EasyCloneMulti: A set of vectors for simultaneous and multiple genomic integrations in saccharomyces cerevisiae

PLoS ONE

Volumn 11, Issue 3, 2016, Pages

  Maury, Jérôme ^a   Germann, Susanne M ^a   Baallal Jacobsen, Simo Abdessamad ^a   Jensen, Niels B ^a,c   Kildegaard, Kanchana R ^a   Herrgàrd, Markus J ^a   Schneider, Konstantin ^a   Koza, Anna ^a   Forster, Jochen ^a   Nielsen, Jens ^a,b   Borodina, Irina ^a  

^a Chalmers University of Technology   (Denmark)

^b CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^c EVOLVA SA   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BETA ALANINE; GREEN FLUORESCENT PROTEIN; HYDRACRYLIC ACID; LACTIC ACID;

ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; ENZYME ACTIVITY; FUNGAL GENETICS; FUNGAL STRAIN; GENE EXPRESSION; GENE IDENTIFICATION; GENE INTERACTION; GENE LOCUS; GENE TARGETING; GENE VECTOR; GENETIC VARIABILITY; LONG TERMINAL REPEAT; MOLECULAR CLONING; NEXT GENERATION SEQUENCING; NONHUMAN; RETROPOSON; SACCHAROMYCES CEREVISIAE; ANALOGS AND DERIVATIVES; GENETICS; GENOMICS; METABOLISM; MICROBIOLOGY; PROCEDURES;

BETA-ALANINE; CLONING, MOLECULAR; GENETIC VECTORS; GENOMICS; INDUSTRIAL MICROBIOLOGY; LACTIC ACID; METABOLIC NETWORKS AND PATHWAYS; SACCHAROMYCES CEREVISIAE;

EID: 84960906175     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0150394     Document Type: Article

References (51)

1. Borodina I, Nielsen J. Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals. Biotechnol J. 2014; 9: 609-20. doi: 10.1002/biot.201300445 PMID: 24677744
2. Li M, Borodina I. Application of synthetic biology for production of chemicals in yeast S. cerevisiae. FEMS Yeast Res. 2014; Sep 19. doi: 10.1111/1567-1364.12213
3. Hong K-K, Nielsen J. Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform forfuture biorefineries. Cell Mol Life Sci. 2012; 69: 2671-90. doi: 10.1007/s00018-012-0945-1 PMID: 22388689
4. Tippmann S, Chen Y, Siewers V, Nielsen J. From flavors and pharmaceuticals to advanced biofuels: production of isoprenoids in Saccharomyces cerevisiae. Biotechnol J. 2013; 8:1435-44. doi: 10.1002/biot.201300028 PMID: 24227704
5. Krivoruchko A, Siewers V, Nielsen J. Opportunities foryeast metabolic engineering: Lessons from synthetic biology. Biotechnol J. 2011; 6: 262-76. doi: 10.1002/biot.201000308 PMID: 21328545
6. David F, Siewers V. Advances in yeast genome engineering. FEMS Yeast Res. 2014; Aug 26. doi: 10.1111/1567-1364.12200
7. Paddon CJ, Westfall PJ, Pitera DJ, Benjamin K, Fisher K, McPhee D, et al. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature. 2013; 496: 526-32. doi: 10.1038/nature12051
8. Asadollahi MA, Maury J, Moller K, Nielsen KF, Schalk M, Clark A, et al. Production of plant sesquiterpenes in Saccharomyces cerevisiae: effect of ERG9 repression on sesquiterpene biosynthesis. Biotechnol Bioeng. 2008; 99: 666-77. doi: 10.1002/bit.21581 PMID: 17705244
9. Brochado AR, Matos C, Moller BL, Hansen J, Mortensen UH, Patil KR. Improved vanillin production in baker's yeast through in silico design. MicrobCell Fact. 2010; 9: 84. doi: 10.1186/1475-2859-9-84 PMID: 21059201
10. Katz M, Durhuus T, Smits H, Förster J. Production of metabolites. 2011. WO2011147818.
11. Mikkelsen MD, Buron LD, Salomonsen B, Olsen CE, Hansen BG, Mortensen UH, et al. Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform. Metab Eng. 2012; 14:104-11. doi: 10.1016/j.ymben.2012.01.006 PMID: 22326477
12. Jensen MK, Keasling JD. Recent applications of synthetic biology tools for yeast metabolic engineering. FEMS Yeast Res. 2014 Jul 16. doi: 10.1111/1567-1364.12185
13. Redden H, Morse N, Alper HS. The synthetic biology toolbox for tuning gene expression in yeast. FEMS Yeast Res. 2014 Jul 22. doi: 10.1111/1567-1364.12188
14. Bitter BGA, Egan KM, Koski RA, Jones MO, Elliott SG, Giffin JC. Expression and secretion vectors for yeast. Methods Enzymol. 1987; 153: 516-44. PMID: 2828848
15. Kanaya E, Higashizaki T, Ozawa F, Hirai K, Nishizawa M, Tokunaga M, et al. Synthesis and secretion of human nerve growth factor by Saccharomyces cerevisiae. Gene. 1989; 83: 65-74. PMID: 2687117
16. Jensen NB, Strucko T, Kildegaard KR, David F, Maury J, Mortensen UH, et al. EasyClone: method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae. FEMS Yeast Res. 2014; 1-11. doi: 10.1111/1567-1364.12118
17. Cameron JR, Loh EY, Davis RW. Evidence for transposition of dispersed repetitive DNA families in yeast. Cell. 1979; 16: 739-751. doi: 10.1016/0092-8674(79)90090-4 PMID: 378399
18. Kazazian HH. Mobile elements: drivers of genome evolution. Science. 2004; 303:1626-1632. doi: 10.1126/science.1089670 PMID: 15016989
19. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007; 8: 973-82. doi: 10.1038/nrg2165 PMID: 17984973
20. Dujon B. Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution. Trends Genet. 2006; 22: 375-87. doi: 10.1016/j.tig.2006.05.007 PMID: 16730849
21. Boeke JD, Garfinkel DJ, Styles CA, Fink GR. Ty elements transpose through an RNA intermediate. Cell. 1985; 40: 491-500. doi: 10.1016/0092-8674(85)90197-7 PMID: 2982495
22. Bleykasten-Grosshans C, Neuvéglise C. Transposable elements in yeasts. C R Biol. 2011; 334: 679-86. doi: 10.1016/j.crvi.2011.05.017 PMID: 21819950
23. Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF. Transposable Elements and Genome Organization : A Comprehensive Survey of Retrotransposons Revealed by the Complete Saccharomyces cere-visiae Genome Sequence. Genome Res. 1998;8:464-78. PMID: 9582191
24. Sakai A, Shimizu Y, Hishinuma F. Integration of heterologous genes into the chromosome of Saccharomyces cerevisiae using a delta sequence of yeast retrotransposon Ty. Appl Microbiol Biotechnol. 1990; 33: 302-306. PMID: 1369269
25. Parekh RN, Shaw MR, Wittrup KD. An integrating vectorfortunable, high copy, stable integration into the dispersed Ty delta sites of Saccharomyces cerevisiae. Biotechnol Prog. 1996; 12:16-21. doi: 10.1021/bp9500627 PMID: 8845105
26. Oliveira C, Teixeira JA, Lima N, Da Silva NA, Domingues L. Development of stable flocculent Saccharomyces cerevisiae strain for continuous Aspergillus niger beta-galactosidase production. J Biosci Bioeng. 2007; 103: 318-324. doi: 10.1263/jbb.103.318 PMID: 17502272
27. Lee W, DaSilva NA. Application of sequential integration for metabolic engineering of 1, 2-propanediol production in yeast. Metab Eng. 2006; 8: 58-65. doi: 10.1016/j.ymben.2005.09.001 PMID: 16242982
28. Yamada R, Taniguchi N, Tanaka T, Ogino C, Fukuda H, Kondo A. Cocktail delta-integration: a novel method to construct cellulolytic enzyme expression ratio-optimized yeast strains. Microb Cell Fact. 2010; 9: 32. doi: 10.1186/1475-2859-9-32 PMID: 20465850
29. Yuan J, Ching CB. Combinatorial assembly of large biochemical pathways into yeast chromosomes for improved production of value-added compounds. ACS Synth Biol. 2014; 4: 23-31. doi: 10.1021/sb500079f PMID: 24847678
30. Lopes TS, Klootwijk J, Veenstra AE, van der Aar PC, van Heerikhuizen H, Raúe HA, et al. High-copy-number integration into the ribosomal DNA of Saccharomyces cerevisiae: a new vector for high-level expression. Gene. 1989; 79:199-206. doi: 10.1016/0378-1119(89)90202-3 PMID: 2676725
31. Stovicek V, Borja GM, Forster J, Borodina I. EasyClone2.0 : expanded toolkit of integrative vectors for stable gene expression in industrial Saccharomyces cerevisiae strains. J Ind Microbiol Biotechnol. 2015; doi: 10.1007/s10295-015-1684-8
32. Borodina I, Kildegaard KR, Jensen NB, Blicher TH, Maury J, Sherstyk S, et al. Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via ß-ala-nine. Metab Eng.; 2014; 27: 57-64. doi: 10.1016/j.ymben.2014.10.003 PMID: 25447643
33. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013; 30: 2725-9. doi: 10.1093/molbev/mst197 PMID: 24132122
34. Inoue H, Nojima H, Okayama H. High efficiency transformation of Escherichia coli with plasmids. Gene. 1990; 96: 23-28. doi: 10.1016/0378-1119(90)90336-P PMID: 2265755
35. Gilon T, Chomsky O, Kulka RG. Degradation signals for ubiquitin system proteolysis in Saccharomyces cerevisiae. EMBO J. 1998; 17: 2759-66. doi: 10.1093/emboj/17.10.2759 PMID: 9582269
36. Norholm MHH. A mutant Pfu DNA polymerase designed for advanced uracil-excision DNA engineering. BMC Biotechnol. 2010; 16:10-21. doi: 10.1186/1472-6750-10-21
37. Gietz RD, Schiestl RH. High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat Protoc. 2007; 2: 31-4. PMID: 17401334
38. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie2. Nat Methods. 2012; 9: 357-9. doi: 10.1038/nmeth.1923 PMID: 22388286
39. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformat-ics. 2010; 26: 841-2 doi: 10.1093/bioinformatics/btq033 PMID: 20110278
40. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25: 2078-9. doi: 10.1093/bioinformatics/btp352 PMID: 19505943
41. Milne I, Stephen G, Bayer M, Cock PJA, Pritchard L, Cardle L, et al. Using Tablet for visual exploration of second-generation sequencing data. Brief Bioinform. 2013; 14:193-202. doi: 10.1093/bib/bbs012 PMID: 22445902
42. Gilon T, Chomsky O, Kulka RG. Degradation signals recognized by the Ubc6p-Ubc7p ubiquitin-conju-gating enzyme pair. Mol Cell Biol. 2000; 20: 7214-9. PMID: 10982838
43. Shi S, Valle-Rodríguez JO, Siewers V, Nielsen J. Engineering of chromosomal wax ester synthase integrated Saccharomyces cerevisiae mutants for improved biosynthesis of fatty acid ethyl esters. Biotechnol Bioeng. 2014; 111:1740-1747. doi: 10.1002/bit.25234 PMID: 24752598
44. Siddiqui MS, Choksi A, Smolke CD. A system for multi-locus chromosomal integration and transformation-free selection marker rescue. FEMS Yeast Res. 2014; 14:1171-1185. doi: 10.1111/1567-1364. 12210 PMID: 25226817
45. Loison G. High level of expression of a protective antigen of schistosomes in Saccharomyces cerevi-siae. Yeast. 1989; 5: 497-507. PMID: 2694678
46. Chen Y, Partow S, Scalcinati G, Siewers V, Nielsen J. Enhancing the copy number of episomal plasmids in Saccharomyces cerevisiae for improved protein production. FEMS Yeast Res. 2012; 12: 598-607. doi: 10.1111/j.1567-1364.2012.00809.x PMID: 22487308
47. Li M, Kildegaard KR, Chen Y, Rodriguez A, Borodina I, Nielsen J. De novo production of resveratrol from glucose or ethanol by engineered Saccharomyces cerevisiae. Metab Eng. Elsevier; 2015; 32:1-11. doi: 10.1016/j.ymben.2015.08.007
48. Alper H, Fischer C, Nevoigt E, Stephanopoulos G. Tuning genetic control through promoter engineering. Proc Natl Acad Sci USA. 2005; 102:12678-83. doi: 10.1073/pnas.0504604102 PMID: 16123130
49. Nevoigt E, Kohnke J, Fischer CR, Alper H, Stahl U, Stephanopoulos G. Engineering of promoter replacement cassettes for fine-tuning of gene expression in Saccharomyces cerevisiae. Appl Environ Microbiol. 2006; 72: 5266-73. doi: 10.1128/AEM.00530-06 PMID: 16885275
50. Dunn B, Richter C, Kvitek DJ, Pugh T, Sherlock G. Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments. Genome Res. 2012; 22: 908-24. doi: 10.1101/gr.130310.111 PMID: 22369888
51. Leite FCB, Dos Anjos RSG, Basilio ACM, Leal GFC, Simöes DA, de Morais MA. Construction of integrative plasmids suitable for genetic modification of industrial strains of Saccharomyces cerevisiae. Plasmid. Elsevier Inc.; 2012; 10-13. doi: 10.1016/j.plasmid.2012.09.004