1
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McGaw C, Garrity AJ, Munoz GZ, Haswell JR, Sengupta S, Keston-Smith E, Hunnewell P, Ornstein A, Bose M, Wessells Q, Jakimo N, Yan P, Zhang H, Alfonse LE, Ziblat R, Carte JM, Lu WC, Cerchione D, Hilbert B, Sothiselvam S, Yan WX, Cheng DR, Scott DA, DiTommaso T, Chong S. Engineered Cas12i2 is a versatile high-efficiency platform for therapeutic genome editing. Nat Commun 2022; 13:2833. [PMID: 35595757 PMCID: PMC9122993 DOI: 10.1038/s41467-022-30465-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/03/2022] [Indexed: 12/11/2022] Open
Abstract
The CRISPR-Cas type V-I is a family of Cas12i-containing programmable nuclease systems guided by a short crRNA without requirement for a tracrRNA. Here we present an engineered Type V-I CRISPR system (Cas12i), ABR-001, which utilizes a tracr-less guide RNA. The compact Cas12i effector is capable of self-processing pre-crRNA and cleaving dsDNA targets, which facilitates versatile delivery options and multiplexing, respectively. We apply an unbiased mutational scanning approach to enhance initially low editing activity of Cas12i2. The engineered variant, ABR-001, exhibits broad genome editing capability in human cell lines, primary T cells, and CD34+ hematopoietic stem and progenitor cells, with both robust efficiency and high specificity. In addition, ABR-001 achieves a high level of genome editing when delivered via AAV vector to HEK293T cells. This work establishes ABR-001 as a versatile, specific, and high-performance platform for ex vivo and in vivo gene therapy.
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Affiliation(s)
- Colin McGaw
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Anthony J Garrity
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Gabrielle Z Munoz
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Jeffrey R Haswell
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Sejuti Sengupta
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Elise Keston-Smith
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | | | - Alexa Ornstein
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Mishti Bose
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Quinton Wessells
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Noah Jakimo
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Paul Yan
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Huaibin Zhang
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Lauren E Alfonse
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Roy Ziblat
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Jason M Carte
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Wei-Cheng Lu
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Derek Cerchione
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Brendan Hilbert
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | | | - Winston X Yan
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - David R Cheng
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - David A Scott
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Tia DiTommaso
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA.
| | - Shaorong Chong
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
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2
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Liu Y, Wang B. A Novel Eukaryote-Like CRISPR Activation Tool in Bacteria: Features and Capabilities. Bioessays 2020; 42:e1900252. [PMID: 32310310 DOI: 10.1002/bies.201900252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/03/2020] [Indexed: 11/09/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) activation (CRISPRa) in bacteria is an attractive method for programmable gene activation. Recently, a eukaryote-like, σ54 -dependent CRISPRa system has been reported. It exhibits high dynamic ranges and permits flexible target site selection. Here, an overview of the existing strategies of CRISPRa in bacteria is presented, and the characteristics and design principles of the CRISPRa system are introduced. Possible scenarios for applying the eukaryote-like CRISPRa system is discussed with corresponding suggestions for performance optimization and future functional expansion. The authors envision the new eukaryote-like CRISPRa system enabling novel designs in multiplexed gene regulation and promoting research in the σ54 -dependent gene regulatory networks among a variety of biotechnology relevant or disease-associated bacterial species.
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Affiliation(s)
- Yang Liu
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK.,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK.,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
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3
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Arter WE, Levin A, Krainer G, Knowles TPJ. Microfluidic approaches for the analysis of protein-protein interactions in solution. Biophys Rev 2020; 12:575-585. [PMID: 32266673 PMCID: PMC7242286 DOI: 10.1007/s12551-020-00679-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/02/2020] [Indexed: 12/15/2022] Open
Abstract
Exploration and characterisation of the human proteome is a key objective enabling a heightened understanding of biological function, malfunction and pharmaceutical design. Since proteins typically exhibit their behaviour by binding to other proteins, the challenge of probing protein-protein interactions has been the focus of new and improved experimental approaches. Here, we review recently developed microfluidic techniques for the study and quantification of protein-protein interactions. We focus on methodologies that utilise the inherent strength of microfluidics for the control of mass transport on the micron scale, to facilitate surface and membrane-free interrogation and quantification of interacting proteins. Thus, the microfluidic tools described here provide the capability to yield insights on protein-protein interactions under physiological conditions. We first discuss the defining principles of microfluidics, and methods for the analysis of protein-protein interactions that utilise the diffusion-controlled mixing characteristic of fluids at the microscale. We then describe techniques that employ electrophoretic forces to manipulate and fractionate interacting protein systems for their biophysical characterisation, before discussing strategies that use microdroplet compartmentalisation for the analysis of protein interactions. We conclude by highlighting future directions for the field, such as the integration of microfluidic experiments into high-throughput workflows for the investigation of protein interaction networks.
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Affiliation(s)
- William E Arter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Aviad Levin
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Georg Krainer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK.
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4
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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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5
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Li M, Li X, Zhang Y, Wu H, Zhou H, Ding X, Zhang X, Jin X, Wang Y, Yin X, Li C, Yang P, Xu H. Micropeptide MIAC Inhibits HNSCC Progression by Interacting with Aquaporin 2. J Am Chem Soc 2020; 142:6708-6716. [PMID: 32176498 DOI: 10.1021/jacs.0c00706] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Several important micropeptides encoded by noncoding RNAs have been identified in recent years; however, there have never been any reports of micropeptides in head and neck squamous cell carcinoma (HNSCC). Here we report the discovery and characterization of a human endogenous peptide named micropeptide inhibiting actin cytoskeleton (MIAC). Comprehensive analysis of the TCGA (The Cancer Genome Atlas) database (n = 500), clinical fresh samples (n = 94), and tissue microarrays (n = 60) revealed that lower MIAC expression is correlated with poor overall survival of HNSCC patients. Meanwhile, RNA-sequencing analysis of 9657 human tissues across 32 cancer types from TCGA cohorts found that MIAC is significantly associated with the progression of 5 other different tumors. Mechanistically, MIAC directly interacts with AQP2 (Aquaporin 2) to inhibit the actin cytoskeleton by regulating SEPT2 (Septin 2)/ITGB4 (Integrin Beta 4) and ultimately suppressing the tumor growth and metastasis of HNSCC. Collectively, the mechanism investigation and evaluation of MIAC activity in vivo and in vitro highlights that MIAC plays an important role in HNSCC tumorigenesis.
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Affiliation(s)
| | | | | | - Heming Wu
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing 210029, P. R. China
| | | | - Xu Ding
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing 210029, P. R. China
| | - Xiaomin Zhang
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing 210029, P. R. China
| | | | | | | | - Chencheng Li
- Nanjing Anji Biotechnology Co. Ltd., Nanjing, Jiangsu 210009, P. R. China
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6
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Ding R, Hung KC, Mitra A, Ung LW, Lightwood D, Tu R, Starkie D, Cai L, Mazutis L, Chong S, Weitz DA, Heyman JA. Rapid isolation of antigen-specific B-cells using droplet microfluidics. RSC Adv 2020; 10:27006-27013. [PMID: 35515810 PMCID: PMC9055518 DOI: 10.1039/d0ra04328a] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022] Open
Abstract
Monoclonal antibodies are powerful tools for scientific research and are the basis of numerous therapeutics. However, traditional approaches to generate monoclonal antibodies against a desired target, such as hybridoma-based techniques and display library methods, are laborious and suffer from fusion inefficiency and display bias, respectively. Here we present a platform, featuring droplet microfluidics and a bead-based binding assay, to rapidly identify and verify antigen-binding antibody sequences from primary cells. We used a defined mixture of hybridoma cells to characterize the system, sorting droplets at up to 100 Hz and isolating desired hybridoma cells, comprising 0.1% of the input, with a false positive rate of less than 1%. We then applied the system to once-frozen primary B-cells to isolate rare cells secreting target-binding antibody. We performed RT-PCR on individual sorted cells to recover the correctly paired heavy- and light-chain antibody sequences, and we used rapid cell-free protein synthesis to generate single-chain variable fragment-format (scFv) antibodies from fourteen of the sorted cells. Twelve of these showed antigen-specific binding by ELISA. Our platform facilitates screening animal B-cell repertoires within days at low cost, increasing both rate and range of discovering antigen-specific antibodies from living organisms. Further, these techniques can be adapted to isolate cells based on virtually any secreted product. We use a droplet-microfluidics-based platform to rapidly identify and isolate individual primary cells that secrete desired antibodies. We then retrieve the antibody-encoding sequences and create recombinant antibodies that bind the target protein.![]()
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Affiliation(s)
- Ruihua Ding
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
- Department of Chemistry and Chemical Biology
| | - Kuo-Chan Hung
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
| | - Anindita Mitra
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
| | - Lloyd W. Ung
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
| | | | - Ran Tu
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
- CAS Key Laboratory of Systems Microbial Biotechnology
| | | | - Liheng Cai
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
- Department of Materials Science and Engineering
| | - Linas Mazutis
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
- Vilnius University
| | | | - David A. Weitz
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
- Department of Physics
| | - John A. Heyman
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
- SphereBio
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7
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Liu Y, Wan X, Wang B. Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria. Nat Commun 2019; 10:3693. [PMID: 31451697 PMCID: PMC6710252 DOI: 10.1038/s41467-019-11479-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/16/2019] [Indexed: 11/21/2022] Open
Abstract
Transcriptional regulation by nuclease-deficient CRISPR/Cas is a popular and valuable tool for routine control of gene expression. CRISPR interference in bacteria can be reliably achieved with high efficiencies. Yet, options for CRISPR activation (CRISPRa) remained limited in flexibility and activity because they relied on σ70 promoters. Here we report a eukaryote-like bacterial CRISPRa system based on σ54-dependent promoters, which supports long distance, and hence multi-input regulation with high dynamic ranges. Our CRISPRa device can activate σ54-dependent promoters with biotechnology relevance in non-model bacteria. It also supports orthogonal gene regulation on multiple levels. Combining our CRISPRa with dxCas9 further expands flexibility in DNA targeting, and boosts dynamic ranges into regimes that enable construction of cascaded CRISPRa circuits. Application-wise, we construct a reusable scanning platform for readily optimizing metabolic pathways without library reconstructions. This eukaryote-like CRISPRa system is therefore a powerful and versatile synthetic biology tool for diverse research and industrial applications.
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Affiliation(s)
- Yang Liu
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Xinyi Wan
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK.
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8
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Berry KE, Hochschild A. A bacterial three-hybrid assay detects Escherichia coli Hfq-sRNA interactions in vivo. Nucleic Acids Res 2018; 46:e12. [PMID: 29140461 PMCID: PMC5778611 DOI: 10.1093/nar/gkx1086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/21/2017] [Accepted: 10/20/2017] [Indexed: 01/08/2023] Open
Abstract
The interaction of RNA molecules with proteins is a critical aspect of gene regulation across all domains of life. Here, we report the development of a bacterial three-hybrid (B3H) assay to genetically detect RNA-protein interactions. The basis for this three-hybrid assay is a transcription-based bacterial two-hybrid assay that has been used widely to detect and dissect protein-protein interactions. In the three-hybrid assay, a DNA-bound protein with a fused RNA-binding moiety (the coat protein of bacteriophage MS2 (MS2CP)) is used to recruit a hybrid RNA upstream of a test promoter. The hybrid RNA consists of a constant region that binds the tethered MS2CP and a variable region. Interaction between the variable region of the hybrid RNA and a target RNA-binding protein that is fused to a subunit of Escherichia coli RNA polymerase (RNAP) stabilizes the binding of RNAP to the test promoter, thereby activating transcription of a reporter gene. We demonstrate that this three-hybrid assay detects interaction between non-coding small RNAs (sRNAs) and the hexameric RNA chaperone Hfq from E. coli and enables the identification of Hfq mutants with sRNA-binding defects. Our findings suggest that this B3H assay will be broadly applicable for the study of RNA-protein interactions.
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Affiliation(s)
- Katherine E Berry
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ann Hochschild
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
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9
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Maddalena LLD, Niederholtmeyer H, Turtola M, Swank ZN, Belogurov GA, Maerkl SJ. GreA and GreB Enhance Expression of Escherichia coli RNA Polymerase Promoters in a Reconstituted Transcription-Translation System. ACS Synth Biol 2016; 5:929-35. [PMID: 27186988 DOI: 10.1021/acssynbio.6b00017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell-free environments are becoming viable alternatives for implementing biological networks in synthetic biology. The reconstituted cell-free expression system (PURE) allows characterization of genetic networks under defined conditions but its applicability to native bacterial promoters and endogenous genetic networks is limited due to the poor transcription rate of Escherichia coli RNA polymerase in this minimal system. We found that addition of transcription elongation factors GreA and GreB to the PURE system increased transcription rates of E. coli RNA polymerase from sigma factor 70 promoters up to 6-fold and enhanced the performance of a genetic network. Furthermore, we reconstituted activation of natural E. coli promoters controlling flagella biosynthesis by the transcriptional activator FlhDC and sigma factor 28. Addition of GreA/GreB to the PURE system allows efficient expression from natural and synthetic E. coli promoters and characterization of their regulation in minimal and defined reaction conditions, making the PURE system more broadly applicable to study genetic networks and bottom-up synthetic biology.
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Affiliation(s)
- Lea L. de Maddalena
- Institute
of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Henrike Niederholtmeyer
- Institute
of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Matti Turtola
- Department
of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Zoe N. Swank
- Institute
of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Sebastian J. Maerkl
- Institute
of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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10
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Srivastava A, Asahara H, Zhang M, Zhang W, Liu H, Cui S, Jin Q, Chong S. Reconstitution of Protein Translation of Mycobacterium Reveals Functional Conservation and Divergence with the Gram-Negative Bacterium Escherichia coli. PLoS One 2016; 11:e0162020. [PMID: 27564552 PMCID: PMC5001721 DOI: 10.1371/journal.pone.0162020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/16/2016] [Indexed: 12/12/2022] Open
Abstract
Protein translation is essential for all bacteria pathogens. It has also been a major focus of structural and functional studies and an important target of antibiotics. Here we report our attempts to biochemically reconstitute mycobacterial protein translation in vitro from purified components. This mycobacterial translation system consists of individually purified recombinant translation factors from Mycobacterium tuberculosis (M. tuberculosis), purified tRNAs and ribosomes from Mycobacterium smegmatis (M. smegmatis), and an aminoacyl-tRNA synthetase (AARS) mixture from the cell-extract of M. smegmatis. We demonstrate that such mycobacterial translation system was efficient in in vitro protein synthesis, and enabled functional comparisons of translational components between the gram-positive Mycobacterium and the gram-negative E. coli. Although mycobacterial translation factors and ribosomes were highly compatible with their E. coli counterparts, M. smegmatis tRNAs were not properly charged by the E. coli AARSs to allow efficient translation of a reporter. In contrast, both E. coli and M. smegmatis tRNAs exhibited similar activity with the semi-purified M. smegmatis AARSs mixture for in vitro translation. We further demonstrated the use of both mycobacterial and E. coli translation systems as comparative in vitro assays for small-molecule antibiotics that target protein translation. While mycobacterial and E. coli translation were both inhibited at the same IC50 by the antibiotic spectinomycin, mycobacterial translation was preferentially inhibited by the antibiotic tetracycline, suggesting that there may be structural differences at the antibiotic binding sites between the ribosomes of Mycobacterium and E. coli. Our results illustrate an alternative approach for antibiotic discovery and functional studies of protein translation in mycobacteria and possibly other bacterial pathogens.
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Affiliation(s)
- Aashish Srivastava
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, United States of America
| | - Haruichi Asahara
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, United States of America
| | - Meng Zhang
- Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Weijia Zhang
- Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Haiying Liu
- Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Sheng Cui
- Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Qi Jin
- Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Shaorong Chong
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, United States of America
- * E-mail:
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11
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A mix-and-read drop-based in vitro two-hybrid method for screening high-affinity peptide binders. Sci Rep 2016; 6:22575. [PMID: 26940078 PMCID: PMC4778045 DOI: 10.1038/srep22575] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/17/2016] [Indexed: 11/08/2022] Open
Abstract
Drop-based microfluidics have recently become a novel tool by providing a stable linkage between phenotype and genotype for high throughput screening. However, use of drop-based microfluidics for screening high-affinity peptide binders has not been demonstrated due to the lack of a sensitive functional assay that can detect single DNA molecules in drops. To address this sensitivity issue, we introduced in vitro two-hybrid system (IVT2H) into microfluidic drops and developed a streamlined mix-and-read drop-IVT2H method to screen a random DNA library. Drop-IVT2H was based on the correlation between the binding affinity of two interacting protein domains and transcriptional activation of a fluorescent reporter. A DNA library encoding potential peptide binders was encapsulated with IVT2H such that single DNA molecules were distributed in individual drops. We validated drop-IVT2H by screening a three-random-residue library derived from a high-affinity MDM2 inhibitor PMI. The current drop-IVT2H platform is ideally suited for affinity screening of small-to-medium-sized libraries (10(3)-10(6)). It can obtain hits within a single day while consuming minimal amounts of reagents. Drop-IVT2H simplifies and accelerates the drop-based microfluidics workflow for screening random DNA libraries, and represents a novel alternative method for protein engineering and in vitro directed protein evolution.
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12
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Abbaspourrad A, Zhang H, Tao Y, Cui N, Asahara H, Zhou Y, Yue D, Koehler SA, Ung LW, Heyman J, Ren Y, Ziblat R, Chong S, Weitz DA. Label-free single-cell protein quantification using a drop-based mix-and-read system. Sci Rep 2015; 5:12756. [PMID: 26234416 PMCID: PMC4522677 DOI: 10.1038/srep12756] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/22/2015] [Indexed: 12/14/2022] Open
Abstract
Quantitative protein analysis of single cells is rarely achieved due to technical difficulties of detecting minute amounts of proteins present in one cell. We develop a mix-and-read assay for drop-based label-free protein analysis of single cells. This high-throughput method quantifies absolute, rather than relative, amounts of proteins and does not involve antibody labeling or mass spectrometry.
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Affiliation(s)
- Alireza Abbaspourrad
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Huidan Zhang
- 1] School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA [2] Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110001, China
| | - Ye Tao
- 1] School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA [2] School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Naiwen Cui
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Haruichi Asahara
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Ying Zhou
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Dongxian Yue
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Stephan A Koehler
- 1] School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA [2] Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Lloyd W Ung
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - John Heyman
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Yukun Ren
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Roy Ziblat
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Shaorong Chong
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - David A Weitz
- 1] School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA [2] Department of Physics, Harvard University, Cambridge, MA 02138, USA
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Kwon YC, Jewett MC. High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Sci Rep 2015; 5:8663. [PMID: 25727242 PMCID: PMC4345344 DOI: 10.1038/srep08663] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/15/2015] [Indexed: 12/24/2022] Open
Abstract
Crude extract based cell-free protein synthesis (CFPS) has emerged as a powerful technology platform for high-throughput protein production and genetic part characterization. Unfortunately, robust preparation of highly active extracts generally requires specialized and costly equipment and can be labor and time intensive. Moreover, cell lysis procedures can be hard to standardize, leading to different extract performance across laboratories. These challenges limit new entrants to the field and new applications, such as comprehensive genome engineering programs to improve extract performance. To address these challenges, we developed a generalizable and easily accessible high-throughput crude extract preparation method for CFPS based on sonication. To validate our approach, we investigated two Escherichia coli strains: BL21 Star™ (DE3) and a K12 MG1655 variant, achieving similar productivity (defined as CFPS yield in g/L) by varying only a few parameters. In addition, we observed identical productivity of cell extracts generated from culture volumes spanning three orders of magnitude (10 mL culture tubes to 10 L fermentation). We anticipate that our rapid and robust extract preparation method will speed-up screening of genomically engineered strains for CFPS applications, make possible highly active extracts from non-model organisms, and promote a more general use of CFPS in synthetic biology and biotechnology.
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Affiliation(s)
- Yong-Chan Kwon
- 1] Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA [2] Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- 1] Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA [2] Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA [3] Robert H. Lurie Comprehensive Cancer Center, Medicine Northwestern University, Chicago, IL 60611, USA [4] Institute of Bionanotechnology in Medicine Northwestern University, Chicago, IL 60611, USA
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