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Dramé-Maigné A, Espada R, McCallum G, Sieskind R, Gines G, Rondelez Y. In Vitro Enzyme Self-Selection Using Molecular Programs. ACS Synth Biol 2024; 13:474-484. [PMID: 38206581 DOI: 10.1021/acssynbio.3c00385] [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: 01/12/2024]
Abstract
Directed evolution provides a powerful route for in vitro enzyme engineering. State-of-the-art techniques functionally screen up to millions of enzyme variants using high throughput microfluidic sorters, whose operation remains technically challenging. Alternatively, in vitro self-selection methods, analogous to in vivo complementation strategies, open the way to even higher throughputs, but have been demonstrated only for a few specific activities. Here, we leverage synthetic molecular networks to generalize in vitro compartmentalized self-selection processes. We introduce a programmable circuit architecture that can link an arbitrary target enzymatic activity to the replication of its encoding gene. Microencapsulation of a bacterial expression library with this autonomous selection circuit results in the single-step and screening-free enrichment of genetic sequences coding for programmed enzymatic phenotypes. We demonstrate the potential of this approach for the nicking enzyme Nt.BstNBI (NBI). We applied autonomous selection conditions to enrich for thermostability or catalytic efficiency, manipulating up to 107 microcompartments and 5 × 105 variants at once. Full gene reads of the libraries using nanopore sequencing revealed detailed mutational activity landscapes, suggesting a key role of electrostatic interactions with DNA in the enzyme's turnover. The most beneficial mutations, identified after a single round of self-selection, provided variants with, respectively, 20 times and 3 °C increased activity and thermostability. Based on a modular molecular programming architecture, this approach does not require complex instrumentation and can be repurposed for other enzymes, including those that are not related to DNA chemistry.
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Affiliation(s)
- Adèle Dramé-Maigné
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Rocío Espada
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Giselle McCallum
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Rémi Sieskind
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Guillaume Gines
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Yannick Rondelez
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
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2
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Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
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Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
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3
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Chaturvedi S, Pablo M, Wolf M, Rosas-Rivera D, Calia G, Kumar AJ, Vardi N, Du K, Glazier J, Ke R, Chan MF, Perelson AS, Weinberger LS. Disrupting autorepression circuitry generates "open-loop lethality" to yield escape-resistant antiviral agents. Cell 2022; 185:2086-2102.e22. [PMID: 35561685 PMCID: PMC9097017 DOI: 10.1016/j.cell.2022.04.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 03/01/2022] [Accepted: 04/14/2022] [Indexed: 12/27/2022]
Abstract
Across biological scales, gene-regulatory networks employ autorepression (negative feedback) to maintain homeostasis and minimize failure from aberrant expression. Here, we present a proof of concept that disrupting transcriptional negative feedback dysregulates viral gene expression to therapeutically inhibit replication and confers a high evolutionary barrier to resistance. We find that nucleic-acid decoys mimicking cis-regulatory sites act as "feedback disruptors," break homeostasis, and increase viral transcription factors to cytotoxic levels (termed "open-loop lethality"). Feedback disruptors against herpesviruses reduced viral replication >2-logs without activating innate immunity, showed sub-nM IC50, synergized with standard-of-care antivirals, and inhibited virus replication in mice. In contrast to approved antivirals where resistance rapidly emerged, no feedback-disruptor escape mutants evolved in long-term cultures. For SARS-CoV-2, disruption of a putative feedback circuit also generated open-loop lethality, reducing viral titers by >1-log. These results demonstrate that generating open-loop lethality, via negative-feedback disruption, may yield a class of antimicrobials with a high genetic barrier to resistance.
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Affiliation(s)
- Sonali Chaturvedi
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA.
| | - Michael Pablo
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Marie Wolf
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Daniel Rosas-Rivera
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Giuliana Calia
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Arjun J Kumar
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Noam Vardi
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Kelvin Du
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joshua Glazier
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Matilda F Chan
- Francis I. Proctor Foundation, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Leor S Weinberger
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
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4
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Nawimanage R, Yuan Z, Casares M, Joshi R, Lohman JR, Gimble FS. Structure-function studies of two yeast homing endonucleases that evolved to cleave identical targets with dissimilar rates and specificities. J Mol Biol 2022; 434:167550. [DOI: 10.1016/j.jmb.2022.167550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 10/18/2022]
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González Castro N, Bjelic J, Malhotra G, Huang C, Alsaffar SH. Comparison of the Feasibility, Efficiency, and Safety of Genome Editing Technologies. Int J Mol Sci 2021; 22:10355. [PMID: 34638696 PMCID: PMC8509008 DOI: 10.3390/ijms221910355] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 08/26/2021] [Accepted: 09/24/2021] [Indexed: 12/15/2022] Open
Abstract
Recent advances in programmable nucleases including meganucleases (MNs), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) have propelled genome editing from explorative research to clinical and industrial settings. Each technology, however, features distinct modes of action that unevenly impact their applicability across the entire genome and are often tested under significantly different conditions. While CRISPR-Cas is currently leading the field due to its versatility, quick adoption, and high degree of support, it is not without limitations. Currently, no technology can be regarded as ideal or even applicable to every case as the context dictates the best approach for genetic modification within a target organism. In this review, we implement a four-pillar framework (context, feasibility, efficiency, and safety) to assess the main genome editing platforms, as a basis for rational decision-making by an expanding base of users, regulators, and consumers. Beyond carefully considering their specific use case with the assessment framework proposed here, we urge stakeholders interested in genome editing to independently validate the parameters of their chosen platform prior to commitment. Furthermore, safety across all applications, particularly in clinical settings, is a paramount consideration and comprehensive off-target detection strategies should be incorporated within workflows to address this. Often neglected aspects such as immunogenicity and the inadvertent selection of mutants deficient for DNA repair pathways must also be considered.
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Affiliation(s)
- Nicolás González Castro
- School of Biosciences, Faculty of Science, University of Melbourne, Parkville 3052, Australia; (N.G.C.); (G.M.); (C.H.); (S.H.A.)
| | - Jan Bjelic
- School of Biosciences, Faculty of Science, University of Melbourne, Parkville 3052, Australia; (N.G.C.); (G.M.); (C.H.); (S.H.A.)
| | - Gunya Malhotra
- School of Biosciences, Faculty of Science, University of Melbourne, Parkville 3052, Australia; (N.G.C.); (G.M.); (C.H.); (S.H.A.)
| | - Cong Huang
- School of Biosciences, Faculty of Science, University of Melbourne, Parkville 3052, Australia; (N.G.C.); (G.M.); (C.H.); (S.H.A.)
| | - Salman Hasan Alsaffar
- School of Biosciences, Faculty of Science, University of Melbourne, Parkville 3052, Australia; (N.G.C.); (G.M.); (C.H.); (S.H.A.)
- Biotechnology Department, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Shuwaikh 13109, Kuwait
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6
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Bouzetos E, Ganar KA, Mastrobattista E, Deshpande S, van der Oost J. (R)evolution-on-a-chip. Trends Biotechnol 2021; 40:60-76. [PMID: 34049723 DOI: 10.1016/j.tibtech.2021.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 01/17/2023]
Abstract
Billions of years of Darwinian evolution has led to the emergence of highly sophisticated and diverse life forms on Earth. Inspired by natural evolution, similar principles have been adopted in laboratory evolution for the fast optimization of genes and proteins for specific applications. In this review, we highlight state-of-the-art laboratory evolution strategies for protein engineering, with a special emphasis on in vitro strategies. We further describe how recent progress in microfluidic technology has allowed the generation and manipulation of artificial compartments for high-throughput laboratory evolution experiments. Expectations for the future are high: we foresee a revolution on-a-chip.
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Affiliation(s)
- Evgenios Bouzetos
- Laboratory of Microbiology, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands
| | - Ketan Ashok Ganar
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands
| | - Enrico Mastrobattista
- Pharmaceutics Division, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Siddharth Deshpande
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands.
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands.
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7
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Mckay A, Burgio G. Harnessing CRISPR-Cas system diversity for gene editing technologies. J Biomed Res 2021; 35:91-106. [PMID: 33797415 PMCID: PMC8038530 DOI: 10.7555/jbr.35.20200184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The discovery and utilization of RNA-guided surveillance complexes, such as CRISPR-Cas9, for sequence-specific DNA or RNA cleavage, has revolutionised the process of gene modification or knockdown. To optimise the use of this technology, an exploratory race has ensued to discover or develop new RNA-guided endonucleases with the most flexible sequence targeting requirements, coupled with high cleavage efficacy and specificity. Here we review the constraints of existing gene editing and assess the merits of exploiting the diversity of CRISPR-Cas effectors as a methodology for surmounting these limitations.
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Affiliation(s)
- Alexander Mckay
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
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8
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Lindenburg L, Huovinen T, van de Wiel K, Herger M, Snaith MR, Hollfelder F. Split & mix assembly of DNA libraries for ultrahigh throughput on-bead screening of functional proteins. Nucleic Acids Res 2020; 48:e63. [PMID: 32383757 PMCID: PMC7293038 DOI: 10.1093/nar/gkaa270] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/02/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022] Open
Abstract
Site-saturation libraries reduce protein screening effort in directed evolution campaigns by focusing on a limited number of rationally chosen residues. However, uneven library synthesis efficiency leads to amino acid bias, remedied at high cost by expensive custom synthesis of oligonucleotides, or through use of proprietary library synthesis platforms. To address these shortcomings, we have devised a method where DNA libraries are constructed on the surface of microbeads by ligating dsDNA fragments onto growing, surface-immobilised DNA, in iterative split-and-mix cycles. This method-termed SpliMLiB for Split-and-Mix Library on Beads-was applied towards the directed evolution of an anti-IgE Affibody (ZIgE), generating a 160,000-membered, 4-site, saturation library on the surface of 8 million monoclonal beads. Deep sequencing confirmed excellent library balance (5.1% ± 0.77 per amino acid) and coverage (99.3%). As SpliMLiB beads are monoclonal, they were amenable to direct functional screening in water-in-oil emulsion droplets with cell-free expression. A FACS-based sorting of the library beads allowed recovery of hits improved in Kd over wild-type ZIgE by up to 3.5-fold, while a consensus mutant of the best hits provided a 10-fold improvement. With SpliMLiB, directed evolution workflows are accelerated by integrating high-quality DNA library generation with an ultra-high throughput protein screening platform.
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Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Tuomas Huovinen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Kayleigh van de Wiel
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Michael Herger
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
- AstraZeneca Medimmune Cambridge, Antibody Discovery and Protein Engineering, Cambridge, UK
| | - Michael R Snaith
- AstraZeneca Medimmune Cambridge, Antibody Discovery and Protein Engineering, Cambridge, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
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9
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Maule G, Arosio D, Cereseto A. Gene Therapy for Cystic Fibrosis: Progress and Challenges of Genome Editing. Int J Mol Sci 2020; 21:E3903. [PMID: 32486152 PMCID: PMC7313467 DOI: 10.3390/ijms21113903] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 02/07/2023] Open
Abstract
Since the early days of its conceptualization and application, human gene transfer held the promise of a permanent solution to genetic diseases including cystic fibrosis (CF). This field went through alternated periods of enthusiasm and distrust. The development of refined technologies allowing site specific modification with programmable nucleases highly revived the gene therapy field. CRISPR nucleases and derived technologies tremendously facilitate genome manipulation offering diversified strategies to reverse mutations. Here we discuss the advancement of gene therapy, from therapeutic nucleic acids to genome editing techniques, designed to reverse genetic defects in CF. We provide a roadmap through technologies and strategies tailored to correct different types of mutations in the cystic fibrosis transmembrane regulator (CFTR) gene, and their applications for the development of experimental models valuable for the advancement of CF therapies.
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Affiliation(s)
- Giulia Maule
- Department of Cellular Computational Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy;
- National Council of Research, CNR, 38123 Trento, Italy;
| | | | - Anna Cereseto
- Department of Cellular Computational Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy;
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10
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Laforet M, McMurrough TA, Vu M, Brown CM, Zhang K, Junop MS, Gloor GB, Edgell DR. Modifying a covarying protein-DNA interaction changes substrate preference of a site-specific endonuclease. Nucleic Acids Res 2019; 47:10830-10841. [PMID: 31602462 PMCID: PMC6847045 DOI: 10.1093/nar/gkz866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/17/2019] [Accepted: 10/09/2019] [Indexed: 12/23/2022] Open
Abstract
Identifying and validating intermolecular covariation between proteins and their DNA-binding sites can provide insights into mechanisms that regulate selectivity and starting points for engineering new specificity. LAGLIDADG homing endonucleases (meganucleases) can be engineered to bind non-native target sites for gene-editing applications, but not all redesigns successfully reprogram specificity. To gain a global overview of residues that influence meganuclease specificity, we used information theory to identify protein-DNA covariation. Directed evolution experiments of one predicted pair, 227/+3, revealed variants with surprising shifts in I-OnuI substrate preference at the central 4 bases where cleavage occurs. Structural studies showed significant remodeling distant from the covarying position, including restructuring of an inter-hairpin loop, DNA distortions near the scissile phosphates, and new base-specific contacts. Our findings are consistent with a model whereby the functional impacts of covariation can be indirectly propagated to neighboring residues outside of direct contact range, allowing meganucleases to adapt to target site variation and indirectly expand the sequence space accessible for cleavage. We suggest that some engineered meganucleases may have unexpected cleavage profiles that were not rationally incorporated during the design process.
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Affiliation(s)
- Marc Laforet
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Thomas A McMurrough
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Michael Vu
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Christopher M Brown
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Kun Zhang
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Murray S Junop
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Gregory B Gloor
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
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11
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McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR. Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases. Nucleic Acids Res 2019; 46:11990-12007. [PMID: 30357419 PMCID: PMC6294521 DOI: 10.1093/nar/gky976] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/05/2018] [Indexed: 12/30/2022] Open
Abstract
LAGLIDADG homing endonucleases (meganucleases) are site-specific mobile endonucleases that can be adapted for genome-editing applications. However, one problem when reprogramming meganucleases on non-native substrates is indirect readout of DNA shape and flexibility at the central 4 bases where cleavage occurs. To understand how the meganuclease active site regulates DNA cleavage, we used functional selections and deep sequencing to profile the fitness landscape of 1600 I-LtrI and I-OnuI active site variants individually challenged with 67 substrates with central 4 base substitutions. The wild-type active site was not optimal for cleavage on many substrates, including the native I-LtrI and I-OnuI targets. Novel combinations of active site residues not observed in known meganucleases supported activity on substrates poorly cleaved by the wild-type enzymes. Strikingly, combinations of E or D substitutions in the two metal-binding residues greatly influenced cleavage activity, and E184D variants had a broadened cleavage profile. Analyses of I-LtrI E184D and the wild-type proteins co-crystallized with the non-cognate AACC central 4 sequence revealed structural differences that correlated with kinetic constants for cleavage of individual DNA strands. Optimizing meganuclease active sites to enhance cleavage of non-native central 4 target sites is a straightforward addition to engineering workflows that will expand genome-editing applications.
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Affiliation(s)
- Thomas A McMurrough
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Christopher M Brown
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Kun Zhang
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
| | - Murray S Junop
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Gregory B Gloor
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
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12
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Porter SN, Levine RM, Pruett-Miller SM. A Practical Guide to Genome Editing Using Targeted Nuclease Technologies. Compr Physiol 2019; 9:665-714. [PMID: 30873595 DOI: 10.1002/cphy.c180022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome engineering using programmable nucleases is a rapidly evolving technique that enables precise genetic manipulations within complex genomes. Although this technology first surfaced with the creation of meganucleases, zinc finger nucleases, and transcription activator-like effector nucleases, CRISPR-Cas9 has been the most widely adopted platform because of its ease of use. This comprehensive review presents a basic overview of genome engineering and discusses the major technological advances in the field. In addition to nucleases, we discuss CRISPR-derived base editors and epigenetic modifiers. We also delve into practical applications of these tools, including creating custom-edited cell and animal models as well as performing genetic screens. Finally, we discuss the potential for therapeutic applications and ethical considerations related to employing this technology in humans. © 2019 American Physiological Society. Compr Physiol 9:665-714, 2019.
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Affiliation(s)
- Shaina N Porter
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rachel M Levine
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shondra M Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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13
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Contreras-Llano LE, Tan C. High-throughput screening of biomolecules using cell-free gene expression systems. Synth Biol (Oxf) 2018; 3:ysy012. [PMID: 32995520 PMCID: PMC7445777 DOI: 10.1093/synbio/ysy012] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/31/2018] [Accepted: 06/25/2018] [Indexed: 01/13/2023] Open
Abstract
The incorporation of cell-free transcription and translation systems into high-throughput screening applications enables the in situ and on-demand expression of peptides and proteins. Coupled with modern microfluidic technology, the cell-free methods allow the screening, directed evolution and selection of desired biomolecules in minimal volumes within a short timescale. Cell-free high-throughput screening applications are classified broadly into in vitro display and on-chip technologies. In this review, we outline the development of cell-free high-throughput screening methods. We further discuss operating principles and representative applications of each screening method. The cell-free high-throughput screening methods may be advanced by the future development of new cell-free systems, miniaturization approaches, and automation technologies.
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Affiliation(s)
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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14
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Bogdanove AJ, Bohm A, Miller JC, Morgan RD, Stoddard BL. Engineering altered protein-DNA recognition specificity. Nucleic Acids Res 2018; 46:4845-4871. [PMID: 29718463 PMCID: PMC6007267 DOI: 10.1093/nar/gky289] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 02/07/2023] Open
Abstract
Protein engineering is used to generate novel protein folds and assemblages, to impart new properties and functions onto existing proteins, and to enhance our understanding of principles that govern protein structure. While such approaches can be employed to reprogram protein-protein interactions, modifying protein-DNA interactions is more difficult. This may be related to the structural features of protein-DNA interfaces, which display more charged groups, directional hydrogen bonds, ordered solvent molecules and counterions than comparable protein interfaces. Nevertheless, progress has been made in the redesign of protein-DNA specificity, much of it driven by the development of engineered enzymes for genome modification. Here, we summarize the creation of novel DNA specificities for zinc finger proteins, meganucleases, TAL effectors, recombinases and restriction endonucleases. The ease of re-engineering each system is related both to the modularity of the protein and the extent to which the proteins have evolved to be capable of readily modifying their recognition specificities in response to natural selection. The development of engineered DNA binding proteins that display an ideal combination of activity, specificity, deliverability, and outcomes is not a fully solved problem, however each of the current platforms offers unique advantages, offset by behaviors and properties requiring further study and development.
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Affiliation(s)
- Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Bohm
- Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Jeffrey C Miller
- Sangamo Therapeutics Inc. 501 Canal Blvd., Richmond, CA 94804, USA
| | - Richard D Morgan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98019, USA
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15
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Guha TK, Edgell DR. Applications of Alternative Nucleases in the Age of CRISPR/Cas9. Int J Mol Sci 2017; 18:ijms18122565. [PMID: 29186020 PMCID: PMC5751168 DOI: 10.3390/ijms18122565] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 01/10/2023] Open
Abstract
Breakthroughs in the development of programmable site-specific nucleases, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), meganucleases (MNs), and most recently, the clustered regularly interspaced short palindromic repeats (CRISPR) associated proteins (including Cas9) have greatly enabled and accelerated genome editing. By targeting double-strand breaks to user-defined locations, the rates of DNA repair events are greatly enhanced relative to un-catalyzed events at the same sites. However, the underlying biology of each genome-editing nuclease influences the targeting potential, the spectrum of off-target cleavages, the ease-of-use, and the types of recombination events at targeted double-strand breaks. No single genome-editing nuclease is optimized for all possible applications. Here, we focus on the diversity of nuclease domains available for genome editing, highlighting biochemical properties and the potential applications that are best suited to each domain.
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Affiliation(s)
- Tuhin K Guha
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada.
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada.
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16
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Macias VM, Ohm JR, Rasgon JL. Gene Drive for Mosquito Control: Where Did It Come from and Where Are We Headed? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14091006. [PMID: 28869513 PMCID: PMC5615543 DOI: 10.3390/ijerph14091006] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 02/08/2023]
Abstract
Mosquito-borne pathogens place an enormous burden on human health. The existing toolkit is insufficient to support ongoing vector-control efforts towards meeting disease elimination and eradication goals. The perspective that genetic approaches can potentially add a significant set of tools toward mosquito control is not new, but the recent improvements in site-specific gene editing with CRISPR/Cas9 systems have enhanced our ability to both study mosquito biology using reverse genetics and produce genetics-based tools. Cas9-mediated gene-editing is an efficient and adaptable platform for gene drive strategies, which have advantages over innundative release strategies for introgressing desirable suppression and pathogen-blocking genotypes into wild mosquito populations; until recently, an effective gene drive has been largely out of reach. Many considerations will inform the effective use of new genetic tools, including gene drives. Here we review the lengthy history of genetic advances in mosquito biology and discuss both the impact of efficient site-specific gene editing on vector biology and the resulting potential to deploy new genetic tools for the abatement of mosquito-borne disease.
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Affiliation(s)
- Vanessa M Macias
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Johanna R Ohm
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA.
| | - Jason L Rasgon
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA.
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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17
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Affiliation(s)
| | - Michael J. Wade
- Department of Biology; Indiana University; Bloomington IN USA
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18
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Werther R, Hallinan JP, Lambert AR, Havens K, Pogson M, Jarjour J, Galizi R, Windbichler N, Crisanti A, Nolan T, Stoddard BL. Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity. Nucleic Acids Res 2017; 45:8621-8634. [PMID: 28637173 PMCID: PMC5737575 DOI: 10.1093/nar/gkx544] [Citation(s) in RCA: 11] [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: 04/27/2017] [Revised: 06/02/2017] [Accepted: 06/12/2017] [Indexed: 12/11/2022] Open
Abstract
The retargeting of protein-DNA specificity, outside of extremely modular DNA binding proteins such as TAL effectors, has generally proved to be quite challenging. Here, we describe structural analyses of five different extensively retargeted variants of a single homing endonuclease, that have been shown to function efficiently in ex vivo and in vivo applications. The redesigned proteins harbor mutations at up to 53 residues (18%) of their amino acid sequence, primarily distributed across the DNA binding surface, making them among the most significantly reengineered ligand-binding proteins to date. Specificity is derived from the combined contributions of DNA-contacting residues and of neighboring residues that influence local structural organization. Changes in specificity are facilitated by the ability of all those residues to readily exchange both form and function. The fidelity of recognition is not precisely correlated with the fraction or total number of residues in the protein-DNA interface that are actually involved in DNA contacts, including directional hydrogen bonds. The plasticity of the DNA-recognition surface of this protein, which allows substantial retargeting of recognition specificity without requiring significant alteration of the surrounding protein architecture, reflects the ability of the corresponding genetic elements to maintain mobility and persistence in the face of genetic drift within potential host target sites.
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Affiliation(s)
- Rachel Werther
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Jazmine P. Hallinan
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Abigail R. Lambert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Kyle Havens
- Bluebird Bio Inc., Suite 207 1616 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Mark Pogson
- Bluebird Bio Inc., Suite 207 1616 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Jordan Jarjour
- Bluebird Bio Inc., Suite 207 1616 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Roberto Galizi
- Imperial College of London, Department of Life Sciences, South Kensington Campus, London SW7 2AZ, UK
| | - Nikolai Windbichler
- Imperial College of London, Department of Life Sciences, South Kensington Campus, London SW7 2AZ, UK
| | - Andrea Crisanti
- Imperial College of London, Department of Life Sciences, South Kensington Campus, London SW7 2AZ, UK
| | - Tony Nolan
- Imperial College of London, Department of Life Sciences, South Kensington Campus, London SW7 2AZ, UK
| | - Barry L. Stoddard
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
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19
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Niyonzima N, Lambert AR, Werther R, De Silva Feelixge H, Roychoudhury P, Greninger AL, Stone D, Stoddard BL, Jerome KR. Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses. Protein Eng Des Sel 2017; 30:503-522. [PMID: 28873986 PMCID: PMC5914421 DOI: 10.1093/protein/gzx037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/19/2017] [Accepted: 07/06/2017] [Indexed: 11/14/2022] Open
Abstract
The combination of yeast surface display and flow cytometric analyses and selections is being used with increasing frequency to alter specificity of macromolecular recognition, including both protein-protein and protein-nucleic acid interactions. Here we describe the use of yeast surface display and cleavage-dependent flow cytometric assays to increase the specificity of an engineered meganuclease. The re-engineered meganuclease displays a significantly tightened specificity profile, while binding its cognate target site with a slightly lower, but still sub-nanomolar affinity. When incorporated into otherwise identical megaTAL protein scaffolds, these two nucleases display significantly different activity and toxicity profiles in cellulo. The structural basis for reprogrammed DNA cleavage specificity was further examined via high-resolution X-ray crystal structures of both enzymes. This analysis illustrated the altered protein-DNA contacts produced by mutagenesis and selection, that resulted both in altered readout of those based and a necessary reduction in DNA binding affinity that were necessary to improve specificity across the target site. The results of this study provide an illustrative example of the potential (and the challenges) associated with the use of surface display and flow cytometry for the retargeting and optimization of enzymes that act on nucleic acid substrates in a sequence-specific manner.
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Affiliation(s)
- Nixon Niyonzima
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Abigail R. Lambert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Rachel Werther
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Harshana De Silva Feelixge
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Alexander L. Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
- Virology Division, Department of Laboratory Medicine, University of Washington, 1616 Eastlake Ave. E, Seattle WA 98102, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Barry L. Stoddard
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
- Virology Division, Department of Laboratory Medicine, University of Washington, 1616 Eastlake Ave. E, Seattle WA 98102, USA
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20
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Bilto IM, Guha TK, Wai A, Hausner G. Three new active members of the I-OnuI family of homing endonucleases. Can J Microbiol 2017; 63:671-681. [PMID: 28414922 DOI: 10.1139/cjm-2017-0067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In vitro characterization of 3 LAGLIDADG-type homing endonucleases (HEs) (I-CcaI, I-CcaII, and I-AstI) that belong to the I-OnuI family showed that they are functional HEs that cleave their respective cognate target sites. These endonucleases are encoded within group ID introns and appear to be orthologues that have inserted into 3 different mitochondrial genes: rns, rnl, and cox3. The endonuclease activity of I-CcaI was tested using various substrates, and its minimum DNA recognition sequence was estimated to be 26 nt. This set of HEs may provide some insight into how these types of mobile elements can migrate into new locations. This study provides additional endonucleases that can be added to the catalog of currently available HEs that may have various biotechnology applications.
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Affiliation(s)
- Iman M Bilto
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Tuhin K Guha
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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21
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Calos MP. Genome Editing Techniques and Their Therapeutic Applications. Clin Pharmacol Ther 2016; 101:42-51. [PMID: 27783398 DOI: 10.1002/cpt.542] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 12/13/2022]
Abstract
Fueled by advances in the field of genetics, the methods available to edit DNA sequences in living cells have continued to develop steadily. These technologies directly impact the fields of gene and cell therapy, where changes in the DNA sequence of target cells offer a route to correct genetic diseases and manipulate disorders like cancer. We review here the expanding menu of genome editing techniques and how they are being applied to therapeutic targets. The methods encompass a myriad of approaches to modify the covalent structure of DNA, including the targeted creation of double-strand breaks that can catalyze genomic changes, as well as the use of retroviruses and transposons to mediate gene addition, recombinases for sequence-specific gene addition and deletion, and base repair for direct sequence changes. The continued growth of the exciting field of genome editing is opening new possibilities for therapeutic intervention.
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Affiliation(s)
- M P Calos
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
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22
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Chemical Biology Approaches to Genome Editing: Understanding, Controlling, and Delivering Programmable Nucleases. Cell Chem Biol 2016; 23:57-73. [PMID: 26933736 DOI: 10.1016/j.chembiol.2015.12.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 12/28/2015] [Accepted: 12/29/2015] [Indexed: 12/15/2022]
Abstract
Programmable DNA nucleases have provided scientists with the unprecedented ability to probe, regulate, and manipulate the human genome. Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeat-Cas9 system (CRISPR-Cas9) represent a powerful array of tools that can bind to and cleave a specified DNA sequence. In their canonical forms, these nucleases induce double-strand breaks at a DNA locus of interest that can trigger cellular DNA repair processes that disrupt or replace genes. The fusion of these programmable nucleases with a variety of other protein domains has led to a rapidly growing suite of tools for activating, repressing, visualizing, and modifying loci of interest. Maximizing the usefulness and therapeutic relevance of these tools, however, requires precisely controlling their activity and specificity to minimize potentially toxic side effects arising from off-target activities. This need has motivated the application of chemical biology principles and methods to genome-editing proteins, including the engineering of variants of these proteins with improved or altered specificities, and the development of genetic, chemical, optical, and protein delivery methods that control the activity of these agents in cells. Advancing the capabilities, safety, effectiveness, and therapeutic relevance of genome-engineering proteins will continue to rely on chemical biology strategies that manipulate their activity, specificity, and localization.
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23
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Yee JK. Off-target effects of engineered nucleases. FEBS J 2016; 283:3239-48. [PMID: 27208701 DOI: 10.1111/febs.13760] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 05/09/2016] [Accepted: 05/18/2016] [Indexed: 12/26/2022]
Abstract
Recent advances in gene editing with engineered nucleases have transformed our ability to manipulate the genome from diverse organisms for applications ranging from biomedical research to disease treatment. A major complication with these engineered nucleases is the binding of the nuclease to unintended genomic sites that share sequence homology with the on-target site. Cleavage of these off-target sites followed by DNA repair using normal cellular DNA repair mechanisms can cause gene mutation or gross chromosome rearrangement. Identification of nuclease-generated off-target sites is a daunting task due to the size and complexity of the mammalian genome. Five unbiased, genome-wide strategies have been developed to detect the off-target cleavage. Some of these strategies reach the sensitivity near the detection limit of directed deep sequencing and have sufficient precision and resolution to objectively assessing the off-target effect of any engineered nuclease. Significant progress has also been made recently to boost the nuclease targeting specificity by protein engineering to modify the structure of the nuclease and alter the interaction with its genomic target. In several studied cases, the off-target effect generated by the modified nuclease is completely eliminated. These modified nucleases significantly improve the overall fidelity of gene editing. These developments will enable gene editing tools to be applied more broadly and safely in basic research and disease treatment.
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Affiliation(s)
- Jiing-Kuan Yee
- Department of Diabetes and Metabolic Diseases Research, City of Hope National Medical Center, Duarte, CA, USA
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24
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Jasin M, Haber JE. The democratization of gene editing: Insights from site-specific cleavage and double-strand break repair. DNA Repair (Amst) 2016; 44:6-16. [PMID: 27261202 DOI: 10.1016/j.dnarep.2016.05.001] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA double-strand breaks (DSBs) are dangerous lesions that if not properly repaired can lead to genomic change or cell death. Organisms have developed several pathways and have many factors devoted to repairing DSBs, which broadly occurs by homologous recombination, which relies on an identical or homologous sequence to template repair, or nonhomologous end-joining. Much of our understanding of these repair mechanisms has come from the study of induced DNA cleavage by site-specific endonucleases. In addition to their biological role, these cellular pathways can be co-opted for gene editing to study gene function or for gene therapy or other applications. While the first gene editing experiments were done more than 20 years ago, the recent discovery of RNA-guided endonucleases has simplified approaches developed over the years to make gene editing an approach that is available to the entire biomedical research community. Here, we review DSB repair mechanisms and site-specific cleavage systems that have provided insight into these mechanisms and led to the current gene editing revolution.
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Affiliation(s)
- Maria Jasin
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 02454-9110, USA.
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25
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Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM, Stoddard BL. Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity. Structure 2016; 24:862-73. [PMID: 27133026 DOI: 10.1016/j.str.2016.03.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/07/2016] [Accepted: 03/21/2016] [Indexed: 11/29/2022]
Abstract
LAGLIDADG meganucleases are DNA cleaving enzymes used for genome engineering. While their cleavage specificity can be altered using several protein engineering and selection strategies, their overall targetability is limited by highly specific indirect recognition of the central four base pairs within their recognition sites. In order to examine the physical basis of indirect sequence recognition and to expand the number of such nucleases available for genome engineering, we have determined the target sites, DNA-bound structures, and central four cleavage fidelities of nine related enzymes. Subsequent crystallographic analyses of a meganuclease bound to two noncleavable target sites, each containing a single inactivating base pair substitution at its center, indicates that a localized slip of the mutated base pair causes a small change in the DNA backbone conformation that results in a loss of metal occupancy at one binding site, eliminating cleavage activity.
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Affiliation(s)
- Abigail R Lambert
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA
| | - Jazmine P Hallinan
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA
| | - Betty W Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA
| | - Jennifer K Chik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA
| | - Jill M Bolduc
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA
| | - Nadia Kulshina
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA
| | - Lori I Robins
- Physical Sciences Division, School of STEM, University of Washington, 18115 Campus Way Northeast, Bothell, WA 98011, USA
| | - Brett K Kaiser
- Department of Biology, Seattle University, 901 12th Avenue, Seattle, WA 98122, USA
| | - Jordan Jarjour
- bluebird bio Inc. Suite 207, 1616 Eastlake Avenue East, Seattle, WA 98102, USA
| | - Kyle Havens
- bluebird bio Inc. Suite 207, 1616 Eastlake Avenue East, Seattle, WA 98102, USA
| | - Andrew M Scharenberg
- Seattle Children's Research Institute, 1900 Ninth Avenue, Seattle, WA 98101, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA.
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26
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Reid W, O'Brochta DA. Applications of genome editing in insects. CURRENT OPINION IN INSECT SCIENCE 2016; 13:43-54. [PMID: 27436552 DOI: 10.1016/j.cois.2015.11.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/23/2015] [Accepted: 11/01/2015] [Indexed: 05/14/2023]
Abstract
Insect genome editing was first reported 1991 in Drosophila melanogaster but the technology used was not portable to other species. Not until the recent development of facile, engineered DNA endonuclease systems has gene editing become widely available to insect scientists. Most applications in insects to date have been technical in nature but this is rapidly changing. Functional genomics and genetics-based insect control efforts will be major beneficiaries of the application of contemporary gene editing technologies. Engineered endonucleases like Cas9 make it possible to create powerful and effective gene drive systems that could be used to reduce or even eradicate specific insect populations. 'Best practices' for using Cas9-based editing are beginning to emerge making it easier and more effective to design and use but gene editing technologies still require traditional means of delivery in order to introduce them into somatic and germ cells of insects-microinjection of developing embryos. This constrains the use of these technologies by insect scientists. Insects created using editing technologies challenge existing governmental regulatory structures designed to manage genetically modified organisms.
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Affiliation(s)
- William Reid
- Institute for Bioscience and Biotechnology Research, Department of Entomology, University of Maryland, College Park, 9600 Gudelsky Drive, Rockville, MD 20850, United States
| | - David A O'Brochta
- Institute for Bioscience and Biotechnology Research, Department of Entomology, University of Maryland, College Park, 9600 Gudelsky Drive, Rockville, MD 20850, United States.
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27
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Salient Features of Endonuclease Platforms for Therapeutic Genome Editing. Mol Ther 2016; 24:422-9. [PMID: 26796671 DOI: 10.1038/mt.2016.21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/07/2016] [Indexed: 12/11/2022] Open
Abstract
Emerging gene-editing technologies are nearing a revolutionary phase in genetic medicine: precisely modifying or repairing causal genetic defects. This may include any number of DNA sequence manipulations, such as knocking out a deleterious gene, introducing a particular mutation, or directly repairing a defective sequence by site-specific recombination. All of these edits can currently be achieved via programmable rare-cutting endonucleases to create targeted DNA breaks that can engage and exploit endogenous DNA repair pathways to impart site-specific genetic changes. Over the past decade, several distinct technologies for introducing site-specific DNA breaks have been developed, yet the different biological origins of these gene-editing technologies bring along inherent differences in parameters that impact clinical implementation. This review aims to provide an accessible overview of the various endonuclease-based gene-editing platforms, highlighting the strengths and weakness of each with respect to therapeutic applications.
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28
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29
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Abstract
The development of a facile genome engineering technology based on transcription activator-like effector nucleases (TALENs) has led to significant advances in diverse areas of science and medicine. In this review, we provide a broad overview of the development of TALENs and the use of this technology in basic science, biotechnology, and biomedical applications. This includes the discovery of DNA recognition by TALEs, engineering new TALE proteins to diverse targets, general advances in nuclease-based editing strategies, and challenges that are specific to various applications of the TALEN technology. We review examples of applying TALENs for studying gene function and regulation, generating disease models, and developing gene therapies. The current status of genome editing and future directions for other uses of these technologies are also discussed.
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Affiliation(s)
- David G Ousterout
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Room 136 Hudson Hall, Box 90281, Durham, NC, 27708-0281, USA. .,Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA. .,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
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30
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DiCarlo JE, Chavez A, Dietz SL, Esvelt KM, Church GM. Safeguarding CRISPR-Cas9 gene drives in yeast. Nat Biotechnol 2015; 33:1250-1255. [PMID: 26571100 PMCID: PMC4675690 DOI: 10.1038/nbt.3412] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 10/19/2015] [Indexed: 01/07/2023]
Abstract
RNA-guided gene drives capable of spreading genomic alterations made in laboratory organisms through wild populations could be used to address environmental and public health problems. However, the possibility of unintended genome editing occurring through the escape of strains from laboratories, coupled with the prospect of unanticipated ecological change, demands caution. We report the efficacy of CRISPR-Cas9 gene drive systems in wild and laboratory strains of the yeast Saccharomyces cerevisiae. Furthermore, we address concerns surrounding accidental genome editing by developing and validating methods of molecular confinement that minimize the risk of unwanted genome editing. We also present a drive system capable of overwriting the changes introduced by an earlier gene drive. These molecular safeguards should enable the development of safe CRISPR gene drives for diverse organisms.
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Affiliation(s)
- James E DiCarlo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Alejandro Chavez
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sven L Dietz
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA.,Department for Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Kevin M Esvelt
- Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
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31
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Abstract
Directed evolution has proved to be an effective strategy for improving or altering the activity of biomolecules for industrial, research and therapeutic applications. The evolution of proteins in the laboratory requires methods for generating genetic diversity and for identifying protein variants with desired properties. This Review describes some of the tools used to diversify genes, as well as informative examples of screening and selection methods that identify or isolate evolved proteins. We highlight recent cases in which directed evolution generated enzymatic activities and substrate specificities not known to exist in nature.
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Affiliation(s)
- Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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32
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Takeuchi R, Choi M, Stoddard BL. Engineering of customized meganucleases via in vitro compartmentalization and in cellulo optimization. Methods Mol Biol 2015; 1239:105-132. [PMID: 25408403 PMCID: PMC4416406 DOI: 10.1007/978-1-4939-1862-1_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
LAGLIDADG homing endonucleases (also referred to as "meganucleases") are compact DNA cleaving enzymes that specifically recognize long target sequences (approximately 20 base pairs), and thus serve as useful tools for therapeutic genome engineering. While stand-alone meganucleases are sufficiently active to introduce targeted genome modification, they can be fused to additional sequence-specific DNA binding domains in order to improve their performance in target cells. In this chapter, we describe an approach to retarget meganucleases to DNA targets of interest (such as sequences found in genes and cis regulatory regions), which is feasible in an academic laboratory environment. A combination of two selection systems, in vitro compartmentalization and two-plasmid cleavage assay in bacteria, allow for efficient engineering of meganucleases that specifically cleave a wide variety of DNA sequences.
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Affiliation(s)
- Ryo Takeuchi
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., A3-025, Seattle, WA, 98109-1024, USA
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33
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Lane MD, Seelig B. Advances in the directed evolution of proteins. Curr Opin Chem Biol 2014; 22:129-36. [PMID: 25309990 DOI: 10.1016/j.cbpa.2014.09.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/13/2014] [Indexed: 12/21/2022]
Abstract
Natural evolution has produced a great diversity of proteins that can be harnessed for numerous applications in biotechnology and pharmaceutical science. Commonly, specific applications require proteins to be tailored by protein engineering. Directed evolution is a type of protein engineering that yields proteins with the desired properties under well-defined conditions and in a practical time frame. While directed evolution has been employed for decades, recent creative developments enable the generation of proteins with previously inaccessible properties. Novel selection strategies, faster techniques, the inclusion of unnatural amino acids or modifications, and the symbiosis of rational design approaches and directed evolution continue to advance protein engineering.
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Affiliation(s)
- Michael D Lane
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.
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34
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Gajula KS, Huwe PJ, Mo CY, Crawford DJ, Stivers JT, Radhakrishnan R, Kohli RM. High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase. Nucleic Acids Res 2014; 42:9964-75. [PMID: 25064858 PMCID: PMC4150791 DOI: 10.1093/nar/gku689] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Antibody maturation is a critical immune process governed by the enzyme activation-induced deaminase (AID), a member of the AID/APOBEC DNA deaminase family. AID/APOBEC deaminases preferentially target cytosine within distinct preferred sequence motifs in DNA, with specificity largely conferred by a small 9–11 residue protein loop that differs among family members. Here, we aimed to determine the key functional characteristics of this protein loop in AID and to thereby inform our understanding of the mode of DNA engagement. To this end, we developed a methodology (Sat-Sel-Seq) that couples saturation mutagenesis at each position across the targeting loop, with iterative functional selection and next-generation sequencing. This high-throughput mutational analysis revealed dominant characteristics for residues within the loop and additionally yielded enzymatic variants that enhance deaminase activity. To rationalize these functional requirements, we performed molecular dynamics simulations that suggest that AID and its hyperactive variants can engage DNA in multiple specific modes. These findings align with AID's competing requirements for specificity and flexibility to efficiently drive antibody maturation. Beyond insights into the AID-DNA interface, our Sat-Sel-Seq approach also serves to further expand the repertoire of techniques for deep positional scanning and may find general utility for high-throughput analysis of protein function.
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Affiliation(s)
- Kiran S Gajula
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter J Huwe
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlie Y Mo
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J Crawford
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rahul M Kohli
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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35
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Esvelt KM, Smidler AL, Catteruccia F, Church GM. Concerning RNA-guided gene drives for the alteration of wild populations. eLife 2014; 3:e03401. [PMID: 25035423 PMCID: PMC4117217 DOI: 10.7554/elife.03401] [Citation(s) in RCA: 449] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 07/09/2014] [Indexed: 12/13/2022] Open
Abstract
Gene drives may be capable of addressing ecological problems by altering entire populations of wild organisms, but their use has remained largely theoretical due to technical constraints. Here we consider the potential for RNA-guided gene drives based on the CRISPR nuclease Cas9 to serve as a general method for spreading altered traits through wild populations over many generations. We detail likely capabilities, discuss limitations, and provide novel precautionary strategies to control the spread of gene drives and reverse genomic changes. The ability to edit populations of sexual species would offer substantial benefits to humanity and the environment. For example, RNA-guided gene drives could potentially prevent the spread of disease, support agriculture by reversing pesticide and herbicide resistance in insects and weeds, and control damaging invasive species. However, the possibility of unwanted ecological effects and near-certainty of spread across political borders demand careful assessment of each potential application. We call for thoughtful, inclusive, and well-informed public discussions to explore the responsible use of this currently theoretical technology.
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Affiliation(s)
- Kevin M Esvelt
- Synthetic Biology
Platform, Wyss Institute for Biologically Inspired
Engineering, Harvard Medical School, Boston, United
States
| | - Andrea L Smidler
- Synthetic Biology
Platform, Wyss Institute for Biologically Inspired
Engineering, Harvard Medical School, Boston, United
States; Department of Immunology and
Infectious Diseases, Harvard School of Public
Health, Boston, United States
| | - Flaminia Catteruccia
- Department of Immunology and Infectious
Diseases, Harvard School of Public
Health, Boston, United States;
Dipartimento di Medicina Sperimentale e Scienze
Biochimiche, Università degli Studi di
Perugia, Terni, Italy
| | - George M Church
- Synthetic Biology
Platform, Wyss Institute for Biologically Inspired
Engineering, Harvard Medical School, Boston, United
States
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36
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Wolfs JM, DaSilva M, Meister SE, Wang X, Schild-Poulter C, Edgell DR. MegaTevs: single-chain dual nucleases for efficient gene disruption. Nucleic Acids Res 2014; 42:8816-29. [PMID: 25013171 PMCID: PMC4117789 DOI: 10.1093/nar/gku573] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Targeting gene disruptions in complex genomes relies on imprecise repair by the non-homologous end-joining DNA pathway, creating mutagenic insertions or deletions (indels) at the break point. DNA end-processing enzymes are often co-expressed with genome-editing nucleases to enhance the frequency of indels, as the compatible cohesive ends generated by the nucleases can be precisely repaired, leading to a cycle of cleavage and non-mutagenic repair. Here, we present an alternative strategy to bias repair toward gene disruption by fusing two different nuclease active sites from I-TevI (a GIY-YIG enzyme) and I-OnuI E2 (an engineered meganuclease) into a single polypeptide chain. In vitro, the MegaTev enzyme generates two double-strand breaks to excise an intervening 30-bp fragment. In HEK 293 cells, we observe a high frequency of gene disruption without co-expression of DNA end-processing enzymes. Deep sequencing of disrupted target sites revealed minimal processing, consistent with the MegaTev sequestering the double-strand breaks from the DNA repair machinery. Off-target profiling revealed no detectable cleavage at sites where the I-TevI CNNNG cleavage motif is not appropriately spaced from the I-OnuI binding site. The MegaTev enzyme represents a small, programmable nuclease platform for extremely specific genome-engineering applications.
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Affiliation(s)
- Jason M Wolfs
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Matthew DaSilva
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Sarah E Meister
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Xu Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5B7, Canada
| | - Caroline Schild-Poulter
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5B7, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
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37
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Abstract
Xanthomonas phytopathogenic bacteria produce unique transcription activator-like effector (TALE) proteins that recognize and activate specific plant promoters through a set of tandem repeats. A unique TALE-DNA-binding code uses two polymorphic amino acids in each repeat to mediate recognition of specific nucleotides. The order of repeats determines effector’s specificity toward the cognate nucleotide sequence of the sense DNA strand. Artificially designed TALE-DNA-binding domains fused to nuclease or activation and repressor domains provide an outstanding toolbox for targeted gene editing and gene regulation in research, biotechnology and gene therapy. Gene editing with custom-designed TALE nucleases (TALENs) extends the repertoire of targeted genome modifications across a broad spectrum of organisms ranging from plants and insect to mammals.
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38
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Steentoft C, Bennett EP, Schjoldager KTBG, Vakhrushev SY, Wandall HH, Clausen H. Precision genome editing: a small revolution for glycobiology. Glycobiology 2014; 24:663-80. [PMID: 24861053 DOI: 10.1093/glycob/cwu046] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Precise and stable gene editing in mammalian cell lines has until recently been hampered by the lack of efficient targeting methods. While different gene silencing strategies have had tremendous impact on many biological fields, they have generally not been applied with wide success in the field of glycobiology, primarily due to their low efficiencies, with resultant failure to impose substantial phenotypic consequences upon the final glycosylation products. Here, we review novel nuclease-based precision genome editing techniques enabling efficient and stable gene editing, including gene disruption, insertion, repair, modification and deletion. The nuclease-based techniques comprised of homing endonucleases, zinc finger nucleases, transcription activator-like effector nucleases, as well as the RNA-guided clustered regularly interspaced short palindromic repeat/Cas nuclease system, all function by introducing single or double-stranded breaks at a defined genomic sequence. We here compare and contrast the different techniques and summarize their current applications, highlighting cases from the field of glycobiology as well as pointing to future opportunities. The emerging potential of precision gene editing for the field is exemplified by applications to xenotransplantation; to probing O-glycoproteomes, including differential O-GalNAc glycoproteomes, to decipher the function of individual polypeptide GalNAc-transferases, as well as for engineering Chinese Hamster Ovary host cells for production of improved therapeutic biologics.
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Affiliation(s)
- Catharina Steentoft
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Katrine T-B G Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
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