101
|
Yang J, Kim B, Kim GY, Jung GY, Seo SW. Synthetic biology for evolutionary engineering: from perturbation of genotype to acquisition of desired phenotype. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:113. [PMID: 31086565 PMCID: PMC6506968 DOI: 10.1186/s13068-019-1460-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
With the increased attention on bio-based industry, demands for techniques that enable fast and effective strain improvement have been dramatically increased. Evolutionary engineering, which is less dependent on biological information, has been applied to strain improvement. Currently, synthetic biology has made great innovations in evolutionary engineering, particularly in the development of synthetic tools for phenotypic perturbation. Furthermore, discovering biological parts with regulatory roles and devising novel genetic circuits have promoted high-throughput screening and selection. In this review, we first briefly explain basics of synthetic biology tools for mutagenesis and screening of improved variants, and then describe how these strategies have been improved and applied to phenotypic engineering. Evolutionary engineering using advanced synthetic biology tools will enable further innovation in phenotypic engineering through the development of novel genetic parts and assembly into well-designed logic circuits that perform complex tasks.
Collapse
Affiliation(s)
- Jina Yang
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
- Institute of Chemical Process, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| | - Beomhee Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| | - Gi Yeon Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering and School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673 South Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
- Institute of Chemical Process, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| |
Collapse
|
102
|
Roth TB, Woolston BM, Stephanopoulos G, Liu DR. Phage-Assisted Evolution of Bacillus methanolicus Methanol Dehydrogenase 2. ACS Synth Biol 2019; 8:796-806. [PMID: 30856338 PMCID: PMC6479731 DOI: 10.1021/acssynbio.8b00481] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Synthetic methylotrophy, the modification of organisms such as E. coli to grow on methanol, is a longstanding goal of metabolic engineering and synthetic biology. The poor kinetic properties of NAD-dependent methanol dehydrogenase, the first enzyme in most methanol assimilation pathways, limit pathway flux and present a formidable challenge to synthetic methylotrophy. To address this bottleneck, we used a formaldehyde biosensor to develop a phage-assisted noncontinuous evolution (PANCE) selection for variants of Bacillus methanolicus methanol dehydrogenase 2 (Bm Mdh2). Using this selection, we evolved Mdh2 variants with up to 3.5-fold improved Vmax. The mutations responsible for enhanced activity map to the predicted active site region homologous to that of type III iron-dependent alcohol dehydrogenases, suggesting a new critical region for future methanol dehydrogenase engineering strategies. Evolved Mdh2 variants enable twice as much 13C-methanol assimilation into central metabolites than previously reported state-of-the-art methanol dehydrogenases. This work provides improved Mdh2 variants and establishes a laboratory evolution approach for metabolic pathways in bacterial cells.
Collapse
Affiliation(s)
- Timothy B. Roth
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Benjamin M. Woolston
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
103
|
Pu J, Disare M, Dickinson BC. Evolution of C-Terminal Modification Tolerance in Full-Length and Split T7 RNA Polymerase Biosensors. Chembiochem 2019; 20:1547-1553. [PMID: 30694596 DOI: 10.1002/cbic.201800707] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/27/2019] [Indexed: 01/23/2023]
Abstract
T7 RNA polymerase (RNAP) is a powerful protein scaffold for the construction of synthetic biology tools and biosensors. However, both T7 RNAP and its split variants are intolerant to C-terminal modifications or fusions, thus placing a key limitation on their engineering and deployment. Here, we use rapid continuous-evolution approaches to evolve both full-length and split T7 RNAP variants that tolerate modified C termini and fusions to entire other proteins. Moreover, we show that the evolved split C-terminal RNAP variants can function as small-molecule biosensors, even in the context of large C-terminal fusions. This work provides a panel of modified RNAP variants with robust activity and tolerance to C-terminal fusions, and provides insights into the biophysical requirements of the C-terminal carboxylic acid functional group of T7 RNAP.
Collapse
Affiliation(s)
- Jinyue Pu
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - Michael Disare
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| |
Collapse
|
104
|
Abbott TR, Qi LS. Evolution at the Cutting Edge: CRISPR-Mediated Directed Evolution. Mol Cell 2019; 72:402-403. [PMID: 30388408 DOI: 10.1016/j.molcel.2018.10.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In a recent issue of Nature, Halperin et al. (2018) develop a new technology to continuously diversify specific genomic loci by combining CRISPR-Cas9 with error-prone DNA polymerases.
Collapse
Affiliation(s)
- Timothy R Abbott
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
105
|
Kim JY, Yoo HW, Lee PG, Lee SG, Seo JH, Kim BG. In vivo Protein Evolution, Next Generation Protein Engineering Strategy: from Random Approach to Target-specific Approach. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-018-0394-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
106
|
Ravikumar A, Arzumanyan GA, Obadi MKA, Javanpour AA, Liu CC. Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds. Cell 2018; 175:1946-1957.e13. [PMID: 30415839 PMCID: PMC6343851 DOI: 10.1016/j.cell.2018.10.021] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 08/16/2018] [Accepted: 10/04/2018] [Indexed: 11/17/2022]
Abstract
Directed evolution is a powerful approach for engineering biomolecules and understanding adaptation. However, experimental strategies for directed evolution are notoriously labor intensive and low throughput, limiting access to demanding functions, multiple functions in parallel, and the study of molecular evolution in replicate. We report OrthoRep, an orthogonal DNA polymerase-plasmid pair in yeast that stably mutates ∼100,000-fold faster than the host genome in vivo, exceeding the error threshold of genomic replication that causes single-generation extinction. User-defined genes in OrthoRep continuously and rapidly evolve through serial passaging, a highly straightforward and scalable process. Using OrthoRep, we evolved drug-resistant malarial dihydrofolate reductases (DHFRs) in 90 independent replicates. We uncovered a more complex fitness landscape than previously realized, including common adaptive trajectories constrained by epistasis, rare outcomes that avoid a frequent early adaptive mutation, and a suboptimal fitness peak that occasionally traps evolving populations. OrthoRep enables a new paradigm of routine, high-throughput evolution of biomolecular and cellular function.
Collapse
Affiliation(s)
- Arjun Ravikumar
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Garri A Arzumanyan
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Muaeen K A Obadi
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Alex A Javanpour
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Chang C Liu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA.
| |
Collapse
|
107
|
Schmied WH, Tnimov Z, Uttamapinant C, Rae CD, Fried SD, Chin JW. Controlling orthogonal ribosome subunit interactions enables evolution of new function. Nature 2018; 564:444-448. [PMID: 30518861 PMCID: PMC6525102 DOI: 10.1038/s41586-018-0773-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/15/2018] [Indexed: 11/09/2022]
Abstract
Orthogonal ribosomes are unnatural ribosomes that are directed towards orthogonal messenger RNAs in Escherichia coli, through an altered version of the 16S ribosomal RNA of the small subunit1. Directed evolution of orthogonal ribosomes has provided access to new ribosomal function, and the evolved orthogonal ribosomes have enabled the encoding of multiple non-canonical amino acids into proteins2-4. The original orthogonal ribosomes shared the pool of 23S ribosomal RNAs, contained in the large subunit, with endogenous ribosomes. Selectively directing a new 23S rRNA to an orthogonal mRNA, by controlling the association between the orthogonal 16S rRNAs and 23S rRNAs, would enable the evolution of new function in the large subunit. Previous work covalently linked orthogonal 16S rRNA and a circularly permuted 23S rRNA to create orthogonal ribosomes with low activity5,6; however, the linked subunits in these ribosomes do not associate specifically with each other, and mediate translation by associating with endogenous subunits. Here we discover engineered orthogonal 'stapled' ribosomes (with subunits linked through an optimized RNA staple) with activities comparable to that of the parent orthogonal ribosome; they minimize association with endogenous subunits and mediate translation of orthogonal mRNAs through the association of stapled subunits. We evolve cells with genomically encoded stapled ribosomes as the sole ribosomes, which support cellular growth at similar rates to natural ribosomes. Moreover, we visualize the engineered stapled ribosome structure by cryo-electron microscopy at 3.0 Å, revealing how the staple links the subunits and controls their association. We demonstrate the utility of controlling subunit association by evolving orthogonal stapled ribosomes which efficiently polymerize a sequence of monomers that the natural ribosome is intrinsically unable to translate. Our work provides a foundation for evolving the rRNA of the entire orthogonal ribosome for the encoded cellular synthesis of non-canonical biological polymers7.
Collapse
MESH Headings
- Base Sequence
- Cross-Linking Reagents/chemistry
- Cryoelectron Microscopy
- Directed Molecular Evolution
- Escherichia coli/classification
- Escherichia coli/cytology
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Models, Molecular
- Peptides/genetics
- Peptides/metabolism
- Protein Biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 16S/ultrastructure
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA, Ribosomal, 23S/ultrastructure
- Ribosome Subunits/chemistry
- Ribosome Subunits/metabolism
- Ribosome Subunits/ultrastructure
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Ribosomes/ultrastructure
Collapse
Affiliation(s)
| | - Zakir Tnimov
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Chayasith Uttamapinant
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Christopher D Rae
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Stephen D Fried
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| |
Collapse
|
108
|
Ghaddar N, Hashemidahaj M, Findlay BL. Access to high-impact mutations constrains the evolution of antibiotic resistance in soft agar. Sci Rep 2018; 8:17023. [PMID: 30451932 PMCID: PMC6242871 DOI: 10.1038/s41598-018-34911-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/27/2018] [Indexed: 01/21/2023] Open
Abstract
Despite widespread resistance to many important antibiotics, the factors that govern the emergence and prevalence of antibiotic-resistant bacteria are still unclear. When exposed to antibiotic gradients in soft agar plates measuring as little as 1.25 × 11 cm we found that Escherichia coli rapidly became resistant to representatives from every class of antibiotics active against Gram-negative bacteria. Evolution kinetics were independent of the frequency of spontaneous mutations that confer antibiotic resistance or antibiotic dose-response curves, and were only loosely correlated to maximal antibiotic concentrations. Instead, rapid evolution required unrealized mutations that could markedly decrease antibiotic susceptibility. When bacteria could not evolve through these “high-impact” mutations, populations frequently bottlenecked, reducing the number of cells from which mutants could arise and prolonging evolution times. This effect was independent of the antibiotic’s mechanism of action, and may affect the evolution of antibiotic resistance in clinical settings.
Collapse
Affiliation(s)
- Nour Ghaddar
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Québec, Canada.,Lady Davis Institute for Medical Research, McGill University, Montreal, Québec, Canada
| | - Mona Hashemidahaj
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Québec, Canada
| | - Brandon L Findlay
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Québec, Canada.
| |
Collapse
|
109
|
Simone BW, Martínez-Gálvez G, WareJoncas Z, Ekker SC. Fishing for understanding: Unlocking the zebrafish gene editor's toolbox. Methods 2018; 150:3-10. [PMID: 30076892 PMCID: PMC6590056 DOI: 10.1016/j.ymeth.2018.07.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/23/2018] [Accepted: 07/30/2018] [Indexed: 02/06/2023] Open
Abstract
The rapid growth of the field of gene editing can largely be attributed to the discovery and optimization of designer endonucleases. These include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regular interspersed short palindromic repeat (CRISPR) systems including Cas9, Cas12a, and structure-guided nucleases. Zebrafish (Danio rerio) have proven to be a powerful model system for genome engineering testing and applications due to their external development, high fecundity, and ease of housing. As the zebrafish gene editing toolkit continues to grow, it is becoming increasingly important to understand when and how to utilize which of these technologies for maximum efficacy in a particular project. While CRISPR-Cas9 has brought broad attention to the field of genome engineering in recent years, designer endonucleases have been utilized in genome engineering for more than two decades. This chapter provides a brief overview of designer endonuclease and other gene editing technologies in zebrafish as well as some of their known functional benefits and limitations depending on specific project goals. Finally, selected prospects for additional gene editing tools are presented, promising additional options for directed genomic programming of this versatile animal model system.
Collapse
Affiliation(s)
- Brandon W Simone
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Zachary WareJoncas
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
| |
Collapse
|
110
|
Yao R, Liu D, Jia X, Zheng Y, Liu W, Xiao Y. CRISPR-Cas9/Cas12a biotechnology and application in bacteria. Synth Syst Biotechnol 2018; 3:135-149. [PMID: 30345399 PMCID: PMC6190536 DOI: 10.1016/j.synbio.2018.09.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas technologies have greatly reshaped the biology field. In this review, we discuss the CRISPR-Cas with a particular focus on the associated technologies and applications of CRISPR-Cas9 and CRISPR-Cas12a, which have been most widely studied and used. We discuss the biological mechanisms of CRISPR-Cas as immune defense systems, recently-discovered anti-CRISPR-Cas systems, and the emerging Cas variants (such as xCas9 and Cas13) with unique characteristics. Then, we highlight various CRISPR-Cas biotechnologies, including nuclease-dependent genome editing, CRISPR gene regulation (including CRISPR interference/activation), DNA/RNA base editing, and nucleic acid detection. Last, we summarize up-to-date applications of the biotechnologies for synthetic biology and metabolic engineering in various bacterial species.
Collapse
Affiliation(s)
- Ruilian Yao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Di Liu
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Xiao Jia
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuan Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
111
|
d’Oelsnitz S, Ellington A. Continuous directed evolution for strain and protein engineering. Curr Opin Biotechnol 2018; 53:158-163. [DOI: 10.1016/j.copbio.2017.12.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 10/18/2022]
|
112
|
Wang T, Badran AH, Huang TP, Liu DR. Continuous directed evolution of proteins with improved soluble expression. Nat Chem Biol 2018; 14:972-980. [PMID: 30127387 PMCID: PMC6143403 DOI: 10.1038/s41589-018-0121-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/17/2018] [Indexed: 01/20/2023]
Abstract
We report the development of soluble expression phage-assisted continuous evolution (SE-PACE), a system for rapidly evolving proteins with increased soluble expression. Through use of a PACE-compatible AND gate that uses a split-intein pIII, SE-PACE enables two simultaneous positive selections to evolve proteins with improved expression while maintaining their desired activities. In as little as three days, SE-PACE evolved several antibody fragments with >5-fold improvement in expression yield while retaining binding activity. We also developed an activity-independent form of SE-PACE to correct folding-defective variants of maltose-binding protein (MBP) and to evolve variants of the eukaryotic cytidine deaminase APOBEC1 with improved expression properties. These evolved APOBEC1 variants were found to improve the expression and apparent activity of Cas9-derived base editors when used in place of the wild-type cytidine deaminase. Together, these results suggest that SE-PACE can be applied to a wide variety of proteins to rapidly improve their soluble expression.
Collapse
Affiliation(s)
- Tina Wang
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ahmed H Badran
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Tony P Huang
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
113
|
Vargas-Rodriguez O, Sevostyanova A, Söll D, Crnković A. Upgrading aminoacyl-tRNA synthetases for genetic code expansion. Curr Opin Chem Biol 2018; 46:115-122. [PMID: 30059834 PMCID: PMC6214156 DOI: 10.1016/j.cbpa.2018.07.014] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/04/2018] [Accepted: 07/13/2018] [Indexed: 01/06/2023]
Abstract
Synthesis of proteins with non-canonical amino acids via genetic code expansion is at the forefront of synthetic biology. Progress in this field has enabled site-specific incorporation of over 200 chemically and structurally diverse amino acids into proteins in an increasing number of organisms. This has been facilitated by our ability to repurpose aminoacyl-tRNA synthetases to attach non-canonical amino acids to engineered tRNAs. Current efforts in the field focus on overcoming existing limitations to the simultaneous incorporation of multiple non-canonical amino acids or amino acids that differ from the l-α-amino acid structure (e.g. d-amino acid or β-amino acid). Here, we summarize the progress and challenges in developing more selective and efficient aminoacyl-tRNA synthetases for genetic code expansion.
Collapse
Affiliation(s)
- Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Anastasia Sevostyanova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| |
Collapse
|
114
|
Moore CL, Papa LJ, Shoulders MD. A Processive Protein Chimera Introduces Mutations across Defined DNA Regions In Vivo. J Am Chem Soc 2018; 140:11560-11564. [PMID: 29991261 PMCID: PMC6166643 DOI: 10.1021/jacs.8b04001] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Laboratory time scale evolution in vivo relies on the generation of large, mutationally diverse gene libraries to rapidly explore biomolecule sequence landscapes. Traditional global mutagenesis methods are problematic because they introduce many off-target mutations that are often lethal and can engender false positives. We report the development and application of the MutaT7 chimera, a potent and highly targeted in vivo mutagenesis agent. MutaT7 utilizes a DNA-damaging cytidine deaminase fused to a processive RNA polymerase to continuously direct mutations to specific, well-defined DNA regions of any relevant length. MutaT7 thus provides a mechanism for in vivo targeted mutagenesis across multi-kb DNA sequences. MutaT7 should prove useful in diverse organisms, opening the door to new types of in vivo evolution experiments.
Collapse
Affiliation(s)
- Christopher L Moore
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Louis J Papa
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Matthew D Shoulders
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| |
Collapse
|
115
|
Halperin SO, Tou CJ, Wong EB, Modavi C, Schaffer DV, Dueber JE. CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature 2018; 560:248-252. [PMID: 30069054 DOI: 10.1038/s41586-018-0384-8] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/19/2018] [Indexed: 12/24/2022]
Abstract
The capacity to diversify genetic codes advances our ability to understand and engineer biological systems1,2. A method for continuously diversifying user-defined regions of a genome would enable forward genetic approaches in systems that are not amenable to efficient homology-directed oligonucleotide integration. It would also facilitate the rapid evolution of biotechnologically useful phenotypes through accelerated and parallelized rounds of mutagenesis and selection, as well as cell-lineage tracking through barcode mutagenesis. Here we present EvolvR, a system that can continuously diversify all nucleotides within a tunable window length at user-defined loci. This is achieved by directly generating mutations using engineered DNA polymerases targeted to loci via CRISPR-guided nickases. We identified nickase and polymerase variants that offer a range of targeted mutation rates that are up to 7,770,000-fold greater than rates seen in wild-type cells, and editing windows with lengths of up to 350 nucleotides. We used EvolvR to identify novel ribosomal mutations that confer resistance to the antibiotic spectinomycin. Our results demonstrate that CRISPR-guided DNA polymerases enable multiplexed and continuous diversification of user-defined genomic loci, which will be useful for a broad range of basic and biotechnological applications.
Collapse
Affiliation(s)
- Shakked O Halperin
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
| | - Connor J Tou
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Eric B Wong
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Cyrus Modavi
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - David V Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA. .,Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA. .,Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - John E Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA. .,Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA. .,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| |
Collapse
|
116
|
Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance. Proc Natl Acad Sci U S A 2018; 115:E5726-E5735. [PMID: 29871954 PMCID: PMC6016788 DOI: 10.1073/pnas.1801646115] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. Standard laboratory evolution approaches explore only a small fraction of the sequence space and fail to identify exceedingly rare resistance mutations and combinations thereof. Therefore, new rapid and exhaustive methods are needed to accurately assess the potential of resistance evolution and uncover the underlying mutational mechanisms. Here, we introduce directed evolution with random genomic mutations (DIvERGE), a method that allows an up to million-fold increase in mutation rate along the full lengths of multiple predefined loci in a range of bacterial species. In a single day, DIvERGE generated specific mutation combinations, yielding clinically significant resistance against trimethoprim and ciprofloxacin. Many of these mutations have remained previously undetected or provide resistance in a species-specific manner. These results indicate pathogen-specific resistance mechanisms and the necessity of future narrow-spectrum antibacterial treatments. In contrast to prior claims, we detected the rapid emergence of resistance against gepotidacin, a novel antibiotic currently in clinical trials. Based on these properties, DIvERGE could be applicable to identify less resistance-prone antibiotics at an early stage of drug development. Finally, we discuss potential future applications of DIvERGE in synthetic and evolutionary biology.
Collapse
|
117
|
Dumas L, Zito F, Auroy P, Johnson X, Peltier G, Alric J. Structure-Function Analysis of Chloroplast Proteins via Random Mutagenesis Using Error-Prone PCR. PLANT PHYSIOLOGY 2018; 177:465-475. [PMID: 29703866 PMCID: PMC6001340 DOI: 10.1104/pp.17.01618] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/31/2018] [Indexed: 05/14/2023]
Abstract
Site-directed mutagenesis of chloroplast genes was developed three decades ago and has greatly advanced the field of photosynthesis research. Here, we describe a new approach for generating random chloroplast gene mutants that combines error-prone polymerase chain reaction of a gene of interest with chloroplast complementation of the knockout Chlamydomonas reinhardtii mutant. As a proof of concept, we targeted a 300-bp sequence of the petD gene that encodes subunit IV of the thylakoid membrane-bound cytochrome b6f complex. By sequencing chloroplast transformants, we revealed 149 mutations in the 300-bp target petD sequence that resulted in 92 amino acid substitutions in the 100-residue target subunit IV sequence. Our results show that this method is suited to the study of highly hydrophobic, multisubunit, and chloroplast-encoded proteins containing cofactors such as hemes, iron-sulfur clusters, and chlorophyll pigments. Moreover, we show that mutant screening and sequencing can be used to study photosynthetic mechanisms or to probe the mutational robustness of chloroplast-encoded proteins, and we propose that this method is a valuable tool for the directed evolution of enzymes in the chloroplast.
Collapse
Affiliation(s)
- Louis Dumas
- Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Aix-Marseille Université, Unité Mixte de Recherche 7265, BIAM, Commissariat à l'Energie Atomique Cadarache, 13115 Saint-Paul-lez-Durance, France
| | - Francesca Zito
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7099, University Paris Diderot, Sorbonne Paris Cité, PSL Research University, F-75005 Paris, France
| | - Pascaline Auroy
- Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Aix-Marseille Université, Unité Mixte de Recherche 7265, BIAM, Commissariat à l'Energie Atomique Cadarache, 13115 Saint-Paul-lez-Durance, France
| | - Xenie Johnson
- Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Aix-Marseille Université, Unité Mixte de Recherche 7265, BIAM, Commissariat à l'Energie Atomique Cadarache, 13115 Saint-Paul-lez-Durance, France
| | - Gilles Peltier
- Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Aix-Marseille Université, Unité Mixte de Recherche 7265, BIAM, Commissariat à l'Energie Atomique Cadarache, 13115 Saint-Paul-lez-Durance, France
| | - Jean Alric
- Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Aix-Marseille Université, Unité Mixte de Recherche 7265, BIAM, Commissariat à l'Energie Atomique Cadarache, 13115 Saint-Paul-lez-Durance, France jean.alric@cea
| |
Collapse
|
118
|
Hu JH, Miller SM, Geurts MH, Tang W, Chen L, Sun N, Zeina CM, Gao X, Rees HA, Lin Z, Liu DR. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature 2018; 556:57-63. [PMID: 29512652 PMCID: PMC5951633 DOI: 10.1038/nature26155] [Citation(s) in RCA: 1023] [Impact Index Per Article: 170.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/21/2018] [Indexed: 12/18/2022]
Abstract
A key limitation to the use of CRISPR-Cas9 proteins for genome editing and other applications is the requirement that a protospacer adjacent motif (PAM) be present at the target site. For the most commonly used Cas9 from Streptococcus pyogenes (SpCas9), this PAM requirement is NGG. No natural or engineered Cas9 variants shown to function efficiently in mammalian cells offer a PAM less restrictive than NGG. Here we used phage-assisted continuous evolution (PACE) to evolve an expanded PAM SpCas9 variant (xCas9) that can recognize a broad range of PAM sequences including NG, GAA, and GAT. The PAM compatibility of xCas9 is the broadest reported to date among Cas9s active in mammalian cells, and supports applications in human cells including targeted transcriptional activation, nuclease-mediated gene disruption, and both cytidine and adenine base editing. Remarkably, despite its broadened PAM compatibility, xCas9 has much greater DNA specificity than SpCas9, with substantially lower genome-wide off-target activity at all NGG target sites tested, as well as minimal off-target activity when targeting genomic sites with non-NGG PAMs. These findings expand the DNA targeting scope of CRISPR systems and establish that there is no necessary trade-off between Cas9 editing efficiency, PAM compatibility, and DNA specificity.
Collapse
Affiliation(s)
- Johnny H Hu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Shannon M Miller
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Maarten H Geurts
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Weixin Tang
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Liwei Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ning Sun
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Christina M Zeina
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Xue Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Holly A Rees
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Zhi Lin
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
119
|
Bryson DI, Fan C, Guo LT, Miller C, Söll D, Liu DR. Continuous directed evolution of aminoacyl-tRNA synthetases. Nat Chem Biol 2017; 13:1253-1260. [PMID: 29035361 PMCID: PMC5724969 DOI: 10.1038/nchembio.2474] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/08/2017] [Indexed: 12/19/2022]
Abstract
Directed evolution of orthogonal aminoacyl-tRNA synthetases (AARSs) enables site-specific installation of noncanonical amino acids (ncAAs) into proteins. Traditional evolution techniques typically produce AARSs with greatly reduced activity and selectivity compared to their wild-type counterparts. We designed phage-assisted continuous evolution (PACE) selections to rapidly produce highly active and selective orthogonal AARSs through hundreds of generations of evolution. PACE of a chimeric Methanosarcina spp. pyrrolysyl-tRNA synthetase (PylRS) improved its enzymatic efficiency (kcat/KMtRNA) 45-fold compared to the parent enzyme. Transplantation of the evolved mutations into other PylRS-derived synthetases improved yields of proteins containing noncanonical residues up to 9.7-fold. Simultaneous positive and negative selection PACE over 48 h greatly improved the selectivity of a promiscuous Methanocaldococcus jannaschii tyrosyl-tRNA synthetase variant for site-specific incorporation of p-iodo-L-phenylalanine. These findings offer new AARSs that increase the utility of orthogonal translation systems and establish the capability of PACE to efficiently evolve orthogonal AARSs with high activity and amino acid specificity.
Collapse
Affiliation(s)
- David I. Bryson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701
| | - Li-Tao Guo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520
| | - Corwin Miller
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520
- Department of Chemistry, Yale University, New Haven, CT, 06520
| | - David R. Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142
| |
Collapse
|
120
|
Bratulic S, Badran AH. Modern methods for laboratory diversification of biomolecules. Curr Opin Chem Biol 2017; 41:50-60. [PMID: 29096324 PMCID: PMC6062405 DOI: 10.1016/j.cbpa.2017.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/03/2017] [Accepted: 10/08/2017] [Indexed: 11/29/2022]
Abstract
Genetic variation fuels Darwinian evolution, yet spontaneous mutation rates are maintained at low levels to ensure cellular viability. Low mutation rates preclude the exhaustive exploration of sequence space for protein evolution and genome engineering applications, prompting scientists to develop methods for efficient and targeted diversification of nucleic acid sequences. Directed evolution of biomolecules relies upon the generation of unbiased genetic diversity to discover variants with desirable properties, whereas genome-engineering applications require selective modifications on a genomic scale with minimal off-targets. Here, we review the current toolkit of mutagenesis strategies employed in directed evolution and genome engineering. These state-of-the-art methods enable facile modifications and improvements of single genes, multicomponent pathways, and whole genomes for basic and applied research, while simultaneously paving the way for genome editing therapeutic interventions.
Collapse
Affiliation(s)
- Sinisa Bratulic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmed H Badran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
121
|
Brödel AK, Isalan M, Jaramillo A. Engineering of biomolecules by bacteriophage directed evolution. Curr Opin Biotechnol 2017; 51:32-38. [PMID: 29175708 DOI: 10.1016/j.copbio.2017.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/10/2017] [Accepted: 11/09/2017] [Indexed: 01/21/2023]
Abstract
Conventional in vivo directed evolution methods have primarily linked the biomolecule's activity to bacterial cell growth. Recent developments instead rely on the conditional growth of bacteriophages (phages), viruses that infect and replicate within bacteria. Here we review recent phage-based selection systems for in vivo directed evolution. These approaches have been applied to evolve a wide range of proteins including transcription factors, polymerases, proteases, DNA-binding proteins, and protein-protein interactions. Advances in this field expand the possible applications of protein and RNA engineering. This will ultimately result in new biomolecules with tailor-made properties, as well as giving us a better understanding of basic evolutionary processes.
Collapse
Affiliation(s)
- Andreas K Brödel
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; CNRS-UMR8030, Laboratoire iSSB, Évry 91000, France; Université Paris-Saclay, Évry 91000, France; Université d'Évry, Évry 91000, France; CEA, DRF, IG, Genoscope, Évry 91000, France; Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, 46980 Paterna, Spain.
| |
Collapse
|
122
|
Suzuki T, Miller C, Guo LT, Ho JML, Bryson DI, Wang YS, Liu DR, Söll D. Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase. Nat Chem Biol 2017; 13:1261-1266. [PMID: 29035363 PMCID: PMC5698177 DOI: 10.1038/nchembio.2497] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/13/2017] [Indexed: 11/16/2022]
Abstract
Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion with non-canonical amino acids, yet understanding of its structure and activity is incomplete. Here we describe the crystal structure of the previously uncharacterized essential N-terminal domain of this unique enzyme in complex with tRNAPyl. This structure explains why PylRS remains orthogonal in a broad range of organisms, from bacteria to humans. The structure also illustrates why tRNAPyl recognition by PylRS is anticodon-independent; the anticodon does not contact the enzyme. Using standard microbiological culture equipment, we then established a new method for laboratory evolution – a non-continuous counterpart of the previously developed phage-assisted continuous evolution. With this method, we evolved novel PylRS variants with enhanced activity and amino acid specificity. We finally employed an evolved PylRS variant to determine its N-terminal domain structure and show how its mutations improve PylRS activity in the genetic encoding of a non-canonical amino acid.
Collapse
Affiliation(s)
- Tateki Suzuki
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Corwin Miller
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Li-Tao Guo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Joanne M L Ho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - David I Bryson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Yane-Shih Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.,Department of Chemistry, Yale University, New Haven, Connecticut, USA
| |
Collapse
|
123
|
Packer MS, Rees HA, Liu DR. Phage-assisted continuous evolution of proteases with altered substrate specificity. Nat Commun 2017; 8:956. [PMID: 29038472 PMCID: PMC5643515 DOI: 10.1038/s41467-017-01055-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/14/2017] [Indexed: 01/15/2023] Open
Abstract
Here we perform phage-assisted continuous evolution (PACE) of TEV protease, which canonically cleaves ENLYFQS, to cleave a very different target sequence, HPLVGHM, that is present in human IL-23. A protease emerging from ∼2500 generations of PACE contains 20 non-silent mutations, cleaves human IL-23 at the target peptide bond, and when pre-mixed with IL-23 in primary cultures of murine splenocytes inhibits IL-23-mediated immune signaling. We characterize the substrate specificity of this evolved enzyme, revealing shifted and broadened specificity changes at the six positions in which the target amino acid sequence differed. Mutational dissection and additional protease specificity profiling reveal the molecular basis of some of these changes. This work establishes the capability of changing the substrate specificity of a protease at many positions in a practical time scale and provides a foundation for the development of custom proteases that catalytically alter or destroy target proteins for biotechnological and therapeutic applications.Proteases are promising therapeutics to treat diseases such as hemophilia which are due to endogenous protease deficiency. Here the authors use phage-assisted continuous evolution to evolve a variant TEV protease with altered target peptide sequence specificities.
Collapse
Affiliation(s)
- Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.,Graduate Program in Biophysics Program, Harvard University, 240 Longwood Avenue, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Holly A Rees
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.,Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA. .,Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA. .,Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.
| |
Collapse
|
124
|
Davis AM, Plowright AT, Valeur E. Directing evolution: the next revolution in drug discovery? Nat Rev Drug Discov 2017; 16:681-698. [PMID: 28935911 DOI: 10.1038/nrd.2017.146] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The strong biological rationale to pursue challenging drug targets such as protein-protein interactions has stimulated the development of novel screening strategies, such as DNA-encoded libraries, to allow broader areas of chemical space to be searched. There has also been renewed interest in screening natural products, which are the result of evolutionary selection for a function, such as interference with a key signalling pathway of a competing organism. However, recent advances in several areas, such as understanding of the biosynthetic pathways for natural products, synthetic biology and the development of biosensors to detect target molecules, are now providing new opportunities to directly harness evolutionary pressure to identify and optimize compounds with desired bioactivities. Here, we describe innovations in the key components of such strategies and highlight pioneering examples that indicate the potential of the directed-evolution concept. We also discuss the scientific gaps and challenges that remain to be addressed to realize this potential more broadly in drug discovery.
Collapse
Affiliation(s)
- Andrew M Davis
- AstraZeneca R&D Gothenburg, Pepparedsleden 1, Mölndal, 43150, Sweden
| | - Alleyn T Plowright
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Eric Valeur
- AstraZeneca R&D Gothenburg, Pepparedsleden 1, Mölndal, 43150, Sweden
| |
Collapse
|
125
|
Brödel AK, Jaramillo A, Isalan M. Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication. Nat Protoc 2017; 12:1830-1843. [PMID: 28796233 DOI: 10.1038/nprot.2017.084] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Directed evolution is a powerful tool to improve the characteristics of biomolecules. Here we present a protocol for the intracellular evolution of proteins with distinct differences and advantages in comparison with established techniques. These include the ability to select for a particular function from a library of protein variants inside cells, minimizing undesired coevolution and propagation of nonfunctional library members, as well as allowing positive and negative selection logics using basally active promoters. A typical evolution experiment comprises the following stages: (i) preparation of a combinatorial M13 phagemid (PM) library expressing variants of the gene of interest (GOI) and preparation of the Escherichia coli host cells; (ii) multiple rounds of an intracellular selection process toward a desired activity; and (iii) the characterization of the evolved target proteins. The system has been developed for the selection of new orthogonal transcription factors (TFs) but is capable of evolving any gene-or gene circuit function-that can be linked to conditional M13 phage replication. Here we demonstrate our approach using as an example the directed evolution of the bacteriophage λ cI TF against two synthetic bidirectional promoters. The evolved TF variants enable simultaneous activation and repression against their engineered promoters and do not cross-react with the wild-type promoter, thus ensuring orthogonality. This protocol requires no special equipment, allowing synthetic biologists and general users to evolve improved biomolecules within ∼7 weeks.
Collapse
Affiliation(s)
- Andreas K Brödel
- Department of Life Sciences, Imperial College London, London, UK
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, UK.,Laboratoire iSSB, UMR 8030, Université Paris-Saclay, Université d'Évry-Val d'Essonne, CNRS, CEA, IG/Genoscope, CEA DRF, Évry, France.,Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Paterna, Spain
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, UK
| |
Collapse
|
126
|
Standley M, Allen J, Cervantes L, Lilly J, Camps M. Fluorescence-Based Reporters for Detection of Mutagenesis in E. coli. Methods Enzymol 2017. [PMID: 28645368 DOI: 10.1016/bs.mie.2017.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Mutagenesis in model organisms following exposure to chemicals is used as an indicator of genotoxicity. Mutagenesis assays are also used to study mechanisms of DNA homeostasis. This chapter focuses on detection of mutagenesis in prokaryotes, which boils down to two approaches: reporter inactivation (forward mutation assay) and reversion of an inactivating mutation (reversion mutation assay). Both methods are labor intensive, involving visual screening, quantification of colonies on solid media, or determining a Poisson distribution in liquid culture. Here, we present two reversion reporters for in vivo mutagenesis that produce a quantitative output, and thus have the potential to greatly reduce the amount of test chemical and labor involved in these assays. This output is obtained by coupling a TEM β lactamase-based reversion assay with GFP fluorescence, either by placing the two genes on the same plasmid or by fusing them translationally and interrupting the N-terminus of the chimeric ORF with a stop codon. We also describe a reporter aimed at facilitating the monitoring of continuous mutagenesis in mutator strains. This reporter couples two reversion markers, allowing the temporal separation of mutation events in time, thus providing information about the dynamics of mutagenesis in mutator strains. Here, we describe these reporter systems, provide protocols for use, and demonstrate their key functional features using error-prone Pol I mutagenesis as a source of mutations.
Collapse
Affiliation(s)
- Melissa Standley
- University of California-Santa Cruz, Santa Cruz, CA, United States
| | - Jennifer Allen
- University of California-Santa Cruz, Santa Cruz, CA, United States
| | - Layla Cervantes
- University of California-Santa Cruz, Santa Cruz, CA, United States
| | - Joshua Lilly
- University of California-Santa Cruz, Santa Cruz, CA, United States
| | - Manel Camps
- University of California-Santa Cruz, Santa Cruz, CA, United States.
| |
Collapse
|
127
|
Zheng X, Xing XH, Zhang C. Targeted mutagenesis: A sniper-like diversity generator in microbial engineering. Synth Syst Biotechnol 2017; 2:75-86. [PMID: 29062964 PMCID: PMC5636951 DOI: 10.1016/j.synbio.2017.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/26/2022] Open
Abstract
Mutations, serving as the raw materials of evolution, have been extensively utilized to increase the chances of engineering molecules or microbes with tailor-made functions. Global and targeted mutagenesis are two main methods of obtaining various mutations, distinguished by the range of action they can cover. While the former one stresses the mining of novel genetic loci within the whole genomic background, targeted mutagenesis performs in a more straightforward manner, bringing evolutionary escape and error catastrophe under control. In this review, we classify the existing techniques of targeted mutagenesis into two categories in terms of whether the diversity is generated in vitro or in vivo, and briefly introduce the mechanisms and applications of them separately. The inherent connections and development trends of the two classes are also discussed to provide an insight into the next generation evolution research.
Collapse
Key Words
- 3′-LTR, 3’-long terminal repeat
- 5-FOA, 5-fluoro-orotic acid
- CRISPR/Cas9, clustered regularly interspaced short palindromic repeats and associated protein 9
- DNA Pol III, DNA polymerase III
- DNA PolI, DNA polymerase I
- DSB, double strand break
- Evolution
- FLASH, fast ligation-based automatable solid-phase high-throughput
- HDR, homology-directed repair
- HIV, human immunodeficiency virus
- ICE, in vivo continuous evolution
- LIC, ligation-independent cloning
- MAGE, multiplex automated genome engineering
- MMEJ, microhomology-mediated end-joining
- Mutations
- NHEJ, error-prone non-homologous end-joining
- ORF, open reading frame
- PAM, protospacer-adjacent motif
- RVD, repeat variable di-residue
- Synthetic biology
- TALE, transcription activator-like effector
- TALEN, transcription activator-like effector nuclease
- TP, terminal protein
- TP-DNAP, TP-DNA polymerase fusion
- TaGTEAM, targeting glycosylase to embedded arrays for mutagenesis
- Targeted mutagenesis
- YOGE, yeast oligo-mediated genome engineering
- ZF, zinc-finger protein
- ZFN, zinc-finger nuclease
- dCas9, catalytically dead Cas9
- dNTP, deoxy-ribonucleoside triphosphate
- dsDNA, double-stranded DNA
- error-prone PCR, error-prone polymerase chain reaction
- non-GMO, non-genetically modified organism
- pre-crRNA, pre-CRISPR RNA
- sctetR, single chain tetR
- sgRNA, single-guide RNA
- ssDNA, single-stranded DNA
- tracrRNA, trans-encoded RNA
Collapse
Affiliation(s)
| | | | - Chong Zhang
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Institute of Biochemical Engineering, Department of Chemical Engineering, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
| |
Collapse
|
128
|
Geng F, Ma CW, Zeng AP. Reengineering substrate specificity of E. coli glutamate dehydrogenase using a position-based prediction method. Biotechnol Lett 2017; 39:599-605. [DOI: 10.1007/s10529-017-2297-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/10/2016] [Indexed: 01/11/2023]
|
129
|
Schlegel S, Genevaux P, de Gier JW. Isolating Escherichia coli strains for recombinant protein production. Cell Mol Life Sci 2016; 74:891-908. [PMID: 27730255 PMCID: PMC5306230 DOI: 10.1007/s00018-016-2371-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/22/2016] [Accepted: 09/16/2016] [Indexed: 12/14/2022]
Abstract
Escherichia coli has been widely used for the production of recombinant proteins. To improve protein production yields in E. coli, directed engineering approaches have been commonly used. However, there are only few reported examples of the isolation of E. coli protein production strains using evolutionary approaches. Here, we first give an introduction to bacterial evolution and mutagenesis to set the stage for discussing how so far selection- and screening-based approaches have been used to isolate E. coli protein production strains. Finally, we discuss how evolutionary approaches may be used in the future to isolate E. coli strains with improved protein production characteristics.
Collapse
Affiliation(s)
- Susan Schlegel
- Department of Environmental Systems Science, ETH Zürich, 8092, Zürich, Switzerland
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrheniusväg 16C, 106 91, Stockholm, Sweden.
| |
Collapse
|
130
|
Csörgő B, Nyerges Á, Pósfai G, Fehér T. System-level genome editing in microbes. Curr Opin Microbiol 2016; 33:113-122. [PMID: 27472027 DOI: 10.1016/j.mib.2016.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/09/2016] [Accepted: 07/06/2016] [Indexed: 11/16/2022]
Abstract
The release of the first complete microbial genome sequences at the end of the past century opened the way for functional genomics and systems-biology to uncover the genetic basis of various phenotypes. The surge of available sequence data facilitated the development of novel genome editing techniques for system-level analytical studies. Recombineering allowed unprecedented throughput and efficiency in microbial genome editing and the recent discovery and widespread use of RNA-guided endonucleases offered several further perspectives: (i) previously recalcitrant species became editable, (ii) the efficiency of recombineering could be elevated, and as a result (iii) diverse genomic libraries could be generated more effectively. Supporting recombineering by RNA-guided endonucleases has led to success stories in metabolic engineering, but their use for system-level analysis is mostly unexplored. For the full exploitation of opportunities that are offered by the genome editing proficiency, future development of large scale analytical procedures is also vitally needed.
Collapse
Affiliation(s)
- Bálint Csörgő
- Systems and Synthetic Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ákos Nyerges
- Systems and Synthetic Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - György Pósfai
- Systems and Synthetic Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.
| | - Tamás Fehér
- Systems and Synthetic Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| |
Collapse
|
131
|
Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance. Nature 2016; 533:58-63. [PMID: 27120167 PMCID: PMC4865400 DOI: 10.1038/nature17938] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 03/23/2016] [Indexed: 12/17/2022]
Abstract
The Bacillus thuringiensis δ-endotoxins (Bt toxins) are widely used insecticidal proteins in engineered crops that provide agricultural, economic, and environmental benefits. The development of insect resistance to Bt toxins endangers their long-term effectiveness. Here we have developed a phage-assisted continuous evolution selection that rapidly evolves high-affinity protein-protein interactions, and applied this system to evolve variants of the Bt toxin Cry1Ac that bind a cadherin-like receptor from the insect pest Trichoplusia ni (TnCAD) that is not natively bound by wild-type Cry1Ac. The resulting evolved Cry1Ac variants bind TnCAD with high affinity (dissociation constant Kd = 11-41 nM), kill TnCAD-expressing insect cells that are not susceptible to wild-type Cry1Ac, and kill Cry1Ac-resistant T. ni insects up to 335-fold more potently than wild-type Cry1Ac. Our findings establish that the evolution of Bt toxins with novel insect cell receptor affinity can overcome insect Bt toxin resistance and confer lethality approaching that of the wild-type Bt toxin against non-resistant insects.
Collapse
|
132
|
Efficient in vivo mutagenesis in bacteria. Nat Methods 2015. [DOI: 10.1038/nmeth.3672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|