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Kay JE, Jewett MC. A cell-free system for production of 2,3-butanediol is robust to growth-toxic compounds. Metab Eng Commun 2020; 10:e00114. [PMID: 31934547 PMCID: PMC6951449 DOI: 10.1016/j.mec.2019.e00114] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 11/14/2019] [Accepted: 11/19/2019] [Indexed: 11/23/2022] Open
Abstract
The need for sustainable, low-cost production of bioenergy and commodity chemicals is increasing. Unfortunately, the engineering potential of whole-cell catalysts to address this need can be hampered by cellular toxicity. When such bottlenecks limit the commercial feasibility of whole-cell fermentation, cell-free, or in vitro, based approaches may offer an alternative. Here, we assess the impact of three classes of growth toxic compounds on crude extract-based, cell-free chemical conversions. As a model system, we test a metabolic pathway for conversion of glucose to 2,3-butanediol (2,3-BDO) in lysates of Escherichia coli. First, we characterized 2,3-BDO production with different classes of antibiotics and found, as expected, that the system is uninhibited by compounds that prevent cell growth by means of cell wall replication and DNA, RNA, and protein synthesis. Second, we considered the impact of polar solvent addition (e.g., methanol, n-butanol). We observed that volumetric productivities (g/L/h) were slowed with increasing hydrophobicity of added alcohols. Finally, we investigated the effects of using pretreated biomass hydrolysate as a feed stock, observing a 25% reduction in 2,3-BDO production as a result of coumaroyl and feruloyl amides. Overall, we find the cell-free system to be robust to working concentrations of antibiotics and other compounds that are toxic to cell growth, but do not denature or inhibit relevant enzymes.
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Affiliation(s)
- Jennifer E. Kay
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center and Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
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2
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Laohakunakorn N, Grasemann L, Lavickova B, Michielin G, Shahein A, Swank Z, Maerkl SJ. Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:213. [PMID: 32266240 PMCID: PMC7105575 DOI: 10.3389/fbioe.2020.00213] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-free systems offer a promising approach to engineer biology since their open nature allows for well-controlled and characterized reaction conditions. In this review, we discuss the history and recent developments in engineering recombinant and crude extract systems, as well as breakthroughs in enabling technologies, that have facilitated increased throughput, compartmentalization, and spatial control of cell-free protein synthesis reactions. Combined with a deeper understanding of the cell-free systems themselves, these advances improve our ability to address a range of scientific questions. By mastering control of the cell-free platform, we will be in a position to construct increasingly complex biomolecular systems, and approach natural biological complexity in a bottom-up manner.
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Affiliation(s)
- Nadanai Laohakunakorn
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura Grasemann
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbora Lavickova
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Grégoire Michielin
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Amir Shahein
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zoe Swank
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J. Maerkl
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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3
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Deaner M, Alper HS. Enhanced scale and scope of genome engineering and regulation using CRISPR/Cas in Saccharomyces cerevisiae. FEMS Yeast Res 2019; 19:foz076. [PMID: 31665284 DOI: 10.1093/femsyr/foz076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022] Open
Abstract
Although only 6 years old, the CRISPR system has blossomed into a tool for rapid, on-demand genome engineering and gene regulation in Saccharomyces cerevisiae. In this minireview, we discuss fundamental CRISPR technologies, tools to improve the efficiency and capabilities of gene targeting, and cutting-edge techniques to explore gene editing and transcriptional regulation at genome scale using pooled approaches. The focus is on applications to metabolic engineering with topics including development of techniques to edit the genome in multiplex, tools to enable large numbers of genetic modifications using pooled single-guide RNA libraries and efforts to enable programmable transcriptional regulation using endonuclease-null Cas enzymes.
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Affiliation(s)
- Matthew Deaner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA
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4
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Pandi A, Grigoras I, Borkowski O, Faulon JL. Optimizing Cell-Free Biosensors to Monitor Enzymatic Production. ACS Synth Biol 2019; 8:1952-1957. [PMID: 31335131 DOI: 10.1021/acssynbio.9b00160] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cell-free systems are promising platforms for rapid and high-throughput prototyping of biological parts in metabolic engineering and synthetic biology. One main limitation of cell-free system applications is the low fold repression of transcriptional repressors. Hence, prokaryotic biosensor development, which mostly relies on repressors, is limited. In this study, we demonstrate how to improve these biosensors in cell-free systems by applying a transcription factor (TF)-doped extract, a preincubation strategy with the TF plasmid, or reinitiation of the cell-free reaction (two-step cell-free reaction). We use the optimized biosensor to sense the enzymatic production of a rare sugar, D-psicose. This work provides a methodology to optimize repressor-based systems in cell-free to further increase the potential of cell-free systems for bioproduction.
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Affiliation(s)
- Amir Pandi
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas 78352, France
| | - Ioana Grigoras
- iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
| | - Olivier Borkowski
- iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas 78352, France
- iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
- SYNBIOCHEM Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
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5
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Kelwick R, Ricci L, Chee SM, Bell D, Webb AJ, Freemont PS. Cell-free prototyping strategies for enhancing the sustainable production of polyhydroxyalkanoates bioplastics. Synth Biol (Oxf) 2018; 3:ysy016. [PMID: 32995523 PMCID: PMC7445755 DOI: 10.1093/synbio/ysy016] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 07/29/2018] [Accepted: 08/21/2018] [Indexed: 12/31/2022] Open
Abstract
The polyhydroxyalkanoates (PHAs) are microbially-produced biopolymers that could potentially be used as sustainable alternatives to oil-derived plastics. However, PHAs are currently more expensive to produce than oil-derived plastics. Therefore, more efficient production processes would be desirable. Cell-free metabolic engineering strategies have already been used to optimize several biosynthetic pathways and we envisioned that cell-free strategies could be used for optimizing PHAs biosynthetic pathways. To this end, we developed several Escherichia coli cell-free systems for in vitro prototyping PHAs biosynthetic operons, and also for screening relevant metabolite recycling enzymes. Furthermore, we customized our cell-free reactions through the addition of whey permeate, an industrial waste that has been previously used to optimize in vivo PHAs production. We found that the inclusion of an optimal concentration of whey permeate enhanced relative cell-free GFPmut3b production by approximately 50%. In cell-free transcription-translation prototyping reactions, gas chromatography-mass spectrometry quantification of cell-free 3-hydroxybutyrate (3HB) production revealed differences between the activities of the Native ΔPhaC_C319A (1.18 ± 0.39 µM), C104 ΔPhaC_C319A (4.62 ± 1.31 µM) and C101 ΔPhaC_C319A (2.65 ± 1.27 µM) phaCAB operons that were tested. Interestingly, the most active operon, C104 produced higher levels of PHAs (or PHAs monomers) than the Native phaCAB operon in both in vitro and in vivo assays. Coupled cell-free biotransformation/transcription-translation reactions produced greater yields of 3HB (32.87 ± 6.58 µM), and these reactions were also used to characterize a Clostridium propionicum Acetyl-CoA recycling enzyme. Together, these data demonstrate that cell-free approaches complement in vivo workflows for identifying additional strategies for optimizing PHAs production.
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Affiliation(s)
- Richard Kelwick
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
| | - Luca Ricci
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Soo Mei Chee
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- The London DNA Foundry, Imperial College London, London, UK
| | - David Bell
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- The London DNA Foundry, Imperial College London, London, UK
| | - Alexander J Webb
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
| | - Paul S Freemont
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
- The London DNA Foundry, Imperial College London, London, UK
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Deaner M, Holzman A, Alper HS. Modular Ligation Extension of Guide RNA Operons (LEGO) for Multiplexed dCas9 Regulation of Metabolic Pathways in Saccharomyces cerevisiae. Biotechnol J 2018; 13:e1700582. [PMID: 29663663 DOI: 10.1002/biot.201700582] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/23/2018] [Indexed: 02/01/2023]
Abstract
Metabolic engineering typically utilizes a suboptimal step-wise gene target optimization approach to parse a highly connected and regulated cellular metabolism. While the endonuclease-null CRISPR/Cas system has enabled gene expression perturbations without genetic modification, it has been mostly limited to small sets of gene targets in eukaryotes due to inefficient methods to assemble and express large sgRNA operons. In this work, we develop a TEF1p-tRNA expression system and demonstrate that the use of tRNAs as splicing elements flanking sgRNAs provides higher efficiency than both Pol III and ribozyme-based expression across a variety of single sgRNA and multiplexed contexts. Next, we devise and validate a scheme to allow modular construction of tRNA-sgRNA (TST) operons using an iterative Type IIs digestion/ligation extension approach, termed CRISPR-Ligation Extension of sgRNA Operons (LEGO). This approach enables facile construction of large TST operons. We demonstrate this utility by constructing a metabolic rewiring prototype for 2,3-butanediol production in 2 distinct yeast strain backgrounds. These results demonstrate that our approach can act as a surrogate for traditional genetic modification on a much shorter design-cycle timescale.
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Affiliation(s)
- Matthew Deaner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712
| | - Allison Holzman
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712
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7
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Casini A, Chang FY, Eluere R, King AM, Young EM, Dudley QM, Karim A, Pratt K, Bristol C, Forget A, Ghodasara A, Warden-Rothman R, Gan R, Cristofaro A, Borujeni AE, Ryu MH, Li J, Kwon YC, Wang H, Tatsis E, Rodriguez-Lopez C, O’Connor S, Medema MH, Fischbach MA, Jewett MC, Voigt C, Gordon DB. A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology. J Am Chem Soc 2018; 140:4302-4316. [DOI: 10.1021/jacs.7b13292] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Arturo Casini
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Fang-Yuan Chang
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Raissa Eluere
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Andrew M. King
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Eric M. Young
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Quentin M. Dudley
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty Karim
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Katelin Pratt
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Cassandra Bristol
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Anthony Forget
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Amar Ghodasara
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Robert Warden-Rothman
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Rui Gan
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexander Cristofaro
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Amin Espah Borujeni
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Min-Hyung Ryu
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Jian Li
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Yong-Chan Kwon
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - He Wang
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Evangelos Tatsis
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | | | - Sarah O’Connor
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Michael A. Fischbach
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Bioengineering and Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, California 94305, United States
| | - Michael C. Jewett
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Christopher Voigt
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - D. Benjamin Gordon
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
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Deaner M, Mejia J, Alper HS. Enabling Graded and Large-Scale Multiplex of Desired Genes Using a Dual-Mode dCas9 Activator in Saccharomyces cerevisiae. ACS Synth Biol 2017; 6:1931-1943. [PMID: 28700213 DOI: 10.1021/acssynbio.7b00163] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Standard approaches for dCas9-based modification of gene expression are limited in the ability to multiplex targets, establish streamlined cassettes, and utilize commonly studied Pol II promoters. In this work, we repurpose the dCas9-VPR activator to act as a dual-mode activator/repressor that can be programmed solely on the basis of target position at gene loci. Furthermore, we implement this approach using a streamlined Pol II-ribozyme system that allows expression of many sgRNAs from a single transcript. By "stepping" dCas9-VPR within the promoter region and ORF we create graded activation and repression (respectively) of target genes, allowing precise control over multiplexed gene modulation. Expression from the Pol II system increased the net amount of sgRNA production in cells by 3.88-fold relative to the Pol III SNR52 promoter, leading to a significant improvement in dCas9-VPR repression strength. Finally, we utilize our Pol II system to create galactose-inducible switching of gene expression states and multiplex constructs capable of modulating up to 4 native genes from a single vector. Our approach represents a significant step toward minimizing DNA required to assemble CRISPR systems in eukaryotes while enhancing the efficacy (greater repression strength), scale (more sgRNAs), and scope (inducibility) of dCas9-mediated gene regulation.
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Affiliation(s)
- Matthew Deaner
- McKetta
Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Julio Mejia
- McKetta
Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Hal S. Alper
- McKetta
Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
- Institute
for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas 78712, United States
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