Synthetic evolution

The combination of modern biotechnologies such as DNA synthesis, λ red recombineering, CRISPR-based editing and next-generation high-throughput sequencing increasingly enables precise manipulation of genes and genomes. Beyond rational design, these technologies also enable the targeted, and potentially continuous, introduction of multiple mutations. While this might seem to be merely a return to natural selection, the ability to target evolution greatly reduces fitness burdens and focuses mutation and selection on those genes and traits that best contribute to a desired phenotype, ultimately throwing evolution into fast forward.From unbiased mutagenesis to precision modification, in genes or whole genomes, researchers have a panoply of tools to direct evolution.

[1]  Hal S Alper,et al.  In vivo continuous evolution of genes and pathways in yeast , 2016, Nature Communications.

[2]  Jameson K. Rogers,et al.  Evolution-guided optimization of biosynthetic pathways , 2014, Proceedings of the National Academy of Sciences.

[3]  J. Keasling,et al.  CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9. , 2018, Metabolic engineering.

[4]  David R. Liu,et al.  Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage , 2016, Nature.

[5]  Cédric R. Weber,et al.  High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis , 2018, bioRxiv.

[6]  Feng Zhang,et al.  Engineered Cpf1 variants with altered PAM specificities increase genome targeting range , 2017, Nature Biotechnology.

[7]  M Boutabout,et al.  DNA synthesis fidelity by the reverse transcriptase of the yeast retrotransposon Ty1. , 2001, Nucleic acids research.

[8]  Yan Zhang,et al.  Metabolic engineering of Escherichia coli using CRISPR-Cas9 meditated genome editing. , 2015, Metabolic engineering.

[9]  Stan Wang,et al.  The Future of Multiplexed Eukaryotic Genome Engineering. , 2017, ACS chemical biology.

[10]  David A. Scott,et al.  Functionally diverse type V CRISPR-Cas systems , 2019, Science.

[11]  David A. Scott,et al.  Genome engineering using the CRISPR-Cas9 system , 2013, Nature Protocols.

[12]  D. Botstein,et al.  Identification of amino acid substitutions that alter the substrate specificity of TEM-1 beta-lactamase , 1992, Journal of bacteriology.

[13]  P. Jennings,et al.  Random mutagenesis of the substrate-binding site of a serine protease can generate enzymes with increased activities and altered primary specificities. , 1993, Biochemistry.

[14]  Farren J. Isaacs,et al.  Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.

[15]  Andrew D. Ellington,et al.  Synthetic evolutionary origin of a proofreading reverse transcriptase , 2016, Science.

[16]  Dan S. Tawfik,et al.  Man-made cell-like compartments for molecular evolution , 1998, Nature Biotechnology.

[17]  S. Benkovic,et al.  Hybrid enzymes: manipulating enzyme design. , 1998, Trends in biotechnology.

[18]  Merja Penttilä,et al.  Yeast oligo-mediated genome engineering (YOGE). , 2013, ACS synthetic biology.

[19]  K. Struhl,et al.  An efficient method for generating proteins with altered enzymatic properties: application to beta-lactamase. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[20]  G. Stephanopoulos,et al.  Global transcription machinery engineering: a new approach for improving cellular phenotype. , 2007, Metabolic engineering.

[21]  W. Stemmer,et al.  DNA shuffling of a family of genes from diverse species accelerates directed evolution , 1998, Nature.

[22]  Ping Wang,et al.  Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance , 2016 .

[23]  J. Boeke,et al.  Replication infidelity during a single cycle of Ty1 retrotransposition. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Jeff F. Miller,et al.  Diversity-generating retroelements. , 2007, Current opinion in microbiology.

[25]  Martin J. Aryee,et al.  In vivo CRISPR editing with no detectable genome-wide off-target mutations , 2018, Nature.

[26]  Andrew D Ellington,et al.  Directed evolution of a synthetic phylogeny of programmable Trp repressors , 2018, Nature Chemical Biology.

[27]  Yan Song,et al.  Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells , 2016, Nature Methods.

[28]  George M. Church,et al.  Developmental barcoding of whole mouse via homing CRISPR , 2018, Science.

[29]  C. Auerbach CHEMICAL MUTAGENESIS , 1949, Biological Reviews of The Cambridge Philosophical Society.

[30]  T. Lu,et al.  Genomically encoded analog memory with precise in vivo DNA writing in living cell populations , 2014, Science.

[31]  G. F. Joyce,et al.  Directed evolution of an RNA enzyme. , 1992, Science.

[32]  J. Keasling,et al.  High-throughput metabolic engineering: advances in small-molecule screening and selection. , 2010, Annual review of biochemistry.

[33]  G. F. Joyce,et al.  Randomization of genes by PCR mutagenesis. , 1992, PCR methods and applications.

[34]  Joel S. Bader,et al.  Synthetic chromosome arms function in yeast and generate phenotypic diversity by design , 2011, Nature.

[35]  George M. Church,et al.  Rapidly evolving homing CRISPR barcodes , 2016, Nature Methods.

[36]  Feng Zhang,et al.  Engineered Cpf1 variants with altered PAM specificities increase genome targeting range , 2017, Nature Biotechnology.

[37]  J. H. Shim,et al.  Combinatorial protein engineering by incremental truncation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[38]  A. Rasheed,et al.  Combinatorial Chemistry: A Review , 2014 .

[39]  George M. Church,et al.  Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems , 2013, Nucleic acids research.

[40]  A. Ellington,et al.  Compartmentalized partnered replication for the directed evolution of genetic parts and circuits , 2017, Nature Protocols.

[41]  D. Gordenin,et al.  Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[42]  David R. Liu,et al.  Continuous evolution of B. thuringiensis toxins overcomes insect resistance , 2016, Nature.

[43]  Gaelen T. Hess,et al.  Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions , 2017, Nature Biotechnology.

[44]  A. Camilli,et al.  Tn-seq; high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms , 2009, Nature Methods.

[45]  R. Simons,et al.  Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements , 2004, Nature.

[46]  S. Kosuri,et al.  Highly parallel genome variant engineering with CRISPR/Cas9 , 2018, Nature Genetics.

[47]  Andrew D Ellington,et al.  Generalized bacterial genome editing using mobile group II introns and Cre-lox , 2013, Molecular systems biology.

[48]  Jennifer A. Doudna,et al.  Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering , 2016, Cell.

[49]  O. Gamborg,et al.  Plant protoplast fusion and growth of intergeneric hybrid cells , 2004, Planta.

[50]  J. Toscano-Garibay,et al.  RNA Aptamer Evolution: Two Decades of SELEction , 2011, International journal of molecular sciences.

[51]  Gaelen T. Hess,et al.  Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells , 2016, Nature Methods.

[52]  Ryan T Gill,et al.  Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides , 2010, Nature Biotechnology.

[53]  Dan S. Tawfik,et al.  Evolution of new protein topologies through multistep gene rearrangements , 2006, Nature Genetics.

[54]  Marc Ostermeier,et al.  A combinatorial approach to hybrid enzymes independent of DNA homology , 1999, Nature Biotechnology.

[55]  Jennifer A. Doudna,et al.  CRISPR-Cas guides the future of genetic engineering , 2018, Science.

[56]  K. Lam,et al.  Combinatorial chemistry in drug discovery. , 2017, Current opinion in chemical biology.

[57]  M. Maluszynski,et al.  Global impact of mutation-derived varieties , 2004, Euphytica.

[58]  Feng Zhang,et al.  CRISPR-assisted editing of bacterial genomes , 2013, Nature Biotechnology.

[59]  David R. Liu,et al.  Phage-assisted continuous evolution of proteases with altered substrate specificity , 2017, Nature Communications.

[60]  Arjun Ravikumar,et al.  Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds , 2018, Cell.

[61]  K. Struhl,et al.  Saturation mutagenesis of a yeast his3 "TATA element": genetic evidence for a specific TATA-binding protein. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[62]  S. Harayama,et al.  Novel family shuffling methods for the in vitro evolution of enzymes. , 1999, Gene.

[63]  Dieter Söll,et al.  Continuous directed evolution of aminoacyl-tRNA synthetases , 2017, Nature chemical biology.

[64]  L. Loeb,et al.  On the fidelity of DNA replication: manganese mutagenesis in vitro. , 1985, Biochemistry.

[65]  Ki-Hyun Kim,et al.  Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications. , 2019, Trends in biochemical sciences.

[66]  D. M. Brown,et al.  An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. , 1996, Journal of molecular biology.

[67]  Barrett R. Morrow,et al.  Retroelement-Based Genome Editing and Evolution. , 2018, ACS synthetic biology.

[68]  D. Court,et al.  High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[69]  Michael J. Shen,et al.  Precise control of SCRaMbLE in synthetic haploid and diploid yeast , 2018, Nature Communications.

[70]  Bryan C Dickinson,et al.  Evolution of a split RNA polymerase as a versatile biosensor platform. , 2017, Nature chemical biology.

[71]  W. Stemmer DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[72]  John E. Dueber,et al.  CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window , 2018, Nature.

[73]  Joseph C. Hogan,et al.  Combinatorial chemistry in drug discovery , 1997, Nature Biotechnology.

[74]  A. Ellington,et al.  Directed Evolution of a Panel of Orthogonal T7 RNA Polymerase Variants for in Vivo or in Vitro Synthetic Circuitry. , 2015, ACS synthetic biology.

[75]  Prashant Mali,et al.  Rapidly evolving homing CRISPR barcodes , 2017, Nature Methods.

[76]  S. Epstein,et al.  Chemical Mutagenesis , 1971, Nature.

[77]  David R. Liu,et al.  Negative selection and stringency modulation in phage-assisted constinuous evolution , 2014, Nature chemical biology.

[78]  Jennifer L. Ong,et al.  Directed evolution of polymerase function by compartmentalized self-replication , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[79]  Mario Hupfeld,et al.  A functional type II-A CRISPR–Cas system from Listeria enables efficient genome editing of large non-integrating bacteriophage , 2018, Nucleic acids research.

[80]  Frank Buchholz,et al.  A new logic for DNA engineering using recombination in Escherichia coli , 1998, Nature Genetics.

[81]  Farren J. Isaacs,et al.  Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes , 2017, Cell.

[82]  F. Sherman,et al.  Transformation of yeast with synthetic oligonucleotides. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[83]  Christopher A. Voigt,et al.  Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors , 2018, Nature Chemical Biology.

[84]  D. Valentine,et al.  Targeted diversity generation by intraterrestrial archaea and archaeal viruses , 2015, Nature Communications.

[85]  H J Muller,et al.  ARTIFICIAL TRANSMUTATION OF THE GENE. , 1927, Science.

[86]  Farren J. Isaacs,et al.  Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA , 2014, Nature Protocols.

[87]  S. Inouye,et al.  Retrons, msDNA, and the bacterial genome , 2005, Cytogenetic and Genome Research.

[88]  N. Costantino,et al.  Recombineering: Genetic Engineering in Bacteria Using Homologous Recombination , 2003 .

[89]  Vitor B. Pinheiro,et al.  Evolving a polymerase for hydrophobic base analogues. , 2009, Journal of the American Chemical Society.

[90]  W. Stemmer,et al.  Genome shuffling leads to rapid phenotypic improvement in bacteria , 2002, Nature.

[91]  David R. Liu,et al.  A System for the Continuous Directed Evolution of Biomolecules , 2011, Nature.

[92]  W. Stemmer Rapid evolution of a protein in vitro by DNA shuffling , 1994, Nature.

[93]  Feng Zhang,et al.  Genome engineering using CRISPR-Cas9 system. , 2015, Methods in molecular biology.

[94]  J. Peberdy Developments in protoplast fusion in fungi. , 1987, Microbiological sciences.

[95]  R. Simons,et al.  Reverse Transcriptase-Mediated Tropism Switching in Bordetella Bacteriophage , 2002, Science.

[96]  Alex Toftgaard Nielsen,et al.  CRMAGE: CRISPR Optimized MAGE Recombineering , 2016, Scientific Reports.

[97]  E. M. DeGennaro,et al.  Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array , 2016, Nature Biotechnology.

[98]  D. Court,et al.  Recombineering: a homologous recombination-based method of genetic engineering , 2009, Nature Protocols.

[99]  S. Pääbo,et al.  Molecular breeding of polymerases for amplification of ancient DNA , 2007, Nature Biotechnology.

[100]  R. Tsien,et al.  Evolution of new nonantibody proteins via iterative somatic hypermutation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[101]  Vincent L. Butty,et al.  An Adaptable Platform for Directed Evolution in Human Cells. , 2018, Journal of the American Chemical Society.

[102]  Tony P. Huang,et al.  Continuous directed evolution of proteins with improved soluble expression , 2018, Nature Chemical Biology.

[103]  Daniel E. Deatherage,et al.  Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli , 2013, Proceedings of the National Academy of Sciences.

[104]  Xintian Li,et al.  Recombineering: Genetic Engineering in Bacteria Using Homologous Recombination , 2003, Current protocols in molecular biology.

[105]  B. González,et al.  Positive selection of DNA-protein interactions in mammalian cells through phenotypic coupling with retrovirus production , 2009, Nature Structural &Molecular Biology.

[106]  S. Zimmerly,et al.  An Unexplored Diversity of Reverse Transcriptases in Bacteria , 2015, Microbiology spectrum.

[107]  David R. Liu,et al.  Evolved Cas9 variants with broad PAM compatibility and high DNA specificity , 2018, Nature.

[108]  David R. Liu,et al.  Development of potent in vivo mutagenesis plasmids with broad mutational spectra , 2015, Nature Communications.

[109]  C. Craik,et al.  Substrate specificity of trypsin investigated by using a genetic selection. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[110]  A. Ellington,et al.  Library Generation by Gene Shuffling , 2014, Current protocols in molecular biology.

[111]  Arjun Ravikumar,et al.  An orthogonal DNA replication system in yeast. , 2014, Nature chemical biology.

[112]  Andrew D Griffiths,et al.  Amplification of complex gene libraries by emulsion PCR , 2006, Nature Methods.

[113]  Frances H Arnold,et al.  General method for sequence-independent site-directed chimeragenesis. , 2003, Journal of molecular biology.

[114]  Harri Savilahti,et al.  Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment. , 2009, Analytical biochemistry.

[115]  M. Ditzler,et al.  In vitro evolution of distinct self-cleaving ribozymes in diverse environments , 2015, Nucleic acids research.

[116]  Michael R. Green,et al.  CRISPR-Cas9–mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy , 2017, Proceedings of the National Academy of Sciences.

[117]  Harleen Kaur,et al.  Recent developments in cell-SELEX technology for aptamer selection. , 2018, Biochimica et biophysica acta. General subjects.

[118]  Frances H. Arnold,et al.  Enzyme Engineering for Nonaqueous Solvents: Random Mutagenesis to Enhance Activity of Subtilisin E in Polar Organic Media , 1991, Bio/Technology.

[119]  G. Weiss,et al.  Protein Engineering with Biosynthesized Libraries from Bordetella bronchiseptica Bacteriophage , 2013, PloS one.

[120]  G. Church,et al.  Genome-scale promoter engineering by Co-Selection MAGE , 2012, Nature Methods.

[121]  István Nagy,et al.  Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance , 2018, Proceedings of the National Academy of Sciences.

[122]  Ryan T Gill,et al.  Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering , 2016, Nature Biotechnology.

[123]  Manel Camps,et al.  Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[124]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[125]  R. Sauer,et al.  Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. , 1988, Science.

[126]  M. Neuberger,et al.  Generation and iterative affinity maturation of antibodies in vitro using hypermutating B-cell lines , 2002, Nature Biotechnology.

[127]  Kyung-Soon Park,et al.  Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors , 2003, Nature Biotechnology.

[128]  Alaksh Choudhury,et al.  Iterative genome editing of Escherichia coli for 3-hydroxypropionic acid production. , 2018, Metabolic engineering.

[129]  A. Ellington,et al.  Compartmentalized Self‐Replication for Evolution of a DNA Polymerase , 2018, Current protocols in chemical biology.

[130]  F. Arnold,et al.  Evolving strategies for enzyme engineering. , 2005, Current opinion in structural biology.

[131]  D. Gokhale,et al.  Protoplast fusion: a tool for intergeneric gene transfer in bacteria. , 1993, Biotechnology advances.

[132]  S. Jinks-Robertson,et al.  Oligonucleotide transformation of yeast reveals mismatch repair complexes to be differentially active on DNA replication strands , 2007, Proceedings of the National Academy of Sciences.

[133]  Jeff F. Miller,et al.  Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey , 2017, Nucleic acids research.

[134]  Brian C. Thomas,et al.  Retroelement guided protein diversification abounds in vast lineages of bacteria and archaea , 2017, Nature Microbiology.

[135]  Andrew D. Ellington,et al.  Directed evolution of genetic parts and circuits by compartmentalized partnered replication , 2013, Nature Biotechnology.

[136]  G. Stephanopoulos,et al.  Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production , 2006, Science.

[137]  Joseph D. Janizek,et al.  Accurate classification of BRCA1 variants with saturation genome editing , 2018, Nature.

[138]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[139]  Robert P. St.Onge,et al.  Multiplexed precision genome editing with trackable genomic barcodes in yeast , 2018, Nature Biotechnology.

[140]  Qi-li Zhu,et al.  Using global transcription machinery engineering (gTME) to improve ethanol tolerance of Zymomonas mobilis , 2016, Microbial Cell Factories.

[141]  Farren J. Isaacs,et al.  Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection , 2012, Nucleic acids research.

[142]  J. Doudna,et al.  The new frontier of genome engineering with CRISPR-Cas9 , 2014, Science.

[143]  D. Goeddel,et al.  A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction , 1989 .