Strategies for the multiplex mapping of genes to traits

Microbial Cell Factories

Volumn 12, Issue 1, 2013, Pages

  Garst, Andrew ^a   Lynch, Michael ^b   Evans, Ron ^c   Gill, Ryan T ^a  

^a UCB 450   (United States)

^b Duke University   (United States)

^c OPX Biotechnologies Inc   (United States)

Author keywords

Genomic vector libraries; Multiplexed recombineering; Transposon saturation mutagenesis; Whole genome sequencing

Indexed keywords

ALCOHOL; COMPLEMENTARY DNA; GENOMIC DNA; LYCOPENE; MESSENGER RNA; OLIGONUCLEOTIDE; RIBOSOME RNA; RNA 16S; RNA POLYMERASE II; TRANSCRIPTOME; TYROSINE; VALINE;

ALCOHOL TOLERANCE; BACILLUS SUBTILIS; BACTERIAL STRAIN; DNA BINDING; DNA MICROARRAY; DNA SEQUENCE; ESCHERICHIA COLI; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE LIBRARY; GENE MAPPING; GENE SEQUENCE; GENE VECTOR; GENETIC ENGINEERING; GENETIC TRAIT; GENETIC VARIABILITY; GENOTYPE; GENOTYPE PHENOTYPE CORRELATION; HOMOLOGOUS RECOMBINATION; METABOLIC ENGINEERING; METAGENOMICS; MICROARRAY ANALYSIS; MICROBIAL COMMUNITY; MICROBIAL GENETICS; MUTAGENESIS; NONHUMAN; OPERON; PHENOTYPE; PROMOTER REGION; REVIEW; SACCHAROMYCES CEREVISIAE; TRANSPOSON; WILD TYPE;

CHROMOSOME MAPPING; DNA PROBES; GENETIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; MUTAGENESIS;

EID: 84886550456     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-12-99     Document Type: Review

References (86)

1. Zhou H, Cheng J-S, Wang BL, Fink GR, Stephanopoulos G. 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 2012, 14:611-622. 10.1016/j.ymben.2012.07.011, 22921355.
2. Koffas MAG, Jung GY, Stephanopoulos G. Engineering metabolism and product formation in corynebacterium glutamicum by coordinated gene overexpression. Metab Eng 2003, 5:32-41. 10.1016/S1096-7176(03)00002-8, 12749842.
3. Lee KH, Park JH, Kim TY, Kim HU, Lee SY. Systems metabolic engineering of Escherichia coli for L-threonine production. Mol Syst Biol 2007, 3:149. 2174629, 18059444.
4. Leonard E, Ajikumar PK, Thayer K, Xiao W-H, Mo JD, Tidor B, Stephanopoulos G, Prather KLJ. Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc Natl Acad Sci 2010, 107:13654-13659. 10.1073/pnas.1006138107, 2922259, 20643967.
5. Bailey JE. Toward a science of metabolic engineering. Science 1991, 252:1668-1675. 10.1126/science.2047876, 2047876.
6. Keasling JD. Manufacturing molecules through metabolic engineering. Science 2010, 330:1355-1358. 10.1126/science.1193990, 21127247.
7. Lynch MD, Gill RT, Stephanopoulos G. Mapping phenotypic landscapes using DNA micro-arrays. Metab Eng 2004, 6:177-185. 10.1016/j.ymben.2004.01.002, 15256207.
8. Boyle NR, Gill RT. Tools for genome-wide strain design and construction. Curr Opin Biotechnol 2012, 23:666-671. 10.1016/j.copbio.2012.01.012, 22357141.
9. Zhang Y-X, Perry K, Vinci VA, Powell K, Stemmer WP, del Cardayré SB. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 2002, 415:644-646. 10.1038/415644a, 11832946.
10. Kaplan NL, Hudson RR, Langley CH. The" hitchhiking effect" revisited. Genetics 1989, 123:887-899. 1203897, 2612899.
11. Patnaik R. Engineering complex phenotypes in industrial strains. Biotechnol Prog 2008, 24:38-47. 10.1021/bp0701214, 17914860.
12. Woodruff LB, Gill RT. Engineering genomes in multiplex. Curr Opin Biotechnol 2011, 22:576-583. 10.1016/j.copbio.2011.04.019, 21592776.
13. Romero PA, Arnold FH. Exploring protein fitness landscapes by directed evolution. Nat Rev Mol Cell Biol 2009, 10:866-876. 10.1038/nrm2805, 2997618, 19935669.
14. Lynch SA, Gill RT. Synthetic biology: new strategies for directing design. Metab Eng 2012, 14:205-211. 10.1016/j.ymben.2011.12.007, 22227399.
15. Leproust EM, Peck BJ, Spirin K, McCuen HB, Moore B, Namsaraev E, Caruthers MH. Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res 2010, 38:2522-2540. 10.1093/nar/gkq163, 2860131, 20308161.
16. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460:894-U133.
17. Zhang Y, Buchholz F, Muyrers JPP, Stewart AF. A new logic for DNA engineering using recombination in Escherichia coli. Nat Genet 1998, 20:123-128. 10.1038/2417, 9771703.
18. Court DL, Sawitzke JA, Thomason LC. Genetic engineering using homologous recombination. Annu Rev Genet 2002, 36:361-388. 10.1146/annurev.genet.36.061102.093104, 12429697.
19. Shoemaker DD, Lashkari DA, Morris D, Mittmann M, Davis RW. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat Genet 1996, 14:450-456. 10.1038/ng1296-450, 8944025.
20. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-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, Güldener U, Hegemann JH, Hempel S, Herman Z, et al. Functional profiling of the saccharomyces cerevisiae genome. Nature 2002, 418:387-391. 10.1038/nature00935, 12140549.
21. Warner JR, Reeder PJ, Karimpour-Fard A, Woodruff LBA, Gill RT. Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides. Nat Biotechnol 2010, 28:856-862. 10.1038/nbt.1653, 20639866.
22. Cho RJ, Fromont-Racine M, Wodicka L, Feierbach B, Stearns T, Legrain P, Lockhart DJ, Davis RW. Parallel analysis of genetic selections using whole genome oligonucleotide arrays. Proc Natl Acad Sci USA 1998, 95:3752-3757. 10.1073/pnas.95.7.3752, 19909, 9520439.
23. Gill RT, Wildt S, Yang YT, Ziesman S, Stephanopoulos G. Genome-wide screening for trait conferring genes using DNA microarrays. Proc Natl Acad Sci USA 2002, 99:7033-7038. 10.1073/pnas.102154799, 124523, 11997466.
24. Reyes LH, Almario MP, Kao KC. Genomic library screens for genes involved in n-butanol tolerance in Escherichia coli. PLoS ONE 2011, 6:e17678. 10.1371/journal.pone.0017678, 3050900, 21408113.
25. Lynch MD, Warnecke T, Gill RT. SCALEs: multiscale analysis of library enrichment. Nat Methods 2007, 4:87-93. 10.1038/nmeth946, 17099705.
26. Bonomo J, Lynch MD, Warnecke T, Price JV, Gill RT. Genome-scale analysis of anti-metabolite directed strain engineering. Metab Eng 2008, 10:109-120. 10.1016/j.ymben.2007.10.002, 18093856.
27. Singh A, Lynch MD, Gill RT. Genes restoring redox balance in fermentation-deficient E. coli NZN111. Metab Eng 2009, 11:347-354. 10.1016/j.ymben.2009.07.002, 19628049.
28. Mills TY, Sandoval NR, Gill RT. Cellulosic hydrolysate toxicity and tolerance mechanisms in Escherichia coli. Biotechnol Biofuels 2009, 2:26. 10.1186/1754-6834-2-26, 2770041, 19832972.
29. Sandoval NR, Mills TY, Zhang M, Gill RT. Elucidating acetate tolerance in E. coli using a genome-wide approach. Metab Eng 2011, 13:214-224. 10.1016/j.ymben.2010.12.001, 21163359.
30. Woodruff LBA, Boyle NR, Gill RT. Engineering improved ethanol production in Escherichia coli with a genome-wide approach. Metab Eng 2013, 17:1-11.
31. Woodruff LBA, May BL, Warner JR, Gill RT. Towards a metabolic engineering strain " commons": an Escherichia coli platform strain for ethanol production. Biotechnol Bioeng 2013, 110:1520-1526. 10.1002/bit.24840, 23322646.
32. Gall S, Lynch MD, Sandoval NR, Gill RT. Parallel mapping of genotypes to phenotypes contributing to overall biological fitness. Metab Eng 2008, 10:382-393. 10.1016/j.ymben.2008.08.003, 18789396.
33. Nicolaou SA, Gaida SM, Papoutsakis ET. Coexisting/coexpressing genomic libraries (CoGeL) identify interactions among distantly located genetic loci for developing complex microbial phenotypes. Nucleic Acids Res 2011, 39:e152. 10.1093/nar/gkr817, 3239195, 21976725.
34. Schmidt TM, DeLong EF, Pace NR. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 1991, 173:4371-4378. 208098, 2066334.
35. Alper H, Stephanopoulos G. Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?. Nat Rev Micro 2009, 7:715-723.
36. Warner JR, Patnaik R, Gill RT. Genomics enabled approaches in strain engineering. Curr Opin Microbiol 2009, 12:223-230. 10.1016/j.mib.2009.04.005, 19467921.
37. Lämmle K, Zipper H, Breuer M, Hauer B, Buta C, Brunner H, Rupp S. Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning. J Biotechnol 2007, 127:575-592. 10.1016/j.jbiotec.2006.07.036, 16963141.
38. Li L-L, McCorkle SR, Monchy S, Taghavi S, van der Lelie D. Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. Biotechnol Biofuels 2009, 2:10. 10.1186/1754-6834-2-10, 2694162, 19450243.
39. Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, McHardy AC, Szeto E, Salamov A, Grigoriev IV, Suciu D, Levine SR, Markowitz VM, Rigoutsos I, Tringe SG, Bruce DC, Richardson PM, Lidstrom ME, Chistoserdova L. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol 2008, 26:1029-1034. 10.1038/nbt.1488, 18711340.
40. Wang Q, Wu H, Wang A, Du P, Pei X, Li H, Yin X, Huang L, Xiong X. Prospecting metagenomic enzyme subfamily genes for DNA family shuffling by a novel PCR-based approach. J Biol Chem 2010, 285:41509-41516. 10.1074/jbc.M110.139659, 3009877, 20962349.
41. Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Müller R, Stewart AF, Zhang Y. Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat Biotechnol 2012, 30:440-446. 10.1038/nbt.2183, 22544021.
42. Yuzawa S, Kim W, Katz L, Keasling JD. Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli. Curr Opin Biotechnol 2012, 23:727-735. 10.1016/j.copbio.2011.12.029, 22244790.
43. Kapur S, Chen AY, Cane DE, Khosla C. Molecular recognition between ketosynthase and acyl carrier protein domains of the 6-deoxyerythronolide B synthase. Proc Natl Acad Sci 2010, 107:22066-22071. 10.1073/pnas.1014081107, 3009775, 21127271.
44. Badarinarayana V, Estep PW, Shendure J, Edwards J, Tavazoie S, Lam F, Church GM. Selection analyses of insertional mutants using subgenic-resolution arrays. Nat Biotechnol 2001, 19:1060-1065. 10.1038/nbt1101-1060, 11689852.
45. van Opijnen T, Bodi KL, Camilli A. Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat Methods 2009, 6:767-772. 10.1038/nmeth.1377, 2957483, 19767758.
46. Gawronski JD, Wong SMS, Giannoukos G, Ward DV, Akerley BJ. Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung. Proc Natl Acad Sci USA 2009, 106:16422-16427. 10.1073/pnas.0906627106, 2752563, 19805314.
47. Girgis HS, Liu Y, Ryu WS, Tavazoie S. A comprehensive genetic characterization of bacterial motility. PLoS Genet 2007, 3:1644-1660. 1976333, 17941710.
48. Li MA, Turner DJ, Ning Z, Yusa K, Liang Q, Eckert S, Rad L, Fitzgerald TW, Craig NL, Bradley A. Mobilization of giant piggyBac transposons in the mouse genome. Nucleic Acids Res 2011, 39:e148. 10.1093/nar/gkr764, 3239208, 21948799.
49. Rostovskaya M, Fu J, Obst M, Baer I, Weidlich S, Wang H, Smith AJH, Anastassiadis K, Stewart AF. Transposon-mediated BAC transgenesis in human ES cells. Nucleic Acids Res 2012, 40:e150. 10.1093/nar/gks643, 3479164, 22753106.
50. van Opijnen T, Camilli A. A fine scale phenotype-genotype virulence map of a bacterial pathogen. Genome Res 2012, 22:2541-2551. 10.1101/gr.137430.112, 3514683, 22826510.
51. Amini S, Goodarzi H, Tavazoie S. Genetic dissection of an exogenously induced biofilm in laboratory and clinical isolates of E. coli. PLoS Pathog 2009, 5:e1000432. 10.1371/journal.ppat.1000432, 2675270, 19436718.
52. Goodarzi H, Bennett BD, Amini S, Reaves ML, Hottes AK, Rabinowitz JD, Tavazoie S. Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli. Mol Syst Biol 2010, 6:1-12.
53. Alper H, Miyaoku K, Stephanopoulos G. Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat Biotechnol 2005, 23:612-616. 10.1038/nbt1083, 15821729.
54. Alper H, Stephanopoulos G. Uncovering the gene knockout landscape for improved lycopene production in E. coli. Appl Microbiol Biotechnol 2008, 78:801-810. 10.1007/s00253-008-1373-x, 18239914.
55. Murphy KC. Use of bacteriophage lambda recombination functions to promote gene replacement in Escherichia coli. J Bacteriol 1998, 180:2063-2071. 107131, 9555887.
56. Costantino N, Court DL. Enhanced levels of lambda red-mediated recombinants in mismatch repair mutants. Proc Natl Acad Sci USA 2003, 100:15748-15753. 10.1073/pnas.2434959100, 307639, 14673109.
57. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006, 2:2006.0008. 1681482, 16738554.
58. Baudin A, Ozier-Kalogeropoulos O, Denouel A, Lacroute F, Cullin C. A simple and efficient method for direct gene deletion in saccharomyces cerevisiae. Nucleic Acids Res 1993, 21:3329-3330. 10.1093/nar/21.14.3329, 309783, 8341614.
59. Ryan O, Shapiro RS, Kurat CF, Mayhew D, Baryshnikova A, Chin B, Lin Z-Y, Cox MJ, Vizeacoumar F, Cheung D, Bahr S, Tsui K, Tebbji F, Sellam A, Istel F, Schwarzmüller T, Reynolds TB, Kuchler K, Gifford DK, Whiteway M, Giaever G, Nislow C, Costanzo M, Gingras A-C, Mitra RD, Andrews B, Fink GR, Cowen LE, Boone C. Global gene deletion analysis exploring yeast filamentous growth. Science 2012, 337:1353-1356. 10.1126/science.1224339, 22984072.
60. Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol 1999, 17:974-978. 10.1038/13664, 10504697.
61. Gao X, LeProust E, Zhang H, Srivannavit O, Gulari E, Yu P, Nishiguchi C, Xiang Q, Zhou X. A flexible light-directed DNA chip synthesis gated by deprotection using solution photogenerated acids. Nucleic Acids Res 2001, 29:4744-4750. 10.1093/nar/29.22.4744, 92522, 11713325.
62. Cleary MA, Kilian K, Wang Y, Bradshaw J, Cavet G, Ge W, Kulkarni A, Paddison PJ, Chang K, Sheth N, Leproust E, Coffey EM, Burchard J, McCombie WR, Linsley P, Hannon GJ. Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis. Nat Methods 2004, 1:241-248. 10.1038/nmeth724, 15782200.
63. Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM. Genome-scale promoter engineering by coselection MAGE. Nat Methods 2012, 9:591-593. 10.1038/nmeth.1971, 3428217, 22484848.
64. Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 2011, 333:348-353. 10.1126/science.1205822, 21764749.
65. Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, Montague MG, Venter JC, Smith HO, Hutchison CA. One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic mycoplasma genitalium genome. Proc Natl Acad Sci 2008, 105:20404-20409. 10.1073/pnas.0811011106, 2600582, 19073939.
66. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA, Smith HO. Complete chemical synthesis, assembly, and cloning of a mycoplasma genitalium genome. Science 2008, 319:1215-1220. 10.1126/science.1151721, 18218864.
67. Sandoval NR, Kim JYH, Glebes TY, Reeder PJ, Aucoin HR, Warner JR, Gill RT. Strategy for directing combinatorial genome engineering in Escherichia coli. Proc Natl Acad Sci 2012, 109:10540-10545. 10.1073/pnas.1206299109, 3387050, 22689973.
68. Cho B-K, Zengler K, Qiu Y, Park YS, Knight EM, Barrett CL, Gao Y, Palsson B. The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol 2009, 27:1043-1049. 10.1038/nbt.1582, 3832199, 19881496.
69. Mäder U, Homuth G, Scharf C, Büttner K, Bode R, Hecker M. Transcriptome and proteome analysis of bacillus subtilis gene expression modulated by amino acid availability. J Bacteriol 2002, 184:4288-4295. 10.1128/JB.184.15.4288-4295.2002, 135197, 12107147.
70. Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, et al. Condition-dependent transcriptome reveals high-level regulatory architecture in bacillus subtilis. Science 2012, 335:1103-1106. 10.1126/science.1206848, 22383849.
71. Silberbach M, Schäfer M, Hüser AT, Kalinowski J, Pühler A, Krämer R, Burkovski A. Adaptation of corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques. Aemasmorg 2005, 71:2391-2402.
72. Park JH, Lee KH, Kim TY, Lee SY. Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci 2007, 104:7797-7802. 10.1073/pnas.0702609104, 1857225, 17463081.
73. Mutz K-O, Heilkenbrinker A, Lönne M, Walter J-G, Stahl F. Transcriptome analysis using next-generation sequencing. Curr Opin Biotechnol 2012, 24:22-30.
74. Ozsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, McInerney P, Thompson JF, Bowers J, Jarosz M, Milos PM. Direct RNA sequencing. Nature 2009, 461:814-818. 10.1038/nature08390, 19776739.
75. Horinouchi T, Tamaoka K, Furusawa C, Ono N, Suzuki S, Hirasawa T, Yomo T, Shimizu H. Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress. BMC Genomics 2010, 11:579. 10.1186/1471-2164-11-579, 3091726, 20955615.
76. Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G. Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 2006, 314:1565-1568. 10.1126/science.1131969, 17158319.
77. Klein-Marcuschamer D, Stephanopoulos G. Assessing the potential of mutational strategies to elicit new phenotypes in industrial strains. Proc Natl Acad Sci 2008, 105:2319-2324. 10.1073/pnas.0712177105, 2268134, 18252819.
78. Santos CNS, Xiao W, Stephanopoulos G. Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli. Proc Natl Acad Sci 2012, 109:13538-13543. 10.1073/pnas.1206346109, 3427108, 22869698.
79. Mardis ER. A decade's perspective on DNA sequencing technology. Nature 2011, 470:198-203. 10.1038/nature09796, 21307932.
80. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, et al. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323:133-138. 10.1126/science.1162986, 19023044.
81. Howorka S, Cheley S, Bayley H. Sequence-specific detection of individual DNA strands using engineered nanopores. Nat Biotechnol 2001, 19:636-639. 10.1038/90236, 11433274.
82. Lieberman KR, Cherf GM, Doody MJ, Olasagasti F, Kolodji Y, Akeson M. Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase. J Am Chem Soc 2010, 132:17961-17972. 10.1021/ja1087612, 3076064, 21121604.
83. Blount ZD, Barrick JE, Davidson CJ, Lenski RE. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 2012, 489:513-518. 10.1038/nature11514, 3461117, 22992527.
84. Tenaillon O, Rodríguez-Verdugo A, Gaut RL, McDonald P, Bennett AF, Long AD, Gaut BS. The molecular diversity of adaptive convergence. Science 2012, 335:457-461. 10.1126/science.1212986, 22282810.
85. Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY. Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol 2013, 31:170-174. 10.1038/nbt.2461, 23334451.
86. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013, 152:1173-1183. 10.1016/j.cell.2013.02.022, 3664290, 23452860.