Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway

Microbial Cell Factories

Volumn 15, Issue 1, 2016, Pages

  Kildegaard, Kanchana R ^a   Jensen, Niels B ^a,d   Schneider, Konstantin ^a   Czarnotta, Eik ^b   Özdemir, Emre ^a   Klein, Tobias ^a   Maury, Jérôme ^a   Ebert, Birgitta E ^b   Christensen, Hanne B ^a   Chen, Yun ^c   Kim, Il Kwon ^c,e   Herrgård, Markus J ^a   Blank, Lars M ^b   Forster, Jochen ^a   Nielsen, Jens ^a,c   Borodina, Irina ^a  

^a Chalmers University of Technology   (Denmark)

^b RWTH AACHEN UNIVERSITY   (Germany)

^c CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^d Evolva Biotech A S   (Denmark)

^e Paikkwang Industrial Co Ltd   (South Korea)

Author keywords

3 Hydroxypropionic acid; Metabolic engineering; Redox metabolism; Saccharomyces cerevisiae

Indexed keywords

ACETYL COENZYME A SYNTHASE; ALDEHYDE DEHYDROGENASE; GLUCOSE; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; GLYCEROL; HYDRACRYLIC ACID; MALONYL COENZYME A REDUCTASE; OXIDOREDUCTASE; PYRUVATE DECARBOXYLASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; SYNTHETASE; UNCLASSIFIED DRUG; LACTIC ACID; MALONYL-COA REDUCTASE;

13C METABOLIC FLUX ANALYSIS; ARTICLE; BIOSYNTHESIS; CHLOROFLEXUS; CHLOROFLEXUS AURANTIACUS; CONTROLLED STUDY; ENZYME PHOSPHORYLATION; ENZYME SPECIFICITY; FED BATCH FERMENTATION; GENE OVEREXPRESSION; GENOME; METABOLIC ENGINEERING; METABOLIC FLUX ANALYSIS; METABOLISM; NONHUMAN; REDOX METABOLISM; SACCHAROMYCES CEREVISIAE; SALMONELLA ENTERICA; TRANSCRIPTOMICS; YEAST; ANALOGS AND DERIVATIVES; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; OXIDATION REDUCTION REACTION; PROCEDURES; TRANSGENIC ORGANISM;

CHLOROFLEXUS; GENE EXPRESSION REGULATION, FUNGAL; LACTIC ACID; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; ORGANISMS, GENETICALLY MODIFIED; OXIDATION-REDUCTION; OXIDOREDUCTASES; SACCHAROMYCES CEREVISIAE; SALMONELLA ENTERICA;

EID: 84960936931     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-016-0451-5     Document Type: Article

References (34)

1. Borodina I, Nielsen J. Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals. Biotechnol J. 2014;9:609-20.
2. van Dien S. From the first drop to the first truckload: commercialization of microbial processes for renewable chemicals. Curr Opin Biotechnol. 2013;24:1061-8.
3. Gokarn RR, Selifonova OV, Jessen HJ, Gort SJ, Selmer T, Buckel W. 3-Hydroxypropionic acid and other organic compounds. 2012. Patent application WO2002042418 A3.
4. Lynch MD, Gill RT, Warnecke-Lipscomb T. Method for producing 3-hydroxypropionic acid and other products. 2011. Patent application WO2011038364 A1.
5. Borodina I, Kildegaard KR, Jensen NB, Blicher TH, Maury J, Sherstyk S, Schneider K, Lamosa P, Herrgård MJ, Rosenstand I, Öberg F, Forster J, Nielsen J. Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine. Metab Eng. 2015;27:57-64.
6. Chen Y, Bao J, Kim I-K, Siewers V, Nielsen J. Coupled incremental precursor and co-factor supply improves 3-hydroxypropionic acid production in Saccharomyces cerevisiae. Metab Eng. 2014;22:104-9.
7. Tehlivets O, Scheuringer K, Kohlwein SD. Fatty acid synthesis and elongation in yeast. Biochim Biophys Acta. 2007;1771:255-70.
8. Shi S, Chen Y, Siewers V, Nielsen J. Improving production of malonyl coenzyme A-derived metabolites by abolishing Snf1-dependent regulation of Acc1. MBio. 2014;5:e01130-14.
9. Maury J, Germann SM, Jacobsen SAB, Jensen NB, Kildegaard KR, Herrgård MJ, Schneider K, Koza A, Forster J, Nielsen J, Borodina I. EasyCloneMulti: a set of vectors for simultaneous and multiple genomic integrations in Saccharomyces cerevisiae. PLoS One. 2016;11:e0150394.
10. Jensen NB, Strucko T, Kildegaard KR, David F, Maury J, Mortensen UH, Forster J, Nielsen J, Borodina I. EasyClone: method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae. FEMS Yeast Res. 2014;14:238-48.
11. Davis MS, Solbiati J, Cronan JE. Overproduction of acetyl-CoA carboxylase activity increases the rate of fatty acid biosynthesis in Escherichia coli. J Biol Chem. 2000;275:28593-8.
12. Shiba Y, Paradise EM, Kirby J, Ro D-K, Keasling JD. Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids. Metab Eng. 2007;9:160-8.
13. Gunawardena U, Meinhold P, Peters MW, Urano J, Feldman RMR. Butanol production by metabolically engineered yeast. 2008. Patent application WO2008080124 A2.
14. Bro C, Regenberg B, Förster J, Nielsen J. In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab Eng. 2006;8:102-11.
15. Guo Z, Zhang L, Ding Z, Shi G. Minimization of glycerol synthesis in industrial ethanol yeast without influencing its fermentation performance. Metab Eng. 2011;13:49-59.
16. Martínez I, Zhu J, Lin H, Bennett GN, San K-Y. Replacing Escherichia coli NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with a NADP-dependent enzyme from Clostridium acetobutylicum facilitates NADPH dependent pathways. Metab Eng. 2008;10:352-9.
17. Verho R, Richard P, Jonson PH, Sundqvist L, Londesborough J, Penttilä M. Identification of the first fungal NADP-GAPDH from Kluyveromyces lactis. Biochemistry. 2002;41:13833-8.
18. Frick O, Wittmann C. Characterization of the metabolic shift between oxidative and fermentative growth in Saccharomyces cerevisiae by comparative 13C flux analysis. Microb Cell Fact. 2005;4:30.
19. McAlister L, Holland MJ. Isolation and characterization of yeast strains carrying mutations in the glyceraldehyde-3-phosphate dehydrogenase genes. J Biol Chem. 1985;260:15013-8.
20. Albers E, Larsson C, Andlid T, Walsh MC, Gustafsson L. Effect of nutrient starvation on the cellular composition and metabolic capacity of Saccharomyces cerevisiae. Appl Environ Microbiol. 2007;73:4839-48.
21. Celton M, Sanchez I, Goelzer A, Fromion V, Camarasa C, Dequin S. A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation. BMC Genom. 2012;13:317.
22. Zamboni N, Fischer E, Sauer U. FiatFlux-a software for metabolic flux analysis from 13C-glucose experiments. BMC Bioinform. 2005;6:209.
23. Ida Y, Furusawa C, Hirasawa T, Shimizu H. Stable disruption of ethanol production by deletion of the genes encoding alcohol dehydrogenase isozymes in Saccharomyces cerevisiae. J Biosci Bioeng. 2012;113:192-5.
24. Oud B, Flores C-L, Gancedo C, Zhang X, Trueheart J, Daran J-M, Pronk JT, van Maris AJ. An internal deletion in MTH1 enables growth on glucose of pyruvate-decarboxylase negative, non-fermentative Saccharomyces cerevisiae. Microb Cell Fact. 2012;11:131.
25. Kozak BU, van Rossum HM, Luttik MAH, Akeroyd M, Benjamin KR, Wu L, de Vries S, Daran J-M, Pronk JT, van Maris AJA. Engineering acetyl coenzyme A supply: functional expression of a bacterial pyruvate dehydrogenase complex in the cytosol of Saccharomyces cerevisiae. MBio. 2014;5:e01696-14.
26. Hubmann G, Guillouet S, Nevoigt E. Gpd1 and Gpd2 fine-tuning for sustainable reduction of glycerol formation in Saccharomyces cerevisiae. Appl Environ Microbiol. 2011;77:5857-67.
27. Gietz RD, Woods RA. Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol. 2002;350:87-96.
28. Nanchen A, Schicker A, Sauer U. Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli. Appl Environ Microbiol. 2006;72:1164-72.
29. Blank LM, Kuepfer L, Sauer U. Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol. 2005;6:R49.
30. Blank LM, Sauer U. TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates. Microbiology. 2004;150:1085-93.
31. Kildegaard KR, Hallström BM, Blicher TH, Sonnenschein N, Jensen NB, Sherstyk S, Harrison SJ, Maury J, Herrgård MJ, Juncker AS, Forster J, Nielsen J, Borodina I. Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance. Metab Eng. 2014;26:57-66.
32. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562-78.
33. 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.
34. King ZA, Dräger A, Abghari A, Sonnenschein N, Lewis NE, Palsson BØ. Escher. A web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS Comput Biol. 2015;11(8):e1004321.