Yeast as a cell factory: Current state and perspectives

Microbial Cell Factories

Volumn 14, Issue 1, 2015, Pages

  Kavšček, Martin ^a   Stražar, Martin ^b   Curk, Tomaž ^b   Natter, Klaus ^a   Petrovič, Uroš ^c  

^a UNIVERSITY OF GRAZ   (Austria)

^b UNIVERSITY OF LJUBLJANA   (Slovenia)

^c JO EF STEFAN INSTITUTE   (Slovenia)

Author keywords

Genome editing; Orthogonality; QTL; Robustness development; Substrate utilization

Indexed keywords

CRISPR CAS SYSTEM; ENVIRONMENTAL STRESS; FUNGAL GENOME; GENE DELETION; GENE INSERTION; GENETIC CODE; MULTIFACTORIAL INHERITANCE; NONHUMAN; OXIDATION REDUCTION STATE; PREDICTION; QUANTITATIVE TRAIT LOCUS; REVIEW; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; STRESS; SYNTHETIC BIOLOGY; YEAST CELL; GENETICS; METABOLIC ENGINEERING; METABOLISM; MICROBIOLOGY; TRENDS;

SACCHAROMYCES CEREVISIAE;

INDUSTRIAL MICROBIOLOGY; METABOLIC ENGINEERING; SACCHAROMYCES CEREVISIAE;

EID: 84933514460     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-015-0281-x     Document Type: Review

References (75)

1. Delgado A, Porcar M (2013) Designing de novo: interdisciplinary debates in synthetic biology. Syst Synth Biol 7:41-50
2. Serrano L (2007) Synthetic biology: promises and challenges. Mol Syst Biol 3:158
3. Mattanovich D, Sauer M, Gasser B (2014) Yeast biotechnology: teaching the old dog new tricks. Microb Cell Fact 13:34
4. Annaluru N, Muller H, Mitchell La, Ramalingam S, Stracquadanio G, Richardson SM et al (2014) Total synthesis of a functional designer eukaryotic chromosome. Science 344:55-58
5. Brochado AR, Patil KR (2013) Overexpression of O-methyltransferase leads to improved vanillin production in baker's yeast only when complemented with model-guided network engineering. Biotechnol Bioeng 110:656-659
6. Westfall PJ, Pitera DJ, Lenihan JR, Eng D, Woolard FX, Regentin R et al (2012) Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. Proc Natl Acad Sci USA 109:E111-E118
7. Horecka J, Davis RW (2014) The 50:50 method for PCR-based seamless genome editing in yeast. Yeast 31:103-112
8. Carroll D (2011) Genome engineering with zinc-finger nucleases. Genetics 188:773-782
9. Dicarlo JE, Conley AJ, Penttilä M, Jäntti J, Wang HH, Church GM (2013) Yeast oligo-mediated genome engineering (YOGE). ACS Synth Biol 2:741-749
10. Bogdanove AJ, Voytas DF (2011) TAL effectors: customizable proteins for DNA targeting. Science 333:1843-1846
11. DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 41:4336-4343
12. Ryan OW, Cate JHD (2014) Multiplex engineering of industrial yeast genomes using CRISPRm, vol 546, 1st edn. Elsevier Inc, NewYork
13. Jakočiunas T, Bonde I, Herrgård M, Harrison SJ, Kristensen M, Pedersen LE et al (2015) Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. Metab Eng 28:213-222
14. Mans R, Rossum HM Van, Wijsman M, Backx A, Kuijpers NGA, Daran-lapujade P et al (2015) CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae. FEMS Yeast Res 15:fov004
15. Yuan J, Ching CB (2014) Combinatorial assembly of large biochemical pathways into yeast chromosomes for improved production of value-added compounds. ACS Synth Biol 4:23-31
16. Shao Z, Zhao H, Zhao H (2009) DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res 37:1-10
17. Jakočiunas T, Rajkumar AS, Zhang J, Arsovska D, Rodriguez A, Jendresen CB et al (2015) CasEMBLR: Cas9-Facilitated Multiloci Genomic Integration of in Vivo Assembled DNA Parts in Saccharomyces cerevisiae. ACS Synth Biol. doi: 10.1021/acssynbio.5b00007
18. Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, Kuznetsov G, Norville JE et al (2015) Biocontainment of genetically modified organisms by synthetic protein design. Nature 518:55-60
19. Rovner AJ, Haimovich AD, Katz SR, Li Z, Grome MW, Gassaway BM et al (2015) Recoded organisms engineered to depend on synthetic amino acids. Nature 518:89-93
20. Callaway E (2014) First synthetic yeast chromosome revealed. In: News & Comment. Nature. http://www.nature.com/news/first-synthetic-yeast-chromosome-revealed-1.14941 . Accessed 3 June 2015
21. Chin JW, Cropp TA, Anderson JC, Mukherji M, Zhang Z, Schultz PG (2003) An expanded eukaryotic genetic code. Science 301:964-967
22. Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ (2004) Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol 22:841-847
23. Rackham O, Chin JW (2005) A network of orthogonal ribosome x mRNA pairs. Nat Chem Biol 1:159-166
24. Hwang YW, Miller DL (1987) A mutation that alters the nucleotide specificity of elongation factor Tu, a GTP regulatory protein. J Biol Chem 262:13081-13085
25. Weinhandl K, Winkler M, Glieder A, Camattari A (2014) Carbon source dependent promoters in yeasts. Microb Cell Fact 13:5
26. Garí E, Piedrafita L, Aldea M, Herrero E (1997) A set of vectors with a tetracycline-regulatable promoter system for modulated gene expression in Saccharomyces cerevisiae. Yeast 13:837-848
27. Quintero MJ, Maya D, Arévalo-Rodríguez M, Cebolla A, Chávez S (2007) An improved system for estradiol-dependent regulation of gene expression in yeast. Microb Cell Fact 6:10
28. Doyle DF, Braasch DA, Jackson LK, Weiss HE, Boehm MF, Mangelsdorf DJ et al (2001) Engineering orthogonal ligand-receptor pairs from "near drugs". J Am Chem Soc 123:11367-11371
29. Collins CH, Arnold FH, Leadbetter JR (2005) Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones. Mol Microbiol 55:712-723
30. Blount BA, Weenink T, Vasylechko S, Ellis T (2012) Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology. PLoS One 7:e33279
31. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S et al (2013) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 31:833-838
32. Bloom J, Ehrenreich I, Loo W, Lite T, Kruglyak L (2013) Finding the sources of missing heritability in a yeast cross. Nature 494:234-237
33. Sirr A, Cromie GA, Jeffery EW, Gilbert TL, Ludlow CL, Scott AC et al (2014) Allelic variation, aneuploidy, and nongenetic mechanisms suppress a monogenic trait in yeast. Genetics 199:247-262
34. Parts L (2014) Genome-wide mapping of cellular traits using yeast. Yeast 31:197-205
35. Chandrasekaran S, Price ND (2010) Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad Sci USA 107:17845-17850
36. Kim S, Sohn K-A, Xing EP (2009) A multivariate regression approach to association analysis of a quantitative trait network. Bioinformatics 25:i204-i212
37. Sun W, Yu T, Li K-C (2007) Detection of eQTL modules mediated by activity levels of transcription factors. Bioinformatics 23:2290-2297
38. Stegle O, Parts L, Durbin R, Winn J (2010) A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies. PLoS Comput Biol 6:e1000770
39. Žitnik M, Zupan B (2014) Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold. Biocomput 2013:400-411
40. Lanckriet GRG, Cristianini N, Bartlett P, Ghaoui L El, Jordan MI (2004) Learning the Kernel matrix with semidefinite programming. J Mach Learn Res 5:27-72
41. Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F et al (2006) Gene prioritization through genomic data fusion. Nat Biotechnol 24:537-544
42. Krivoruchko A, Siewers V, Nielsen J (2011) Opportunities for yeast metabolic engineering: lessons from synthetic biology. Biotechnol 6:262-276
43. Klipp E, Nordlander B, Krüger R, Gennemark P, Hohmann S (2005) Integrative model of the response of yeast to osmotic shock. Nat Biotechnol 23:975-982
44. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G et al (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241-4257
45. Kim S, Baek S-H, Lee K, Hahn J-S (2013) Cellulosic ethanol production using a yeast consortium displaying a minicellulosome and β-glucosidase. Microb Cell Fact 12:14
46. Yu KO, Kim SW, Han SO (2010) Engineering of glycerol utilization pathway for ethanol production by Saccharomyces cerevisiae. Bioresour Technol 101:4157-4161
47. Hong J, Yang H, Zhang K, Liu C, Zou S, Zhang M (2014) Development of a cellulolytic Saccharomyces cerevisiae strain with enhanced cellobiohydrolase activity. World J Microbiol Biotechnol 30:2985-2993
48. Liang Y, Si T, Ang EL, Zhao H (2014) An engineered penta-functional minicellulosome for simultaneous saccharification and ethanol fermentation in Saccharomyces cerevisiae. Appl Environ Microbiol 80:6677-6684
49. Van Zyl C, Prior AB, Kilian GS, Kock LFJ (1989) D-Xylose Utilization by Saccharomyces cerevisiae. J Gen Microbiol
50. Richard P, Toivari MH, Penttilä M (1999) Evidence that the gene YLR070c of Saccharomyces cerevisiae encodes a xylitol dehydrogenase. FEBS Lett 457:135-138
51. Attfield PV, Bell PJL (2006) Use of population genetics to derive nonrecombinant Saccharomyces cerevisiae strains that grow using xylose as a sole carbon source. FEMS Yeast Res 6:862-868
52. Wenger JW, Schwartz K, Sherlock G (2010) Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae. PLoS Genet 6:e1000942
53. Demeke MM, Dietz H, Li Y, Foulquié-Moreno MR, Mutturi S, Deprez S et al (2013) Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering. Biotechnol Biofuels 6:89
54. Peplow M (2014) Cellulosic ethanol fights for life. Nature 507:152-153
55. Demeke MM, Dumortier F, Li Y, Broeckx T, Foulquié-Moreno MR, Thevelein JM (2013) Combining inhibitor tolerance and D-xylose fermentation in industrial Saccharomyces cerevisiae for efficient lignocellulose-based bioethanol production. Biotechnol Biofuels 6:120
56. Kricka W, Fitzpatrick J, Bond U (2014) Metabolic engineering of yeasts by heterologous enzyme production for degradation of cellulose and hemicellulose from biomass: a perspective. Front Microbiol 5:174
57. Huberts DHEW, Niebel B, Heinemann M (2012) A flux-sensing mechanism could regulate the switch between respiration and fermentation. FEMS Yeast Res 12:118-128
58. Henricsson C, de Jesus Ferreira MC, Hedfalk K, Elbing K, Larsson C, Bill RM et al (2005) Engineering of a novel Saccharomyces cerevisiae wine strain with a respiratory phenotype at high external glucose concentrations. Appl Environ Microbiol 71:6185-6192
59. Ferndahl C, Bonander N, Logez C, Wagner R, Gustafsson L, Larsson C et al (2010) Increasing cell biomass in Saccharomyces cerevisiae increases recombinant protein yield: the use of a respiratory strain as a microbial cell factory. Microb Cell Fact 9:47
60. 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
61. Tokuhiro K, Ishida N, Nagamori E, Saitoh S, Onishi T, Kondo A et al (2009) Double mutation of the PDC1 and ADH1 genes improves lactate production in the yeast Saccharomyces cerevisiae expressing the bovine lactate dehydrogenase gene. Appl Microbiol Biotechnol 82:883-890
62. Kealey JT, Liu L, Santi DV, Betlach MC, Barr PJ (1998) Production of a polyketide natural product in nonpolyketide-producing prokaryotic and eukaryotic hosts. Proc Natl Acad Sci USA 95:505-509
63. Shiba Y, Paradise EM, Kirby J, Ro D-K, Keasling JD (2007) Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids. Metab Eng 9:160-168
64. Hong S-Y, Zurbriggen AS, Melis A (2012) Isoprene hydrocarbons production upon heterologous transformation of Saccharomyces cerevisiae. J Appl Microbiol 113:52-65
65. Mikkelsen MD, Hansen J, Simon E, Brianza F, Semmler A, Olsson K et al (2014) Methods for improved production of rebaudioside d and rebaudioside m
66. Thodey K, Galanie S, Smolke CD (2014) A microbial biomanufacturing platform for natural and semisynthetic opioids. Nat Chem Biol 10:837-844
67. Heavner BD, Smallbone K, Price ND, Walker LP (2013) Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. Database (Oxford) 2013:bat059
68. Zanghellini J, Ruckerbauer DE, Hanscho M, Jungreuthmayer C (2013) Elementary flux modes in a nutshell: properties, calculation and applications. Biotechnol J 8:1009-1016
69. Larhlimi A, Bockmayr A (2009) A new constraint-based description of the steady-state flux cone of metabolic networks. Discret Appl Math 157:2257-2266
70. Pais TM, Foulquié-Moreno MR, Hubmann G, Duitama J, Swinnen S, Goovaerts A et al (2013) Comparative polygenic analysis of maximal ethanol accumulation capacity and tolerance to high ethanol levels of cell proliferation in yeast. PLoS Genet 9:e1003548
71. Hubmann G, Foulquié-Moreno MR, Nevoigt E, Duitama J, Meurens N, Pais TM et al (2013) Quantitative trait analysis of yeast biodiversity yields novel gene tools for metabolic engineering. Metab Eng 17:68-81
72. Hubmann G, Mathé L, Foulquié-Moreno MR, Duitama J, Nevoigt E, Thevelein JM (2013) Identification of multiple interacting alleles conferring low glycerol and high ethanol yield in Saccharomyces cerevisiae ethanolic fermentation. Biotechnol Biofuels 6:87
73. Brion C, Ambroset C, Delobel P, Sanchez I, Blondin B (1085) Deciphering regulatory variation of THI genes in alcoholic fermentation indicate an impact of Thi3p on PDC1 expression. BMC Genom 2014:15
74. Greetham D, Wimalasena TT, Leung K, Marvin ME, Chandelia Y, Hart AJ et al (2014) The genetic basis of variation in clean lineages of Saccharomyces cerevisiae in response to stresses encountered during bioethanol fermentations. PLoS One 9:233
75. Brice C, Sanchez I, Bigey F, Legras J, Blondin B (2014) A genetic approach of wine yeast fermentation capacity in nitrogen-starvation reveals the key role of nitrogen signaling. BMC Genom 15:495