Abstract
Due to limited knowledge of complicated cellular networks, directed evolution has played critical roles in strain improvement, especially for complex traits with hundreds of genetic determinants and for organisms with few genetic tools. Directed evolution mimics natural evolution in the laboratory via iterative cycles of diversity generation and functional selection or screening to isolate evolved mutants with desirable phenotypes. In this chapter, we summarize recent technological advances and applications of directed evolution in strain development, focusing on the efforts for accelerating evolution workflows, expanding the range of target phenotypes, and facilitating mechanistic understanding of evolved mutations.
$Tong Si and Jiazhang Lian contributed equally to this work
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abbott DA, Zelle RM, Pronk JT, Maris AJA (2009) Metabolic engineering of Saccharomyces cerevisiae for production of carboxylic acids: current status and challenges. FEMS Yeast Res 9(8):1123–1136
Alexeyev MF, Shokolenko IN (1995) Mini-Tn10 transposon derivatives for insertion mutagenesis and gene delivery into the chromosome of gram-negative bacteria. Gene 160(1):59–62
Almario MP, Reyes LH, Kao KC (2013) Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass. Biotechnol Bioeng 110(10):2616–2623
Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314(5805):1565–1568
Alper H, Stephanopoulos G (2007) Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab Eng 9(3):258–267
Atsumi S, Liao JC (2008) Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli. Appl Environ Microbiol 74(24):7802–7808
Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2:2006.0008
Bailey JE (1991) Toward a science of metabolic engineering. Science 252(5013):1668–1675
Bailey JE, Sburlati A, Hatzimanikatis V, Lee K, Renner WA, Tsai PS (1996) Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol Bioeng 52(1):109–121
Bao Z, Xiao H, Liang J, Zhang L, Xiong X, Sun N, Si T, Zhao H (2015) Homology-integrated CRISPR-Cas (HI-CRISPR) system for one-step multigene disruption in Saccharomyces cerevisiae. ACS Synth Biol 4(5):585–594
Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461(7268):1243–1247
Biot-Pelletier D, Martin VJ (2014) Evolutionary engineering by genome shuffling. Appl Microbiol Biotechnol 98(9):3877–3887
Blank D, Wolf L, Ackermann M, Silander OK (2014) The predictability of molecular evolution during functional innovation. Proc Natl Acad Sci U S A 111(8):3044–3049
Brennan TC, Williams TC, Schulz BL, Palfreyman RW, Kromer JO, Nielsen LK (2015) Evolutionary engineering improves tolerance for replacement jet fuels in Saccharomyces cerevisiae. Appl Environ Microbiol 81(10):3316–3325
Burgard AP, Pharkya P, Maranas CD (2003) Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84(6):647–657
Cadiere A, Aguera E, Caille S, Ortiz-Julien A, Dequin S (2012) Pilot-scale evaluation the enological traits of a novel, aromatic wine yeast strain obtained by adaptive evolution. Food Microbiol 32(2):332–337
Cadiere A, Ortiz-Julien A, Camarasa C, Dequin S (2011) Evolutionary engineered Saccharomyces cerevisiae wine yeast strains with increased in vivo flux through the pentose phosphate pathway. Metab Eng 13(3):263–271
Cakar ZP, Turanli-Yildiz B, Alkim C, Yilmaz U (2012) Evolutionary engineering of Saccharomyces cerevisiae for improved industrially important properties. FEMS Yeast Res 12(2):171–182
Carr PA, Church GM (2009) Genome engineering. Nat Biotechnol 27(12):1151–1162
Caspeta L, Chen Y, Ghiaci P, Feizi A, Buskov S, Hallstrom BM, Petranovic D, Nielsen J (2014) Altered sterol composition renders yeast thermotolerant. Science 346(6205):75–78
Caspeta L, Nielsen J (2015) Thermotolerant yeast strains adapted by laboratory evolution show trade-off at ancestral temperatures and preadaptation to other stresses. MBio 6(4):e00431
Chen Y, Sheng J, Jiang T, Stevens J, Feng X, Wei N (2016) Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae. Biotechnol Biofuels 9:9
Chou HH, Keasling JD (2013) Programming adaptive control to evolve increased metabolite production. Nat Commun 4:2595
Cobb RE, Wang Y, Zhao H (2015) High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 4(6):723–728
Cong L, Ran FA, Cox D, Lin SL, Barretto R, Habib N, Hsu PD, Wu XB, Jiang WY, Marraffini LA, Zhang F (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339(6121):819–823
Dean AM, Thornton JW (2007) Mechanistic approaches to the study of evolution: the functional synthesis. Nat Rev Genet 8(9):675–688
Demeke MM, Foulquie-Moreno MR, Dumortier F, Thevelein JM (2015) Rapid evolution of recombinant Saccharomyces cerevisiae for Xylose fermentation through formation of extra-chromosomal circular DNA. PLoS Genet 11(3):e1005010
DiCarlo JE, Conley AJ, Penttila M, Jantti J, Wang HH, Church GM (2013) Yeast oligo-mediated genome engineering (YOGE). ACS Synth Biol 2(12):741–749
Dietrich JA, McKee AE, Keasling JD (2010) High-throughput metabolic engineering: advances in small-molecule screening and selection. Annu Rev Biochem 79:563–590
Dietrich JA, Shis DL, Alikhani A, Keasling JD (2013) Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. ACS Synth Biol 2(1):47–58
Dörr M, Fibinger MPC, Last D, Schmidt S, Santos-Aberturas J, Böttcher D, Hummel A, Vickers C, Voss M, Bornscheuer UT (2016) Fully automatized high-throughput enzyme library screening using a robotic platform. Biotechnol Bioeng. doi:10.1002/bit.25925
Dragosits M, Mattanovich D (2013) Adaptive laboratory evolution – principles and applications for biotechnology. Microb Cell Fact 12:64
Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD (2011) Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477(7365):471–476
Ellis HM, Yu D, Di Tizio T, Court DL (2001) High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc Natl Acad Sci U S A 98(12):6742–6746
Enquist-Newman M, Faust AM, Bravo DD, Santos CN, Raisner RM, Hanel A, Sarvabhowman P, Le C, Regitsky DD, Cooper SR, Peereboom L, Clark A, Martinez Y, Goldsmith J, Cho MY, Donohoue PD, Luo L, Lamberson B, Tamrakar P, Kim EJ, Villari JL, Gill A, Tripathi SA, Karamchedu P, Paredes CJ, Rajgarhia V, Kotlar HK, Bailey RB, Miller DJ, Ohler NL, Swimmer C, Yoshikuni Y (2014) Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform. Nature 505(7482):239–243
Esvelt KM, Wang HH (2013) Genome-scale engineering for systems and synthetic biology. Mol Syst Biol 9:641
Flikweert MT, Swaaf M, Dijken JP, Pronk JT (1999) Growth requirements of pyruvate-decarboxylase-negative Saccharomyces cerevisiae. FEMS Microbiol Lett 174(1):73–79
Fondi M, Liò P (2015) Multi-omics and metabolic modelling pipelines: challenges and tools for systems microbiology. Microbiol Res 171:52–64
Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO (2005) In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 91(5):643–648
Fullwood MJ, Wei CL, Liu ET, Ruan Y (2009) Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res 19(4):521–532
Geertman JM, Maris AJ, Dijken JP, Pronk JT (2006) Physiological and genetic engineering of cytosolic redox metabolism in Saccharomyces cerevisiae for improved glycerol production. Metab Eng 8(6):532–542
Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian K-D, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang C-Y, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418(6896):387–391
Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS (2014) Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159(3):647–661
Greener A, Callahan M, Jerpseth B (1997) An efficient random mutagenesis technique using an E. coli mutator strain. Mol Biotechnol 7(2):189–195
Gresham D, Dunham MJ (2014) The enduring utility of continuous culturing in experimental evolution. Genomics 104(6 Pt A):399–405
Guadalupe-Medina V, Metz B, Oud B, Graaf CM, Mans R, Pronk JT, Maris AJ (2014) Evolutionary engineering of a glycerol-3-phosphate dehydrogenase-negative, acetate-reducing Saccharomyces cerevisiae strain enables anaerobic growth at high glucose concentrations. J Microbial Biotechnol 7(1):44–53
Guimaraes PM, Berre V, Sokol S, Francois J, Teixeira JA, Domingues L (2008) Comparative transcriptome analysis between original and evolved recombinant lactose-consuming Saccharomyces cerevisiae strains. Biotechnol J 3(12):1591–1597
Hasunuma T, Sakamoto T, Kondo A (2016) Inverse metabolic engineering based on transient acclimation of yeast improves acid-containing xylose fermentation and tolerance to formic and acetic acids. Appl Microbiol Biotechnol 100(2):1027–1038
Hawkins GM, Doran-Peterson J (2011) A strain of Saccharomyces cerevisiae evolved for fermentation of lignocellulosic biomass displays improved growth and fermentative ability in high solids concentrations and in the presence of inhibitory compounds. Biotechnol Biofuels 4(1):49
Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S, Natarajan P, Koh JL, Porter J, Gray CA, Andersen RJ, Giaever G, Nislow C, Andrews B, Botstein D, Graham TR, Yoshida M, Boone C (2009) A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nat Biotechnol 27(4):369–377
Hong KK, Nielsen J (2013) Adaptively evolved yeast mutants on galactose show trade-offs in carbon utilization on glucose. Metab Eng 16:78–86
Horinouchi T, Minamoto T, Suzuki S, Shimizu H, Furusawa C (2014) Development of an automated culture system for laboratory evolution. J Lab Autom 19(5):478–482
Hosaka T, Ohnishi-Kameyama M, Muramatsu H, Murakami K, Tsurumi Y, Kodani S, Yoshida M, Fujie A, Ochi K (2009) Antibacterial discovery in actinomycetes strains with mutations in RNA polymerase or ribosomal protein S12. Nat Biotechnol 27(5):462–464
Huang M, Bai Y, Sjostrom SL, Hallstrom BM, Liu Z, Petranovic D, Uhlen M, Joensson HN, Andersson-Svahn H, Nielsen J (2015) Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast. Proc Natl Acad Sci U S A 112(34):E4689–E4696
Hutchison CA, Peterson SN, Gill SR, Cline RT, White O, Fraser CM, Smith HO, Venter JC (1999) Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286(5447):2165–2169
Jakiela S, Kaminski TS, Cybulski O, Weibel DB, Garstecki P (2013) Bacterial growth and adaptation in microdroplet chemostats. Angew Chem Int Ed 52(34):8908–8911
Jakociunas T, Bonde I, Herrgard M, Harrison SJ, Kristensen M, Pedersen LE, Jensen MK, Keasling JD (2015) Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. Metab Eng 28:213–222
Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31(3):233–239
Keasling JD (2010) Manufacturing molecules through metabolic engineering. Science 330(6009):1355–1358
Kim HJ, Ha S, Lee HY, Lee KJ (2015) ROSics: chemistry and proteomics of cysteine modifications in redox biology. Mass Spectrum Rev 34(2):184–208
Kim SJ, Seo SO, Jin YS, Seo JH (2013) Production of 2,3-butanediol by engineered Saccharomyces cerevisiae. Bioresour Technol 146:274–281
Kim SJ, Seo SO, Park YC, Jin YS, Seo JH (2014) Production of 2,3-butanediol from xylose by engineered Saccharomyces cerevisiae. J Biotechnol 192:376–382
Kim SR, Skerker JM, Kang W, Lesmana A, Wei N, Arkin AP, Jin YS (2013) Rational and evolutionary engineering approaches uncover a small set of genetic changes efficient for rapid xylose fermentation in Saccharomyces cerevisiae. PLoS One 8(2):e57048
Kim SR, Xu H, Lesmana A, Kuzmanovic U, Au M, Florencia C, Oh EJ, Zhang G, Kim KH, Jin YS (2015) Deletion of PHO13, encoding haloacid dehalogenase type IIA phosphatase, results in upregulation of the pentose phosphate pathway in Saccharomyces cerevisiae. Appl Environ Microbiol 81(5):1601–1609
Kinnersley M, Wenger J, Kroll E, Adams J, Sherlock G, Rosenzweig F (2014) Ex uno plures: clonal reinforcement drives evolution of a simple microbial community. PLoS Genet 10(6):e1004430
Klein-Marcuschamer D, Stephanopoulos G (2008) Assessing the potential of mutational strategies to elicit new phenotypes in industrial strains. Proc Natl Acad Sci U S A 105(7):2319–2324
Klimacek M, Kirl E, Krahulec S, Longus K, Novy V, Nidetzky B (2014) Stepwise metabolic adaption from pure metabolization to balanced anaerobic growth on xylose explored for recombinant Saccharomyces cerevisiae. Microb Cell Fact 13(1):37
Koffas M (2005) Evolutionary metabolic engineering. Metab Eng 7(1):1–3
Konermann S, Brigham MD, Trevino AE, Joung J, Abudayyeh OO, Barcena C, Hsu PD, Habib N, Gootenberg JS, Nishimasu H, Nureki O, Zhang F (2015) Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517(7536):583–588
Koppram R, Albers E, Olsson L (2012) Evolutionary engineering strategies to enhance tolerance of xylose utilizing recombinant yeast to inhibitors derived from spruce biomass. Biotechnol Biofuels 5(1):32
Koren S, Phillippy AM (2015) One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr Opin Microbiol 23:110–120
Kryazhimskiy S, Rice DP, Jerison ER, Desai MM (2014) Global epistasis makes adaptation predictable despite sequence-level stochasticity. Science 344(6191):1519–1522
Kucukgoze G, Alkim C, Yilmaz U, Kisakesen HI, Gunduz S, Akman S, Cakar ZP (2013) Evolutionary engineering and transcriptomic analysis of nickel-resistant Saccharomyces cerevisiae. FEMS Yeast Res 13(8):731–746
Lang GI, Botstein D, Desai MM (2011) Genetic variation and the fate of beneficial mutations in asexual populations. Genetics 188(3):647–661
Lang GI, Desai MM (2014) The spectrum of adaptive mutations in experimental evolution. Genomics 104(6):412–416
Lang GI, Murray AW (2008) Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae. Genetics 178(1):67–82
Lang GI, Rice DP, Hickman MJ, Sodergren E, Weinstock GM, Botstein D, Desai MM (2013) Pervasive genetic hitchhiking and clonal interference in fourty evolving yeast populations. Nature 500(7464):571–574
Lee H, Popodi E, Tang H, Foster PL (2012) Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc Natl Acad Sci U S A 109(41):E2774–E2783
Lee HJ, Kim SJ, Yoon JJ, Kim KH, Seo JH, Park YC (2015) Evolutionary engineering of Saccharomyces cerevisiae for efficient conversion of red algal biosugars to bioethanol. Bioresour Technol 191:445–451
Lee JW, Na D, Park JM, Lee J, Choi S, Lee SY (2012) Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol 8(6):536–546
Lee KS, Hong ME, Jung SC, Ha SJ, Yu BJ, Koo HM, Park SM, Seo JH, Kweon DH, Park JC, Jin YS (2011) Improved galactose fermentation of Saccharomyces cerevisiae through inverse metabolic engineering. Biotechnol Bioeng 108(3):621–631
Lee SM, Jellison T, Alper HS (2014) Systematic and evolutionary engineering of a xylose isomerase-based pathway in Saccharomyces cerevisiae for efficient conversion yields. Biotechnol Biofuels 7(1):122
Lee SY, Kim HU (2015) Systems strategies for developing industrial microbial strains. Nat Biotechnol 33(10):1061–1072
Lenski RE, Mongold JA, Sniegowski PD, Travisano M, Vasi F, Gerrish PJ, Schmidt TM (1998) Evolution of competitive fitness in experimental populations of E. coli: what makes one genotype a better competitor than another? Antonie Van Leeuwenhoek 73(1):35–47
Li P, Sun H, Chen Z, Li Y, Zhu T (2015) Construction of efficient xylose utilizing Pichia pastoris for industrial enzyme production. Microb Cell Fact 14:22
Li S, Si T, Wang M, Zhao H (2015) Development of a synthetic Malonyl-CoA sensor in Saccharomyces cerevisiae for intracellular metabolite monitoring and genetic screening. ACS Synth Biol 4(12):1308–1315
Lian J, Chao R, Zhao H (2014) Metabolic engineering of a Saccharomyces cerevisiae strain capable of simultaneously utilizing glucose and galactose to produce enantiopure (2R,3R)-butanediol. Metab Eng 23:92–99
Lind PA, Andersson DI (2008) Whole-genome mutational biases in bacteria. Proc Natl Acad Sci U S A 105(46):17878–17883
Ling H, Pratomo Juwono NK, Teo WS, Liu R, Leong SS, Chang MW (2015) Engineering transcription factors to improve tolerance against alkane biofuels in Saccharomyces cerevisiae. Biotechnol Biofuels 8:231
Lopez-Malo M, Garcia-Rios E, Melgar B, Sanchez MR, Dunham MJ, Guillamon JM (2015) Evolutionary engineering of a wine yeast strain revealed a key role of inositol and mannoprotein metabolism during low-temperature fermentation. BMC Genomics 16:537
Lou DI, Hussmann JA, McBee RM, Acevedo A, Andino R, Press WH, Sawyer SL (2013) High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proc Natl Acad Sci U S A 110(49):19872–19877
Luan G, Cai Z, Li Y, Ma Y (2013) Genome replication engineering assisted continuous evolution (GREACE) to improve microbial tolerance for biofuels production. Biotechnol Biofuels 6(1):137
Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, Dickinson WJ, Okamoto K, Kulkarni S, Hartl DL, Thomas WK (2008) A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci U S A 105(27):9272–9277
Lynch MD, Warnecke T, Gill RT (2007) SCALEs: multiscale analysis of library enrichment. Nat Methods 4(1):87–93
Maharjan R, Seeto S, Notley-McRobb L, Ferenci T (2006) Clonal adaptive radiation in a constant environment. Science 313(5786):514–517
Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM (2013) RNA-guided human genome engineering via Cas9. Science 339(6121):823–826
Martinez JL, Bordel S, Hong KK, Nielsen J (2014) Gcn4p and the Crabtree effect of yeast: drawing the causal model of the Crabtree effect in Saccharomyces cerevisiae and explaining evolutionary trade-offs of adaptation to galactose through systems biology. FEMS Yeast Res 14(4):654–662
Michener JK, Smolke CD (2012) High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metab Eng 14(4):306–316
Mitsumasu K, Liu ZS, Tang YQ, Akamatsu T, Taguchi H, Kida K (2014) Development of industrial yeast strain with improved acid- and thermo-tolerance through evolution under continuous fermentation conditions followed by haploidization and mating. J Biosci Bioeng 118(6):689–695
Mukherjee K, Bhattacharyya S, Peralta-Yahya P (2015) GPCR-based chemical biosensors for medium-chain fatty acids. ACS Synth Biol 4(12):1261–1269
Nan H, Seo SO, Oh EJ, Seo JH, Cate JH, Jin YS (2014) 2,3-butanediol production from cellobiose by engineered Saccharomyces cerevisiae. Appl Microbiol Biotechnol 98(12):5757–5764
Nielsen J, Keasling Jay D (2016) Engineering cellular metabolism. Cell 164(6):1185–1197
Nijland JG, Shin HY, Jong RM, Waal PP, Klaassen P, Driessen AJ (2014) Engineering of an endogenous hexose transporter into a specific D-xylose transporter facilitates glucose-xylose co-consumption in Saccharomyces cerevisiae. Biotechnol Biofuels 7(1):168
Notley-McRobb L, King T, Ferenci T (2002) rpoS mutations and loss of general stress resistance in Escherichia coli populations as a consequence of conflict between competing stress responses. J Bacteriol 184(3):806–811
Novick A, Szilard L (1950) Description of the chemostat. Science 112(2920):715–716
Ochi K (2007) From microbial differentiation to ribosome engineering. Biosci Biotechnol Biochem 71(6):1373–1386
Oud B, Flores CL, Gancedo C, Zhang X, Trueheart J, Daran JM, Pronk JT, Maris AJ (2012) An internal deletion in MTH1 enables growth on glucose of pyruvate-decarboxylase negative, non-fermentative Saccharomyces cerevisiae. Microb Cell Fact 11:131
Oud B, Maris AJ, Daran JM, Pronk JT (2012) Genome-wide analytical approaches for reverse metabolic engineering of industrially relevant phenotypes in yeast. FEMS Yeast Res 12(2):183–196
Park K-S, Lee D-K, Lee H, Lee Y, Jang Y-S, Kim YH, Yang H-Y, Lee S-I, Seol W, Kim J-S (2003) Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors. Nat Biotechnol 21(10):1208–1214
Park KS, Jang YS, Lee H, Kim JS (2005) Phenotypic alteration and target gene identification using combinatorial libraries of zinc finger proteins in prokaryotic cells. J Bacteriol 187(15):5496–5499
Patzschke A, Steiger MG, Holz C, Lang C, Mattanovich D, Sauer M (2015) Enhanced glutathione production by evolutionary engineering of Saccharomyces cerevisiae strains. Biotechnol J 10(11):1719–1726
Pereira SR, Sanchez INV, Frazao CJ, Serafim LS, Gorwa-Grauslund MF, Xavier AM (2015) Adaptation of Scheffersomyces stipitis to hardwood spent sulfite liquor by evolutionary engineering. Biotechnol Biofuels 8:50
Pinel D, Colatriano D, Jiang H, Lee H, Martin VJ (2015) Deconstructing the genetic basis of spent sulphite liquor tolerance using deep sequencing of genome-shuffled yeast. Biotechnol Biofuels 8:53
Pinel D, D’Aoust F, Cardayre SB, Bajwa PK, Lee H, Martin VJ (2011) Saccharomyces cerevisiae genome shuffling through recursive population mating leads to improved tolerance to spent sulfite liquor. Appl Environ Microbiol 77(14):4736–4743
Qi X, Zha J, Liu GG, Zhang W, Li BZ, Yuan YJ (2015) Heterologous xylose isomerase pathway and evolutionary engineering improve xylose utilization in Saccharomyces cerevisiae. Front Microbiol 6:1165
Quandt EM, Deatherage DE, Ellington AD, Georgiou G, Barrick JE (2014) Recursive genome-wide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli. Proc Natl Acad Sci U S A 111(6):2217–2222
Rabinovitch-Deere CA, Oliver JWK, Rodriguez GM, Atsumi S (2013) Synthetic biology and metabolic engineering approaches to produce biofuels. Chem Rev 113(7):4611–4632
Reyes LH, Gomez JM, Kao KC (2014) Improving carotenoids production in yeast via adaptive laboratory evolution. Metab Eng 21:26–33
Rodriguez-Verdugo A, Carrillo-Cisneros D, Gonzalez-Gonzalez A, Gaut BS, Bennett AF (2014) Different tradeoffs result from alternate genetic adaptations to a common environment. Proc Natl Acad Sci U S A 111(33):12121–12126
Rosenzweig F, Sherlock G (2014) Experimental evolution: prospects and challenges. Genomics 104(6, Part A):v–vi
Sanchez BJ, Nielsen J (2015) Genome scale models of yeast: towards standardized evaluation and consistent omic integration. Integr Biol 7(8):846–858
Santos CNS, Stephanopoulos G (2008) Combinatorial engineering of microbes for optimizing cellular phenotype. Curr Opin Chem Biol 12(2):168–176
Sauer U (2001) Evolutionary engineering of industrially important microbial phenotypes. Adv Biochem Eng Biotechnol 73:129–169
Scalcinati G, Otero JM, Vleet JR, Jeffries TW, Olsson L, Nielsen J (2012) Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption. FEMS Yeast Res 12(5):582–597
Serero A, Jubin C, Loeillet S, Legoix-Ne P, Nicolas AG (2014) Mutational landscape of yeast mutator strains. Proc Natl Acad Sci U S A 111(5):1897–1902
Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F (2014) Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343(6166):84–87
Sharan SK, Thomason LC, Kuznetsov SG, Court DL (2009) Recombineering: a homologous recombination-based method of genetic engineering. Nat Protoc 4(2):206–223
Shen Y, Stracquadanio G, Wang Y, Yang K, Mitchell LA, Xue Y, Cai Y, Chen T, Dymond JS, Kang K, Gong J, Zeng X, Zhang Y, Li Y, Feng Q, Xu X, Wang J, Wang J, Yang H, Boeke JD, Bader JS (2016) SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Res 26(1):36–49
Shi S, Liang Y, Zhang MM, Ang EL, Zhao H (2016) A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae. Metab Eng 33:19–27
Shima J, Hesketh A, Okamoto S, Kawamoto S, Ochi K (1996) Induction of actinorhodin production by rpsL (encoding ribosomal protein S12) mutations that confer streptomycin resistance in Streptomyces lividans and Streptomyces coelicolor A3(2). J Bacteriol 178(24):7276–7284
Shin HY, Nijland JG, Waal PP, Jong RM, Klaassen P, Driessen AJ (2015) An engineered cryptic Hxt11 sugar transporter facilitates glucose-xylose co-consumption in Saccharomyces cerevisiae. Biotechnol Biofuels 8:176
Shui W, Xiong Y, Xiao W, Qi X, Zhang Y, Lin Y, Guo Y, Zhang Z, Wang Q, Ma Y (2015) Understanding the mechanism of thermotolerance distinct from heat shock response through proteomic analysis of industrial strains of Saccharomyces cerevisiae. Mol Cell Proteomics 14(7):1885–1897
Si T, Luo Y, Bao Z, Zhao H (2015) RNAi-assisted genome evolution in Saccharomyces cerevisiae for complex phenotype engineering. ACS Synth Biol 4(3):283–291
Si T, Xiao H, Zhao H (2015) Rapid prototyping of microbial cell factories via genome-scale engineering. Biotechnol Adv 33(7):1420–1432
Sjostrom SL, Bai Y, Huang M, Liu Z, Nielsen J, Joensson HN, Andersson Svahn H (2014) High-throughput screening for industrial enzyme production hosts by droplet microfluidics. Lab Chip 14(4):806–813
Skretas G, Kolisis FN (2012) Combinatorial approaches for inverse metabolic engineering applications. Comput Struct Biotechnol J 3:e201210021
Smith KM, Liao JC (2011) An evolutionary strategy for isobutanol production strain development in Escherichia coli. Metab Eng 13(6):674–681
Snoek T, Picca Nicolino M, Bremt S, Mertens S, Saels V, Verplaetse A, Steensels J, Verstrepen KJ (2015) Large-scale robot-assisted genome shuffling yields industrial Saccharomyces cerevisiae yeasts with increased ethanol tolerance. Biotechnol Biofuels 8:32
Sonderegger M, Sauer U (2003) Evolutionary engineering of Saccharomyces cerevisiae for anaerobic growth on xylose. Appl Environ Microbiol 69(4):1990–1998
Standage-Beier K, Zhang Q, Wang X (2015) Targeted large-scale deletion of bacterial genomes using CRISPR-nickases. ACS Synth Biol 4(11):1217–1225
Steensels J, Snoek T, Meersman E, Picca Nicolino M, Voordeckers K, Verstrepen KJ (2014) Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol Rev 38(5):947–995
Stovicek V, Borodina I, Forster J (2015) CRISPR–Cas system enables fast and simple genome editing of industrial Saccharomyces cerevisiae strains. Metab Eng Commun 2:13–22
Sung W, Ackerman MS, Miller SF, Doak TG, Lynch M (2012) Drift-barrier hypothesis and mutation-rate evolution. Proc Natl Acad Sci U S A 109(45):18488–18492
Tenaillon O, Rodriguez-Verdugo A, Gaut RL, McDonald P, Bennett AF, Long AD, Gaut BS (2012) The molecular diversity of adaptive convergence. Science 335(6067):457–461
Teoh ST, Putri S, Mukai Y, Bamba T, Fukusaki E (2015) A metabolomics-based strategy for identification of gene targets for phenotype improvement and its application to 1-butanol tolerance in Saccharomyces cerevisiae. Biotechnol Biofuels 8:144
Tilloy V, Cadiere A, Ehsani M, Dequin S (2015) Reducing alcohol levels in wines through rational and evolutionary engineering of Saccharomyces cerevisiae. Int J Food Microbiol 213:49–58
Toprak E, Veres A, Michel JB, Chait R, Hartl DL, Kishony R (2012) Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat Genet 44(1):101–105
Torres EM, Dephoure N, Panneerselvam A, Tucker CM, Whittaker CA, Gygi SP, Dunham MJ, Amon A (2010) Identification of aneuploidy-tolerating mutations. Cell 143(1):71–83
Maris AJ, Geertman JM, Vermeulen A, Groothuizen MK, Winkler AA, Piper MD, Dijken JP, Pronk JT (2004) Directed evolution of pyruvate decarboxylase-negative Saccharomyces cerevisiae, yielding a C2-independent, glucose-tolerant, and pyruvate-hyperproducing yeast. Appl Environ Microbiol 70(1):159–166
Vanee N, Fisher AB, Fong SS (2012) Evolutionary engineering for industrial microbiology. Subcell Biochem 64:43–71
Vilela Lde F, de Araujo VP, Paredes Rde S, Bon EP, Torres FA, Neves BC, Eleutherio EC (2015) Enhanced xylose fermentation and ethanol production by engineered Saccharomyces cerevisiae strain. AMB Express 5:16
Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460(7257):894–U133
Wang M, Li S, Zhao H (2016) Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in Saccharomyces cerevisiae. Biotechnol Bioeng 113(1):206–215
Wang T, Wei JJ, Sabatini DM, Lander ES (2014) Genetic screens in human cells using the CRISPR-Cas9 system. Science 343(6166):80–84
Wang Y, Zhang S, Liu H, Zhang L, Yi C, Li H (2015) Changes and roles of membrane compositions in the adaptation of Saccharomyces cerevisiae to ethanol. J Basic Microbiol 55(12):1417–1426
Wargacki AJ, Leonard E, Win MN, Regitsky DD, Santos CN, Kim PB, Cooper SR, Raisner RM, Herman A, Sivitz AB, Lakshmanaswamy A, Kashiyama Y, Baker D, Yoshikuni Y (2012) An engineered microbial platform for direct biofuel production from brown macroalgae. Science 335(6066):308–313
Warner JR, Reeder PJ, Karimpour-Fard A, Woodruff LB, Gill RT (2010) Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides. Nat Biotechnol 28(8):856–862
Wei N, Quarterman J, Jin YS (2013) Marine macroalgae: an untapped resource for producing fuels and chemicals. Trends Biotechnol 31(2):70–77
Winkler JD, Kao KC (2014) Recent advances in the evolutionary engineering of industrial biocatalysts. Genomics 104(6 Pt A):406–411
Wisselink HW, Cipollina C, Oud B, Crimi B, Heijnen JJ, Pronk JT, Maris AJ (2010) Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae. Metab Eng 12(6):537–551
Woodruff LBA, Gill RT (2011) Engineering genomes in multiplex. Curr Opin Biotechnol 22(4):576–583
Wright J, Bellissimi E, Hulster E, Wagner A, Pronk JT, Maris AJ (2011) Batch and continuous culture-based selection strategies for acetic acid tolerance in xylose-fermenting Saccharomyces cerevisiae. FEMS Yeast Res 11(3):299–306
Xiao H, Zhao H (2014) Genome-wide RNAi screen reveals the E3 SUMO-protein ligase gene SIZ1 as a novel determinant of furfural tolerance in Saccharomyces cerevisiae. Biotechnol Biofuels 7:78
Xu H, Kim S, Sorek H, Lee Y, Jeong D, Kim J, Oh EJ, Yun EJ, Wemmer DE, Kim KH, Kim SR, Jin YS (2016) PHO13 deletion-induced transcriptional activation prevents sedoheptulose accumulation during xylose metabolism in engineered Saccharomyces cerevisiae. Metab Eng 34:88–96
Yan D, Wang C, Zhou J, Liu Y, Yang M, Xing J (2014) Construction of reductive pathway in Saccharomyces cerevisiae for effective succinic acid fermentation at low pH value. Bioresour Technol 156:232–239
Zelle RM, Hulster E, Winden WA, Waard P, Dijkema C, Winkler AA, Geertman JM, Dijken JP, Pronk JT, Maris AJ (2008) Malic acid production by Saccharomyces cerevisiae: engineering of pyruvate carboxylation, oxaloacetate reduction, and malate export. Appl Environ Microbiol 74(9):2766–2777
Zha J, Shen M, Hu M, Song H, Yuan Y (2014) Enhanced expression of genes involved in initial xylose metabolism and the oxidative pentose phosphate pathway in the improved xylose-utilizing Saccharomyces cerevisiae through evolutionary engineering. J Ind Microbiol Biotechnol 41(1):27–39
Zhang Y, Liu G, Engqvist MK, Krivoruchko A, Hallstrom BM, Chen Y, Siewers V, Nielsen J (2015) Adaptive mutations in sugar metabolism restore growth on glucose in a pyruvate decarboxylase negative yeast strain. Microb Cell Fact 14:116
Zhou H, Cheng JS, Wang BL, Fink GR, Stephanopoulos G (2012) Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae. Metab Eng 14(6):611–622
Zhu L, Li Y, Cai Z (2015) Development of a stress-induced mutagenesis module for autonomous adaptive evolution of Escherichia coli to improve its stress tolerance. Biotechnol Biofuels 8:93
Ziv N, Brandt NJ, Gresham D (2013) The use of chemostats in microbial systems biology. J Vis Exp 80:18
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this chapter
Cite this chapter
Si, T., Lian, J., Zhao, H. (2017). Strain Development by Whole-Cell Directed Evolution. In: Alcalde, M. (eds) Directed Enzyme Evolution: Advances and Applications. Springer, Cham. https://doi.org/10.1007/978-3-319-50413-1_7
Download citation
DOI: https://doi.org/10.1007/978-3-319-50413-1_7
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-50411-7
Online ISBN: 978-3-319-50413-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)