101
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Abstract
Cell-free protein synthesis (CFPS) has become an established tool for rapid protein synthesis in order to accelerate the discovery of new enzymes and the development of proteins with improved characteristics. Over the past years, progress in CFPS system preparation has been made towards simplification, and many applications have been developed with regard to tailor-made solutions for specific purposes. In this review, various preparation methods of CFPS systems are compared and the significance of individual supplements is assessed. The recent applications of CFPS are summarized and the potential for biocatalyst development discussed. One of the central features is the high-throughput synthesis of protein variants, which enables sophisticated approaches for rapid prototyping of enzymes. These applications demonstrate the contribution of CFPS to enhance enzyme functionalities and the complementation to in vivo protein synthesis. However, there are different issues to be addressed, such as the low predictability of CFPS performance and transferability to in vivo protein synthesis. Nevertheless, the usage of CFPS for high-throughput enzyme screening has been proven to be an efficient method to discover novel biocatalysts and improved enzyme variants.
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102
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Silverman AD, Kelley-Loughnane N, Lucks JB, Jewett MC. Deconstructing Cell-Free Extract Preparation for in Vitro Activation of Transcriptional Genetic Circuitry. ACS Synth Biol 2019; 8:403-414. [PMID: 30596483 PMCID: PMC6584022 DOI: 10.1021/acssynbio.8b00430] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent advances in cell-free gene expression (CFE) systems have enabled their use for a host of synthetic biology applications, particularly for rapid prototyping of genetic circuits and biosensors. Despite the proliferation of cell-free protein synthesis platforms, the large number of currently existing protocols for making CFE extracts muddles the collective understanding of how the extract preparation method affects its functionality. A key aspect of extract performance relevant to many applications is the activity of the native host transcriptional machinery that can mediate protein synthesis. However, protein yields from genes transcribed in vitro by the native Escherichia coli RNA polymerase are variable for different extract preparation techniques, and specifically low in some conventional crude extracts originally optimized for expression by the bacteriophage transcriptional machinery. Here, we show that cell-free expression of genes under bacterial σ70 promoters is constrained by the rate of transcription in crude extracts, and that processing the extract with a ribosomal runoff reaction and subsequent dialysis alleviates this constraint. Surprisingly, these processing steps only enhance protein synthesis in genes under native regulation, indicating that the translation rate is unaffected. We further investigate the role of other common extract preparation process variants on extract performance and demonstrate that bacterial transcription is inhibited by including glucose in the growth culture but is unaffected by flash-freezing the cell pellet prior to lysis. Our final streamlined and detailed protocol for preparing extract by sonication generates extract that facilitates expression from a diverse set of sensing modalities including protein and RNA regulators. We anticipate that this work will clarify the methodology for generating CFE extracts that are active for biosensing using native transcriptional machinery and will encourage the further proliferation of cell-free gene expression technology for new applications.
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Affiliation(s)
- Adam D. Silverman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Nancy Kelley-Loughnane
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Member, Robert H. Lurie Comprehensive Cancer Center, and Member, Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Member, Robert H. Lurie Comprehensive Cancer Center, and Member, Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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103
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Westbrook A, Tang X, Marshall R, Maxwell CS, Chappell J, Agrawal DK, Dunlop MJ, Noireaux V, Beisel CL, Lucks J, Franco E. Distinct timescales of RNA regulators enable the construction of a genetic pulse generator. Biotechnol Bioeng 2019; 116:1139-1151. [DOI: 10.1002/bit.26918] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/25/2018] [Accepted: 01/06/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Alexandra Westbrook
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University Ithaca New York
| | - Xun Tang
- Department of Mechanical Engineering University of California at Riverside Riverside California
| | - Ryan Marshall
- School of Physics and Astronomy, University of Minnesota Minneapolis Minnesota
| | - Colin S. Maxwell
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina
| | | | - Deepak K. Agrawal
- Biomedical Engineering Department Boston University Boston Massachusetts
| | - Mary J. Dunlop
- Biomedical Engineering Department Boston University Boston Massachusetts
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota Minneapolis Minnesota
| | - Chase L. Beisel
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina
- Helmholtz Institute for RNA‐based Infection Research (HIRI) Helmholtz‐Centre for Infection Research (HZI), Würzburg Germany
- Faculty of Medicine, University of Würzburg Würzburg Germany
| | - Julius Lucks
- Department of Chemical and Biological Engineering Northwestern University Evanston Illinois
| | - Elisa Franco
- Department of Mechanical Engineering University of California at Riverside Riverside California
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104
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Hwang S, Maxwell KL. Meet the Anti-CRISPRs: Widespread Protein Inhibitors of CRISPR-Cas Systems. CRISPR J 2019; 2:23-30. [DOI: 10.1089/crispr.2018.0052] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Sungwon Hwang
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Karen L. Maxwell
- Department of Biochemistry, University of Toronto, Toronto, Canada
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105
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Collias D, Marshall R, Collins SP, Beisel CL, Noireaux V. An educational module to explore CRISPR technologies with a cell-free transcription-translation system. Synth Biol (Oxf) 2019; 4:ysz005. [PMID: 32995532 PMCID: PMC7445873 DOI: 10.1093/synbio/ysz005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/30/2018] [Accepted: 11/19/2018] [Indexed: 12/26/2022] Open
Abstract
Within the last 6 years, CRISPR-Cas systems have transitioned from adaptive defense systems in bacteria and archaea to revolutionary genome-editing tools. The resulting CRISPR technologies have driven innovations for treating genetic diseases and eradicating human pests while raising societal questions about gene editing in human germline cells as well as crop plants. Bringing CRISPR into the classroom therefore offers a means to expose students to cutting edge technologies and to promote discussions about ethical questions at the intersection of science and society. However, working with these technologies in a classroom setting has been difficult because typical experiments rely on cellular systems such as bacteria or mammalian cells. We recently reported the use of an E. coli cell-free transcription-translation (TXTL) system that simplifies the demonstration and testing of CRISPR technologies with shorter experiments and limited equipment. Here, we describe three educational modules intended to expose undergraduate students to CRISPR technologies using TXTL. The three sequential modules comprise (i) designing the RNAs that guide DNA targeting, (ii) measuring DNA cleavage activity in TXTL and (iii) testing how mutations to the targeting sequence or RNA backbone impact DNA binding and cleavage. The modules include detailed protocols, questions for group discussions or individual evaluation, and lecture slides to introduce CRISPR and TXTL. We expect these modules to allow students to experience the power and promise of CRISPR technologies in the classroom and to engage with their instructor and peers about the opportunities and potential risks for society.
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Affiliation(s)
- Daphne Collias
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Ryan Marshall
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Scott P Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Chase L Beisel
- Helmholtz Institute of RNA-based Infection Research, D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
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106
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Nakamura M, Srinivasan P, Chavez M, Carter MA, Dominguez AA, La Russa M, Lau MB, Abbott TR, Xu X, Zhao D, Gao Y, Kipniss NH, Smolke CD, Bondy-Denomy J, Qi LS. Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells. Nat Commun 2019; 10:194. [PMID: 30643127 PMCID: PMC6331597 DOI: 10.1038/s41467-018-08158-x] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 12/20/2018] [Indexed: 11/24/2022] Open
Abstract
Repurposed CRISPR-Cas molecules provide a useful tool set for broad applications of genomic editing and regulation of gene expression in prokaryotes and eukaryotes. Recent discovery of phage-derived proteins, anti-CRISPRs, which serve to abrogate natural CRISPR anti-phage activity, potentially expands the ability to build synthetic CRISPR-mediated circuits. Here, we characterize a panel of anti-CRISPR molecules for expanded applications to counteract CRISPR-mediated gene activation and repression of reporter and endogenous genes in various cell types. We demonstrate that cells pre-engineered with anti-CRISPR molecules become resistant to gene editing, thus providing a means to generate "write-protected" cells that prevent future gene editing. We further show that anti-CRISPRs can be used to control CRISPR-based gene regulation circuits, including implementation of a pulse generator circuit in mammalian cells. Our work suggests that anti-CRISPR proteins should serve as widely applicable tools for synthetic systems regulating the behavior of eukaryotic cells.
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Affiliation(s)
- Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | | | - Michael Chavez
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Matthew A Carter
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Antonia A Dominguez
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Marie La Russa
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Matthew B Lau
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- International Christian School, 1 On Muk Ln, Sha Tin, 999077, Hong Kong SAR, China
| | - Timothy R Abbott
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Xiaoshu Xu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Dehua Zhao
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Yuchen Gao
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Cancer Biology Program, Stanford University, Stanford, CA, 94305, USA
| | - Nathan H Kipniss
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, CA, 94158, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA.
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA.
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107
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Doerr A, de Reus E, van Nies P, van der Haar M, Wei K, Kattan J, Wahl A, Danelon C. Modelling cell-free RNA and protein synthesis with minimal systems. Phys Biol 2019; 16:025001. [DOI: 10.1088/1478-3975/aaf33d] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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108
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109
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Abstract
In recent years, Cas9 has revolutionized the genome-editing field and enabled a broad range of applications from basic biology to biotechnology and medicine. Cas9 specificity is dictated by base pairing of the guide RNA to the complementary DNA strand, however to initiate hybridization, a short protospacer adjacent motif (PAM) sequence is required in the vicinity of the target sequence. The PAM is recognized by the Cas9 protein and varies between Cas9s. There are thousands of type II CRISPR-Cas9 sequences available in sequence databases. To characterize the PAM recognition diversity provided by Cas9 orthologs, we developed a phylogeny-guided bioinformatics approach and streamlined our experimental procedures for Cas9 expression and RNP complex assembly using cell lysates and in vitro translation mixtures. This approach could be easily adapted for the characterization of other CRISPR-Cas nucleases that require PAM sequences and generate double-strand breaks following target recognition.
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Affiliation(s)
| | - Joshua K Young
- Department of Molecular Engineering, Corteva Agriscience™ Agriculture Division of DowDuPont™, Johnston, IA, United States
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110
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Dubuc E, Pieters PA, van der Linden AJ, van Hest JC, Huck WT, de Greef TF. Cell-free microcompartmentalised transcription-translation for the prototyping of synthetic communication networks. Curr Opin Biotechnol 2018; 58:72-80. [PMID: 30594098 PMCID: PMC6723619 DOI: 10.1016/j.copbio.2018.10.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 10/14/2018] [Indexed: 12/21/2022]
Abstract
Recent efforts in synthetic biology have shown the possibility of engineering distributed functions in populations of living cells, which requires the development of highly orthogonal, genetically encoded communication pathways. Cell-free transcription-translation (TXTL) reactions encapsulated in microcompartments enable prototyping of molecular communication channels and their integration into engineered genetic circuits by mimicking critical cell features, such as gene expression, cell size, and cell individuality within a community. In this review, we discuss the uses of cell-free transcription-translation reactions for the development of synthetic genetic circuits, with a special focus on the use of microcompartments supporting this reaction. We highlight several studies where molecular communication between non-living microcompartments and living cells have been successfully engineered.
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Affiliation(s)
- Emilien Dubuc
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Pascal A Pieters
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Ardjan J van der Linden
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Jan Cm van Hest
- Department of Biomedical Engineering & Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Wilhelm Ts Huck
- Department of Physical Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen 6525 HP, The Netherlands
| | - Tom Fa de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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111
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Yelleswarapu M, van der Linden AJ, van Sluijs B, Pieters PA, Dubuc E, de Greef TFA, Huck WTS. Sigma Factor-Mediated Tuning of Bacterial Cell-Free Synthetic Genetic Oscillators. ACS Synth Biol 2018; 7:2879-2887. [PMID: 30408412 PMCID: PMC6305555 DOI: 10.1021/acssynbio.8b00300] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Cell-free
transcription–translation provides a simplified
prototyping environment to rapidly design and study synthetic networks.
Despite the presence of a well characterized toolbox of genetic elements,
examples of genetic networks that exhibit complex temporal behavior
are scarce. Here, we present a genetic oscillator implemented in an E. coli-based cell-free system under steady-state conditions
using microfluidic flow reactors. The oscillator has an activator–repressor
motif that utilizes the native transcriptional machinery of E. coli: the RNAP and its associated sigma factors.
We optimized a kinetic model with experimental data using an evolutionary
algorithm to quantify the key regulatory model parameters. The functional
modulation of the RNAP was investigated by coupling two oscillators
driven by competing sigma factors, allowing the modification of network
properties by means of passive transcriptional regulation.
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Affiliation(s)
- Maaruthy Yelleswarapu
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Ardjan J. van der Linden
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Computational Biology Group, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Bob van Sluijs
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Pascal A. Pieters
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Computational Biology Group, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Emilien Dubuc
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Computational Biology Group, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Tom F. A. de Greef
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Computational Biology Group, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Wilhelm T. S. Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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112
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Caschera F, Karim AS, Gazzola G, d’Aquino AE, Packard NH, Jewett MC. High-Throughput Optimization Cycle of a Cell-Free Ribosome Assembly and Protein Synthesis System. ACS Synth Biol 2018; 7:2841-2853. [PMID: 30354075 DOI: 10.1021/acssynbio.8b00276] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Building variant ribosomes offers opportunities to reveal fundamental principles underlying ribosome biogenesis and to make ribosomes with altered properties. However, cell viability limits mutations that can be made to the ribosome. To address this limitation, the in vitro integrated synthesis, assembly and translation (iSAT) method for ribosome construction from the bottom up was recently developed. Unfortunately, iSAT is complex, costly, and laborious to researchers, partially due to the high cost of reaction buffer containing over 20 components. In this study, we develop iSAT in Escherichia coli BL21Rosetta2 cell lysates, a commonly used bacterial strain, with a cost-effective poly sugar and nucleotide monophosphate-based metabolic scheme. We achieved a 10-fold increase in protein yield over our base case with an evolutionary design of experiments approach, screening 490 reaction conditions to optimize the reaction buffer. The computationally guided, cell-free, high-throughput technology presented here augments the way we approach multicomponent synthetic biology projects and efforts to repurpose ribosomes.
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Affiliation(s)
| | | | - Gianluca Gazzola
- Rutgers Center for Operations Research, Rutgers Business School, 100 Rockafeller Road, Piscataway, New Jersey 08854, United States
| | | | - Norman H. Packard
- ProtoLife, Inc., 57 Post Street Suite 908, San Francisco, California 94104, United States
| | - Michael C. Jewett
- Rutgers Center for Operations Research, Rutgers Business School, 100 Rockafeller Road, Piscataway, New Jersey 08854, United States
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113
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Watters KE, Fellmann C, Bai HB, Ren SM, Doudna JA. Systematic discovery of natural CRISPR-Cas12a inhibitors. Science 2018; 362:236-239. [PMID: 30190307 DOI: 10.1126/science.aau5138] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/23/2018] [Indexed: 12/18/2022]
Abstract
Cas12a (Cpf1) is a CRISPR-associated nuclease with broad utility for synthetic genome engineering, agricultural genomics, and biomedical applications. Although bacteria harboring CRISPR-Cas9 or CRISPR-Cas3 adaptive immune systems sometimes acquire mobile genetic elements encoding anti-CRISPR proteins that inhibit Cas9, Cas3, or the DNA-binding Cascade complex, no such inhibitors have been found for CRISPR-Cas12a. Here we use a comprehensive bioinformatic and experimental screening approach to identify three different inhibitors that block or diminish CRISPR-Cas12a-mediated genome editing in human cells. We also find a widespread connection between CRISPR self-targeting and inhibitor prevalence in prokaryotic genomes, suggesting a straightforward path to the discovery of many more anti-CRISPRs from the microbial world.
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Affiliation(s)
- Kyle E Watters
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone Institutes, San Francisco, CA 94158, USA
| | - Hua B Bai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shawn M Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. .,Gladstone Institutes, San Francisco, CA 94158, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Li Ka Shing Biomedical and Health Sciences Center, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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114
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Mendoza BJ, Trinh CT. In Silico Processing of the Complete CRISPR-Cas Spacer Space for Identification of PAM Sequences. Biotechnol J 2018; 13:e1700595. [PMID: 30076736 DOI: 10.1002/biot.201700595] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/23/2018] [Indexed: 12/16/2022]
Abstract
Despite extensive exploration of the diversity of CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR associated) systems, biological applications have been mostly confined to Class 2 systems, specifically the Cas9 and Cas12 (formerly Cpf1) single effector proteins. A key limitation of exploring and utilizing other CRISPR-Cas systems with unique functionalities, particularly Class I types and their multi-protein effector complex, is the knowledge of the system's protospacer adjacent motif (PAM) sequence identity. In this work, the authors developed a systematic pipeline, named CASPERpam, that enables a comprehensive assessment of the PAM sequences of all the available CRISPR-Cas systems in the NCBI database of bacterial genomes. The CASPERpam analysis reveals that within the 30 389 assemblies previously screened for CRISPR arrays, there exists 26 364 spacers that match somewhere in the viral, bacterial, and plasmid databases of NCBI, using the constraints of 95% sequence identity and 95% sequence coverage for blast hits. When grouping these results by species, the authors identified putative PAM sequences for 1049 among 1493 unique species. The remaining species either have insufficient data or an undetermined result from the analysis. Finally, the authors assigned a confidence score to each species' PAM prediction and generate categories that largely cover the revealed diversity of PAM motifs, providing a baseline for further experimental studies including PAM assays. The authors envision CASPERpam is a useful bioinformatic tool for understanding and harnessing the diversity of CRISPR-Cas systems.
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Affiliation(s)
- Brian J Mendoza
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996, USA
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115
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Kassaw TK, Donayre-Torres AJ, Antunes MS, Morey KJ, Medford JI. Engineering synthetic regulatory circuits in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:13-22. [PMID: 29907304 DOI: 10.1016/j.plantsci.2018.04.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 04/05/2018] [Accepted: 04/07/2018] [Indexed: 05/21/2023]
Abstract
Plant synthetic biology is a rapidly emerging field that aims to engineer genetic circuits to function in plants with the same reliability and precision as electronic circuits. These circuits can be used to program predictable plant behavior, producing novel traits to improve crop plant productivity, enable biosensors, and serve as platforms to synthesize chemicals and complex biomolecules. Herein we introduce the importance of developing orthogonal plant parts and the need for quantitative part characterization for mathematical modeling of complex circuits. In particular, transfer functions are important when designing electronic-like genetic controls such as toggle switches, positive/negative feedback loops, and Boolean logic gates. We then discuss potential constraints and challenges in synthetic regulatory circuit design and integration when using plants. Finally, we highlight current and potential plant synthetic regulatory circuit applications.
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Affiliation(s)
- Tessema K Kassaw
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Alberto J Donayre-Torres
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Mauricio S Antunes
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Kevin J Morey
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - June I Medford
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA.
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116
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Accessing Structure, Dynamics and Function of Biological Macromolecules by NMR Through Advances in Isotope Labeling. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0085-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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117
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Hynes AP, Rousseau GM, Agudelo D, Goulet A, Amigues B, Loehr J, Romero DA, Fremaux C, Horvath P, Doyon Y, Cambillau C, Moineau S. Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins. Nat Commun 2018; 9:2919. [PMID: 30046034 PMCID: PMC6060171 DOI: 10.1038/s41467-018-05092-w] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/13/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are bacterial anti-viral systems, and bacterial viruses (bacteriophages, phages) can carry anti-CRISPR (Acr) proteins to evade that immunity. Acrs can also fine-tune the activity of CRISPR-based genome-editing tools. While Acrs are prevalent in phages capable of lying dormant in a CRISPR-carrying host, their orthologs have been observed only infrequently in virulent phages. Here we identify AcrIIA6, an Acr encoded in 33% of virulent Streptococcus thermophilus phage genomes. The X-ray structure of AcrIIA6 displays some features unique to this Acr family. We compare the activity of AcrIIA6 to those of other Acrs, including AcrIIA5 (also from S. thermophilus phages), and characterize their effectiveness against a range of CRISPR-Cas systems. Finally, we demonstrate that both Acr families from S. thermophilus phages inhibit Cas9-mediated genome editing of human cells.
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Affiliation(s)
- Alexander P Hynes
- Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University. Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Daniel Agudelo
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
| | - Beatrice Amigues
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
| | - Jeremy Loehr
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada
| | - Dennis A Romero
- DuPont Nutrition and Health, 3329 Agriculture Dr, Madison, WI, 53716, USA
| | | | - Philippe Horvath
- DuPont Nutrition and Health, BP 10, 86220, Dangé-Saint-Romain, France
| | - Yannick Doyon
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.
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118
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Maxwell CS, Jacobsen T, Marshall R, Noireaux V, Beisel CL. A detailed cell-free transcription-translation-based assay to decipher CRISPR protospacer-adjacent motifs. Methods 2018; 143:48-57. [PMID: 29486239 PMCID: PMC6051895 DOI: 10.1016/j.ymeth.2018.02.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 12/21/2022] Open
Abstract
The RNA-guided nucleases derived from the CRISPR-Cas systems in bacteria and archaea have found numerous applications in biotechnology, including genome editing, imaging, and gene regulation. However, the discovery of novel Cas nucleases has outpaced their characterization and subsequent exploitation. A key step in characterizing Cas nucleases is determining which protospacer-adjacent motif (PAM) sequences they recognize. Here, we report advances to an in vitro method based on an E. coli cell-free transcription-translation system (TXTL) to rapidly elucidate PAMs recognized by Cas nucleases. The method obviates the need for cloning Cas nucleases or gRNAs, does not require the purification of protein or RNA, and can be performed in less than a day. To advance our previously published method, we incorporated an internal GFP cleavage control to assess the extent of library cleavage as well as Sanger sequencing of the cleaved library to assess PAM depletion prior to next-generation sequencing. We also detail the methods needed to construct all relevant DNA constructs, and how to troubleshoot the assay. We finally demonstrate the technique by determining PAM sequences recognized by the Neisseria meningitidis Cas9, revealing subtle sequence requirements of this highly specific PAM. The overall method offers a rapid means to identify PAMs recognized by diverse CRISPR nucleases, with the potential to greatly accelerate our ability to characterize and harness novel CRISPR nucleases across their many uses.
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Affiliation(s)
- Colin S Maxwell
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Thomas Jacobsen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Ryan Marshall
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, United States
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, United States
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States; Helmholtz Institute for RNA-based Infection Research (HIRI), Josef-Schneider-Str. 2/D15, D-97080 Würzburg, Germany.
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119
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Agrawal DK, Tang X, Westbrook A, Marshall R, Maxwell CS, Lucks J, Noireaux V, Beisel CL, Dunlop MJ, Franco E. Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression. ACS Synth Biol 2018; 7:1219-1228. [PMID: 29709170 DOI: 10.1021/acssynbio.8b00040] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Feedback allows biological systems to control gene expression precisely and reliably, even in the presence of uncertainty, by sensing and processing environmental changes. Taking inspiration from natural architectures, synthetic biologists have engineered feedback loops to tune the dynamics and improve the robustness and predictability of gene expression. However, experimental implementations of biomolecular control systems are still far from satisfying performance specifications typically achieved by electrical or mechanical control systems. To address this gap, we present mathematical models of biomolecular controllers that enable reference tracking, disturbance rejection, and tuning of the temporal response of gene expression. These controllers employ RNA transcriptional regulators to achieve closed loop control where feedback is introduced via molecular sequestration. Sensitivity analysis of the models allows us to identify which parameters influence the transient and steady state response of a target gene expression process, as well as which biologically plausible parameter values enable perfect reference tracking. We quantify performance using typical control theory metrics to characterize response properties and provide clear selection guidelines for practical applications. Our results indicate that RNA regulators are well-suited for building robust and precise feedback controllers for gene expression. Additionally, our approach illustrates several quantitative methods useful for assessing the performance of biomolecular feedback control systems.
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Affiliation(s)
- Deepak K. Agrawal
- Biomedical Engineering Department, Boston University, Boston, Massachusetts 02215, United States
| | - Xun Tang
- Department of Mechanical Engineering, University of California at Riverside, Riverside, California 92521, United States
| | - Alexandra Westbrook
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Ryan Marshall
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Colin S. Maxwell
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Julius Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Chase L. Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Josef-Schneider-Str. 2/D15, D-97080 Würzburg, Germany
| | - Mary J. Dunlop
- Biomedical Engineering Department, Boston University, Boston, Massachusetts 02215, United States
| | - Elisa Franco
- Department of Mechanical Engineering, University of California at Riverside, Riverside, California 92521, United States
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120
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Seamon KJ, Light YK, Saada EA, Schoeniger JS, Harmon B. Versatile High-Throughput Fluorescence Assay for Monitoring Cas9 Activity. Anal Chem 2018; 90:6913-6921. [DOI: 10.1021/acs.analchem.8b01155] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Kyle J. Seamon
- Systems Biology Department, Sandia National Laboratories, P.O. Box
969, Livermore, California 94550, United States
| | - Yooli K. Light
- Systems Biology Department, Sandia National Laboratories, P.O. Box
969, Livermore, California 94550, United States
| | - Edwin A. Saada
- Systems Biology Department, Sandia National Laboratories, P.O. Box
969, Livermore, California 94550, United States
| | - Joseph S. Schoeniger
- Systems Biology Department, Sandia National Laboratories, P.O. Box
969, Livermore, California 94550, United States
| | - Brooke Harmon
- Systems Biology Department, Sandia National Laboratories, P.O. Box
969, Livermore, California 94550, United States
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121
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Jiang L, Zhao J, Lian J, Xu Z. Cell-free protein synthesis enabled rapid prototyping for metabolic engineering and synthetic biology. Synth Syst Biotechnol 2018; 3:90-96. [PMID: 29900421 PMCID: PMC5995451 DOI: 10.1016/j.synbio.2018.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/11/2018] [Accepted: 02/14/2018] [Indexed: 11/15/2022] Open
Abstract
Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade. However, due to complexity of cellular metabolism, the optimization of metabolic pathways for maximal production represents a grand challenge and an unavoidable barrier for metabolic engineering. Recently, cell-free protein synthesis system (CFPS) has been emerging as an enabling alternative to address challenges in biomanufacturing. This review summarizes the recent progresses of CFPS in rapid prototyping of biosynthetic pathways and genetic circuits (biosensors) to speed up design-build-test (DBT) cycles of metabolic engineering and synthetic biology.
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Affiliation(s)
- Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiarun Zhao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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122
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Synthetic Biology with an All E. coli TXTL System: Quantitative Characterization of Regulatory Elements and Gene Circuits. Methods Mol Biol 2018; 1772:61-93. [PMID: 29754223 DOI: 10.1007/978-1-4939-7795-6_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Over the past decade, a new generation of cell-free transcription-translation (TXTL) systems has been devised for emerging multidisciplinary applications. The DNA-dependent in vitro protein synthesis technology has been developed to tackle applications in synthetic biology, biological and chemical engineering, as well as quantitative disciplines such as biophysics. In addition to being convenient at the biosafety level, the new TXTL platforms are user-friendly; more affordable; more versatile at the level of transcription, with a TX repertoire covering hundreds of parts; and more powerful, with protein production reaching a few mg/mL in batch and continuous modes. As a consequence, TXTL is rising up as a popular research tool and is used by a growing research community. While TXTL is proving reliable for an increasing number of applications, it is important to gain appropriate TXTL skills, especially for quantitative applications. TXTL has become particularly useful to rapidly prototype genetic devices , from single regulatory elements to elementary circuit motifs . In this chapter, we describe the basic procedures to develop appropriate TXTL practices for the characterization of such genetic parts. We use an all E. coli TXTL system developed in our lab, now commercialized by Arbor Biosciences under the name myTXTL.
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