Genomes and Genes
directed molecular evolution
Summary: The techniques used to produce molecules exhibiting properties that conform to the demands of the experimenter. These techniques combine methods of generating structural changes with methods of selection. They are also used to examine proposed mechanisms of evolution under in vitro selection conditions.
- Giger L, Caner S, Obexer R, Kast P, Baker D, Ban N, et al. Evolution of a designed retro-aldolase leads to complete active site remodeling. Nat Chem Biol. 2013;9:494-8 pubmed publisher..Such internal competition between alternative reactive sites may have characterized the early evolution of many natural enzymes. ..
- Dalby P. Strategy and success for the directed evolution of enzymes. Curr Opin Struct Biol. 2011;21:473-80 pubmed publisher..Finally, the combined use of several strategies is likely to be required in practice to improve multiple target properties of an enzyme, as successfully shown by a recent industrial example. ..
- García Ruiz E, Gonzalez Perez D, Ruiz Duenas F, Martinez A, Alcalde M. Directed evolution of a temperature-, peroxide- and alkaline pH-tolerant versatile peroxidase. Biochem J. 2012;441:487-98 pubmed publisher..Overall, the directed evolution approach described provides a set of strategies for selecting VPs with improvements in secretion, activity and stability...
- Subach F, Piatkevich K, Verkhusha V. Directed molecular evolution to design advanced red fluorescent proteins. Nat Methods. 2011;8:1019-26 pubmed publisher..We consider advances in library design by mutagenesis, protein expression systems and instrumentation for high-throughput screening that should yield improved fluorescent proteins for advanced imaging applications. ..
- Goldsmith M, Tawfik D. Enzyme engineering by targeted libraries. Methods Enzymol. 2013;523:257-83 pubmed publisher..Finally, the design efficiency and the optimal mutational loads of libraries are assessed by comparing targeted mutational libraries versus libraries of random mutations. ..
- Fallah Araghi A, Baret J, Ryckelynck M, Griffiths A. A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution. Lab Chip. 2012;12:882-91 pubmed publisher..Compared to screening using microtiter plate-based systems, the volume and cost of PCR and IVTT reagents are reduced by almost 10(5)-fold, allowing the screening of 10(6) genes using only 150 ?L of reagents. ..
- Xiong A, Peng R, Zhuang J, Davies J, Zhang J, Yao Q. Advances in directed molecular evolution of reporter genes. Crit Rev Biotechnol. 2012;32:133-42 pubmed publisher..b>Directed molecular evolution is a powerful molecular tool for the creation of designer proteins for industrial and research ..
- Gaj T, Mercer A, Sirk S, Smith H, Barbas C. A comprehensive approach to zinc-finger recombinase customization enables genomic targeting in human cells. Nucleic Acids Res. 2013;41:3937-46 pubmed publisher..This study demonstrates the feasibility of generating customized ZFRs and the potential of ZFR technology for a diverse range of applications, including genome engineering, synthetic biology and gene therapy. ..
- Camarero S, Pardo I, Cañas A, Molina P, Record E, Martinez A, et al. Engineering platforms for directed evolution of Laccase from Pycnoporus cinnabarinus. Appl Environ Microbiol. 2012;78:1370-84 pubmed publisher..Furthermore, some mutations arising in the evolved preproleader highlighted its potential for heterologous expression of fungal laccases in yeast (S. cerevisiae). ..
- Tokuriki N, Jackson C, Afriat Jurnou L, Wyganowski K, Tang R, Tawfik D. Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme. Nat Commun. 2012;3:1257 pubmed publisher..These findings also suggest that the catalytic efficiency and specificity of many natural enzymes may be far from their optimum. ..
- ..This review surveys recent progress in combining computational and evolutionary approaches to enzyme design, together with insights into enzyme function gained from studies of the engineered catalysts. ..
- Seelig B. mRNA display for the selection and evolution of enzymes from in vitro-translated protein libraries. Nat Protoc. 2011;6:540-52 pubmed publisher..This method is demonstrated by the generation of new RNA ligase enzymes. ..
- Mate D, Gonzalez Perez D, Falk M, Kittl R, Pita M, De Lacey A, et al. Blood tolerant laccase by directed evolution. Chem Biol. 2013;20:223-31 pubmed publisher..This proof of concept that laccases can be adapted to function in extreme conditions opens an array of opportunities for implantable nanobiodevices, chemical syntheses, and detoxification. ..
- Guntas G, Kanwar M, Ostermeier M. Circular permutation in the ?-loop of TEM-1 ?-lactamase results in improved activity and altered substrate specificity. PLoS ONE. 2012;7:e35998 pubmed publisher..These variants were circularly permuted in the ?-loop proximal to the active site. Remarkably, one variant was circularly permuted such that the key catalytic residue Glu166 was located at the N-terminus of the mature protein. ..
- Bell G, Gonzalez A. Adaptation and evolutionary rescue in metapopulations experiencing environmental deterioration. Science. 2011;332:1327-30 pubmed publisher..Adaptation was surprisingly frequent and rapid in small peripheral populations. Thus, evolutionary dynamics affect both the persistence and the range of a species after environmental deterioration. ..
- Traxlmayr M, Faissner M, Stadlmayr G, Hasenhindl C, Antes B, Ruker F, et al. Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast. Biochim Biophys Acta. 2012;1824:542-9 pubmed publisher..These data clearly demonstrate the importance and efficacy of the presented strategy for selection of stabilizing mutations in proteins of high intrinsic stability within reasonable time. ..
- Esvelt K, Carlson J, Liu D. A system for the continuous directed evolution of biomolecules. Nature. 2011;472:499-503 pubmed publisher..By greatly accelerating laboratory evolution, PACE may provide solutions to otherwise intractable directed evolution problems and address novel questions about molecular evolution...
- Degeling M, Bovenberg M, Lewandrowski G, de Gooijer M, Vleggeert Lankamp C, Tannous M, et al. Directed molecular evolution reveals Gaussia luciferase variants with enhanced light output stability. Anal Chem. 2013;85:3006-12 pubmed publisher..To overcome these limitations, a library of Gluc variants was generated using directed molecular evolution and screened for relative light output, a shift in emission spectrum, and glow-type light emission ..
- Kries H, Blomberg R, Hilvert D. De novo enzymes by computational design. Curr Opin Chem Biol. 2013;17:221-8 pubmed publisher..Analysis of their evolutionary trajectories provides valuable feedback for the design algorithms and can enhance our understanding of natural protein evolution. ..
- Dettman J, Rodrigue N, Melnyk A, Wong A, Bailey S, Kassen R. Evolutionary insight from whole-genome sequencing of experimentally evolved microbes. Mol Ecol. 2012;21:2058-77 pubmed publisher..We also outline an example of a computational pipeline for use in EE-WGS studies, based on freely available bioinformatics tools. ..
- Owens R, Gu X, Shin M, Springer T, Jin M. Engineering of single Ig superfamily domain of intercellular adhesion molecule 1 (ICAM-1) for native fold and function. J Biol Chem. 2010;285:15906-15 pubmed publisher..The systematic approach demonstrated in this study to engineer a single Ig superfamily fold in ICAM-1 can be broadly applicable to the engineering of modular Ig superfamily domains in other cell surface molecules. ..
- Horinouchi T, Tamaoka K, Furusawa C, Ono N, Suzuki S, Hirasawa T, et al. Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress. BMC Genomics. 2010;11:579 pubmed publisher..The common phenotypic changes in the ethanol-tolerant strains we identified could provide a fundamental basis for designing ethanol-tolerant strains for industrial purposes. ..
- Gao X, Xie X, Pashkov I, Sawaya M, Laidman J, Zhang W, et al. Directed evolution and structural characterization of a simvastatin synthase. Chem Biol. 2009;16:1064-74 pubmed publisher..Comparisons between the structures reveal that beneficial mutations stabilize the structure of G5 in a more compact conformation that is favorable for catalysis. ..
- Lee D, Palsson B. Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol. Appl Environ Microbiol. 2010;76:4158-68 pubmed publisher..These results provide insight into the genetic basis underlying microbial evolution for growth on a nonnative substrate. ..
- Bloom J, Arnold F. In the light of directed evolution: pathways of adaptive protein evolution. Proc Natl Acad Sci U S A. 2009;106 Suppl 1:9995-10000 pubmed publisher..These lessons about the coupling between adaptive and neutral protein evolution in the laboratory offer insight into the evolution of proteins in nature. ..
- Goodarzi H, Bennett B, Amini S, Reaves M, Hottes A, Rabinowitz J, et al. Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli. Mol Syst Biol. 2010;6:378 pubmed publisher..Remarkably, these laboratory-evolved strains, by and large, follow the same adaptive paths as inferred from our coarse-grained search of the fitness landscape. ..
- Kao K, Sherlock G. Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Nat Genet. 2008;40:1499-504 pubmed publisher..These results represent the most detailed molecular characterization of experimental evolution to date and provide direct experimental evidence supporting both the clonal interference and the multiple mutation models. ..
- Bontjer I, Melchers M, Eggink D, David K, Moore J, Berkhout B, et al. Stabilized HIV-1 envelope glycoprotein trimers lacking the V1V2 domain, obtained by virus evolution. J Biol Chem. 2010;285:36456-70 pubmed publisher..These evolved ?V1V2 trimers could be useful reagents for immunogenicity and structural studies. ..
- Brissos V, Pereira L, Munteanu F, Cavaco Paulo A, Martins L. Expression system of CotA-laccase for directed evolution and high-throughput screenings for the oxidation of high-redox potential dyes. Biotechnol J. 2009;4:558-63 pubmed publisher..The enzymatic assays developed were tested for the screening of one mutant library from CotA-laccase created by error-prone PCR...
- Atsumi S, Wu T, Machado I, Huang W, Chen P, Pellegrini M, et al. Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol Syst Biol. 2010;6:449 pubmed publisher..Interestingly, improved isobutanol tolerance did not increase the final titer of isobutanol production...
- Dong S, Rogan S, Roth B. Directed molecular evolution of DREADDs: a generic approach to creating next-generation RASSLs. Nat Protoc. 2010;5:561-73 pubmed publisher..In this study, we describe a generic protocol for the directed molecular evolution of designer receptors exclusively activated by designer drugs (DREADDs)...
- Takeuchi R, Certo M, Caprara M, Scharenberg A, Stoddard B. Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation. Nucleic Acids Res. 2009;37:877-90 pubmed publisher..This implies that mutations that have previously reduced the endonuclease activity of I-AniI are identified and reversed, sometimes in combination with additional 'artificial' mutations, to optimize its in vivo activity. ..
- Cole M, Gaucher E. Exploiting models of molecular evolution to efficiently direct protein engineering. J Mol Evol. 2011;72:193-203 pubmed publisher..We anticipate that the REAP approach will be used in the future to facilitate the engineering of biopolymers with expanded functions and will thus have a significant impact on the developing field of 'evolutionary synthetic biology'. ..
- Paramesvaran J, Hibbert E, Russell A, Dalby P. Distributions of enzyme residues yielding mutants with improved substrate specificities from two different directed evolution strategies. Protein Eng Des Sel. 2009;22:401-11 pubmed publisher..The results suggest ways in which directed evolution by SDSM could be improved for greater efficiency in terms of reducing the library sizes required to obtain beneficial mutations that alter substrate specificity. ..
- García Ruiz E, Maté D, Ballesteros A, Martinez A, Alcalde M. Evolving thermostability in mutant libraries of ligninolytic oxidoreductases expressed in yeast. Microb Cell Fact. 2010;9:17 pubmed publisher..The existing tradeoff between activity and stability determined from many point mutations discovered by directed evolution and other protein engineering means can be circumvented combining different tools of in vitro evolution. ..
- Chahar S, Elsawy H, Ragozin S, Jeltsch A. Changing the DNA recognition specificity of the EcoDam DNA-(adenine-N6)-methyltransferase by directed evolution. J Mol Biol. 2010;395:79-88 pubmed publisher..We conclude that the new methyltransferases are fully functional in vivo and in vitro but show a new target-site specificity. ..
- Conrad T, Joyce A, Applebee M, Barrett C, Xie B, Gao Y, et al. Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol. 2009;10:R118 pubmed publisher..In contrast, a variety of regulators acquire mutations in the different endpoints, suggesting flexibility in overcoming regulatory challenges in the adaptation. ..
- Guo J, Gaj T, Barbas C. Directed evolution of an enhanced and highly efficient FokI cleavage domain for zinc finger nucleases. J Mol Biol. 2010;400:96-107 pubmed publisher..This enhanced and highly efficient cleavage domain will aid in a variety of ZFN applications in medicine and biology. ..
- Jochens H, Bornscheuer U. Natural diversity to guide focused directed evolution. Chembiochem. 2010;11:1861-6 pubmed publisher..2) towards 3-PBA-ethyl ester, a significant number of hits with improved rates (up to 240-fold) and enantioselectivities (up to E(true)=80) were identified in these "smart" libraries. ..
- Gerstein A, Cleathero L, Mandegar M, Otto S. Haploids adapt faster than diploids across a range of environments. J Evol Biol. 2011;24:531-40 pubmed publisher..These results are consistent with theory that predicts haploids should evolve faster than diploids at large population sizes. ..
- Reetz M, Soni P, Fernández L, Gumulya Y, Carballeira J. Increasing the stability of an enzyme toward hostile organic solvents by directed evolution based on iterative saturation mutagenesis using the B-FIT method. Chem Commun (Camb). 2010;46:8657-8 pubmed publisher..Mutants of the lipase from Bacillus subtilis, previously engineered for enhanced thermostability using directed evolution based on the B-FIT method, show significantly increased tolerance to hostile organic solvents. ..
- Reetz M, Bocola M, Wang L, Sanchis J, Cronin A, Arand M, et al. Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stage. J Am Chem Soc. 2009;131:7334-43 pubmed publisher..Predictions regarding substrate scope and enantioselectivity of the best mutant are shown to be possible...
- Nannemann D, KAUFMANN K, Meiler J, Bachmann B. Design and directed evolution of a dideoxy purine nucleoside phosphorylase. Protein Eng Des Sel. 2010;23:607-16 pubmed publisher..The engineered PNP may form the basis for catalysts and pathways for the biosynthesis of ddI. ..