Metabolomic and 13C-metabolic flux analysis of a xylose-consuming Saccharomyces cerevisiae strain expressing xylose isomerase

Biotechnology and Bioengineering

Volumn 112, Issue 3, 2015, Pages 470-483

  Wasylenko, Thomas M ^a   Stephanopoulos, Gregory ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

13C metabolic flux analysis; Carbon catabolite repression; Cellulosic ethanol; Metabolomics; Saccharomyces cerevisiae; Xylose

Indexed keywords

CARBON; CELLULOSIC ETHANOL; ETHANOL; FERMENTATION; GLUCOSE; METABOLISM; PATHOLOGY; STRAIN; XYLOSE;

AEROBIC AND ANAEROBIC CONDITIONS; CARBON CATABOLITE REPRESSION; ETHANOL PRODUCTIVITY; GLUCOSE FERMENTATION; METABOLIC FLUX ANALYSIS; METABOLOMICS; SACCHAROMYCES CEREVISIAE STRAINS; XYLOSE FERMENTATION;

YEAST;

CARBON 13; FUNGAL ENZYME; GLUCOSE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE; XYLOSE; XYLOSE ISOMERASE; ALCOHOL; BIOFUEL; CARBON; ISOMERASE; SACCHAROMYCES CEREVISIAE PROTEIN;

AEROBIC FERMENTATION; ALCOHOL PRODUCTION; ANAEROBIC FERMENTATION; ARTICLE; CARBON SOURCE; CATABOLITE REPRESSION; CITRIC ACID CYCLE; FUNGAL STRAIN; GLYCOLYSIS; METABOLIC FLUX ANALYSIS; METABOLOMICS; NONHUMAN; PENTOSE PHOSPHATE CYCLE; PROTEIN EXPRESSION; SACCHAROMYCES CEREVISIAE; SUGAR INTAKE; METABOLIC ENGINEERING; METABOLISM; PROCEDURES;

SACCHAROMYCES CEREVISIAE;

ALDOSE-KETOSE ISOMERASES; BIOFUELS; CARBON; ETHANOL; METABOLIC ENGINEERING; METABOLIC FLUX ANALYSIS; METABOLIC NETWORKS AND PATHWAYS; METABOLOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; XYLOSE;

EID: 84922782676     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.25447     Document Type: Article

References (89)

1. Almeida JR, Modig T, Petersson A, Hähn-Hägerdal B, Lidén G, Gorwa-Grauslund MF. 2007. Increased tolerance and conversion of inhibitors in lignocellulosic hydrolysates bySaccharomyces cerevisiae. J Chem Technol Biotechnol 82:340-349.
2. Amore R, Wilhelm M, Hollenberg CP. 1989. The fermentation of xylose-an analysis of the expression of Bacillus and Actinoplanes xylose isomerase genes in yeast. Appl Microbiol Biotechnol 30:351-357.
3. Andreasen AA, Stier TJ. 1954. Anaerobic nutrition of Saccharomyces cerevisiae. II. Unsaturated fatty acid requirement for growth in a defined medium. J Cell Physiol 43:271-281.
4. Andreasen AA, Stier TJB. 1953. Anaerobic nutrition of Saccharomyces cerevisiae. I. Ergosterol requirement for growth in a defined medium. J Cell Physiol 41:23-36.
5. Antoniewicz MR, Kelleher JK, Stephanopoulos G. 2006. Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. Metab Eng 8:324-337.
6. Antoniewicz MR, Kelleher JK, Stephanopoulos G. 2007a. Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab Eng 9:68-86.
7. Antoniewicz MR, Kelleher JK, Stephanopoulos G. 2007b. Accurate assessment of amino acid mass isotopomer distributions for metabolic flux analysis. Anal Chem 79:7554-7559.
8. Bakker BM, Overkamp KM, van Maris null AJ, Kötter P, Luttik MA, van Dijken null JP, Pronk JT. 2001. Stoichiometry and compartmentation of NADH metabolism in Saccharomyces cerevisiae. FEMS Microbiol Rev 25:15-37.
9. Belinchón MM, Gancedo JM. 2003. Xylose and some non-sugar carbon sources cause catabolite repression in Saccharomyces cerevisiae. Arch Microbiol 180:293-297.
10. Belinchón MM, Gancedo JM. 2007. Glucose controls multiple processes in Saccharomyces cerevisiae through diverse combinations of signaling pathways. FEMS Yeast Res 7:808-818.
11. Bergdahl B, Heer D, Sauer U, Hahn-Hägerdal B, van Niel EW. 2012. Dynamic metabolomics differentiates between carbon and energy starvation in recombinant Saccharomyces cerevisiae fermenting xylose. Biotechnol Biofuels 5:34.
12. Blank LM, Lehmbeck F, Sauer U. 2005. Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Res 5:545-558.
13. Boles E, Heinisch J, Zimmermann FK. 1993. Different signals control the activation of glycolysis in the yeast Saccharomyces cerevisiae. Yeast Chichester Engl 9:761-770.
14. Boles E, Müller S, Zimmermann FK. 1996. A multi-layered sensory system controls yeast glycolytic gene expression. Mol Microbiol 19:641-642.
15. Boles E, Zimmermann FK. 1993. Induction of pyruvate decarboxylase in glycolysis mutants of Saccharomyces cerevisiae correlates with the concentrations of three-carbon glycolytic metabolites. Arch Microbiol 160:324-328.
16. Bruinenberg PM, Bot PHM, Dijken JP, Scheffers WA. 1983. The role of redox balances in the anaerobic fermentation of xylose by yeasts. Eur J Appl Microbiol Biotechnol 18:287-292.
17. Bruinenberg P, Bot PM, Dijken J, Scheffers WA. 1984. NADH-linked aldose reductase: the key to anaerobic alcoholic fermentation of xylose by yeasts. Appl Microbiol Biotechnol 19:256-260.
18. Canelas AB, ten Pierick, Ras A, Seifar C, van Dam RM, van Gulik JC, Heijnen WM. 2009. Quantitative evaluation of intracellular metabolite extraction techniques for yeast metabolomics. Anal Chem 81:7379-7389.
19. Canelas AB, Ras C, Pierick A, Dam JC, Heijnen JJ, Gulik WM. 2008. Leakage-free rapid quenching technique for yeast metabolomics. Metabolomics 4:226-239.
20. Carroll A, Somerville C. 2009. Cellulosic biofuels. Annu Rev Plant Biol 60:165-182.
21. Cavero S, Vozza A, del Arco A, Palmieri L, Villa A, Blanco E, Runswick MJ, Walker JE, Cerdán S, Palmieri F, Satrústegui J. 2003. Identification and metabolic role of the mitochondrial aspartate-glutamate transporter in Saccharomyces cerevisiae. Mol Microbiol 50:1257-1269.
22. Dihazi H, Kessler R, Eschrich K. 2003. Glucose-induced stimulation of the Ras-cAMP pathway in yeast leads to multiple phosphorylations and activation of 6-phosphofructo-2-kinase. Biochemistry (Mosc) 42:6275-6282.
23. Ewald JC, Heux S, Zamboni N. 2009. High-throughput quantitative metabolomics: Workflow for cultivation, quenching, and analysis of yeast in a multiwell format. Anal Chem 81:3623-3629.
24. Feng X, Zhao H. 2013a. Investigating xylose metabolism in recombinant Saccharomyces cerevisiae via 13C metabolic flux analysis. Microb Cell Factories 12:114.
25. 13C metabolic flux analysis. AIChE J 59:3195-3202.
26. Fiaux J, Cakar ZP, Sonderegger M, Wüthrich K, Szyperski T, Sauer U. 2003. Metabolic-flux profiling of the yeasts Saccharomyces cerevisiae and Pichia stipitis. Eukaryot Cell 2:170-180.
27. Förster J, Famili I, Fu P, Palsson BØ, Nielsen J. 2003. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13:244-253.
28. Gancedo JM, Gancedo C. 1979. Inactivation of gluconeogenic enzymes in glycolytic mutants of Saccharomyces cerevisiae. Eur J Biochem FEBS 101:455-460.
29. Gancedo JM, Mazón MJ, Gancedo C. 1983. Fructose 2, 6-bisphosphate activates the cAMP-dependent phosphorylation of yeast fructose-1, 6-bisphosphatase in vitro. J Biol Chem 258:5998-5999.
30. Gancedo JM. 2008. The early steps of glucose signalling in yeast. FEMS Microbiol Rev 32:673-704.
31. Gárdonyi M, Hahn-Hägerdal B. 2003. The Streptomyces rubiginosus xylose isomerase is misfolded when expressed in Saccharomyces cerevisiae. Enzyme Microb Technol 32:252-259.
32. Gárdonyi M, Jeppsson M, Lidén G, Gorwa-Grauslund MF, Hahn-Hägerdal B. 2003. Control of xylose consumption by xylose transport in recombinant Saccharomyces cerevisiae. Biotechnol Bioeng 82:818-824.
33. Gombert AK, Moreira dos Santos, Christensen M, Nielsen B. 2001. Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J Bacteriol 183:1441-1451.
34. Gonzalez B, François J, Renaud M. 1997. A rapid and reliable method for metabolite extraction in yeast using boiling buffered ethanol. Yeast Chichester Engl 13:1347-1355.
35. Grotkjaer T, Christakopoulos P, Nielsen J, Olsson L. 2005. Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains. Metab Eng 7:437-444.
36. Ha S-J, Galazka JM, Kim SR, Choi J-H, Yang X, Seo J-H, Glass NL, Cate JHD, Jin Y-S. 2011. Engineered Saccharomyces cerevisiae capable of simultaneous cellobiose and xylose fermentation. Proc Natl Acad Sci USA 108:504-509.
37. Harhangi HR, Akhmanova AS, Emmens R, van der Drift C, de Laat WTAM, van Dijken JP, Jetten MSM, Pronk JT, Op den Camp HJM. 2003. Xylose metabolism in the anaerobic fungus Piromyces sp. strain E2 follows the bacterial pathway. Arch Microbiol 180:134-141.
38. Jeppsson M, Träff K, Johansson B, Hahn-Hägerdal B, Gorwa-Grauslund MF. 2003. Effect of enhanced xylose reductase activity on xylose consumption and product distribution in xylose-fermenting recombinant Saccharomyces cerevisiae. FEMS Yeast Res 3:167-175.
39. Jin Y-S, Laplaza JM, Jeffries TW. 2004. Saccharomyces cerevisiae engineered for xylose metabolism exhibits a respiratory response. Appl Environ Microbiol 70:6816-6825.
40. Jin Y-S, Ni H, Laplaza JM, Jeffries TW. 2003. Optimal growth and ethanol production from xylose by recombinant Saccharomyces cerevisiae require moderate D-xylulokinase activity. Appl Environ Microbiol 69:495-503.
41. Karhumaa K, Hahn-Hägerdal B, Gorwa-Grauslund M-F. 2005. Investigation of limiting metabolic steps in the utilization of xylose by recombinant Saccharomyces cerevisiae using metabolic engineering. Yeast Chichester Engl 22:359-368.
42. Kim SR, Ha S-J, Kong II, Jin Y-S. 2012. High expression of XYL2 coding for xylitol dehydrogenase is necessary for efficient xylose fermentation by engineered Saccharomyces cerevisiae. Metab Eng 14:336-343.
43. Kleijn RJ, van Winden WA, van Gulik WM, Heijnen JJ. 2005. Revisiting the 13C-label distribution of the non-oxidative branch of the pentose phosphate pathway based upon kinetic and genetic evidence. FEBS J 272:4970-4982.
44. Klimacek M, Krahulec S, Sauer U, Nidetzky B. 2010. Limitations in xylose-fermenting Saccharomyces cerevisiae, made evident through comprehensive metabolite profiling and thermodynamic analysis. Appl Environ Microbiol 76:7566-7574.
45. Kötter P, Ciriacy M. 1993. Xylose fermentation by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 38:776-783.
46. Kuyper M, Harhangi HR, Stave AK, Winkler AA, Jetten MSM, de Laat WTAM, den Ridder JJJ, Op den Camp HJM, van Dijken JP, Pronk JT. 2003. High-level functional expression of a fungal xylose isomerase: the key to efficient ethanolic fermentation of xylose by Saccharomyces cerevisiae?. FEMS Yeast Res 4:69-78.
47. Kuyper M, Hartog MMP, Toirkens MJ, Almering MJH, Winkler AA, van Dijken JP, Pronk JT. 2005a. Metabolic engineering of a xylose-isomerase-expressing Saccharomyces cerevisiae strain for rapid anaerobic xylose fermentation. FEMS Yeast Res 5:399-409.
48. Kuyper M, Toirkens MJ, Diderich JA, Winkler AA, van Dijken JP, Pronk JT. 2005b. Evolutionary engineering of mixed-sugar utilization by a xylose-fermenting Saccharomyces cerevisiae strain. FEMS Yeast Res 5:925-934.
49. Kuyper M, Winkler AA, van Dijken JP, Pronk JT. 2004. Minimal metabolic engineering of Saccharomyces cerevisiae for efficient anaerobic xylose fermentation: A proof of principle. FEMS Yeast Res 4:655-664.
50. Lau MW, Gunawan C, Balan V, Dale BE. 2010. Comparing the fermentation performance of Escherichia coli KO11, Saccharomyces cerevisiae 424A(LNH-ST) and Zymomonas mobilis AX101 for cellulosic ethanol production. Biotechnol Biofuels 3:11.
51. Lönn A, Träff-Bjerre K, Cordero Otero, van Zyl R, Hahn-Hägerdal W. 2003. Xylose isomerase activity influences xylose fermentation with recombinant Saccharomyces cerevisiae strains expressing mutated xylA from Thermus thermophilus. Enzyme Microb Technol 32:567-573.
52. Luo B, Groenke K, Takors R, Wandrey C, Oldiges M. 2007. Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry. J Chromatogr A 1147:153-164.
53. Maaheimo H, Fiaux J, Cakar ZP, Bailey JE, Sauer U, Szyperski T. 2001. Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional (13)C labeling of common amino acids. Eur J Biochem FEBS 268:2464-2479.
54. Van Maris AJA, Abbott DA, Bellissimi E, van den Brink J, Kuyper M, Luttik MAH, Wisselink HW, Scheffers WA, van Dijken JP, Pronk JT. 2006. Alcoholic fermentation of carbon sources in biomass hydrolysates by Saccharomyces cerevisiae: Current status. Antonie Van Leeuwenhoek 90:391-418.
55. Matsushika A, Nagashima A, Goshima T, Hoshino T. 2013. Fermentation of xylose causes inefficient metabolic state due to carbon/energy starvation and reduced glycolytic flux in recombinant industrial Saccharomyces cerevisiae. PloS ONE 8: e 69005.
56. Minard KI, McAlister-Henn L. 1992. Glucose-induced degradation of the MDH2 isozyme of malate dehydrogenase in yeast. J Biol Chem 267:17458-17464.
57. Minard KI, McAlister-Henn L. 1994. Glucose-induced phosphorylation of the MDH2 isozyme of malate dehydrogenase in Saccharomyces cerevisiae. Arch Biochem Biophys 315:302-309.
58. Müller S, Boles E, May M, Zimmermann FK. 1995. Different internal metabolites trigger the induction of glycolytic gene expression in Saccharomyces cerevisiae. J Bacteriol 177:4517-4519.
59. Navas MA, Gancedo JM. 1996. The regulatory characteristics of yeast fructose-1, 6-bisphosphatase confer only a small selective advantage. J Bacteriol 178:1809-1812.
60. Nissen TL, Schulze U, Nielsen J, Villadsen J. 1997. Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiol Read Engl 143:203-218.
61. Palmieri L, Vozza A, Agrimi G, De Marco V, Runswick MJ, Palmieri F, Walker JE. 1999. Identification of the yeast mitochondrial transporter for oxaloacetate and sulfate. J Biol Chem 274:22184-22190.
62. Pitkänen J-P, Aristidou A, Salusjärvi L, Ruohonen L, Penttilä M. 2003. Metabolic flux analysis of xylose metabolism in recombinant Saccharomyces cerevisiae using continuous culture. Metab Eng 5:16-31.
63. Polakis ES, Bartley W. 1965. Changes in the enzyme activities of Saccharomyces cerevisiae during aerobic growth on different carbon sources. Biochem J 97:284-297.
64. Rolland F, De Winde JH, Lemaire K, Boles E, Thevelein JM, Winderickx J. 2000. Glucose-induced cAMP signalling in yeast requires both a G-protein coupled receptor system for extracellular glucose detection and a separable hexose kinase-dependent sensing process. Mol Microbiol 38:348-358.
65. Runquist D, Fonseca C, Rådström P, Spencer-Martins I, Hahn-Hägerdal B. 2009a. Expression of the Gxf1 transporter from Candida intermedia improves fermentation performance in recombinant xylose-utilizing Saccharomyces cerevisiae. Appl Microbiol Biotechnol 82:123-130.
66. Runquist D, Hahn-Hägerdal B, Bettiga M. 2009b. Increased expression of the oxidative pentose phosphate pathway and gluconeogenesis in anaerobically growing xylose-utilizing Saccharomyces cerevisiae. Microb Cell Factories 8:49.
67. Runquist D, Hahn-Hägerdal B, Rådström P. 2010. Comparison of heterologous xylose transporters in recombinant Saccharomyces cerevisiae. Biotechnol Biofuels 3:5.
68. Salusjärvi L, Kankainen M, Soliymani R, Pitkänen J-P, Penttilä M, Ruohonen L. 2008. Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae. Microb Cell Factories 7:18.
69. Sarthy AV, McConaughy BL, Lobo Z, Sundstrom JA, Furlong CE, Hall BD. 1987. Expression of the Escherichia coli xylose isomerase gene in Saccharomyces cerevisiae. Appl Environ Microbiol 53:1996-2000.
70. Scalcinati G, Otero JM, Van Vleet JRH, Jeffries TW, Olsson L, Nielsen J. 2012. Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption. FEMS Yeast Res 12:582-597.
71. Sonderegger M, Jeppsson M, Hahn-Hägerdal B, Sauer U. 2004. Molecular basis for anaerobic growth of Saccharomyces cerevisiae on xylose, investigated by global gene expression and metabolic flux analysis. Appl Environ Microbiol 70:2307-2317.
72. Stephanopoulos G. 2007. Challenges in engineering microbes for biofuels production. Science 315:801-804.
73. Tantirungkij M, Nakashima N, Seki T, Yoshida T. 1993. Construction of xylose-assimilating Saccharomyces cerevisiae. J Ferment Bioeng 75:83-88.
74. Toivari MH, Aristidou A, Ruohonen L, Penttilä M. 2001. Conversion of xylose to ethanol by recombinant Saccharomyces cerevisiae: importance of xylulokinase (XKS1) and oxygen availability. Metab Eng 3:236-249.
75. Van Winden WA, Wittmann C, Heinzle E, Heijnen JJ. 2002. Correcting mass isotopomer distributions for naturally occurring isotopes. Biotechnol Bioeng 80:477-479.
76. Vaseghi S, Macherhammer F, Zibek S, Reuss M. 2001. Signal transduction dynamics of the protein kinase-A/phosphofructokinase-2 system in Saccharomyces cerevisiae. Metab Eng 3:163-172.
77. Vincent O, Townley R, Kuchin S, Carlson M. 2001. Subcellular localization of the Snf1 kinase is regulated by specific beta subunits and a novel glucose signaling mechanism. Genes Dev 15:1104-1114.
78. Wahlbom CF, Eliasson A, Hahn-Hägerdal B. 2001. Intracellular fluxes in a recombinant xylose-utilizing Saccharomyces cerevisiae cultivated anaerobically at different dilution rates and feed concentrations. Biotechnol Bioeng 72:289-296.
79. Wahlbom CF, Cordero Otero, van Zyl RR, Hahn-Hägerdal WH, Jönsson B. 2003. Molecular analysis of a Saccharomyces cerevisiae mutant with improved ability to utilize xylose shows enhanced expression of proteins involved in transport, initial xylose metabolism, and the pentose phosphate pathway. Appl Environ Microbiol 69:740-746.
80. Walfridsson M, Hallborn J, Penttilä M, Keränen S, Hahn-Hägerdal B. 1995. Xylose-metabolizing Saccharomyces cerevisiae strains overexpressing the TKL1 and TAL1 genes encoding the pentose phosphate pathway enzymes transketolase and transaldolase. Appl Environ Microbiol 61:4184-4190.
81. Wasylenko TM, Stephanopoulos G. 2013. Kinetic isotope effects significantly influence intracellular metabolite (13) C labeling patterns and flux determination. Biotechnol J 8:1080-1089.
82. Wiechert W, de Graaf AA. 1997. Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments. Biotechnol Bioeng 55:101-117.
83. Wisselink HW, Cipollina C, Oud B, Crimi B, Heijnen JJ, Pronk JT, van Maris AJA. 2010. Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae. Metab Eng 12:537-551.
84. Wittmann, Heinzle 1999. Mass spectrometry for metabolic flux analysis. Biotechnol Bioeng 62:739-750.
85. Wu L, Mashego MR, van Dam JC, Proell AM, Vinke JL, Ras C, van Winden WA, van Gulik WM, Heijnen JJ. 2005. Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards. Anal Biochem 336:164-171.
86. Yin Z, Hatton L, Brown AJ. 2000. Differential post-transcriptional regulation of yeast mRNAs in response to high and low glucose concentrations. Mol Microbiol 35:553-565.
87. Young EM, Comer AD, Huang H, Alper HS. 2012. A molecular transporter engineering approach to improving xylose catabolism in Saccharomyces cerevisiae. Metab Eng 14:401-411.
88. Young JD, Shastri AA, Stephanopoulos G, Morgan JA. 2011. Mapping photoautotrophic metabolism with isotopically nonstationary (13)C flux analysis. Metab Eng 13:656-665.
89. Zhou H, Cheng J-S, Wang BL, Fink GR, Stephanopoulos G. 2012. Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae. Metab Eng 14:611-622.