1
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Herring-Nicholas A, Dimig H, Roesing MR, Josephs EA. Selection of extended CRISPR RNAs with enhanced targeting and specificity. Commun Biol 2024; 7:86. [PMID: 38212640 PMCID: PMC10784525 DOI: 10.1038/s42003-024-05776-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024] Open
Abstract
As CRISPR effectors like Cas9 increasingly enter clinical trials for therapeutic gene editing, a future for personalized medicine will require efficient methods to protect individuals from the potential of off-target mutations that may also occur at specific sequences in their genomes that are similar to the therapeutic target. A Cas9 enzyme's ability to recognize their targets (and off-targets) are determined by the sequence of their RNA-cofactors (their guide RNAs or gRNAs). Here, we present a method to screen hundreds of thousands of gRNA variants with short, randomized 5' nucleotide extensions near its DNA-targeting segment-a modification that can increase gene editing specificity by orders of magnitude-to identify extended gRNAs (x-gRNAs) that effectively block any activity at those off-target sites while still maintaining strong activity at their intended targets. X-gRNAs that have been selected for specific target / off-target pairs can significantly out-perform other methods that reduce Cas9 off-target activity overall, like using Cas9 variants engineered for higher specificity in general, and we demonstrate their effectiveness in clinically-relevant gRNAs. Our streamlined approach to efficiently identify highly specific and active x-gRNAs provides a way to move beyond a one-size-fits-all model of high-fidelity CRISPR for safer and more effective personalized gene therapies.
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Affiliation(s)
- Ashley Herring-Nicholas
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Hillary Dimig
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Miranda R Roesing
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Eric A Josephs
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC, USA.
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2
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Ziemann M, Reimann V, Liang Y, Shi Y, Ma H, Xie Y, Li H, Zhu T, Lu X, Hess WR. CvkR is a MerR-type transcriptional repressor of class 2 type V-K CRISPR-associated transposase systems. Nat Commun 2023; 14:924. [PMID: 36801863 PMCID: PMC9938897 DOI: 10.1038/s41467-023-36542-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 02/06/2023] [Indexed: 02/20/2023] Open
Abstract
Certain CRISPR-Cas elements integrate into Tn7-like transposons, forming CRISPR-associated transposon (CAST) systems. How the activity of these systems is controlled in situ has remained largely unknown. Here we characterize the MerR-type transcriptional regulator Alr3614 that is encoded by one of the CAST (AnCAST) system genes in the genome of cyanobacterium Anabaena sp. PCC 7120. We identify a number of Alr3614 homologs across cyanobacteria and suggest naming these regulators CvkR for Cas V-K repressors. Alr3614/CvkR is translated from leaderless mRNA and represses the AnCAST core modules cas12k and tnsB directly, and indirectly the abundance of the tracr-CRISPR RNA. We identify a widely conserved CvkR binding motif 5'-AnnACATnATGTnnT-3'. Crystal structure of CvkR at 1.6 Å resolution reveals that it comprises distinct dimerization and potential effector-binding domains and that it assembles into a homodimer, representing a discrete structural subfamily of MerR regulators. CvkR repressors are at the core of a widely conserved regulatory mechanism that controls type V-K CAST systems.
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Affiliation(s)
- Marcus Ziemann
- Faculty of Biology, Institute of Biology III, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, Freiburg, D-79104, Germany
| | - Viktoria Reimann
- Faculty of Biology, Institute of Biology III, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, Freiburg, D-79104, Germany
| | - Yajing Liang
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,Shandong Energy Institute, Qingdao, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Yue Shi
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,Shandong Energy Institute, Qingdao, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Honglei Ma
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,Shandong Energy Institute, Qingdao, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuman Xie
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Li
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Zhu
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China. .,Shandong Energy Institute, Qingdao, 266101, China. .,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xuefeng Lu
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China. .,Shandong Energy Institute, Qingdao, 266101, China. .,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Wolfgang R Hess
- Faculty of Biology, Institute of Biology III, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, Freiburg, D-79104, Germany.
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3
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Herring-Nicholas A, Dimig H, Roesing M, Josephs EA. Selection of Extended CRISPR RNAs with Enhanced Targeting and Specificity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523593. [PMID: 36711586 PMCID: PMC9882064 DOI: 10.1101/2023.01.11.523593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
For a CRISPR guide RNA (gRNA) with a specific target but activity at known "off-target" sequences, we present a method to screen hundreds of thousands of gRNA variants with short, randomized 5' nucleotide extensions near its DNA-targeting segment-a modification that can increase Cas9 gene editing specificity by orders of magnitude with certain 5'- extension sequences, via some as-yet-unknown mechanism that makes de novo design of the extension sequence difficult to perform manually-to robustly identify extended gRNAs (x-gRNAs) that have been counter-selected against activity at those off-target sites and that exhibit significantly enhanced Cas9 specificity for their intended targets.
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Affiliation(s)
- Ashley Herring-Nicholas
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, North Carolina, 27401, USA
- Authors contributed equally
| | - Hillary Dimig
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, North Carolina, 27401, USA
- Authors contributed equally
| | - Miranda Roesing
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, North Carolina, 27401, USA
| | - Eric A. Josephs
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, North Carolina, 27401, USA
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4
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Roberts A, Nethery MA, Barrangou R. Functional characterization of diverse type I-F CRISPR-associated transposons. Nucleic Acids Res 2022; 50:11670-11681. [PMID: 36384163 PMCID: PMC9723613 DOI: 10.1093/nar/gkac985] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/07/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
CRISPR-Cas systems generally provide adaptive immunity in prokaryotes through RNA-guided degradation of foreign genetic elements like bacteriophages and plasmids. Recently, however, transposon-encoded and nuclease-deficient CRISPR-Cas systems were characterized and shown to be co-opted by Tn7-like transposons for CRISPR RNA-guided DNA transposition. As a genome engineering tool, these CRISPR-Cas systems and their associated transposon proteins can be deployed for programmable, site-specific integration of sizable cargo DNA, circumventing the need for DNA cleavage and homology-directed repair involving endogenous repair machinery. Here, we selected a diverse set of type I-F3 CRISPR-associated transposon systems derived from Gammaproteobacteria, predicted all components essential for transposition activity, and deployed them for functionality testing within Escherichia coli. Our results demonstrate that these systems possess a significant range of integration efficiencies with regards to temperature, transposon size, and flexible PAM requirements. Additionally, our findings support the categorization of these systems into functional compatibility groups for efficient and orthogonal RNA-guided DNA integration. This work expands the CRISPR-based toolbox with new CRISPR RNA-guided DNA integrases that can be applied to complex and extensive genome engineering efforts.
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Affiliation(s)
- Avery Roberts
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC 27695, USA,Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Matthew A Nethery
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC 27695, USA,Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
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5
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Romantseva E, Alperovich N, Ross D, Lund SP, Strychalski EA. Effects of DNA template preparation on variability in cell-free protein production. Synth Biol (Oxf) 2022; 7:ysac015. [PMID: 36046152 PMCID: PMC9425043 DOI: 10.1093/synbio/ysac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/01/2022] [Accepted: 08/12/2022] [Indexed: 08/08/2023] Open
Abstract
DNA templates for protein production remain an unexplored source of variability in the performance of cell-free expression (CFE) systems. To characterize this variability, we investigated the effects of two common DNA extraction methodologies, a postprocessing step and manual versus automated preparation on protein production using CFE. We assess the concentration of the DNA template, the quality of the DNA template in terms of physical damage and the quality of the DNA solution in terms of purity resulting from eight DNA preparation workflows. We measure the variance in protein titer and rate of protein production in CFE reactions associated with the biological replicate of the DNA template, the technical replicate DNA solution prepared with the same workflow and the measurement replicate of nominally identical CFE reactions. We offer practical guidance for preparing and characterizing DNA templates to achieve acceptable variability in CFE performance.
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Affiliation(s)
| | - Nina Alperovich
- National Institute of Standards and Technology, Gaithersburg, MD USA
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, MD USA
| | - Steven P Lund
- National Institute of Standards and Technology, Gaithersburg, MD USA
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6
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Rhea KA, McDonald ND, Cole SD, Noireaux V, Lux MW, Buckley PE. Variability in cell-free expression reactions can impact qualitative genetic circuit characterization. Synth Biol (Oxf) 2022; 7:ysac011. [PMID: 35966404 PMCID: PMC9365049 DOI: 10.1093/synbio/ysac011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/24/2022] [Accepted: 08/01/2022] [Indexed: 09/21/2023] Open
Abstract
Cell-free expression systems provide a suite of tools that are used in applications from sensing to biomanufacturing. One of these applications is genetic circuit prototyping, where the lack of cloning is required and a high degree of control over reaction components and conditions enables rapid testing of design candidates. Many studies have shown utility in the approach for characterizing genetic regulation elements, simple genetic circuit motifs, protein variants or metabolic pathways. However, variability in cell-free expression systems is a known challenge, whether between individuals, laboratories, instruments, or batches of materials. While the issue of variability has begun to be quantified and explored, little effort has been put into understanding the implications of this variability. For genetic circuit prototyping, it is unclear when and how significantly variability in reaction activity will impact qualitative assessments of genetic components, e.g. relative activity between promoters. Here, we explore this question by assessing DNA titrations of seven genetic circuits of increasing complexity using reaction conditions that ostensibly follow the same protocol but vary by person, instrument and material batch. Although the raw activities vary widely between the conditions, by normalizing within each circuit across conditions, reasonably consistent qualitative performance emerges for the simpler circuits. For the most complex case involving expression of three proteins, we observe a departure from this qualitative consistency, offering a provisional cautionary line where normal variability may disrupt reliable reuse of prototyping results. Our results also suggest that a previously described closed loop controller circuit may help to mitigate such variability, encouraging further work to design systems that are robust to variability. Graphical Abstract.
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Affiliation(s)
- Katherine A Rhea
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Nathan D McDonald
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Stephanie D Cole
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Matthew W Lux
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Patricia E Buckley
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
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7
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Wandera KG, Alkhnbashi OS, Bassett HVI, Mitrofanov A, Hauns S, Migur A, Backofen R, Beisel CL. Anti-CRISPR prediction using deep learning reveals an inhibitor of Cas13b nucleases. Mol Cell 2022; 82:2714-2726.e4. [PMID: 35649413 DOI: 10.1016/j.molcel.2022.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/25/2022] [Accepted: 05/03/2022] [Indexed: 11/28/2022]
Abstract
As part of the ongoing bacterial-phage arms race, CRISPR-Cas systems in bacteria clear invading phages whereas anti-CRISPR proteins (Acrs) in phages inhibit CRISPR defenses. Known Acrs have proven extremely diverse, complicating their identification. Here, we report a deep learning algorithm for Acr identification that revealed an Acr against type VI-B CRISPR-Cas systems. The algorithm predicted numerous putative Acrs spanning almost all CRISPR-Cas types and subtypes, including over 7,000 putative type IV and VI Acrs not predicted by other algorithms. By performing a cell-free screen for Acr hits against type VI-B systems, we identified a potent inhibitor of Cas13b nucleases we named AcrVIB1. AcrVIB1 blocks Cas13b-mediated defense against a targeted plasmid and lytic phage, and its inhibitory function principally occurs upstream of ribonucleoprotein complex formation. Overall, our work helps expand the known Acr universe, aiding our understanding of the bacteria-phage arms race and the use of Acrs to control CRISPR technologies.
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Affiliation(s)
- Katharina G Wandera
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Omer S Alkhnbashi
- Information and Computer Science Department, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| | - Harris V I Bassett
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | | | - Sven Hauns
- Universität Freiburg, 79098 Freiburg, Germany
| | - Anzhela Migur
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Rolf Backofen
- Universität Freiburg, 79098 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79098 Freiburg, Germany.
| | - Chase L Beisel
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany.
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8
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Rybnicky GA, Fackler NA, Karim AS, Köpke M, Jewett MC. Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences. Nucleic Acids Res 2022; 50:3523-3534. [PMID: 35258601 PMCID: PMC8990532 DOI: 10.1093/nar/gkac142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022] Open
Abstract
RNA-guided nucleases from CRISPR-Cas systems expand opportunities for precise, targeted genome modification. Endogenous CRISPR-Cas systems in many prokaryotes are attractive to circumvent expression, functionality, and unintended activity hurdles posed by heterologous CRISPR-Cas effectors. However, each CRISPR-Cas system recognizes a unique set of protospacer adjacent motifs (PAMs), which requires identification by extensive screening of randomized DNA libraries. This challenge hinders development of endogenous CRISPR-Cas systems, especially those based on multi-protein effectors and in organisms that are slow-growing or have transformation idiosyncrasies. To address this challenge, we present Spacer2PAM, an easy-to-use, easy-to-interpret R package built to predict and guide experimental determination of functional PAM sequences for any CRISPR-Cas system given its corresponding CRISPR array as input. Spacer2PAM can be used in a 'Quick' method to generate a single PAM prediction or in a 'Comprehensive' method to inform targeted PAM libraries small enough to screen in difficult to transform organisms. We demonstrate Spacer2PAM by predicting PAM sequences for industrially relevant organisms and experimentally identifying seven PAM sequences that mediate interference from the Spacer2PAM-informed PAM library for the type I-B CRISPR-Cas system from Clostridium autoethanogenum. We anticipate that Spacer2PAM will facilitate the use of endogenous CRISPR-Cas systems for industrial biotechnology and synthetic biology.
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Affiliation(s)
- Grant A Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA,Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, 60208, USA
| | | | - Ashty S Karim
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA,Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA,Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | | | - Michael C Jewett
- To whom correspondence should be addressed. Tel: +1 847 467 5007; Fax: +1 847 467 5007;
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9
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Wimmer F, Mougiakos I, Englert F, Beisel CL. Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons. Mol Cell 2022; 82:1210-1224.e6. [PMID: 35216669 DOI: 10.1016/j.molcel.2022.01.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/30/2021] [Accepted: 01/26/2022] [Indexed: 11/25/2022]
Abstract
CRISPR-Cas biology and technologies have been largely shaped to date by the characterization and use of single-effector nucleases. By contrast, multi-subunit effectors dominate natural systems, represent emerging technologies, and were recently associated with RNA-guided DNA transposition. This disconnect stems from the challenge of working with multiple protein subunits in vitro and in vivo. Here, we apply cell-free transcription-translation (TXTL) systems to radically accelerate the characterization of multi-subunit CRISPR effectors and transposons. Numerous DNA constructs can be combined in one TXTL reaction, yielding defined biomolecular readouts in hours. Using TXTL, we mined phylogenetically diverse I-E effectors, interrogated extensively self-targeting I-C and I-F systems, and elucidated targeting rules for I-B and I-F CRISPR transposons using only DNA-binding components. We further recapitulated DNA transposition in TXTL, which helped reveal a distinct branch of I-B CRISPR transposons. These capabilities will facilitate the study and exploitation of the broad yet underexplored diversity of CRISPR-Cas systems and transposons.
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Affiliation(s)
- Franziska Wimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Ioannis Mougiakos
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Frank Englert
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany.
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10
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Romantseva EF, Tack DS, Alperovich N, Ross D, Strychalski EA. Best Practices for DNA Template Preparation Toward Improved Reproducibility in Cell-Free Protein Production. Methods Mol Biol 2022; 2433:3-50. [PMID: 34985735 DOI: 10.1007/978-1-0716-1998-8_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Performance variability is a common challenge in cell-free protein production and hinders a wider adoption of these systems for both research and biomanufacturing. While the inherent stochasticity and complexity of biology likely contributes to variability, other systematic factors may also play a role, including the source and preparation of the cell extract, the composition of the supplemental reaction buffer, the facility at which experiments are conducted, and the human operator (Cole et al. ACS Synth Biol 8:2080-2091, 2019). Variability in protein production could also arise from differences in the DNA template-specifically the amount of functional DNA added to a cell-free reaction and the quality of the DNA preparation in terms of contaminants and strand breakage. Here, we present protocols and suggest best practices optimized for DNA template preparation and quantitation for cell-free systems toward reducing variability in cell-free protein production.
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Affiliation(s)
| | - Drew S Tack
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nina Alperovich
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, MD, USA
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11
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Wimmer F, Englert F, Beisel CL. A TXTL-Based Assay to Rapidly Identify PAMs for CRISPR-Cas Systems with Multi-Protein Effector Complexes. Methods Mol Biol 2022; 2433:391-411. [PMID: 34985758 DOI: 10.1007/978-1-0716-1998-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Type I CRISPR-Cas systems represent the most common and diverse type of these prokaryotic defense systems and are being harnessed for a growing set of applications. As these systems rely on multi-protein effector complexes, their characterization remains challenging. Here, we report a rapid and straightforward method to characterize these systems in a cell-free transcription-translation (TXTL) system. A ribonucleoprotein complex is produced and binds to its target next to a recognized PAM, thereby preventing the targeted sequence from being cleaved by a restriction enzyme. Selection for uncleaved targeted plasmids leads to an enrichment of recognized sequences within a PAM library. This assay will aid the exploration of CRISPR-Cas diversity and evolution and help contribute new systems for CRISPR technologies and applications.
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Affiliation(s)
- Franziska Wimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Frank Englert
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany.
- Medical Faculty, University of Würzburg, Würzburg, Germany.
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12
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Garenne D, Thompson S, Brisson A, Khakimzhan A, Noireaux V. The all-E. coliTXTL toolbox 3.0: new capabilities of a cell-free synthetic biology platform. Synth Biol (Oxf) 2021; 6:ysab017. [PMID: 34712841 PMCID: PMC8546610 DOI: 10.1093/synbio/ysab017] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/19/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
The new generation of cell-free gene expression systems enables the prototyping and engineering of biological systems in vitro over a remarkable scope of applications and physical scales. As the utilization of DNA-directed in vitro protein synthesis expands in scope, developing more powerful cell-free transcription-translation (TXTL) platforms remains a major goal to either execute larger DNA programs or improve cell-free biomanufacturing capabilities. In this work, we report the capabilities of the all-E. coli TXTL toolbox 3.0, a multipurpose cell-free expression system specifically developed for synthetic biology. In non-fed batch-mode reactions, the synthesis of the fluorescent reporter protein eGFP (enhanced green fluorescent protein) reaches 4 mg/ml. In synthetic cells, consisting of liposomes loaded with a TXTL reaction, eGFP is produced at concentrations of >8 mg/ml when the chemical building blocks feeding the reaction diffuse through membrane channels to facilitate exchanges with the outer solution. The bacteriophage T7, encoded by a genome of 40 kb and ∼60 genes, is produced at a concentration of 1013 PFU/ml (plaque forming unit/ml). This TXTL system extends the current cell-free expression capabilities by offering unique strength and properties, for testing regulatory elements and circuits, biomanufacturing biologics or building synthetic cells.
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Affiliation(s)
- David Garenne
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Seth Thompson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Amaury Brisson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
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13
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McSweeney MA, Styczynski MP. Effective Use of Linear DNA in Cell-Free Expression Systems. Front Bioeng Biotechnol 2021; 9:715328. [PMID: 34354989 PMCID: PMC8329657 DOI: 10.3389/fbioe.2021.715328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/06/2021] [Indexed: 12/27/2022] Open
Abstract
Cell-free expression systems (CFEs) are cutting-edge research tools used in the investigation of biological phenomena and the engineering of novel biotechnologies. While CFEs have many benefits over in vivo protein synthesis, one particularly significant advantage is that CFEs allow for gene expression from both plasmid DNA and linear expression templates (LETs). This is an important and impactful advantage because functional LETs can be efficiently synthesized in vitro in a few hours without transformation and cloning, thus expediting genetic circuit prototyping and allowing expression of toxic genes that would be difficult to clone through standard approaches. However, native nucleases present in the crude bacterial lysate (the basis for the most affordable form of CFEs) quickly degrade LETs and limit expression yield. Motivated by the significant benefits of using LETs in lieu of plasmid templates, numerous methods to enhance their stability in lysate-based CFEs have been developed. This review describes approaches to LET stabilization used in CFEs, summarizes the advancements that have come from using LETs with these methods, and identifies future applications and development goals that are likely to be impactful to the field. Collectively, continued improvement of LET-based expression and other linear DNA tools in CFEs will help drive scientific discovery and enable a wide range of applications, from diagnostics to synthetic biology research tools.
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Affiliation(s)
- Megan A McSweeney
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
| | - Mark P Styczynski
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
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14
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Abstract
Cell-free protein synthesis is a powerful tool to produce recombinant proteins, and as an open system, can often integrate all or part of downstream assays. Here we describe in vitro synthesis of the Streptococcus pyogenes type II-A CRISPR-Cas9 ribonucleoproteins (SpCas9 RNPs), consisting of the effector protein and the single guide RNAs (sgRNAs). In spite of its large molecular weight (160kDa), the SpCas9 effector is expressed relatively well from linear DNA templates under T7 promoter in commercial reconstituted cell-free protein synthesis systems. sgRNAs can be added before the effector synthesis reaction, or transcribed directly from linear DNA templates during the synthesis reaction. The newly synthesized SpCas9 effector forms an active RNP complex with sgRNAs. When a reconstituted cell-free system is used, the target DNA templates can also be added in the reactions, thereby combining CRISPR-Cas synthesis and activity assay.
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Affiliation(s)
- Colin McGaw
- Arbor Biotechnologies, Cambridge, MA, United States
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15
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Aliaga Goltsman DS, Alexander LM, Devoto AE, Albers JB, Liu J, Butterfield CN, Brown CT, Thomas BC. Novel Type V-A CRISPR Effectors Are Active Nucleases with Expanded Targeting Capabilities. CRISPR J 2020; 3:454-461. [PMID: 33146573 PMCID: PMC7757703 DOI: 10.1089/crispr.2020.0043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Cas12a enzymes are quickly being adopted for use in a variety of genome-editing applications. These programmable nucleases are part of adaptive microbial immune systems, the natural diversity of which has been largely unexplored. Here, we identified novel families of Type V-A CRISPR nucleases through a large-scale analysis of metagenomes collected from a variety of complex environments, and developed representatives of these systems into gene-editing platforms. The nucleases display extensive protein variation and can be programmed by a single-guide RNA with specific motifs. The majority of these enzymes are part of systems recovered from uncultivated organisms, some of which also encode a divergent Type V effector. Biochemical analysis uncovered unexpected protospacer adjacent motif diversity, indicating that these systems will facilitate a variety of genome-engineering applications. The simplicity of guide sequences and activity in human cell lines suggest utility in gene and cell therapies.
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Affiliation(s)
| | | | | | | | - Jason Liu
- Metagenomi, Inc., Emeryville, California, USA
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16
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Jacobsen T, Ttofali F, Liao C, Manchalu S, Gray BN, Beisel CL. Characterization of Cas12a nucleases reveals diverse PAM profiles between closely-related orthologs. Nucleic Acids Res 2020; 48:5624-5638. [PMID: 32329776 PMCID: PMC7261169 DOI: 10.1093/nar/gkaa272] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems comprise diverse adaptive immune systems in prokaryotes whose RNA-directed nucleases have been co-opted for various technologies. Recent efforts have focused on expanding the number of known CRISPR-Cas subtypes to identify nucleases with novel properties. However, the functional diversity of nucleases within each subtype remains poorly explored. Here, we used cell-free transcription-translation systems and human cells to characterize six Cas12a single-effector nucleases from the V-A subtype, including nucleases sharing high sequence identity. While these nucleases readily utilized each other's guide RNAs, they exhibited distinct PAM profiles and apparent targeting activities that did not track based on phylogeny. In particular, two Cas12a nucleases encoded by Prevotella ihumii (PiCas12a) and Prevotella disiens (PdCas12a) shared over 95% amino-acid identity yet recognized distinct PAM profiles, with PiCas12a but not PdCas12a accommodating multiple G's in PAM positions -2 through -4 and T in position -1. Mutational analyses transitioning PiCas12a to PdCas12a resulted in PAM profiles distinct from either nuclease, allowing more flexible editing in human cells. Cas12a nucleases therefore can exhibit widely varying properties between otherwise related orthologs, suggesting selective pressure to diversify PAM recognition and supporting expansion of the CRISPR toolbox through ortholog mining and PAM engineering.
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Affiliation(s)
- Thomas Jacobsen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Fani Ttofali
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Chunyu Liao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Srinivas Manchalu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | | | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany.,Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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17
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Jacobsen T, Liao C, Beisel CL. The Acidaminococcus sp. Cas12a nuclease recognizes GTTV and GCTV as non-canonical PAMs. FEMS Microbiol Lett 2020; 366:5475644. [PMID: 31004485 DOI: 10.1093/femsle/fnz085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 04/19/2019] [Indexed: 12/19/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) nuclease Acidaminococcus sp. Cas12a (AsCas12a, also known as AsCpf1) has become a popular alternative to Cas9 for genome editing and other applications. AsCas12a has been associated with a TTTV protospacer-adjacent motif (PAM) as part of target recognition. Using a cell-free transcription-translation (TXTL)-based PAM screen, we discovered that AsCas12a can also recognize GTTV and, to a lesser degree, GCTV motifs. Validation experiments involving DNA cleavage in TXTL, plasmid clearance in Escherichia coli, and indel formation in mammalian cells showed that AsCas12a was able to recognize these motifs, with the GTTV motif resulting in higher cleavage efficiency compared to the GCTV motif. We also observed that the -5 position influenced the activity of DNA cleavage in TXTL and in E. coli, with a C at this position resulting in the lowest activity. Together, these results show that wild-type AsCas12a can recognize non-canonical GTTV and GCTV motifs and exemplify why the range of PAMs recognized by Cas nucleases are poorly captured with a consensus sequence.
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Affiliation(s)
- Thomas Jacobsen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Chunyu Liao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Josef-Schnedier-Str. 2, 97080 Würzburg, Germany
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Josef-Schnedier-Str. 2, 97080 Würzburg, Germany.,Medical Faculty, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
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18
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Reimann V, Ziemann M, Li H, Zhu T, Behler J, Lu X, Hess WR. Specificities and functional coordination between the two Cas6 maturation endonucleases in Anabaena sp. PCC 7120 assign orphan CRISPR arrays to three groups. RNA Biol 2020; 17:1442-1453. [PMID: 32453626 DOI: 10.1080/15476286.2020.1774197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many bacteria and archaea possess an RNA-guided adaptive and inheritable immune system that consists of clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. In most CRISPR-Cas systems, the maturation of CRISPR-derived small RNAs (crRNAs) is essential for functionality. Cas6 endonucleases function as the most frequent CRISPR RNA maturation enzymes. In the cyanobacterium Anabaena sp. PCC 7120, ten CRISPR loci are present, but only two cas gene cassettes plus a Tn7-associated eleventh array. In this study, we deleted the two cas6 genes alr1482 (Type III-D) or alr1566 (Type I-D) and tested the specificities of the two corresponding enzymes in the resulting mutant strains, as recombinant proteins and in a cell-free transcription-translation system. The results assign the direct repeats (DRs) to three different groups. While Alr1566 is specific for one group, Alr1482 has a higher preference for the DRs of the second group but can also cleave those of the first group. We found that this cross-recognition limits crRNA accumulation for the Type I-D system in vivo. We also show that the DR of the cas gene-free CRISPR array of cyanophage N-1 is processed by these enzymes, suggesting that it is fully competent in association with host-encoded Cas proteins. The data support the functionality of CRISPR arrays that frequently appear fragmented to multiple genomic loci in multicellular cyanobacteria and disfavour other possibilities, such as the nonfunctionality of these orphan repeat-spacer arrays. Our results show the functional coordination of Cas6 endonucleases with both neighbouring and remote repeat-spacer arrays in the CRISPR-Cas system of cyanobacteria.
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Affiliation(s)
- Viktoria Reimann
- Faculty of Biology, Institute of Biology III, University of Freiburg , Germany
| | - Marcus Ziemann
- Faculty of Biology, Institute of Biology III, University of Freiburg , Germany
| | - Hui Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences , Qingdao, China.,College of Life Sciences, University of Chinese Academy of Sciences , Beijing, China
| | - Tao Zhu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences , Qingdao, China
| | - Juliane Behler
- Faculty of Biology, Institute of Biology III, University of Freiburg , Germany
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences , Qingdao, China
| | - Wolfgang R Hess
- Faculty of Biology, Institute of Biology III, University of Freiburg , Germany
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19
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Fedorova I, Arseniev A, Selkova P, Pobegalov G, Goryanin I, Vasileva A, Musharova O, Abramova M, Kazalov M, Zyubko T, Artamonova T, Artamonova D, Shmakov S, Khodorkovskii M, Severinov K. DNA targeting by Clostridium cellulolyticum CRISPR-Cas9 Type II-C system. Nucleic Acids Res 2020; 48:2026-2034. [PMID: 31943070 PMCID: PMC7038990 DOI: 10.1093/nar/gkz1225] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 01/11/2023] Open
Abstract
Type II CRISPR-Cas9 RNA-guided nucleases are widely used for genome engineering. Type II-A SpCas9 protein from Streptococcus pyogenes is the most investigated and highly used enzyme of its class. Nevertheless, it has some drawbacks, including a relatively big size, imperfect specificity and restriction to DNA targets flanked by an NGG PAM sequence. Cas9 orthologs from other bacterial species may provide a rich and largely untapped source of biochemical diversity, which can help to overcome the limitations of SpCas9. Here, we characterize CcCas9, a Type II-C CRISPR nuclease from Clostridium cellulolyticum H10. We show that CcCas9 is an active endonuclease of comparatively small size that recognizes a novel two-nucleotide PAM sequence. The CcCas9 can potentially broaden the existing scope of biotechnological applications of Cas9 nucleases and may be particularly advantageous for genome editing of C. cellulolyticum H10, a bacterium considered to be a promising biofuel producer.
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Affiliation(s)
- Iana Fedorova
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Anatolii Arseniev
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Polina Selkova
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Georgii Pobegalov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Ignatiy Goryanin
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Aleksandra Vasileva
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Olga Musharova
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Marina Abramova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Maksim Kazalov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Tatyana Zyubko
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Tatyana Artamonova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Daria Artamonova
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Sergey Shmakov
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | | | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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20
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Agrawal DK, Marshall R, Noireaux V, Sontag ED. In vitro implementation of robust gene regulation in a synthetic biomolecular integral controller. Nat Commun 2019; 10:5760. [PMID: 31848346 PMCID: PMC6917713 DOI: 10.1038/s41467-019-13626-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 11/18/2019] [Indexed: 12/20/2022] Open
Abstract
Feedback mechanisms play a critical role in the maintenance of cell homeostasis in the presence of disturbances and uncertainties. Motivated by the need to tune the dynamics and improve the robustness of gene circuits, biological engineers have proposed various designs that mimic natural molecular feedback control mechanisms. However, practical and predictable implementations have proved challenging because of the complexity of synthesis and analysis of complex biomolecular networks. Here, we analyze and experimentally validate a synthetic biomolecular controller executed in vitro. The controller ensures that gene expression rate tracks an externally imposed reference level, and achieves this goal even in the presence of certain kinds of disturbances. Our design relies upon an analog of the well-known principle of integral feedback in control theory. We implement the controller in an Escherichia coli cell-free transcription-translation system, which allows rapid prototyping and implementation. Modeling and theory guide experimental implementation with well-defined operational predictability.
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Affiliation(s)
- Deepak K Agrawal
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Marshall
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Eduardo D Sontag
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA.
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston MA, USA.
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21
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Garenne D, Noireaux V. Cell-free transcription–translation: engineering biology from the nanometer to the millimeter scale. Curr Opin Biotechnol 2019; 58:19-27. [DOI: 10.1016/j.copbio.2018.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/14/2018] [Indexed: 01/01/2023]
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22
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Garenne D, Beisel CL, Noireaux V. Characterization of the all-E. coli transcription-translation system myTXTL by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1036-1048. [PMID: 30900355 DOI: 10.1002/rcm.8438] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 03/05/2019] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Cell-free transcription-translation (TXTL) is becoming a popular technology to prototype and engineer biological systems outside living organisms. TXTL relies commonly on a cytoplasmic extract that provides the molecular components necessary to recapitulate gene expression in vitro, where most of the available systems are derived from E. coli. The proteinic and enzymatic composition of lysates, however, is typically unknown. In this work, we analyzed by mass spectrometry the molecular constituents of the all-E. coli TXTL platform myTXTL prepared from the E. coli strain BL21 Rosetta2. METHODS Standard TXTL reactions were assembled and executed for 10-12 hours at 29°C. In addition to a no-DNA control, four DNA programs were executed in separate reactions to synthesize the reporter protein deGFP as well as the phages MS2, phix174 and T7. The reactions were treated according to standard procedures (trypsin treatment, cleaning) before performing liquid chromatography/mass spectrometry (LC/MS). Data analysis was performed using Sequest and protein identification using Scaffold. RESULTS A total of 500-800 proteins were identified by LC/MS in the blank reactions. We organized the most abundant protein sets into several categories pertaining, in particular, to transcription, translation and ATP regeneration. The synthesis of deGFP was easily measured. The major structural proteins that compose the three phages MS2, phix174 and T7 were also identified. CONCLUSIONS Mass spectrometry is a practical tool to characterize biochemical solutions as complex as a cell-free TXTL reaction and to determine the presence of synthesized proteins. The data presented demonstrate that the composition of TXTL based on lysates can be used to validate some underlying molecular mechanisms implicated in cell-free protein synthesis. The composition of the lysate shows significant differences with respect to similar studies on other E. coli strains.
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Affiliation(s)
- David Garenne
- School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN, 55455, USA
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection (HZI) Research, 97080, Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN, 55455, USA
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23
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24
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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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