Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: A comparison of yeast promoter activities

Microbial Cell Factories

Volumn 14, Issue 1, 2015, Pages

  Peng, Bingyin ^a   Williams, Thomas C ^a   Henry, Matthew ^a   Nielsen, Lars K ^a   Vickers, Claudia E ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Batch cultivation; Fermentation; Flow cytometry; Metabolic engineering; Overexpression; Promoter; Transcription regulation

Indexed keywords

ALCOHOL; CARBON; COPPER; GALACTOSE; GLUCOSE; GREEN FLUORESCENT PROTEIN; SUCROSE; TRANSCRIPTION ELONGATION FACTOR; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CARBON SOURCE; CHEMICAL PARAMETERS; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; CULTURE TECHNIQUE; CUP1 GENE; DIAUXIC SHIFT; FUNGAL GENE; GAL1 GENE; GENE EXPRESSION REGULATION; GLUCOSE BATCH CULTIVATION; GLYCOLYSIS; NONHUMAN; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN STABILITY; SSA1 GENE; TEF1 GENE; UPREGULATION; YEAST CELL; FERMENTATION; GENETICS; METABOLISM; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

CARBON; FERMENTATION; GENE EXPRESSION REGULATION, FUNGAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84933508907     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-015-0278-5     Document Type: Article

References (51)

1. Osterlund T, Nookaew I, Bordel S, Nielsen J (2013) Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling. BMC Syst Biol 7:36
2. Boer VM, de Winde JH, Pronk JT, Piper MD (2003) 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 278:3265-3274
3. Sun J, Shao Z, Zhao H, Nair N, Wen F, Xu JH et al (2012) Cloning and characterization of a panel of constitutive promoters for applications in pathway engineering in Saccharomyces cerevisiae. Biotechnol Bioeng 109:2082-2092
4. Jensen MK, Keasling JD (2015) Recent applications of synthetic biology tools for yeast metabolic engineering. FEMS Yeast Res 15:1-10
5. Weinhandl K, Winkler M, Glieder A, Camattari A (2014) Carbon source dependent promoters in yeasts. Microb Cell Fact 13:5
6. Goncalves PM, Griffioen G, Bebelman JP, Planta RJ (1997) Signalling pathways leading to transcriptional regulation of genes involved in the activation of glycolysis in yeast. Mol Microbiol 25:483-493
7. Lemaire K, Van de Velde S, Van Dijck P, Thevelein JM (2004) Glucose and sucrose act as agonist and mannose as antagonist ligands of the G protein-coupled receptor Gpr1 in the yeast Saccharomyces cerevisiae. Mol Cell 16:293-299
8. Kim SR, Ha SJ, Wei N, Oh EJ, Jin YS (2012) Simultaneous co-fermentation of mixed sugars: a promising strategy for producing cellulosic ethanol. Trends Biotechnol 30:274-282
9. Verduyn C, Zomerdijk TP, van Dijken JP, Scheffers WA (1984) Continuous measurement of ethanol production by aerobic yeast suspensions with an enzyme electrode. Appl Microbiol Biotechnol 19:181-185
10. Renouf M, Wegener M, Nielsen L (2008) An environmental life cycle assessment comparing Australian sugarcane with US corn and UK sugar beet as producers of sugars for fermentation. Biomass Bioenergy 32:1144-1155
11. Archer CT, Kim JF, Jeong H, Park JH, Vickers CE, Lee SY et al (2011) The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli. BMC Genom 12:9
12. 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
13. Basso TO, de Kok S, Dario M, do Espirito-Santo JC, Muller G, Schlolg PS et al (2011) Engineering topology and kinetics of sucrose metabolism in Saccharomyces cerevisiae for improved ethanol yield. Metab Eng 13:694-703
14. Badotti F, Dario MG, Alves SL Jr, Cordioli ML, Miletti LC, de Araujo PS et al (2008) Switching the mode of sucrose utilization by Saccharomyces cerevisiae. Microb Cell Fact 7:4
15. Partow S, Siewers V, Bjorn S, Nielsen J, Maury J (2010) Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae. Yeast (Chichester, England) 27:955-964
16. Chen X, Li S, Liu L (2014) Engineering redox balance through cofactor systems. Trends Biotechnol 32:337-343
17. Heyland J, Blank LM, Schmid A (2011) Quantification of metabolic limitations during recombinant protein production in Escherichia coli. J Biotechnol 155:178-184
18. Williams TC, Nielsen LK, Vickers CE (2013) Engineered quorum sensing using pheromone-mediated cell-to-cell communication in saccharomyces cerevisiae. ACS Synth Biol 2:136-149
19. West RW Jr, Chen SM, Putz H, Butler G, Banerjee M (1987) GAL1-GAL10 divergent promoter region of Saccharomyces cerevisiae contains negative control elements in addition to functionally separate and possibly overlapping upstream activating sequences. Genes Dev 1:1118-1131
20. Butt TR, Ecker DJ (1987) Yeast metallothionein and applications in biotechnology. Microbiol Rev 51:351-364
21. Hauf J, Zimmermann FK, Muller S (2000) Simultaneous genomic overexpression of seven glycolytic enzymes in the yeast Saccharomyces cerevisiae. Enzyme Microb Technol 26:688-698
22. Lee KM, DaSilva NA (2005) Evaluation of the Saccharomyces cerevisiae ADH2 promoter for protein synthesis. Yeast (Chichester, England) 22:431-440
23. Vickers CE, Blank LM, Kromer JO (2010) Grand challenge commentary: chassis cells for industrial biochemical production. Nat Chem Biol 6:875-877
24. Hontz RD, Niederer RO, Johnson JM, Smith JS (2009) Genetic identification of factors that modulate ribosomal DNA transcription in Saccharomyces cerevisiae. Genetics 182:105-119
25. Alexandre H, Ansanay-Galeote V, Dequin S, Blondin B (2001) Global gene expression during short-term ethanol stress in Saccharomyces cerevisiae. FEBS Lett 498:98-103
26. Werner-Washburne M, Becker J, Kosic-Smithers J, Craig EA (1989) Yeast Hsp70 RNA levels vary in response to the physiological status of the cell. J Bacteriol 171:2680-2688
27. Wenzel TJ, Luttik MA, van den Berg JA, de Steensma HY (1993) Regulation of the PDA1 gene encoding the E1 alpha subunit of the pyruvate dehydrogenase complex from Saccharomyces cerevisiae. Eur J Biochem/FEBS 218:405-411
28. Mateus C, Avery SV (2000) Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry. Yeast (Chichester, England) 16:1313-1323
29. Vickers CE, Bydder SF, Zhou Y, Nielsen LK (2013) Dual gene expression cassette vectors with antibiotic selection markers for engineering in Saccharomyces cerevisiae. Microb Cell Fact 12:96
30. Vickers CE, Schenk PM, Li D, Mullineaux PM, Gresshoff PM (2007) pGFPGUSPlus, a new binary vector for gene expression studies and optimising transformation systems in plants. Biotechnol Lett 29:1793-1796
31. Vickers CE, Xue GP, Gresshoff PM (2003) A synthetic xylanase as a novel reporter in plants. Plant Cell Rep 22:135-140
32. Vickers CE, Xue G, Gresshoff PM (2006) A novel cis-acting element, ESP, contributes to high-level endosperm-specific expression in an oat globulin promoter. Plant Mol Biol 62:195-214
33. Buzas DM, Lohar D, Sato S, Nakamura Y, Tabata S, Vickers CE et al (2005) Promoter trapping in Lotus japonicus reveals novel root and nodule GUS expression domains. Plant Cell Physiol 46:1202-1212
34. Schunmann PH, Richardson AE, Vickers CE, Delhaize E (2004) Promoter analysis of the barley Pht1;1 phosphate transporter gene identifies regions controlling root expression and responsiveness to phosphate deprivation. Plant Physiol 136:4205-4214
35. Martinez-Pastor MT, Estruch F (1996) Sudden depletion of carbon source blocks translation, but not transcription, in the yeast Saccharomyces cerevisiae. FEBS Lett 390:319-322
36. Zid BM, O'Shea EK (2014) Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. Nature 514:117-121
37. Ashe MP, De Long SK, Sachs AB (2000) Glucose depletion rapidly inhibits translation initiation in yeast. Mol Biol Cell 11:833-848
38. Chakrabarti S, Liehl P, Buchon N, Lemaitre B (2012) Infection-induced host translational blockage inhibits immune responses and epithelial renewal in the Drosophila gut. Cell Host Microbe 12:60-70
39. Loewith R, Hall MN (2011) Target of rapamycin (TOR) in nutrient signaling and growth control. Genetics 189:1177-1201
40. Chen Y, Daviet L, Schalk M, Siewers V, Nielsen J (2013) Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism. Metab Eng 15:48-54
41. Hahn JS, Thiele DJ (2004) Activation of the Saccharomyces cerevisiae heat shock transcription factor under glucose starvation conditions by Snf1 protein kinase. J Biol Chem 279:5169-5176
42. Cao L, Tang X, Zhang X, Zhang J, Tian X, Wang J et al (2014) Two-stage transcriptional reprogramming in Saccharomyces cerevisiae for optimizing ethanol production from xylose. Metab Eng 24:150-159
43. Hassett R, Kosman DJ (1995) Evidence for Cu (II) reduction as a component of copper uptake by Saccharomyces cerevisiae. J Biol Chem 270:128-134
44. Fay JC, McCullough HL, Sniegowski PD, Eisen MB (2004) Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biol 5:R26
45. Peng B, Shen Y, Li X, Chen X, Hou J, Bao X (2012) Improvement of xylose fermentation in respiratory-deficient xylose-fermenting Saccharomyces cerevisiae. Metab Eng 14:9-18
46. Entian K-D, Kötter P (1998) 23 yeast mutant and plasmid collections. Methods Microbiol 26:431-449
47. Gueldener U, Heinisch J, Koehler GJ, Voss D, Hegemann JH (2002) A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Res 30:e23
48. Van Driessche B, Tafforeau L, Hentges P, Carr AM, Vandenhaute J (2005) Additional vectors for PCR-based gene tagging in Saccharomyces cerevisiae and Schizosaccharomyces pombe using nourseothricin resistance. Yeast (Chichester, England) 22:1061-1068
49. Norrander J, Kempe T, Messing J (1983) Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. Gene 26:101-106
50. Dvir S, Velten L, Sharon E, Zeevi D, Carey LB, Weinberger A et al (2013) Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast. Proc Natl Acad Sci USA 110:E2792-E2801
51. Dietmair S, Timmins NE, Gray PP, Nielsen LK, Kromer JO (2010) Towards quantitative metabolomics of mammalian cells: development of a metabolite extraction protocol. Anal Biochem 404:155-164