CRISPR/Cas9 advances engineering of microbial cell factories

Metabolic Engineering

Volumn 34, Issue , 2016, Pages 44-59

  Jakočiunas, Tadas ^a   Jensen, Michael K ^a   Keasling, Jay D ^a,b,c,d  

^a Chalmers University of Technology   (Denmark)

^b JOINT BIOENERGY INSTITUTE   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d University of California at Berkeley   (United States)

Author keywords

Bacteria; CRISPR Cas9; Genome editing; Metabolic engineering; Recombineering; Yeast

Indexed keywords

BACTERIA; CELL ENGINEERING; COMPUTER AIDED DESIGN; GENES; METABOLISM; NUCLEIC ACIDS; PRECISION ENGINEERING; RNA; YEAST;

CRISPR/CAS9; GENOME ENGINEERING; MICROBIAL CELL FACTORIES; MODEL ORGANISMS; ORTHOGONALITY; RECOMBINEERING; TARGET GENES; TRANSCRIPTIONAL REGULATION;

METABOLIC ENGINEERING;

GUIDE RNA; NUCLEASE; CRISPR ASSOCIATED PROTEIN;

BACTERIAL GENOME; COMPUTER AIDED DESIGN; CRISPR CAS SYSTEM; ESCHERICHIA COLI; GENE DELETION; GENE EXPRESSION REGULATION; METABOLIC ENGINEERING; MICROBIAL GENOME; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA EDITING; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION REGULATION; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; GENETIC ENHANCEMENT; GENETICS; METABOLISM; PROCEDURES;

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-ASSOCIATED PROTEINS; CRISPR-CAS SYSTEMS; GENETIC ENHANCEMENT; GENOME, MICROBIAL; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS;

EID: 84952682854     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2015.12.003     Document Type: Review

References (196)

1. Ajikumar P.K., Xiao W.H., Tyo K.E.J., Wang Y., Simeon F., Leonard E., Mucha O., Phon T.H., Pfeifer B., Stephanopoulos G. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 2010, 330:70-74.
2. Andersson A.F., Banfield J.F. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 2008, 320:1047-1050.
3. Anthony J.R., Anthony L.C., Nowroozi F., Kwon G., Newman J.D., Keasling J.D. Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4,11-diene. Metab. Eng. 2009, 11:13-19.
4. Asadollahi M.A., Maury J., Schalk M., Clark A., Nielsen J. Enhancement of farnesyl diphosphate pool as direct precursor of sesquiterpenes through metabolic engineering of the mevalonate pathway in Saccharomyces cerevisiae. Biotechnol. Bioeng. 2010, 106:86-96.
5. Bao Z., Xiao H., Liang J., Zhang L., Xiong X., Sun N., Si T., Zhao H. Homology-integrated CRISPR-Cas (HI-CRISPR) system for one-step multigene disruption in Saccharomyces cerevisiae. ACS Synth. Biol. 2015, 4:585-594.
6. Barrangou R., Fremaux C., Deveau H., Richards M., Boyaval P., Moineau S., Romero D.A., Horvath P. CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007, 315:1709-1712.
7. Bentley W.E., Mirjalili N., Andersen D.C., Davis R.H., Kompala D.S. Plasmid-encoded protein: the principal factor in the "metabolic burden" associated with recombinant bacteria. Biotechnol. Bioeng. 1990, 35:668-681.
8. Beumer K., Bhattacharyya G., Bibikova M., Trautman J.K., Carroll D. Efficient gene targeting in Drosophila with zinc-finger nucleases. Genetics 2006, 172:2391-2403.
9. Bibikova M., Golic M., Golic K.G., Carroll D. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 2002, 161:1169-1175.
10. Bikard D., Jiang W., Samai P., Hochschild A., Zhang F., Marraffini L.A. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 2013, 41:7429-7437.
11. Boer V.M., de Winde J.H., Pronk J.T., Piper M.D.W. The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J. Biol. Chem. 2003, 278:3265-3274.
12. Bogdanove A.J., Voytas D.F. TAL effectors: customizable proteins for DNA targeting. Science 2011, 333(6051):1843-1846.
13. Bolotin A., Quinquis B., Sorokin A., Dusko Ehrlich S. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 2005, 151:2551-2561.
14. Bonde M.T., Kosuri S., Genee H.J., Sarup-Lytzen K., Church G.M., Sommer M.O.a, Wang H.H. Direct mutagenesis of thousands of genomic targets using microarray-derived oligonucleotides. ACS Synth. Biol. 2014, 4:17-22.
15. Bordel S., Agren R., Nielsen J. Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes. PLoS Comput. Biol. 2010, 6(7):e1000859.
16. Brouns S.J.J., Jore M.M., Lundgren M., Westra E.R., Slijkhuis R.J.H., Snijders A.P.L., Dickman M.J., Makarova K.S., Koonin E.V., van der Oost J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 2008, 321:960-964.
17. Chao R., Yuan Y., Zhao H. Recent advances in DNA assembly technologies. FEMS Yeast Res. 2014, 15(1):1-9.
18. Charpentier E., Marraffini L.A. Harnessing CRISPR-Cas9 immunity for genetic engineering. Curr. Opin. Microbiol. 2014, 19:114-119.
19. Chevalier B.S., Stoddard B.L. Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res. 2001, 29:3757-3774.
20. Chiurazzi M., Ray A., Viret J.F., Perera R., Wang X.H., Lloyd A.M., Signer E.R. Enhancement of somatic intrachromosomal homologous recombination in Arabidopsis by the HO endonuclease. Plant Cell. 1996, 8:2057-2066.
21. Cho S.W., Kim S., Kim Y., Kweon J., Kim H.S., Bae S., Kim J. Analysis of off-target effects of CRISPR Cas-derived RNA-guided endonucleases and nickases sup2. Genome Res. 2014, 24(1):132-141.
22. Choulika A., Perrin A., Dujon B., Nicolas J.F. Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae. Mol. Cell. Biol. 1995, 15:1968-1973.
23. Cobb R.E., Wang Y., Zhao H. High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth. Biol. 2015, 4:723-728.
24. Cong L., Ran F.A., Cox D., Lin S., Barretto R., Habib N., Hsu P.D., Wu X., Jiang W., Marraffini L.A., Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science 2013, 339:819-823.
25. Costantino N., Court D.L. Enhanced levels of lambda Red-mediated recombinants in mismatch repair mutants. Proc. Natl. Acad. Sci. USA 2003, 100:15748-15753.
26. Covert M.W., Knight E.M., Reed J.L., Herrgard M.J., Palsson B.O. Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004, 429:92-96.
27. Cox D.B.T., Platt R.J., Zhang F. Therapeutic genome editing: prospects and challenges. Nat. Med. 2015, 21(2):121-131.
28. Crook N.C., Schmitz A.C., Alper H.S. Optimization of a yeast RNA interference system for controlling gene expression and enabling rapid metabolic engineering. ACS Synth. Biol. 2014, 3:307-313.
29. Da Silva N.A., Srikrishnan S. Introduction and expression of genes for metabolic engineering applications in Saccharomyces cerevisiae. FEMS Yeast Res. 2012, 12:197-214.
30. Dai Z., Liu Y., Guo J., Huang L., Zhang X. Yeast synthetic biology for high-value metabolites. FEMS Yeast Res. 2014, 15(1):1-11.
31. Datsenko K.A., Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 2000, 97:6640-6645.
32. Delneri D., Tomlin G.C., Wixon J.L., Hutter A., Sefton M., Louis E.J., Oliver S.G. Exploring redundancy in the yeast genome: an improved strategy for use of the cre-loxP system. Gene 2000, 252:127-135.
33. Deltcheva E., Chylinski K., Sharma C.M., Gonzales K., Chao Y., Pirzada Z.a, Eckert M.R., Vogel J., Charpentier E. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 2011, 471:602-607.
34. DiCarlo J.E., Conley A.J., Penttila M., Ja J., Wang H.H., Church G.M. Yeast oligo-mediated genome engineering (YOGE). ACS Synth. Biol. 2013, 2:741-749.
35. DiCarlo J.E., Norville J.E., Mali P., Rios X., Aach J., Church G.M. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 2013, 41:4336-4343.
36. DiCarlo J.E., Chavez A., Dietz S.L., Esvelt K.M., Church G.M. Safeguarding CRISPR-Cas9 gene drives in yeast. Nat. Biotechnol. 2015, Ahead of print. 10.1038/nbt.3412.
37. Dickinson D.J., Ward J.D., Reiner D.J., Goldstein B. Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat. Methods 2013, 10:1028-1034.
38. Doudna J.A., Charpentier E. The new frontier of genome engineering with CRISPR-Cas9. Science 2014, 346:6213.
39. Dragosits M., Mattanovich D. Adaptive laboratory evolution - principles and applications for biotechnology. Microb. Cell Factories 2013, 12:64.
40. Duan J., Lu G., Xie Z., Lou M., Luo J., Guo L., Zhang Y. Genome-wide identification of CRISPR/Cas9 off-targets in human genome. Cell Res. 2014, 24:1009-1012.
41. Eckert-Boulet N., Pedersen M.L., Krogh B.O., Lisby M. Optimization of ordered plasmid assembly by gap repair in Saccharomyces cerevisiae. Yeast 2012, 29:323-334.
42. Ellis H.M., Yu D., DiTizio T., Court D.L. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl. Acad. Sci. USA 2001, 98:6742-6746.
43. Esvelt K.M., Mali P., Braff J.L., Moosburner M., Yaung S.J., Church G.M. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods 2013, 10:1116-1121.
44. Esvelt K.M., Wang H.H. Genome-scale engineering for systems and synthetic biology. Mol. Syst. Biol. 2013, 9:641.
45. Farzadfard F., Perli S.D., Lu T.K. Tunable and multi-functional eukaryotic transcription factors based on CRISPR/Cas. ACS Synth. Biol. 2013, 2:604-613.
46. Fields S., Song O. A novel genetic system to detect protein-protein interactions. Nature 1989, 340:245-246.
47. Fu Y., Foden J.A., Khayter C., Maeder M.L., Reyon D., Joung J.K., Sander J.D. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol. 2013, 31:822-826.
48. Gaj T., Gersbach C.A., Barbas C.F. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 2013, 31:397-405.
49. Gao X., Wang P., Tang Y. Engineered polyketide biosynthesis and biocatalysis in Escherichia coli. Appl. Microbiol. Biotechnol. 2010, 88:1233-1242.
50. Gao Y., Zhao Y. Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing. J Integr Plant Biol 2014, (4):343-349.
51. Garneau J.E., Dupuis M.-È., Villion M., Romero D.a, Barrangou R., Boyaval P., Fremaux C., Horvath P., Magadán A.H., Moineau S. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 2010, 468:67-71.
52. Gasiunas G., Barrangou R., Horvath P., Siksnys V. PNAS Plus: Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl. Acad. Sci. USA 2012, 109:2579-2586.
53. Geen H.O., Henry I.M., Bhakta M.S., Meckler J.F., Segal D.J. A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture targeted sequence capture. Nucleic Acids Res. 2014, 43(6):3389-3404.
54. Giaever G., Chu A.M., Ni L., Connelly C., Riles L., Véronneau S., Dow S., Lucau-Danila A., Anderson K., André B., Arkin A.P., 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 D.J., Gerstein M., Gotte D., Güldener U., Hegemann J.H., Hempel S., Herman Z., Jaramillo D.F., Kelly D.E., Kelly S.L., Kötter P., LaBonte D., Lamb D.C., Lan N., Liang H., Liao H., Liu L., Luo C., Lussier M., Mao R., Menard P., Ooi S.L., Revuelta J.L., Roberts C.J., Rose M., Ross-Macdonald P., Scherens B., Schimmack G., Shafer B., Shoemaker D.D., Sookhai-Mahadeo S., Storms R.K., Strathern J.N., Valle G., Voet M., Volckaert G., Wang C., Ward T.R., Wilhelmy J., Winzeler E.A., Yang Y., Yen G., Youngman E., Yu K., Bussey H., Boeke J.D., Snyder M., Philippsen P., Davis R.W., Johnston M. Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002, 418:387-391.
55. Gilbert L.A., Horlbeck M.A., Adamson B., Villalta J.E., Chen Y., Whitehead E.H., Guimaraes C., Panning B., Ploegh H.L., Bassik M.C., Qi L.S., Kampmann M., Weissman J.S. Genome-Scale CRISPR-mediated control of gene repression and activation. Cell 2014, 159:647-661.
56. Gilbert L.A., Larson M.H., Morsut L., Liu Z., Brar G.A., Torres S.E., Stern-Ginossar N., Brandman O., Whitehead E.H., Doudna J.A., Lim W.A., Weissman J.S., Qi L.S. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 2013, 154:442-451.
57. Goldbeter A., Koshland D.E. An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl. Acad. Sci. USA 1981, 78(11):6840-6844.
58. Grav L.M., Lee J.S., Gerling S., Beuchert Kallehauge T., Holmgaard Hansen A., Kol S., Lee G.M., Ebdrup Pedersen L., Faustrup Kildegaard H. One-step generation of triple knockout CHO cell lines using CRISPR Cas9 and fluorescent enrichment. Biotechnol. J. 2015, 10:1446-1456.
59. Guirouilh-Barbat J., Huck S., Bertrand P., Pirzio L., Desmaze C., Sabatier L., Lopez B.S. Impact of the KU80 pathway on NHEJ-induced genome rearrangements in mammalian cells. Mol. Cell 2004, 14:611-623.
60. Haimovich A.D., Muir P., Isaacs F.J. Genomes by design. Nat. Rev. Genet. 2015, 16:501-516.
61. Harner N.K., Bajwa P.K., Formusa P.A., Austin G.D., Habash M.B., Trevors J.T., Chan C.-K., Ho C.-Y., Lee H. Determinants of tolerance to inhibitors in hardwood spent sulfite liquor in genome shuffled Pachysolen tannophilus strains. Antonie Van Leeuwenhoek 2015, 108(4):811-834.
62. He A.S., Rohatgi P.R., Hersh M.N., Rosenberg S.M. Roles of E. coli double-strand-break-repair proteins in stress-induced mutation. DNA Repair 2006, 5:258-273.
63. Heigwer F., Kerr G., Boutros M. E-CRISP: fast CRISPR target site identification. Nat. Methods 2014, 11:122-123.
64. Heler R., Samai P., Modell J.W., Weiner C., Goldberg G.W., Bikard D., Marraffini L.A. Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature 2015, 519:199-202.
65. Hendel A., Fine E.J., Bao G., Porteus M.H. Quantifying on- and off-target genome editing. Trends Biotechnol. 2015, 33(2):132-140.
66. Horii Z., Clark a J. Genetic analysis of the recF pathway to genetic recombination in Escherichia coli K12: isolation and characterization of mutants. J. Mol. Biol. 1973, 80:327-344.
67. Horst J.P., Wu T.H., Marinus M.G. Escherichia coli mutator genes. Trends Microbiol. 1999, 7:29-36.
68. Horvath P., Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science 2010, 327:167-170.
69. Horwitz A.A., Walter J.M., Schubert M.G., Kung S.H., Hawkins K., Platt D.M., Hernday A.D., Mahatdejkul-Meadows T., Szeto W., Chandran S.S., Newman J.D. Efficient multiplexed integration of synergistic alleles and metabolic pathways in yeasts via CRISPR-Cas. Cell Syst. 2015, 1:88-96.
70. Hsu P.D., Scott D.a, Weinstein J.a, Ran F.A., Konermann S., Agarwala V., Li Y., Fine E.J., Wu X., Shalem O., Cradick T.J., Marraffini L.a, Bao G., Zhang F. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 2013, 31:827-832.
71. Hsu P.D., Lander E.S., Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 2014, 157:1262-1278.
72. Huang H., Zheng G., Jiang W., Hu H., Lu Y. One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces. Acta Biochim. Biophys. Sin. 2015, 47:231-243.
73. Isaacs F.J., Carr P.A., Wang H.H., Lajoie M.J., Sterling B., Kraal L., Tolonen A.C., Gianoulis T.A., Goodman D.B., Reppas N.B., Emig C.J., Bang D., Hwang S.J., Jewett M.C., Jacobson J.M., Church G.M. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 2011, 333:348-353.
74. Ishino Y., Shinagawa H., Makino K., Amemura M., Nakata a Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J. Bacteriol. 1987, 169:5429-5433.
75. Jacobs J.Z., Ciccaglione K.M., Tournier V., Zaratiegui M. Implementation of the CRISPR-Cas9 system in fission yeast. Nat. Commun. 2014, 5:1-5.
76. Jakočiunas T., Bonde I., Herrgård M., Harrison S.J., Kristensen M., Pedersen L.E., Jensen M.K., Keasling J.D. Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. Metab. Eng. 2015, 28:213-222.
77. Jakočiunas T., Rajkumar A.S., Zhang J., Arsovska D., Rodriguez A., Jendresen C.B., Skjødt M.L., Nielsen A.T., Borodina I., Jensen M.K., Keasling J.D. CasEMBLR: Cas9-facilitated multiloci genomic integration of in vivo assembled dna parts in Saccharomyces cerevisiae. ACS Synth. Biol. 2015, 4:1226-1234.
78. Jensen N.B., Strucko T., Kildegaard K.R., David F., Maury J., Mortensen U.H., Forster J., Nielsen J., Borodina I. EasyClone: method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae. FEMS Yeast Res. 2014, 14:238-248.
79. Jiang W., Bikard D., Cox D., Zhang F., Marraffini L.A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 2013, 31:233-239.
80. Jiang W., Marraffini L.A. CRISPR-Cas: new tools for genetic manipulations from bacterial immunity systems. Annu. Rev. Microbiol. 2015, 69:209-228.
81. Jiang Y., Chen B., Duan C., Sun B., Yang J., Yang S. Multigene editing in the Escherichia coli genome using the CRISPR-Cas9 system. Appl. Env. Microbiol. 2015, 81:2506-2514.
82. Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337:816-821.
83. Jones K.L., Kim S.W., Keasling J.D. Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Metab. Eng. 2000, 2:328-338.
84. Joshi R., Ho K.K., Tenney K., Chen J.-H., Golden B.L., Gimble F.S. Evolution of I-SceI homing endonucleases with increased DNA recognition site specificity. J. Mol. Biol. 2011, 405:185-200.
85. Jullesson D., David F., Pfleger B., Nielsen J. Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals. Biotechnol. Adv. 2015, 33(7):1395-1402.
86. Katsuyama T., Akmammedov A., Seimiya M., Hess S.C., Sievers C., Paro R. An efficient strategy for TALEN-mediated genome engineering in Drosophila. Nucleic Acids Res. 2013, 41:e163.
87. Khakhar A., Bolten N.J., Nemhauser J., Klavins E. Cell-cell communication in yeast using auxin biosynthesis and auxin responsive CRISPR transcription factors. ACS Synth. Biol. 2015, 10.1021/acssynbio.5b00064.
88. Kistler K.E., Vosshall L.B., Matthews B.J. Genome engineering with CRISPR-Cas9 in the mosquito Aedes aegypti. Cell. Rep. 2015, 11:51-60.
89. Kleinstiver B.P., Prew M.S., Tsai S.Q., Topkar V.V., Nguyen N.T., Zheng Z., Gonzales A.P.W., Li Z., Peterson R.T., Yeh J.-R.J., Aryee M.J., Joung J.K. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 2015, 523:481-485.
90. Konermann S., Brigham M.D., Trevino a E., Joung J., Abudayyeh O.O., Barcena C., Hsu P.D., Habib N., Gootenberg J.S., Nishimasu H., Nureki O., Zhang F. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 2014, 517:583-588.
91. Koopman F., Beekwilder J., Crimi B., van Houwelingen A., Hall R.D., Bosch D., van Maris A.J., Pronk J.T., Daran J.M. De novo production of the flavonoid naringenin in engineered Saccharomyces cerevisiae. Microb. Cell Fact. 2012, 11:155.
92. Kuijpers N.G.A., Chroumpi S., Vos T., Solis-Escalante D., Bosman L., Pronk J.T., Daran J.-M., Daran-Lapujade P. One-step assembly and targeted integration of multigene constructs assisted by the I-SceI meganuclease in Saccharomyces cerevisiae. FEMS Yeast Res. 2013, 13:769-781.
93. Kuscu C., Arslan S., Singh R., Thorpe J., Adli M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat. Biotechnol. 2014, 32:677-683.
94. La Russa M.F., Qi L.S. The new state of the art: Cas9 for gene activation and repression. Mol. Cell. Biol. 2015, 35(22):3800-3809.
95. Lanza A.M., Curran K.A., Rey L.G., Alper H.S. A condition-specific codon optimization approach for improved heterologous gene expression in Saccharomyces cerevisiae. BMC Syst. Biol. 2014, 8:33.
96. Lee J.S., Grav L.M., Lewis N.E., Kildegaard H.F. CRISPR/Cas9-mediated genome engineering of CHO cell factories: application and perspectives. Biotechnol. J. 2015, 10:979-994.
97. Lee J.S., Kallehauge T.B., Pedersen L.E., Kildegaard H.F. Site-specific integration in CHO cells mediated by CRISPR/Cas9 and homology-directed DNA repair pathway. Sci. Rep. 2015, 5:8572.
98. Lee M.E., Aswani A., Han A.S., Tomlin C.J., Dueber J.E. Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay. Nucleic Acids Res. 2013, 41(22):10668-10678.
99. Lennen R.M., Nilsson Wallin A.I., Pedersen M., Bonde M., Luo H., Herrgård M.J., Sommer M.O. Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects. Nucleic Acids Res. 2015, 10.1093/nar/gkv1090.
100. Li J., Neubauer P. Escherichia coli as a cell factory for heterologous production of nonribosomal peptides and polyketides. N. Biotechnol. 2014, 31:579-585.
101. Li Y., Lin Z., Huang C., Zhang Y., Wang Z., Tang Y., Chen T., Zhao X. Metabolic engineering of Escherichia coli using CRISPR-Cas9 meditated genome editing. Metab. Eng. 2015, 31:13-21.
102. Liang F., Han M., Romanienko P.J., Jasin M. Homology-directed repair is a major double-strand break repair pathway in mammalian cells. Proc. Natl. Acad. Sci. USA 1998, 95:5172-5177.
103. Liu R., Chen L., Jiang Y., Zhou Z., Zou G. Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system. Cell Discov. 2015, 1:15007.
104. Luttik M.A., Vuralhan Z., Suir E., Braus G.H., Pronk J.T., Daran J.M. Alleviation of feedback inhibition in Saccharomyces cerevisiae aromatic amino acid biosynthesis: quantification of metabolic impact. Metab. Eng. 2008, 10:141-153.
105. Lv L., Ren Y., Chen J., Wu Q., Chen G. Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes , a case study[U+202F]: controllable P ( 3HB- co -4HB ) biosynthesis. Metab. Eng. 2015, 29:1-9.
106. Ma H., Kunes S., Schatz P.J., Botstein D. Plasmid construction by homologous recombination in yeast. Gene 1987, 58:201-216.
107. Mali P., Aach J., Stranges P.B., Esvelt K.M., Moosburner M., Kosuri S., Yang L., Church G.M. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 2013, 31:833-838.
108. Maniloff J. The minimal cell genome: "on being the right size". Proc. Natl. Acad. Sci. USA 1996, 93:10004-10006.
109. Mans R., van Rossum H.M., Wijsman M., Backx A., Kuijpers N.G.A., van den Broek M., Daran-Lapujade P., Pronk J.T., van Maris A.J.A., Daran J.-M.G. CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae. FEMS Yeast Res. 2015, 15. 10.1093/femsyr/fov004.
110. Marraffini L.A. CRISPR-Cas immunity in prokaryotes. Nature 2015, 526:55-61.
111. Martin V.J.J., Pitera D.J., Withers S.T., Newman J.D., Keasling J.D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 2003, 21:796-802.
112. Miller-Fleming L., Giorgini F., Outeiro T.F. Yeast as a model for studying human neurodegenerative disorders. Biotechnol. J. 2008, 3:325-338.
113. Mitchell L.A., Chuang J., Agmon N., Khunsriraksakul C., Phillips N.A., Cai Y., Truong D.M., Veerakumar A., Wang Y., Mayorga M., Blomquist P., Sadda P., Trueheart J., Boeke J.D. Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae. Nucleic Acids Res. 2015, 43:6620-6630.
114. Mojica F.J.M., Díez-Villaseñor C., García-Martínez J., Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 2005, 60:174-182.
115. Moore J.K., Haber J.E. Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol. Cell. Biol. 1996, 16:2164-2173.
116. Murakami C., Kaeberlein M. Quantifying yeast chronological life span by outgrowth of aged cells. J. Vis. Exp. 2009, 27:1156.
117. Naito Y., Hino K., Bono H., Ui-Tei K. CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics 2014, 31:1120-1123.
118. Nihongaki Y., Yamamoto S., Kawano F., Suzuki H., Sato M. CRISPR-Cas9-based photoactivatable transcription system. Chem. Biol. 2015, 22:169-174.
119. Nishimasu H., Ran F.A., Hsu P.D., Konermann S., Shehata S.I., Dohmae N., Ishitani R., Zhang F., Nureki O. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 2014, 156:935-949.
120. Nødvig C.S., Nielsen J.B., Kogle M.E., Mortensen U.H. A CRISPR-Cas9 system for genetic engineering of filamentous fungi. PLoS One 2015, 10:e0133085.
121. Nyerges Á., Csorgo B., Nagy I., Latinovics D., Szamecz B., Pósfai G., Pál C. Conditional DNA repair mutants enable highly precise genome engineering. Nucleic Acids Res. 2014, 42:e62.
122. Oh J.-H., van Pijkeren J.-P. CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri. Nucleic Acids Res. 2014, 42:e131.
123. Olano C., Méndez C., Salas J.A. Antitumor compounds from actinomycetes: from gene clusters to new derivatives by combinatorial biosynthesis. Nat. Prod. Rep. 2009, 26:628-660.
124. Oldenburg K.R., Vo K.T., Michaelis S., Paddon C. Recombination-mediated PCR-directed plasmid construction in vivo in yeast. Nucleic Acids Res. 1997, 25:451-452.
125. Österlund T., Nookaew I., Bordel S., Nielsen J. Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling. BMC Syst. Biol. 2013, 7:36.
126. Özaydin B., Burd H., Lee T.S., Keasling J.D. Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production. Metab. Eng. 2013, 15:174-183.
127. Paddon C.J., Keasling J.D. Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat. Rev. Microbiol. 2012, 12(5):355-367.
128. Pâques F., Haber J.E. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 1999, 63:349-404.
129. Pardo B., Gómez-González B., Aguilera A. DNA repair in mammalian cells. Cell. Mol. Life Sci. 2009, 66:1039-1056.
130. Patnaik R., Louie S., Gavrilovic V., Perry K., Stemmer W.P.C., Ryan C.M., del Cardayré S. Genome shuffling of Lactobacillus for improved acid tolerance. Nat. Biotechnol. 2002, 20:707-712.
131. Pelletier S., Gingras S., Green D.R. Mouse genome engineering via CRISPR-Cas9 for study of immune function. Immunity 2015, 42:18-27.
132. Peng B., Williams T.C., Henry M., Nielsen L.K., Vickers C.E. Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activities. Microb. Cell Factories 2015, 14:91.
133. Peters J.M., Silvis M.R., Zhao D., Hawkins J.S., Gross C.A., Qi L.S. Bacterial CRISPR: accomplishments and prospects. Curr. Opin. Microbiol. 2015, 27:121-126.
134. Pinel D., Colatriano D., Jiang H., Lee H., Martin V.J. Deconstructing the genetic basis of spent sulphite liquor tolerance using deep sequencing of genome-shuffled yeast. Biotechnol. Biofuels 2015, 8:53.
135. Polstein L.R., Gersbach C.a A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. Nat. Chem. Biol. 2015, 11:198-200.
136. Pourcel C., Salvignol G., Vergnaud G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 2005, 151:653-663.
137. Pyne M.E., Moo-Young M., Chung D.A., Chou C.P. Coupling the CRISPR/Cas9 system to lambda Red recombineering enables simplified chromosomal gene replacement in Escherichia coli. Appl. Env. Microbiol. 2015, 81:5103-5114.
138. Qi L.S., Larson M.H., Gilbert L.a, Doudna J.a, Weissman J.S., Arkin A.P., Lim W. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013, 152:1173-1183.
139. Reyes L.H., Gomez J.M., Kao K.C. Improving carotenoids production in yeast via adaptive laboratory evolution. Metab. Eng. 2014, 21:26-33.
140. Reyon D., Tsai S.Q., Khayter C., Foden J.A., Sander J.D., Joung J.K. FLASH assembly of TALENs for high-throughput genome editing. Nat. Biotechnol. 2012, 30:460-465.
141. Ro D.-K., Paradise E.M., Ouellet M., Fisher K.J., Newman K.L., Ndungu J.M., Ho K.A., Eachus R.A., Ham T.S., Kirby J., Chang M.C.Y., Withers S.T., Shiba Y., Sarpong R., Keasling J.D. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 2006, 440:940-943.
142. Rodríguez-Verdugo A., Carrillo-Cisneros D., González-González A., Gaut B.S., Bennett A.F. Different tradeoffs result from alternate genetic adaptations to a common environment. Proc. Natl. Acad. Sci. USA 2014, 111(33):12121-12126.
143. Romero P.A., Arnold F.H. Exploring protein fitness landscapes by directed evolution. Nat. Rev. Mol. Cell Biol. 2009, 10:866-876.
144. Romagnoli G., Luttik MA., Kötter P., Pronk JT., Daran J.M. Substrate specificity of thiamine pyrophosphate-dependent 2-oxo-acid decarboxylases in Saccharomyces cerevisiae. Appl. Environ. Microbiol 2012, 7538-7548.
145. Ronda C., Maury J., Jakočiunas T., Baallal Jacobsen S.A., Germann S.M., Harrison S.J., Borodina I., Keasling J.D., Jensen M.K., Nielsen A.T. CrEdit: CRISPR mediated multi-loci gene integration in Saccharomyces cerevisiae. Microb. Cell. Factories 2015, 14:97.
146. Ronda C., Pedersen L.E., Hansen H.G., Kallehauge T.B., Betenbaugh M.J., Nielsen A.T., Kildegaard H.F. Accelerating genome editing in CHO cells using CRISPR Cas9 and CRISPy, a web-based target finding tool. Biotechnol. Bioeng. 2014, 111:1604-1616.
147. Roth D.B., Wilson J.H. Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction. Mol. Cell. Biol. 1986, 6:4295-4304.
148. Ryan O.W., Skerker J.M., Maurer M.J., Li X., Tsai J.C., Poddar S., Lee M.E., DeLoache W., Dueber J.E., Arkin A.P., Cate J.H.D. Selection of chromosomal DNA libraries using a multiplex CRISPR system. Elife 2014, e03703.
149. Sandberg T.E., Pedersen M., LaCroix R.A., Ebrahim A., Bonde M., Herrgard M.J., Palsson B.O., Sommer M., Feist A.M. Evolution of Escherichia coli to 42°C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. Mol. Biol. Evol. 2014, 31:2647-2662.
150. Sander J.D., Dahlborg E.J., Goodwin M.J., Cade L., Zhang F., Cifuentes D., Curtin S.J., Blackburn J.S., Thibodeau-Beganny S., Qi Y., Pierick C.J., Hoffman E., Maeder M.L., Khayter C., Reyon D., Dobbs D., Langenau D.M., Stupar R.M., Giraldez A.J., Voytas D.F., Peterson R.T., Yeh J.-R.J., Joung J.K. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat. Methods 2011, 8:67-69.
151. Sander J.D., Joung J.K. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 2014, 32:347-355.
152. Sawitzke J.A., Thomason L.C., Bubunenko M., Li X., Costantino N., Court D.L. Laboratory methods in enzymology: cell, lipid and carbohydrate, methods in enzymology. Methods Enzymol. 2013.
153. Selle K., Barrangou R. Harnessing CRISPR-Cas systems for bacterial genome editing. Trends Microbiol. 2015, 23(4):225-232.
154. Shalem O., Sanjana N.E., Zhang F. High-throughput functional genomics using CRISPR-Cas9. Nat. Rev. Genet. 2015, 16:299-311.
155. Shao Z., Zhao H., Zhao H. DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res. 2009, 37:e16.
156. Sharan S.K., Thomason L.C., Kuznetsov S.G., Court D.L. Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. 2009, 4:206-223.
157. Shi T., Wang G., Wang Z., Fu J., Chen T., Zhao X. Establishment of a markerless mutation delivery system in Bacillus subtilis stimulated by a double-strand break in the chromosome. PLoS One 2013, 8:e81370.
158. Shi S., Liang Y., Zhang M.M., Ang E.L., Zhao H. A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae. Metab. Eng. 2015, 33:19-27.
159. Si T., Xiao H., Zhao H. Rapid prototyping of microbial cell factories via genome-scale engineering. Biotechnol. Adv. 2014, 33(7):1420-1432.
160. Siddiqui M.S., Choksi A., Smolke C.D. A system for multi-locus chromosomal integration and transformation-free selection marker rescue. FEMS Yeast Res. 2014, 14:1171-1185.
161. Silva-Rocha R., Martinez-Garcia E., Calles B., Chavarria M., Arce-Rodriguez A., de las Heras A., Paez-Espino A.D., Durante-Rodriguez G., Kim J., Nikel P.I., Platero R., de Lorenzo V. The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res. 2012, 41:666-675.
162. Simeonidis E., Price N.D. Genome-scale modeling for metabolic engineering. J. Ind. Microbiol. Biotechnol. 2015, 42:327-338.
163. Smith J., Grizot S., Arnould S., Duclert A., Epinat J.-C., Chames P., Prieto J., Redondo P., Blanco F.J., Bravo J., Montoya G., Pâques F., Duchateau P. A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences. Nucleic Acids Res. 2006, 34:e149.
164. Solis-Escalante D., Kuijpers N.G., van der Linden F.H., Pronk J.T., Daran J.M., Daran-Lapujade P. Efficient simultaneous excision of multiple selectable marker cassettes using I-SceI-induced double-strand DNA breaks in Saccharomyces cerevisiae. FEMS Yeast Res. 2014, 14:741-754.
165. Solis-Escalante D., Kuijpers N.G.A., Bongaerts N., Bolat I., Bosman L., Pronk J.T., Daran J.-M., Daran-Lapujade P. amdSYM, a new dominant recyclable marker cassette for Saccharomyces cerevisiae. FEMS Yeast Res. 2013, 13:126-139.
166. Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., Brown P.O., Futcher B. Comprehensive identification of cell cycle - regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 1998, 9:3273-3297.
167. Steensels J., Snoek T., Meersman E., Picca Nicolino M., Voordeckers K., Verstrepen K.J. Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol. Rev. 2014, 38:947-995.
168. Storici F., Durham C.L., Gordenin D.A., Resnick M.A. Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast. Proc. Natl. Acad. Sci. USA 2003, 100:14994-14999.
169. Storici F., Resnick M.A The delitto perfetto approach to in vivo site-directed mutagenesis and chromosome rearrangements with synthetic oligonucleotides in yeast. Methods Enzymol. 2006, 409:329-345.
170. Stovicek V., Borodina I., Forster J. CRISPR-Cas system enables fast and simple genome editing of industrial Saccharomyces cerevisiae strains. Metab. Eng. Commun. 2015, 2:13-22.
171. Sugano S.S., Shirakawa M., Takagi J., Matsuda Y., Shimada T., Hara-Nishimura I., Kohchi T. CRISPR/Cas9-mediated targeted mutagenesis in the liverwort Marchantia polymorpha L. Plant Cell Physiol. 2014, 55:475-481.
172. Sun J., Shao Z., Zhao H., Nair N., Wen F., Xu J.-H., Zhao H. Cloning and characterization of a panel of constitutive promoters for applications in pathway engineering in Saccharomyces cerevisiae. Biotechnol. Bioeng. 2012, 109:2082-2092.
173. Thierry A., Dujon B. Nested chromosomal fragmentation in yeast using the meganuclease I-Sce I: a new method for physical mapping of eukaryotic genomes. Nucleic Acids Res. 1992, 20:5625-5631.
174. Thomason L., Court D.L., Bubunenko M., Costantino N., Wilson H., Datta S., Oppenheim A. Recombineering: genetic engineering in bacteria using homologous recombination. Curr. Protoc. Mol. Biol. 2007, Chapter 1, Unit 1.16.
175. Tong S.I., HamediRad M., Zhao H. Regulatory RNA-assisted genome engineering in microorganisms. Curr. Opin. Biotechnol. 2015, 36:85-90.
176. Tong Y., Charusanti P., Zhang L., Weber T., Lee S.Y. CRISPR-Cas9 based engineering of actinomycetal genomes. ACS Synth. Biol. 2015, 4:1020-1029.
177. Tsai C.-S., Kong I.I., Lesmana A., Million G., Zhang G.-C., Kim S.R., Jin Y.-S. Rapid and marker-free Cas9/CRISPR refactoring yields equivalent xylose-utilization performance in yeast. Biotechnol. Bioeng. 2015, 112:2406-2411.
178. Tsai S.Q., Zheng Z., Nguyen N.T., Liebers M., Topkar V.V., Thapar V., Wyvekens N., Khayter C., Iafrate A.J., Le L.P., Aryee M.J., Joung J.K. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 2014, 33:187-198.
179. Upadhyay S.K., Kumar J., Alok A., Tuli R. RNA-guided genome editing for target gene mutations in wheat. G3 2013, 3:2233-2238.
180. Verwaal R., Wang J., Meijnen J.P., Visser H., Sandmann G., vandenBerg J.A., vanOoyen A.J. High-level production of beta-carotene in Saccharomyces cerevisiae by successive transformation with carotenogenic genes from Xanthophyllomyces dendrorhous. Appl Environ Microbiol 2007, 4342-4350.
181. Wang H.H., Isaacs F.J., Carr P.a, Sun Z.Z., Xu G., Forest C.R., Church G.M. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460:894-898.
182. Wang Q., Wang L. New methods enabling efficient incorporation of unnatural amino acids in yeast new methods enabling efficient incorporation of unnatural amino acids in yeast. Society 2008, 6066-6067.
183. Wang Y., Li Z., Xu J., Zeng B., Ling L., You L., Chen Y., Huang Y., Tan A. The CRISPR/Cas system mediates efficient genome engineering in Bombyx mori. Cell Res. 2013, 23:1414-1416.
184. Wang Y., Zhang Z.-T., Seo S.-O., Choi K., Lu T., Jin Y.-S., Blaschek H.P. Markerless chromosomal gene deletion in Clostridium beijerinckii using CRISPR/Cas9 system. J. Biotechnol. 2015, 200:1-5.
185. Whelan W.L., Gocke E., Manney T.R. The CAN1 locus of Saccharomyces cerevisiae: fine-structure analysis and forward mutation rates. Genetics 1979, 91:35-51.
186. Wood A.J., Lo T.-W., Zeitler B., Pickle C.S., Ralston E.J., Lee A.H., Amora R., Miller J.C., Leung E., Meng X., Zhang L., Rebar E.J., Gregory P.D., Urnov F.D., Meyer B.J. Targeted genome editing across species using ZFNs and TALENs. Science 2011, 333:307.
187. Wu J., Du G., Chen J., Zhou J. Enhancing flavonoid production by systematically tuning the central metabolic pathways based on a CRISPR interference system in Escherichia coli. Sci. Rep. 2015, 5:13477.
188. Wu X., Scott D.a, Kriz A.J., Chiu A.C., Hsu P.D., Dadon D.B., Cheng A.W., Trevino A.E., Konermann S., Chen S., Jaenisch R., Zhang F., Sharp P.A Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat. Biotechnol. 2014, 32:670-676.
189. Xu T., Li Y., Shi Z., Hemme C.L., Li Y., Zhu Y., Van Nostrand J.D., He Z., Zhou J. Efficient genome editing in Clostridium cellulolyticum via CRISPR-Cas9 nickase. Appl. Environ. Microbiol. 2015, 81(13):4423-4431.
190. Yu B.J., Kim C. Minimization of the Escherichia coli genome using the Tn5-targeted Cre/loxP excision system. Methods Mol. Biol. 2008, 416:261-277.
191. Yuan L., Kurek I., English J., Keenan R. Laboratory-directed protein evolution. Microbiol. Mol. Biol. Rev. 2005, 69:373-392.
192. Zalatan J.G., Lee M.E., Almeida R., Gilbert L.A., Whitehead E.H., La Russa M., Tsai J.C., Weissman J.S., Dueber J.E., Qi L.S., Lim W.A. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 2014, 160:339-350.
193. Zeng H., Wen S., Xu W., He Z., Zhai G., Liu Y., Deng Z., Sun Y. Highly efficient editing of the actinorhodin polyketide chain length factor gene in Streptomyces coelicolor M145 using CRISPR/Cas9-CodA(sm) combined system. Appl. Microbiol. Biotechnol. 2015, Ahead of print. 10.1007/s00253-015-6931-4.
194. Zhang G., Lin Y., Qi X., Wang L., He P., Wang Q., Ma Y. Genome shuffling of the nonconventional yeast Pichia anomala for improved sugar alcohol production. Microb. Cell Factories 2015, 14:112.
195. Zhang G.C., Kong I.I., Kim H., Liu J.J., Cate J.H.D., Jin Y.-S. Construction of a quadruple auxotrophic mutant of an industrial polyploid saccharomyces cerevisiae strain by using rna-guided Cas9 nuclease. Appl. Environ. Microbiol. 2014, 80:7694-7701.
196. Zu Y., Tong X., Wang Z., Liu D., Pan R., Li Z., Hu Y., Luo Z., Huang P., Wu Q., Zhu Z., Zhang B., Lin S. TALEN-mediated precise genome modification by homologous recombination in zebrafish. Nat. Methods 2013, 10:329-331.