综述 |
|
|
|
|
体内连续定向进化研究进展 * |
察亚平1,朱牧孜2,李爽1,**() |
1 华南理工大学生物科学与工程学院 广州 510006 2 广东省微生物研究所 广州 510070 |
|
Research Progress on In Vivo Continuous Directed Evolution |
CHA Ya-ping1,ZHU Mu-zi2,LI Shuang1,**() |
1 School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China 2 State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China |
[1] |
Mills D R, Peterson R L, Spiegelman S. An extracellular darwinian experiment with a self-duplicating nucleic acid molecule. Proceedings of the National Academy of Sciences, 1967,58(1):217-224.
|
[2] |
Chen K, Arnold F H. Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proceedings of the National Academy of Sciences, 1993,90(12):5618-5622.
|
[3] |
Stemmer W P. Rapid evolution of a protein in vitro by DNA shuffling. Nature, 1994,370(6488):389-391.
doi: 10.1038/370389a0
pmid: 8047147
|
[4] |
Lutz S. Beyond directed evolution-semi-rational protein engineering and design. Current Opinion in Chemical Biology, 2010,21(6):734-743.
|
[5] |
Avoigt C, Kauffman S, Wang Z G. Rational evolutionary design: the theory of in vitro protein evolution. Evolutionary Protein Design, 2001,55:79-160.
|
[6] |
Arnold F H, Georgiou G. Directed enzyme evolution: screening and selection methods. Totowa: Humana Press, 2003: 1-2.
|
[7] |
Lang G I, Murray A W. Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae. Genetics, 2008,178(1):67-82.
pmid: 18202359
|
[8] |
Camps M, Naukkarinen J, Johnson B P, et al. Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I. Proceedings of the National Academy of Sciences, 2003,100(17):9727-9732.
|
[9] |
Larrea A A, Lujan S A, Kunkel T A. SnapShot: DNA mismatch repair. Cell, 2010,141(4):730-731e1.
pmid: 20478261
|
[10] |
Morrison M S, Podracky C J, Liu D R. The developing toolkit of continuous directed evolution. Nature Chemical Biology, 2020,16(6):610-619.
|
[11] |
Badran A H, Liu D R. In vivo continuous directed evolution. Current Opinion in Chemical Biology, 2015,24:1-10.
pmid: 25461718
|
[12] |
D’Oelsnitz S, Ellington A. Continuous directed evolution for strain and protein engineering. Current Opinion in Chemical Biology, 2018,53:158-163.
|
[13] |
Husimi Y. Selection and evolution of bacteriophages in cellstat. Advances in Biophysics, 1989,25:1-43.
doi: 10.1016/0065-227x(89)90003-8
pmid: 2696338
|
[14] |
Esvelt K M, Carlson J C, Liu D R. A system for the continuous directed evolution of biomolecules. Nature, 2011,472(7344):499-503.
|
[15] |
Carlson J C, Badran A H, Guggiana-Nilo D A, et al. Negative selection and stringency modulation in phage-assisted continuous evolution. Nature Chemical Biology, 2014,10(3):216-222.
doi: 10.1038/NCHEMBIO.1453
|
[16] |
Dickinson B C, Packer M S, Badran A H, et al. A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations. Nature Communications, 2014,5:5352.
|
[17] |
Packer M S, Rees H A, Liu D R. Phage-assisted continuous evolution of proteases with altered substrate specificity. Nature Communications, 2017,8(1):956.
|
[18] |
Badran A H, Guzov V M, Huai Q, et al. Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance. Nature, 2016,533(7601):58-63.
pmid: 27120167
|
[19] |
Wang T, Badran A H, Huang T P, et al. Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 2018,14(10):972-980.
pmid: 30127387
|
[20] |
Bryson D, Fan C, Guo L T, et al. Continuous directed evolution of aminoacyl-tRNA synthetases. Nature Chemical Biology, 2017,13(2):1253-1260.
|
[21] |
Hubbard B P, Badran A H, Zuris J A, et al. Continuous directed evolution of DNA-binding proteins to improve TALEN specificity. Nature Methods, 2015,12(10):939-942.
pmid: 26258293
|
[22] |
Hu J H, Miller S M, Geurts M H, et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature, 2018,556(7699):57-63.
|
[23] |
Miller S M, Wang T, Randolph P B, et al. Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 2020,38(4):471-481.
pmid: 32042170
|
[24] |
Thuronyi B W, Koblan L W, Levy J M, et al. Continuous evolution of base editors with expanded target compatibility and improved activity. Nature Biotechnology, 2019,37(9):1070-1079.
|
[25] |
Wang H H, Isaacs F J, Carr P A, et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature, 2009,460(7257):894-898.
pmid: 19633652
|
[26] |
Luan G, Cai Z, Li Y, et al. Genome replication engineering assisted continuous evolution (GREACE) to improve microbial tolerance for biofuels production. Biotechnology for Biofuels, 2013,6(1):137.
|
[27] |
Luan G D, Cai Z, Luan G, et al. Developing controllable hypermutable clostridium cells through manipulating its methyl-directed mismatch repair system. Protein Cell, 2013,4(11):854-862.
|
[28] |
Lennen R M, Nilsson Wallin A I, Pedersen M, et al. Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects. Nucleic Acids Research, 2016,44(4):e36.
|
[29] |
Nyerges A, Csorgo B, Nagy I, et al. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species. Proceedings of the National Academy of Sciences, 2016,113(9):2502-2507.
|
[30] |
Pham H L, Wong A, Chua N, et al. Engineering a riboswitch-based genetic platform for the self-directed evolution of acid-tolerant phenotypes. Nature Communications, 2017,8(1):411.
|
[31] |
Zhu L J, Li Y, Cai Z. Development of a stress-induced mutagenesis module for autonomous adaptive evolution of Escherichia coli to improve its stress tolerance. Biotechnology for Biofuels, 2015,8:93.
pmid: 26136829
|
[32] |
Halperin S O, Tou C J, Wong E B, et al. CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature, 2018,560(7717):248-252.
|
[33] |
Si T, Chao R, Min Y H, et al. Automated multiplex genome-scale engineering in yeast. Nature Communications, 2017,8:15187.
doi: 10.1038/ncomms15187
pmid: 28469255
|
[34] |
Garst A D, Bassalo M C, Pines G, et al. Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering. Nature Biotechnology, 2017,35(1):48-55.
|
[35] |
Hess G T, Fresard L, Han K, et al. Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. Nature Methods, 2016,13(12):1036-1042.
|
[36] |
Ravikumar A, Arrieta A, Liu C C. An orthogonal DNA replication system in yeast. Nature Chemical Biology, 2014,10(3):175-177.
|
[37] |
Arzumanyan G, Gabriel K N, Ravikumar A, et al. Mutually orthogonal DNA replication systems in vivo. ACS Synthetic Biology, 2018,7(7):1722-1729.
|
[38] |
Ravikumar A, Arzumanyan G A, Obadi M K A, et al. Scalable, continuous evolution of genes at mutation rates above genomic error thresholds. Cell, 2018,175(7):1946-1957.
pmid: 30415839
|
[39] |
Crook N, Abatemarco J, Sun J, et al. In vivo continuous evolution of genes and pathways in yeast. Nature Communications, 2016,7:13051.
doi: 10.1038/ncomms13051
pmid: 27748457
|
[40] |
Romero P A, Arnold F H. Exploring protein fitness landscapes by directed evolution. Nature Reviews Molecular Cell Biology, 2009,10(12):866-876.
|
[41] |
Feist A M, Zielinski D C, Orth J D, et al. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metabolic Engineering, 2010,12(3):173-186.
|
[42] |
Mohamed E T, Wang S, Lennen R M, et al. Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. Microbial Cell Factories, 2017,16(1):204.
|
[43] |
Caspeta L, Chen Y, Ghiaci P, et al. Altered sterol composition renders yeast thermotolerant. Science, 2014,346(6205):75-78.
pmid: 25278608
|
[44] |
Xie W P, Lv X M, Ye L D, et al. Construction of lycopene-overproducing Saccharomyces cerevisiae by combining directed evolution and metabolic engineering. Metabolic Engineering, 2015,30:69-78.
pmid: 25959020
|
[45] |
Engström K, Nyhleén J, Sandström A G, et al. Directed evolution of an enantioselective lipase with broad substrate scope for hydrolysis of α-substituted esters. Journal of the American Chemical Society, 2010,132(20):7038-7042.
|
[46] |
Shepelin D, Hansen A S L, Lennen R, et al. Selecting the best: evolutionary engineering of chemical production in microbes. Genes, 2018,9(5):249.
|
[47] |
Burgard A P, Pharkya P, Maranas C D. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnology and Bioengineering, 2003,84(6):647-657.
doi: 10.1002/bit.10803
pmid: 14595777
|
[48] |
Hassanpour N, Ullah E, Yousofshahi M, et al. Selection finder (SelFi): a computational metabolic engineering tool to enable directed evolution of enzymes. Metabolic Engineering Communications, 2017,4:37-47.
|
[49] |
Zhou S, Shanmugam K T, Ingram L O. Functional replacement of the Escherichia coli D-(-)-lactate dehydrogenase gene (ldhA) with the L-(+)-lactate dehydrogenase gene (ldhL) from Pediococcus acidilactici. Applied and Environmental Microbiology, 2003,69(4):2237-2244.
|
[50] |
Zhang X, Jantama K, Moore J C, et al. Production of L-alanine by metabolically engineered Escherichia coli. Applied and Environmental Microbiology, 2007,77(2):355-366.
|
[51] |
Shen C R, Lan E I, Dekishima Y, et al. Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli enabled by driving forces. Applied and Environmental Microbiology, 2011,77(9):2905-2915.
doi: 10.1128/AEM.03034-10
pmid: 21398484
|
[52] |
Jantama K, Haupt M J, Svoronos S A, et al. Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate. Biotechnology and Bioengineering, 2008,99(5):1140-1153.
|
[53] |
Tai Y S, Xiong M, Jambunathan P, et al. Engineering nonphosphorylative metabolism to generate lignocellulose-derived products. Nature Chemical Biology, 2016,12(4):247-253.
pmid: 26854668
|
[54] |
Reyes L H, Gomez J M, Kao K C. Improving carotenoids production in yeast via adaptive laboratory evolution. Metabolic Engineering, 2014,21:26-33.
doi: 10.1016/j.ymben.2013.11.002
pmid: 24262517
|
[55] |
Minty J J, Lesnefsky A A, Lin F M, et al. Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli. Microbial Cell Factories, 2011,10(1):18.
|
[56] |
Zhuang Y, Yang G Y, Chen X, et al. Biosynthesis of plant-derived ginsenoside Rh2 in yeast via repurposing a key promiscuous microbial enzyme. Metabolic Engineering, 2017,42:25-32.
pmid: 28479190
|
[57] |
Cho S M. Optimizing tyrosine production in yeast via in vivo continuous evolution. Austin: The University of Texas at Austin, 2016.
|
[58] |
Tan Y M, Zhang Y, Han Y B, et al. Directed evolution of an α1, 3-fucosyltransferase using a single-cell ultrahigh-throughput screening method. Science Advances, 2019, 5(10): eaaw8451.
|
[59] |
Kortmann M, Mack C, Baumgart M, et al. Pyruvate carboxylase variants enabling improved Lysine production from glucose identified by biosensor-based high-throughput fluorescence-activated cell sorting screening. ACS Synthetic Biology, 2019,8(2):274-281.
doi: 10.1021/acssynbio.8b00510
pmid: 30707564
|
[60] |
Agresti J J, Antipov E, Abate A R, et al. Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proceedings of the National Academy of Sciences, 2010,107(9):4004-4009.
|
[61] |
Saleski T E, Kerner A R, Chung M T, et al. Syntrophic co-culture amplification of production phenotype for high-throughput screening of microbial strain libraries. Metabolic Engineering, 2019,54:232-243.
|
[62] |
Monod J. La technique de culture continue: theorie et applications. Annales de l Institut Pasteur, 1950,79:390-410.
|
[63] |
De Crecy E, Jaronski S, Lyons B, et al. Directed evolution of a filamentous fungus for thermotolerance. BMC Biotechnology, 2009,9:74.
|
[64] |
Van Gerven N, Klein R D, Hultgren S J, et al. Bacterial amyloid formation: structural insights into curli biogensis. Trends in Microbiology, 2015,23(11):693-706.
|
[65] |
Hope E A, Amorosi C J, Miller A W, et al. Experimental evolution reveals favored adaptive routes to cell aggregation in yeast. Genetics, 2017,206(2):1153-1167.
doi: 10.1534/genetics.116.198895
pmid: 28450459
|
[66] |
Marliere P, Patrouix J, Doring V, et al. Chemical evolution of a bacterium’s genome. Angewandte Chemie International Edition, 2011,50(31):7109-7114.
|
[67] |
Bouzon M, Perret A, Loreau O, et al. A synthetic alternative to canonical one-carbon metabolism. ACS Synthetic Biology, 2017,6(8):1520-1533.
doi: 10.1021/acssynbio.7b00029
pmid: 28467058
|
[68] |
Jian X J, Guo X J, Wang J, et al. Microbial microdroplet culture system (MMC): an integrated platform for automated, high-throughput microbial cultivation and adaptive evolution. Biotechnology and Bioengineering, 2020,117(6):1724-1737.
doi: 10.1002/bit.27327
pmid: 32159223
|
[69] |
Wang J, Jian X J, Xing X H, et al. Empowering a methanol-dependent Escherichia coli via adaptive evolution using a high-throughput microbial microdroplet culture system. Frontiers in Bioengineering and Biotechnology, 2020,8:570.
|
[70] |
Horinouchi T, Minamoto T, Suzuki S, et al. Development of an automated culture system for laboratory evolution. Journal of Laboratory Automation, 2014,19(5):478-482.
doi: 10.1177/2211068214521417
pmid: 24526062
|
[71] |
Miller A W, Befort C, Kerr E O, et al. Design and use of multiplexed chemostat arrays. Journal of Visualized Experiments, 2013,72:e50262.
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
|
Shared |
|
|
|
|
|
Discussed |
|
|
|
|