment. To address this biosafety issue, significant effort has been invested in creating ways to confine these organisms and transgenic materials. Emerging technologies in synthetic biology involving genetic circuit engineering, genome editing, and gene expression regulation have led to the development of novel biocontainment systems. In this perspective, we highlight recent advances in biocontainment and suggest a number of approaches for future development, which may be applied to overcome remaining challenges in safeguard implementation.
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76
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Klompe SE, Sternberg SH. Harnessing "A Billion Years of Experimentation": The Ongoing Exploration and Exploitation of CRISPR-Cas Immune Systems. CRISPR J 2018; 1:141-158. [PMID: 31021200 PMCID: PMC6636882 DOI: 10.1089/crispr.2018.0012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The famed physicist-turned-biologist, Max Delbrück, once remarked that, for physicists, "the field of bacterial viruses is a fine playground for serious children who ask ambitious questions." Early discoveries in that playground helped establish molecular genetics, and half a century later, biologists delving into the same field have ushered in the era of precision genome engineering. The focus has of course shifted-from bacterial viruses and their mechanisms of infection to the bacterial hosts and their mechanisms of immunity-but it is the very same evolutionary arms race that continues to awe and inspire researchers worldwide. In this review, we explore the remarkable diversity of CRISPR-Cas adaptive immune systems, describe the molecular components that mediate nucleic acid targeting, and outline the use of these RNA-guided machines for biotechnology applications. CRISPR-Cas research has yielded far more than just Cas9-based genome-editing tools, and the wide-reaching, innovative impacts of this fascinating biological playground are sure to be felt for years to come.
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Affiliation(s)
- Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York
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77
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Xia PF, Li Q, Tan LR, Liu MM, Jin YS, Wang SG. Synthetic Whole-Cell Biodevices for Targeted Degradation of Antibiotics. Sci Rep 2018; 8:2906. [PMID: 29440690 PMCID: PMC5811551 DOI: 10.1038/s41598-018-21350-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/01/2018] [Indexed: 11/09/2022] Open
Abstract
Synthetic biology enables infinite possibilities in biotechnology via employing genetic modules. However, not many researches have explored the potentials of synthetic biology in environmental bioprocesses. In this study, we introduced a genetic module harboring the codon-optimized tetracycline degrading gene, tetX.co, into the model host, Escherichia coli, and generated a prototypal whole-cell biodevice for the degradation of a target antibiotic. Our results suggested that E. coli with the tetX.co-module driven by either the PJ23119 or PBAD promoters conferred resistance up to 50 μg/mL of tetracycline and degrades over 95% of tetracycline within 24 h. The detoxification ability of tetX was further verified in conditioned media by typical E. coli K-12 and B strains as well as Shewanella oneidensis. Our strategy demonstrated the feasibility of introducing genetic modules into model hosts to enable environmental functions, and this work will inspire more environmental innovations through synthetic biological devices.
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Affiliation(s)
- Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, 27 Shanda Nanlu, Jinan, 250100, P.R. China
| | - Qian Li
- School of Environmental Science and Engineering, Shandong University, 27 Shanda Nanlu, Jinan, 250100, P.R. China
| | - Lin-Rui Tan
- School of Environmental Science and Engineering, Shandong University, 27 Shanda Nanlu, Jinan, 250100, P.R. China
| | - Miao-Miao Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL, 61801, United States
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, United States.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 905k South Goodwin Avenue, Urbana, IL, 61801, United States
| | - Shu-Guang Wang
- School of Environmental Science and Engineering, Shandong University, 27 Shanda Nanlu, Jinan, 250100, P.R. China.
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78
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Donohoue PD, Barrangou R, May AP. Advances in Industrial Biotechnology Using CRISPR-Cas Systems. Trends Biotechnol 2018; 36:134-146. [PMID: 28778606 DOI: 10.1016/j.tibtech.2017.07.007] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 12/14/2022]
Abstract
The term 'clustered regularly interspaced short palindromic repeats' (CRISPR) has recently become synonymous with the genome-editing revolution. The RNA-guided endonuclease CRISPR-associated protein 9 (Cas9), in particular, has attracted attention for its promise in basic research and gene editing-based therapeutics. CRISPR-Cas systems are efficient and easily programmable nucleic acid-targeting tools, with uses reaching beyond research and therapeutic development into the precision breeding of plants and animals and the engineering of industrial microbes. CRISPR-Cas systems have potential for many microbial engineering applications, including bacterial strain typing, immunization of cultures, autoimmunity or self-targeted cell killing, and the engineering or control of metabolic pathways for improved biochemical synthesis. In this review, we explore the fundamental characteristics of CRISPR-Cas systems and highlight how these features can be used in industrial settings.
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Affiliation(s)
- Paul D Donohoue
- Caribou Biosciences, Inc., 2929 7th St., Suite 105, Berkeley, CA 94710, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Andrew P May
- Caribou Biosciences, Inc., 2929 7th St., Suite 105, Berkeley, CA 94710, USA; Current address: Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA.
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79
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Fagen JR, Collias D, Singh AK, Beisel CL. Advancing the design and delivery of CRISPR antimicrobials. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017. [DOI: 10.1016/j.cobme.2017.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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80
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Stirling F, Bitzan L, O'Keefe S, Redfield E, Oliver JWK, Way J, Silver PA. Rational Design of Evolutionarily Stable Microbial Kill Switches. Mol Cell 2017; 68:686-697.e3. [PMID: 29149596 DOI: 10.1016/j.molcel.2017.10.033] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 08/11/2017] [Accepted: 10/24/2017] [Indexed: 12/12/2022]
Abstract
The evolutionary stability of synthetic genetic circuits is key to both the understanding and application of genetic control elements. One useful but challenging situation is a switch between life and death depending on environment. Here are presented "essentializer" and "cryodeath" circuits, which act as kill switches in Escherichia coli. The essentializer element induces cell death upon the loss of a bi-stable cI/Cro memory switch. Cryodeath makes use of a cold-inducible promoter to express a toxin. We employ rational design and a toxin/antitoxin titering approach to produce and screen a small library of potential constructs, in order to select for constructs that are evolutionarily stable. Both kill switches were shown to maintain functionality in vitro for at least 140 generations. Additionally, cryodeath was shown to control the growth environment of a population, with an escape frequency of less than 1 in 105 after 10 days of growth in the mammalian gut.
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Affiliation(s)
- Finn Stirling
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert 536, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
| | - Lisa Bitzan
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert 536, Boston, MA 02115, USA
| | - Samuel O'Keefe
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert 536, Boston, MA 02115, USA
| | - Elizabeth Redfield
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert 536, Boston, MA 02115, USA
| | - John W K Oliver
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert 536, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
| | - Jeffrey Way
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert 536, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert 536, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA.
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81
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Abstract
Biocontainment systems are crucial for preventing genetically modified organisms from escaping into natural ecosystems. Here, we describe the orthogonal ribosome biofirewall, which consists of an activation circuit and a degradation circuit. The activation circuit is a genetic AND gate based on activation of the encrypted pathway by the orthogonal ribosome in response to specific environmental signals. The degradation circuit is a genetic NOT gate with an output of I-SceI homing endonuclease, which conditionally degrades the orthogonal ribosome genes. We demonstrate that the activation circuit can be flexibly incorporated into genetic circuits and metabolic pathways for encryption. The plasmid-based encryption of the deoxychromoviridans pathway and the genome-based encryption of lacZ are tightly regulated and can decrease the expression to 7.3% and 7.8%, respectively. We validated the ability of the degradation circuit to decrease the expression levels of the target plasmids and the orthogonal rRNA (O-rRNA) plasmids to 0.8% in lab medium and 0.76% in nonsterile soil medium, respectively. Our orthogonal ribosome biofirewall is a versatile platform that can be useful in biosafety research and in the biotechnology industry.
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Affiliation(s)
- Bin Jia
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Hao Qi
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Bing-Zhi Li
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Shuo Pan
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Duo Liu
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Hong Liu
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Yizhi Cai
- School
of Biological Sciences, University of Edinburgh, Daniel Rutherford Building G.24,
The King’s Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Ying-Jin Yuan
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
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82
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Jeon S, Lim JM, Lee HG, Shin SE, Kang NK, Park YI, Oh HM, Jeong WJ, Jeong BR, Chang YK. Current status and perspectives of genome editing technology for microalgae. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:267. [PMID: 29163669 PMCID: PMC5686953 DOI: 10.1186/s13068-017-0957-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/04/2017] [Indexed: 05/25/2023]
Abstract
Genome editing techniques are critical for manipulating genes not only to investigate their functions in biology but also to improve traits for genetic engineering in biotechnology. Genome editing has been greatly facilitated by engineered nucleases, dubbed molecular scissors, including zinc-finger nuclease (ZFN), TAL effector endonuclease (TALEN) and clustered regularly interspaced palindromic sequences (CRISPR)/Cas9. In particular, CRISPR/Cas9 has revolutionized genome editing fields with its simplicity, efficiency and accuracy compared to previous nucleases. CRISPR/Cas9-induced genome editing is being used in numerous organisms including microalgae. Microalgae have been subjected to extensive genetic and biological engineering due to their great potential as sustainable biofuel and chemical feedstocks. However, progress in microalgal engineering is slow mainly due to a lack of a proper transformation toolbox, and the same problem also applies to genome editing techniques. Given these problems, there are a few reports on successful genome editing in microalgae. It is, thus, time to consider the problems and solutions of genome editing in microalgae as well as further applications of this exciting technology for other scientific and engineering purposes.
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Affiliation(s)
- Seungjib Jeon
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Jong-Min Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Sung-Eun Shin
- LG Chem, 188 Munji-ro, Yuseong-gu, Daejeon, 34122 Republic of Korea
| | - Nam Kyu Kang
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Won-Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Byeong-ryool Jeong
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Yong Keun Chang
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
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83
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Wang P, Zhang L, Xie Y, Wang N, Tang R, Zheng W, Jiang X. Genome Editing for Cancer Therapy: Delivery of Cas9 Protein/sgRNA Plasmid via a Gold Nanocluster/Lipid Core-Shell Nanocarrier. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2017; 4:1700175. [PMID: 29201613 PMCID: PMC5700650 DOI: 10.1002/advs.201700175] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/28/2017] [Indexed: 05/18/2023]
Abstract
The type II bacterial clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 (CRISPR-associated protein) system (CRISPR-Cas9) is a powerful toolbox for gene-editing, however, the nonviral delivery of CRISPR-Cas9 to cells or tissues remains a key challenge. This paper reports a strategy to deliver Cas9 protein and single guide RNA (sgRNA) plasmid by a nanocarrier with a core of gold nanoclusters (GNs) and a shell of lipids. By modifying the GNs with HIV-1-transactivator of transcription peptide, the cargo (Cas9/sgRNA) can be delivered into cell nuclei. This strategy is utilized to treat melanoma by designing sgRNA targeting Polo-like kinase-1 (Plk1) of the tumor. The nanoparticle (polyethylene glycol-lipid/GNs/Cas9 protein/sgPlk1 plasmid, LGCP) leads to >70% down-regulation of Plk1 protein expression of A375 cells in vitro. Moreover, the LGCP suppresses melanoma progress by 75% on mice. Thus, this strategy can deliver protein-nucleic acid hybrid agents for gene therapy.
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Affiliation(s)
- Peng Wang
- Beijing Engineering Research Center for BioNanotechnologyCAS Key Laboratory for Biological Effects of Nanomaterials and NanosafetyCAS Center for Excellence in NanoscienceNational Center for NanoScience and TechnologyBeijing100190China
| | - Lingmin Zhang
- Beijing Engineering Research Center for BioNanotechnologyCAS Key Laboratory for Biological Effects of Nanomaterials and NanosafetyCAS Center for Excellence in NanoscienceNational Center for NanoScience and TechnologyBeijing100190China
| | - Yangzhouyun Xie
- Beijing Engineering Research Center for BioNanotechnologyCAS Key Laboratory for Biological Effects of Nanomaterials and NanosafetyCAS Center for Excellence in NanoscienceNational Center for NanoScience and TechnologyBeijing100190China
| | - Nuoxin Wang
- Beijing Engineering Research Center for BioNanotechnologyCAS Key Laboratory for Biological Effects of Nanomaterials and NanosafetyCAS Center for Excellence in NanoscienceNational Center for NanoScience and TechnologyBeijing100190China
| | - Rongbing Tang
- Beijing Engineering Research Center for BioNanotechnologyCAS Key Laboratory for Biological Effects of Nanomaterials and NanosafetyCAS Center for Excellence in NanoscienceNational Center for NanoScience and TechnologyBeijing100190China
| | - Wenfu Zheng
- Beijing Engineering Research Center for BioNanotechnologyCAS Key Laboratory for Biological Effects of Nanomaterials and NanosafetyCAS Center for Excellence in NanoscienceNational Center for NanoScience and TechnologyBeijing100190China
| | - Xingyu Jiang
- Beijing Engineering Research Center for BioNanotechnologyCAS Key Laboratory for Biological Effects of Nanomaterials and NanosafetyCAS Center for Excellence in NanoscienceNational Center for NanoScience and TechnologyBeijing100190China
- College of Materials Science and Opto‐Electronic Technology/Sino‐Danish CollegeUniversity of Chinese Academy of SciencesBeijing100049China
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84
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Chaterji S, Ahn EH, Kim DH. CRISPR Genome Engineering for Human Pluripotent Stem Cell Research. Theranostics 2017; 7:4445-4469. [PMID: 29158838 PMCID: PMC5695142 DOI: 10.7150/thno.18456] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
The emergence of targeted and efficient genome editing technologies, such as repurposed bacterial programmable nucleases (e.g., CRISPR-Cas systems), has abetted the development of cell engineering approaches. Lessons learned from the development of RNA-interference (RNA-i) therapies can spur the translation of genome editing, such as those enabling the translation of human pluripotent stem cell engineering. In this review, we discuss the opportunities and the challenges of repurposing bacterial nucleases for genome editing, while appreciating their roles, primarily at the epigenomic granularity. First, we discuss the evolution of high-precision, genome editing technologies, highlighting CRISPR-Cas9. They exist in the form of programmable nucleases, engineered with sequence-specific localizing domains, and with the ability to revolutionize human stem cell technologies through precision targeting with greater on-target activities. Next, we highlight the major challenges that need to be met prior to bench-to-bedside translation, often learning from the path-to-clinic of complementary technologies, such as RNA-i. Finally, we suggest potential bioinformatics developments and CRISPR delivery vehicles that can be deployed to circumvent some of the challenges confronting genome editing technologies en route to the clinic.
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85
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Bikard D, Barrangou R. Using CRISPR-Cas systems as antimicrobials. Curr Opin Microbiol 2017; 37:155-160. [PMID: 28888103 DOI: 10.1016/j.mib.2017.08.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/05/2017] [Accepted: 08/18/2017] [Indexed: 12/26/2022]
Abstract
Although CRISPR-Cas systems naturally evolved to provide adaptive immunity in bacteria and archaea, Cas nucleases can be co-opted to target chromosomal sequences rather than invasive genetic elements. Although genome editing is the primary outcome of self-targeting using CRISPR-based technologies in eukaryotes, self-targeting by CRISPR is typically lethal in bacteria. Here, we discuss how DNA damage introduced by Cas nucleases in bacteria can efficiently and specifically lead to plasmid curing or drive cell death. Specifically, we discuss how various CRISPR-Cas systems can be engineered and delivered using phages or phagemids as vectors. These principles establish CRISPR-Cas systems as potent and programmable antimicrobials, and open new avenues for the development of CRISPR-based tools for selective removal of bacterial pathogens and precise microbiome composition alteration.
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Affiliation(s)
- David Bikard
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris 75015, France.
| | - Rodolphe Barrangou
- Department of Food, Processing and Nutritional Sciences, North Carolina State University, NC, USA.
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86
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Chang HJ, Voyvodic PL, Zúñiga A, Bonnet J. Microbially derived biosensors for diagnosis, monitoring and epidemiology. Microb Biotechnol 2017; 10:1031-1035. [PMID: 28771944 PMCID: PMC5609271 DOI: 10.1111/1751-7915.12791] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 07/04/2017] [Indexed: 11/27/2022] Open
Abstract
Living cells have evolved to detect and process various signals and can self-replicate, presenting an attractive platform for engineering scalable and affordable biosensing devices. Microbes are perfect candidates: they are inexpensive and easy to manipulate and store. Recent advances in synthetic biology promise to streamline the engineering of microbial biosensors with unprecedented capabilities. Here we review the applications of microbially-derived biosensors with a focus on environmental monitoring and healthcare applications. We also identify critical challenges that need to be addressed in order to translate the potential of synthetic microbial biosensors into large-scale, real-world applications.
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Affiliation(s)
- Hung-Ju Chang
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Peter L Voyvodic
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Ana Zúñiga
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Jérôme Bonnet
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
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87
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Jung C, Hawkins JA, Jones SK, Xiao Y, Rybarski JR, Dillard KE, Hussmann J, Saifuddin FA, Savran CA, Ellington AD, Ke A, Press WH, Finkelstein IJ. Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips. Cell 2017; 170:35-47.e13. [PMID: 28666121 DOI: 10.1016/j.cell.2017.05.044] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 04/23/2017] [Accepted: 05/26/2017] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas nucleoproteins target foreign DNA via base pairing with a crRNA. However, a quantitative description of protein binding and nuclease activation at off-target DNA sequences remains elusive. Here, we describe a chip-hybridized association-mapping platform (CHAMP) that repurposes next-generation sequencing chips to simultaneously measure the interactions between proteins and ∼107 unique DNA sequences. Using CHAMP, we provide the first comprehensive survey of DNA recognition by a type I-E CRISPR-Cas (Cascade) complex and Cas3 nuclease. Analysis of mutated target sequences and human genomic DNA reveal that Cascade recognizes an extended protospacer adjacent motif (PAM). Cascade recognizes DNA with a surprising 3-nt periodicity. The identity of the PAM and the PAM-proximal nucleotides control Cas3 recruitment by releasing the Cse1 subunit. These findings are used to develop a model for the biophysical constraints governing off-target DNA binding. CHAMP provides a framework for high-throughput, quantitative analysis of protein-DNA interactions on synthetic and genomic DNA. PAPERCLIP.
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Affiliation(s)
- Cheulhee Jung
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - John A Hawkins
- Institute for Computational Engineering and Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Stephen K Jones
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - James R Rybarski
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kaylee E Dillard
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey Hussmann
- Institute for Computational Engineering and Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Fatema A Saifuddin
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Cagri A Savran
- School of Mechanical Engineering, Birck Nanotechnology Center, Purdue University, 1205 West State Street, West Lafayette, IN 47907, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - William H Press
- Institute for Computational Engineering and Science, The University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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88
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Fu BXH, Wainberg M, Kundaje A, Fire AZ. High-Throughput Characterization of Cascade type I-E CRISPR Guide Efficacy Reveals Unexpected PAM Diversity and Target Sequence Preferences. Genetics 2017; 206:1727-1738. [PMID: 28634160 PMCID: PMC5560783 DOI: 10.1534/genetics.117.202580] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/29/2017] [Indexed: 12/18/2022] Open
Abstract
Interactions between Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs and CRISPR-associated (Cas) proteins form an RNA-guided adaptive immune system in prokaryotes. The adaptive immune system utilizes segments of the genetic material of invasive foreign elements in the CRISPR locus. The loci are transcribed and processed to produce small CRISPR RNAs (crRNAs), with degradation of invading genetic material directed by a combination of complementarity between RNA and DNA and in some cases recognition of adjacent motifs called PAMs (Protospacer Adjacent Motifs). Here we describe a general, high-throughput procedure to test the efficacy of thousands of targets, applying this to the Escherichia coli type I-E Cascade (CRISPR-associated complex for antiviral defense) system. These studies were followed with reciprocal experiments in which the consequence of CRISPR activity was survival in the presence of a lytic phage. From the combined analysis of the Cascade system, we found that (i) type I-E Cascade PAM recognition is more expansive than previously reported, with at least 22 distinct PAMs, with many of the noncanonical PAMs having CRISPR-interference abilities similar to the canonical PAMs; (ii) PAM positioning appears precise, with no evidence for tolerance to PAM slippage in interference; and (iii) while increased guanine-cytosine (GC) content in the spacer is associated with higher CRISPR-interference efficiency, high GC content (>62.5%) decreases CRISPR-interference efficiency. Our findings provide a comprehensive functional profile of Cascade type I-E interference requirements and a method to assay spacer efficacy that can be applied to other CRISPR-Cas systems.
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Affiliation(s)
- Becky Xu Hua Fu
- Department of Genetics, Stanford University School of Medicine, California 94305
| | - Michael Wainberg
- Department of Computer Science, Stanford University, California 94305
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, California 94305
- Department of Computer Science, Stanford University, California 94305
| | - Andrew Z Fire
- Department of Genetics, Stanford University School of Medicine, California 94305
- Department of Pathology, Stanford University School of Medicine, California 94305
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89
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Xiao Y, Luo M, Hayes RP, Kim J, Ng S, Ding F, Liao M, Ke A. Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System. Cell 2017; 170:48-60.e11. [PMID: 28666122 DOI: 10.1016/j.cell.2017.06.012] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/27/2017] [Accepted: 06/08/2017] [Indexed: 01/06/2023]
Abstract
Type I CRISPR systems feature a sequential dsDNA target searching and degradation process, by crRNA-displaying Cascade and nuclease-helicase fusion enzyme Cas3, respectively. Here we present two cryo-EM snapshots of the Thermobifida fusca type I-E Cascade: (1) unwinding 11 bp of dsDNA at the seed-sequence region to scout for sequence complementarity, and (2) further unwinding of the entire protospacer to form a full R-loop. These structures provide the much-needed temporal and spatial resolution to resolve key mechanistic steps leading to Cas3 recruitment. In the early steps, PAM recognition causes severe DNA bending, leading to spontaneous DNA unwinding to form a seed-bubble. The full R-loop formation triggers conformational changes in Cascade, licensing Cas3 to bind. The same process also generates a bulge in the non-target DNA strand, enabling its handover to Cas3 for cleavage. The combination of both negative and positive checkpoints ensures stringent yet efficient target degradation in type I CRISPR-Cas systems.
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Affiliation(s)
- Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Min Luo
- Department of Cell Biology, Harvard Medical School, 250 Longwood Avenue, SGM 509, Boston, MA 02115, USA
| | - Robert P Hayes
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Jonathan Kim
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Sherwin Ng
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Fang Ding
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, 250 Longwood Avenue, SGM 509, Boston, MA 02115, USA.
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.
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90
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A Novel Biocontainment Strategy Makes Bacterial Growth and Survival Dependent on Phosphite. Sci Rep 2017; 7:44748. [PMID: 28317852 PMCID: PMC5357788 DOI: 10.1038/srep44748] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/13/2017] [Indexed: 12/26/2022] Open
Abstract
There is a growing demand to develop biocontainment strategies that prevent unintended proliferation of genetically modified organisms in the open environment. We found that the hypophosphite (H3PO2, HPt) transporter HtxBCDE from Pseudomonas stutzeri WM88 was also capable of transporting phosphite (H3PO3, Pt) but not phosphate (H3PO4, Pi), suggesting the potential for engineering a Pt/HPt-dependent bacterial strain as a biocontainment strategy. We disrupted all Pi and organic Pi transporters in an Escherichia coli strain expressing HtxABCDE and a Pt dehydrogenase, leaving Pt/HPt uptake and oxidation as the only means to obtain Pi. Challenge on non-permissive growth medium revealed that no escape mutants appeared for at least 21 days with a detection limit of 1.94 × 10-13 per colony forming unit. This represents, to the best of our knowledge, the lowest escape frequency among reported strategies. Since Pt/HPt are ecologically rare and not available in amounts sufficient for the growth of the Pt/HPt-dependent bacteria, this strategy offers a reliable and practical method for biocontainment.
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91
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Bikard D, Barrangou R. [CRISPR-Cas systems as weapons against pathogenic bacteria]. Biol Aujourdhui 2017; 211:265-270. [PMID: 29956653 DOI: 10.1051/jbio/2018004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Indexed: 11/15/2022]
Abstract
CRISPR-Cas systems (Clustered Regularly Interspaced Short Palindromic Repeats) are the adaptive immune system of bacteria and archaea. They target foreign genetic elements thanks to small RNAs able to guide Cas nucleases to destroy them. These nucleases can be reprogrammed to target chromosomal sequences rather than invasive genetic elements. Whereas targeting the genome of eukaryotic cells enables the efficient genesis of mutations, DNA breaks induced by Cas nucleases are lethal in bacteria. This property can be used in the development of novel antimicrobial strategies. CRISPR-Cas systems can be delivered to target bacteria using bacteriophage capsids in order to specifically eliminate bacteria carrying antibiotic resistance genes or virulence factors. These technologies enable the development of novel tools based on CRISPR-Cas systems to specifically eliminate pathogenic bacteria and precisely modify the composition of various microbiomes.
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Affiliation(s)
- David Bikard
- Groupe de Biologie de Synthèse, Département de Microbiologie, Institut Pasteur, Paris 75015, France
| | - Rodolphe Barrangou
- Department of Food, Processing and Nutritional Sciences, North Carolina State University, NC, USA
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92
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A CRISPR-Cas9 Assisted Non-Homologous End-Joining Strategy for One-step Engineering of Bacterial Genome. Sci Rep 2016; 6:37895. [PMID: 27883076 PMCID: PMC5121644 DOI: 10.1038/srep37895] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/01/2016] [Indexed: 11/08/2022] Open
Abstract
Homologous recombination-mediated genome engineering has been broadly applied in prokaryotes with high efficiency and accuracy. However, this method is limited in realizing larger-scale genome editing with numerous genes or large DNA fragments because of the relatively complicated procedure for DNA editing template construction. Here, we describe a CRISPR-Cas9 assisted non-homologous end-joining (CA-NHEJ) strategy for the rapid and efficient inactivation of bacterial gene (s) in a homologous recombination-independent manner and without the use of selective marker. Our study show that CA-NHEJ can be used to delete large chromosomal DNA fragments in a single step that does not require homologous DNA template. It is thus a novel and powerful tool for bacterial genomes reducing and possesses the potential for accelerating the genome evolution.
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93
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Mimee M, Citorik RJ, Lu TK. Microbiome therapeutics - Advances and challenges. Adv Drug Deliv Rev 2016; 105:44-54. [PMID: 27158095 PMCID: PMC5093770 DOI: 10.1016/j.addr.2016.04.032] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/21/2016] [Accepted: 04/28/2016] [Indexed: 12/14/2022]
Abstract
The microbial community that lives on and in the human body exerts a major impact on human health, from metabolism to immunity. In order to leverage the close associations between microbes and their host, development of therapeutics targeting the microbiota has surged in recent years. Here, we discuss current additive and subtractive strategies to manipulate the microbiota, focusing on bacteria engineered to produce therapeutic payloads, consortia of natural organisms and selective antimicrobials. Further, we present challenges faced by the community in the development of microbiome therapeutics, including designing microbial therapies that are adapted for specific geographies in the body, stable colonization with microbial therapies, discovery of clinically relevant biosensors, robustness of engineered synthetic gene circuits and addressing safety and biocontainment concerns. Moving forward, collaboration between basic and applied researchers and clinicians to address these challenges will poise the field to herald an age of next-generation, cellular therapies that draw on novel findings in basic research to inform directed augmentation of the human microbiota.
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Affiliation(s)
- Mark Mimee
- MIT Microbiology Program, 77 Massachusetts Avenue, Cambridge, MA, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA, USA; The Center for Microbiome Informatics and Therapeutics, Cambridge, MA, USA
| | - Robert J Citorik
- MIT Microbiology Program, 77 Massachusetts Avenue, Cambridge, MA, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA, USA; The Center for Microbiome Informatics and Therapeutics, Cambridge, MA, USA
| | - Timothy K Lu
- MIT Microbiology Program, 77 Massachusetts Avenue, Cambridge, MA, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; The Center for Microbiome Informatics and Therapeutics, Cambridge, MA, USA.
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94
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Luo ML, Jackson RN, Denny SR, Tokmina-Lukaszewska M, Maksimchuk KR, Lin W, Bothner B, Wiedenheft B, Beisel CL. The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers. Nucleic Acids Res 2016; 44:7385-94. [PMID: 27174938 PMCID: PMC5009729 DOI: 10.1093/nar/gkw421] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/12/2022] Open
Abstract
Bacteria and archaea acquire resistance to foreign genetic elements by integrating fragments of foreign DNA into CRISPR (clustered regularly interspaced short palindromic repeats) loci. In Escherichia coli, CRISPR-derived RNAs (crRNAs) assemble with Cas proteins into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Cascade recognizes DNA targets via protein-mediated recognition of a protospacer adjacent motif and complementary base pairing between the crRNA spacer and the DNA target. Previously determined structures of Cascade showed that the crRNA is stretched along an oligomeric protein assembly, leading us to ask how crRNA length impacts the assembly and function of this complex. We found that extending the spacer portion of the crRNA resulted in larger Cascade complexes with altered stoichiometry and preserved in vitro binding affinity for target DNA. Longer spacers also preserved the in vivo ability of Cascade to repress target gene expression and to recruit the Cas3 endonuclease for target degradation. Finally, longer spacers exhibited enhanced silencing at particular target locations and were sensitive to mismatches within the extended region. These findings demonstrate the flexibility of the Type I-E CRISPR machinery and suggest that spacer length can be modified to fine-tune Cascade activity.
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Affiliation(s)
- Michelle L Luo
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Ryan N Jackson
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Steven R Denny
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Kenneth R Maksimchuk
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Wayne Lin
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
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95
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Abstract
Synthetically engineered organisms hold promise for a broad range of medical, environmental, and industrial applications. Organisms can potentially be designed, for example, for the inexpensive and environmentally benign synthesis of pharmaceuticals and industrial chemicals, for the cleanup of environmental pollutants, and potentially even for biomedical applications such as the targeting of specific diseases or tissues. However, the use of synthetically engineered organisms comes with several reasonable safety concerns, one of which is that the organisms or their genes could escape their intended habitats and cause environmental disruption. Here we review key recent developments in this emerging field of synthetic biocontainment and discuss further developments that might be necessary for the widespread use of synthetic organisms. Specifically, we discuss the history and modern development of three strategies for the containment of synthetic microbes: addiction to an exogenously supplied ligand; self-killing outside of a designated environment; and self-destroying encoded DNA circuitry outside of a designated environment.
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Affiliation(s)
- Anna J Simon
- Department of Chemistry & Biochemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Andrew D Ellington
- Department of Chemistry & Biochemistry, University of Texas at Austin, Austin, TX, 78712, USA
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96
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Savitskaya EE, Musharova OS, Severinov KV. Diversity of CRISPR-Cas-mediated mechanisms of adaptive immunity in prokaryotes and their application in biotechnology. BIOCHEMISTRY (MOSCOW) 2016; 81:653-61. [DOI: 10.1134/s0006297916070026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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97
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Hu L, Li H, Qin R, Xu R, Li J, Li L, Wei P, Yang J. Plant phosphomannose isomerase as a selectable marker for rice transformation. Sci Rep 2016; 6:25921. [PMID: 27174847 PMCID: PMC4865823 DOI: 10.1038/srep25921] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/25/2016] [Indexed: 01/14/2023] Open
Abstract
The E. coli phosphomannose isomerase (EcPMI) gene is widely used as a selectable marker gene (SMG) in mannose (Man) selection-based plant transformation. Although some plant species exhibit significant PMI activity and active PMIs were even identified in Man-sensitive plants, whether plant PMIs can be used as SMGs remains unclear. In this study, we isolated four novel PMI genes from Chlorella variabilis and Oryza sativa. Their isoenzymatic activities were examined in vitro and compared with that of EcPMI. The active plant PMIs were separately constructed into binary vectors as SMGs and then transformed into rice via Agrobacterium. In both Indica and Japonica subspecies, our results indicated that the plant PMIs could select and produce transgenic plants in a pattern similar to that of EcPMI. The transgenic plants exhibited an accumulation of plant PMI transcripts and enhancement of the in vivo PMI activity. Furthermore, a gene of interest was successfully transformed into rice using the plant PMIs as SMGs. Thus, novel SMGs for Man selection were isolated from plants, and our analysis suggested that PMIs encoding active enzymes might be common in plants and could potentially be used as appropriate genetic elements in cisgenesis engineering.
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Affiliation(s)
- Lei Hu
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Hao Li
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Ruiying Qin
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Rongfang Xu
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Juan Li
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Li Li
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Pengcheng Wei
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jianbo Yang
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
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98
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Johns NI, Blazejewski T, Gomes AL, Wang HH. Principles for designing synthetic microbial communities. Curr Opin Microbiol 2016; 31:146-153. [PMID: 27084981 DOI: 10.1016/j.mib.2016.03.010] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 01/21/2023]
Abstract
Advances in synthetic biology to build microbes with defined and controllable properties are enabling new approaches to design and program multispecies communities. This emerging field of synthetic ecology will be important for many areas of biotechnology, bioenergy and bioremediation. This endeavor draws upon knowledge from synthetic biology, systems biology, microbial ecology and evolution. Fully realizing the potential of this discipline requires the development of new strategies to control the intercellular interactions, spatiotemporal coordination, robustness, stability and biocontainment of synthetic microbial communities. Here, we review recent experimental, analytical and computational advances to study and build multi-species microbial communities with defined functions and behavior for various applications. We also highlight outstanding challenges and future directions to advance this field.
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Affiliation(s)
- Nathan I Johns
- Department of Systems Biology, Columbia University Medical Center, New York, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, USA
| | - Tomasz Blazejewski
- Department of Systems Biology, Columbia University Medical Center, New York, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, USA
| | - Antonio Lc Gomes
- Department of Systems Biology, Columbia University Medical Center, New York, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Medical Center, New York, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA.
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99
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Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli. Nature 2016; 530:499-503. [PMID: 26863189 PMCID: PMC5134256 DOI: 10.1038/nature16995] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/14/2016] [Indexed: 12/19/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and the cas (CRISPR-associated) operon form an RNA-based adaptive immune system against foreign genetic elements in prokaryotes. Type I accounts for 95% of CRISPR systems, and has been used to control gene expression and cell fate. During CRISPR RNA (crRNA)-guided interference, Cascade (CRISPR-associated complex for antiviral defence) facilitates the crRNA-guided invasion of double-stranded DNA for complementary base-pairing with the target DNA strand while displacing the non-target strand, forming an R-loop. Cas3, which has nuclease and helicase activities, is subsequently recruited to degrade two DNA strands. A protospacer adjacent motif (PAM) sequence flanking target DNA is crucial for self versus foreign discrimination. Here we present the 2.45 Å crystal structure of Escherichia coli Cascade bound to a foreign double-stranded DNA target. The 5'-ATG PAM is recognized in duplex form, from the minor groove side, by three structural features in the Cascade Cse1 subunit. The promiscuity inherent to minor groove DNA recognition rationalizes the observation that a single Cascade complex can respond to several distinct PAM sequences. Optimal PAM recognition coincides with wedge insertion, initiating directional target DNA strand unwinding to allow segmented base-pairing with crRNA. The non-target strand is guided along a parallel path 25 Å apart, and the R-loop structure is further stabilized by locking this strand behind the Cse2 dimer. These observations provide the structural basis for understanding the PAM-dependent directional R-loop formation process.
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100
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Venturelli OS, Egbert RG, Arkin AP. Towards Engineering Biological Systems in a Broader Context. J Mol Biol 2016; 428:928-44. [DOI: 10.1016/j.jmb.2015.10.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/24/2015] [Accepted: 10/28/2015] [Indexed: 01/18/2023]
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