Genome-wide identification of Saccharomyces cerevisiae genes required for tolerance to acetic acid

Microbial Cell Factories - Tập 9 Số 1 - 2010
Nuno P. Mira1, Margarida Palma1, Joana F. Guerreiro1, Isabel Sá‐Correia1
1Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Technical University of Lisbon, 1049-00, Lisboa, Portugal

Tóm tắt

AbstractBackgroundAcetic acid is a byproduct ofSaccharomyces cerevisiaealcoholic fermentation. Together with high concentrations of ethanol and other toxic metabolites, acetic acid may contribute to fermentation arrest and reduced ethanol productivity. This weak acid is also a present in lignocellulosic hydrolysates, a highly interesting non-feedstock substrate in industrial biotechnology. Therefore, the better understanding of the molecular mechanisms underlyingS. cerevisiaetolerance to acetic acid is essential for the rational selection of optimal fermentation conditions and the engineering of more robust industrial strains to be used in processes in which yeast is explored as cell factory.ResultsThe yeast genes conferring protection against acetic acid were identified in this study at a genome-wide scale, based on the screening of the EUROSCARF haploid mutant collection for susceptibility phenotypes to this weak acid (concentrations in the range 70-110 mM, at pH 4.5). Approximately 650 determinants of tolerance to acetic acid were identified. Clustering of these acetic acid-resistance genes based on their biological function indicated an enrichment of genes involved in transcription, internal pH homeostasis, carbohydrate metabolism, cell wall assembly, biogenesis of mitochondria, ribosome and vacuole, and in the sensing, signalling and uptake of various nutrients in particular iron, potassium, glucose and amino acids. A correlation between increased resistance to acetic acid and the level of potassium in the growth medium was found. The activation of the Snf1p signalling pathway, involved in yeast response to glucose starvation, is demonstrated to occur in response to acetic acid stress but no evidence was obtained supporting the acetic acid-induced inhibition of glucose uptake.ConclusionsApproximately 490 of the 650 determinants of tolerance to acetic acid identified in this work are implicated, for the first time, in tolerance to this weak acid. These are novel candidate genes for genetic engineering to obtain more robust yeast strains against acetic acid toxicity. Among these genes there are number of transcription factors that are documented regulators of a large percentage of the genes found to exert protection against acetic acid thus being considered interesting targets for subsequent genetic engineering. The increase of potassium concentration in the growth medium was found to improve the expression of maximal tolerance to acetic acid, consistent with the idea that the adequate manipulation of nutrient concentration of industrial growth medium can be an interesting strategy to surpass the deleterious effects of this weak acid in yeast cells.

Từ khóa


Tài liệu tham khảo

Gancedo JM, Gancedo C: Catabolite repression mutants of yeast. FEMS Microbiol Rev. 1986, 32: 179-187.

Graves T, Narendranath N, Dawson K, Power R: Effect of pH and lactic or acetic acid on ethanol productivity by Saccharomyces cerevisiae in corn mash. J Ind Microbiol Biotechnol. 2006, 33 (6): 469-474. 10.1007/s10295-006-0091-6.

Rasmussen JE, Schultz E, Snyder RE, Jones RS, Smith CR: Acetic-Acid as a Causative Agent in Producing Stuck Fermentations. Am J Enol Viticult. 1995, 46 (2): 278-280.

Garay-Arroyo A, Covarrubias AA, Clark I, Nino I, Gosset G, Martinez A: Response to different environmental stress conditions of industrial and laboratory Saccharomyces cerevisiae strains. Appl Microbiol Biotechnol. 2004, 63 (6): 734-741. 10.1007/s00253-003-1414-4.

Radler F: Yeasts-Metabolism of organic acids. Wine Microbiology and Biotechnology. 1993, 165-179. Harwood Academic Publishers,

van Maris AJ, Abbott DA, Bellissimi E, van den Brink J, Kuyper M, Luttik MA, Wisselink HW, Scheffers WA, van Dijken JP, Pronk JT: Alcoholic fermentation of carbon sources in biomass hydrolysates by Saccharomyces cerevisiae: current status. Antonie Van Leeuwenhoek. 2006, 90 (4): 391-418. 10.1007/s10482-006-9085-7.

Palmqvist E, Hahn-Hägerdal B: Fermentation of lignocellulosic hydrolysates. I: inhibition and detoxification. Bioresour Technol. 2000, 74 (1): 17-24. 10.1016/S0960-8524(99)00160-1.

Almeida JR, Modig T, Petersson A, Hähn-Hägerdal B, Lidén G, Gorwa-Grauslund MF: Increased tolerance and conversion of inhibitors in lignocellulosic hydrolysates by Saccharomyces cerevisiae. J Chem Technol Biotechnol. 2007, 82 (4): 340-349. 10.1002/jctb.1676.

Casey E, Sedlak M, Ho NW, Mosier NS: Effect of acetic acid and pH on the cofermentation of glucose and xylose to ethanol by a genetically engineered strain of Saccharomyces cerevisiae. FEMS Yeast Res. 2010, 10 (4): 385-393. 10.1111/j.1567-1364.2010.00623.x.

Stratford M: Food and Beverage Spoilage Yeasts. Yeasts in Food and Beverages. Edited by: Querol A, Fleet G. 2006, 335-379. full_text. Berlin: Springer

Guldfeldt LU, Arneborg N: Measurement of the effects of acetic acid and extracellular pH on intracellular pH of nonfermenting, individual Saccharomyces cerevisiae cells by fluorescence microscopy. Appl Environ Microbiol. 1998, 64 (2): 530-534.

Pampulha ME, Loureiro-Dias MC: Activity of glycolytic enzymes of Saccharomyces cerevisiae in the presence of acetic acid. Appl Microbiol Biotechnol. 1990, 34 (3): 375-380. 10.1007/BF00170063.

Pampulha ME, Loureiro-Dias MC: Energetics of the effect of acetic acid on growth of Saccharomyces cerevisiae. FEMS Microbiol Lett. 2000, 184 (1): 69-72. 10.1111/j.1574-6968.2000.tb08992.x.

Mira NP, Teixeira MC, Sá-Correia I: Adaptation and tolerance to weak acid stress in Saccharomyces cerevisiae: a genome-wide view. OMICS: A Journal of Integrative Biology. 2010, 14 (5): 525-540. 10.1089/omi.2010.0072.

Kotyk A, Georghiou G: Protonmotive force in yeasts-pH, buffer and species dependence. Biochem Int. 1991, 24 (4): 641-647.

Carmelo V, Santos H, Sá-Correia I: Effect of extracellular acidification on the activity of plasma membrane ATPase and on the cytosolic and vacuolar pH of Saccharomyces cerevisiae. Biochim Biophys Acta. 1997, 1325: 63-70. 10.1016/S0005-2736(96)00245-3.

Tenreiro S, Nunes PA, Viegas CA, Neves MS, Teixeira MC, Cabral MG, Sá-Correia I: AQR1 gene (ORF YNL065w) encodes a plasma membrane transporter of the major facilitator superfamily that confers resistance to short-chain monocarboxylic acids and quinidine in Saccharomyces cerevisiae. Biochem Biophys Res Commun. 2002, 292 (3): 741-748. 10.1006/bbrc.2002.6703.

Tenreiro S, Rosa PC, Viegas CA, Sá-Correia I: Expression of the AZR1 gene (ORF YGR224w), encoding a plasma membrane transporter of the major facilitator superfamily, is required for adaptation to acetic acid and resistance to azoles in Saccharomyces cerevisiae. Yeast. 2000, 16 (16): 1469-1481. 10.1002/1097-0061(200012)16:16<1469::AID-YEA640>3.0.CO;2-A.

Fernandes AR, Mira NP, Vargas RC, Canelhas I, Sá-Correia I: Saccharomyces cerevisiae adaptation to weak acids involves the transcription factor Haa1p and Haa1p-regulated genes. Biochem Biophys Res Commun. 2005, 337 (1): 95-103. 10.1016/j.bbrc.2005.09.010.

Mira NP, Becker J, Sá-Correia I: Genomic expression program involving the Haa1p-regulon in Saccharomyces cerevisiae response to acetic acid. OMICS: A Journal of Integrative Biology. 2010, 14 (5): 587-601. 10.1089/omi.2010.0048.

Alejandro-Osorio AL, Huebert DJ, Porcaro DT, Sonntag ME, Nillasithanukroh S, Will JL, Gasch AP: The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress. Genome Biol. 2009, 10 (5): R57- 10.1186/gb-2009-10-5-r57.

Goossens A, de la Fuente N, Forment J, Serrano R, Portillo F: Regulation of Yeast H+-ATPase by Protein Kinases Belonging to a Family Dedicated to Activation of Plasma Membrane Transporters. Mol Cell Biol. 2000, 20 (20): 7654-7661. 10.1128/MCB.20.20.7654-7661.2000.

Kawahata M, Masaki K, Fujii T, Iefujii H: Yeast genes involved in response to lactic acid and acetic acid: acidic conditions caused by the organic acids in Saccharomyces cerevisiae cultures induce expression of intracellular metal metabolism genes regulated by Aft1p. FEMS Yeast Res. 2006, 6: 924-936. 10.1111/j.1567-1364.2006.00089.x.

Herman PK: Stationary phase in yeast. Curr Opin Microbiol. 2002, 5 (6): 602-607. 10.1016/S1369-5274(02)00377-6.

Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, Lee W, Proctor M, St Onge RP, Tyers M, Koller D, et al.: The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes. Science. 2008, 320 (5874): 362-365. 10.1126/science.1150021.

Mroczek S, Kufel J: Apoptotic signals induce specific degradation of ribosomal RNA in yeast. Nucleic Acids Res. 2008, 36 (9): 2874-2888. 10.1093/nar/gkm1100.

Viegas CA, Almeida PF, Cavaco M, Sá-Correia I: The H(+)-ATPase in the plasma membrane of Saccharomyces cerevisiae is activated during growth latency in octanoic acid-supplemented medium accompanying the decrease in intracellular pH and cell viability. Appl Environ Microbiol. 1998, 64 (2): 779-783.

Fernandes AR, Durao PJ, Santos PM, Sá-Correia I: Activation and significance of vacuolar H+-ATPase in Saccharomyces cerevisiae adaptation and resistance to the herbicide 2, 4-dichlorophenoxyacetic acid. Biochem Biophys Res Commun. 2003, 312 (4): 1317-1324. 10.1016/j.bbrc.2003.11.072.

Makrantoni V, Dennison P, Stark MJ, Coote PJ: A novel role for the yeast protein kinase Dbf2p in vacuolar H+-ATPase function and sorbic acid stress tolerance. Microbiology. 2007, 153 (Pt 12): 4016-4026. 10.1099/mic.0.2007/010298-0.

Mulet JM, Leube MP, Kron SJ, Rios G, Fink GR, Serrano R: A novel mechanism of ion homeostasis and salt tolerance in yeast: the Hal4 and Hal5 protein kinases modulate the Trk1-Trk2 potassium transporter. Mol Cell Biol. 1999, 19 (5): 3328-3337.

Munson AM, Haydon DH, Love SL, Fell GL, Palanivel VR, Rosenwald AG: Yeast ARL1 encodes a regulator of K+ influx. J Cell Sci. 2004, 117 (Pt 11): 2309-2320. 10.1242/jcs.01050.

Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, Alenquer M, Oliveira A, Freitas AT, Sá-Correia I: The YEASTRACT database: a tool for the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 2006, 34: D446-D451. 10.1093/nar/gkj013.

Almeida B, Ohlmeier S, Almeida AJ, Madeo F, Leão C, Rodrigues F, Ludovico P: Yeast protein expression profile during acetic acid-induced apoptosis indicates causal involvement of the TOR pathway. PROTEOMICS. 2009, 9 (3): 720-732. 10.1002/pmic.200700816.

Hong SP, Carlson M: Regulation of Snf1 protein kinase in response to environmental stress. J Biol Chem. 2007, 282 (23): 16838-16845. 10.1074/jbc.M700146200.

Santangelo GM: Glucose Signaling in Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 2006, 70 (1): 253-282. 10.1128/MMBR.70.1.253-282.2006.

Giannattasio S, Guaragnella N, Corte-Real M, Passarella S, Marra E: Acid stress adaptation protects Saccharomyces cerevisiae from acetic acid-induced programmed cell death. Gene. 2005, 354: 93-98. 10.1016/j.gene.2005.03.030.

Guaragnella N, Antonacci L, Passarella S, Marra E, Giannattasio S: Hydrogen peroxide and superoxide anion production during acetic acid-induced yeast programmed cell death. Folia Microbiol. 2007, 52 (3): 237-240. 10.1007/BF02931304.

Porter NA, Caldwell SE, Mills KA: Mechanisms of free radical oxidation of unsaturated lipids. Lipids. 1995, 30 (4): 277-290. 10.1007/BF02536034.

van der Rest ME, Kamminga AH, Nakano A, Anraku Y, Poolman B, Konings WN: The plasma membrane of Saccharomyces cerevisiae: structure, function, and biogenesis. Microbiol Rev. 1995, 59 (2): 304-322.

Dickson RC: Thematic review series: sphingolipids. New insights into sphingolipid metabolism and function in budding yeast. J Lipid Res. 2008, 49 (5): 909-921. 10.1194/jlr.R800003-JLR200.

Wilson WA, Hawley SA, Hardie DG: Glucose repression/derepression in budding yeast: SNF1 protein kinase is activated by phosphorylation under derepressing conditions, and this correlates with a high AMP:ATP ratio. Curr Biol. 1996, 6 (11): 1426-1434. 10.1016/S0960-9822(96)00747-6.

Mollapour M, Shepherd A, Piper PW: Presence of the Fps1p aquaglyceroporin channel is essential for Hog1p activation, but suppresses the Slt2(Mpk1)p activation, with acetic acid stress of yeast. Microbiology. 2009, 155: 3304-3311. 10.1099/mic.0.030502-0.

Simões T, Mira NP, Fernandes AR, Sá-Correia I: The SPI1 gene, encoding a glycosylphosphatidylinositol (GPI)-anchored cell wall protein, plays a prominent role in the development of yeast resistance to lipophilic weak acids food preservatives. Appl Environ Microb. 2006, 72: 7168-7175. 10.1128/AEM.01476-06.

Mollapour M, Fong D, Balakrishnan K, Harris N, Thompson S, Schuller C, Kuchler K, Piper PW: Screening the yeast deletant mutant collection for hypersensitivity and hyper-resistance to sorbate, a weak organic acid food preservative. Yeast. 2004, 21 (11): 927-946. 10.1002/yea.1141.

Mira NP, Lourenco AB, Fernandes AR, Becker JD, Sá-Correia I: The RIM101 pathway has a role in Saccharomyces cerevisiae adaptive response and resistance to propionic acid and other weak acids. FEMS Yeast Res. 2009, 9 (2): 202-216. 10.1111/j.1567-1364.2008.00473.x.

Perez-Valle J, Jenkins H, Merchan S, Montiel V, Ramos J, Sharma S, Serrano R, Yenush L: Key role for intracellular K+ and protein kinases Sat4/Hal4 and Hal5 in the plasma membrane stabilization of yeast nutrient transporters. Mol Cell Biol. 2007, 27 (16): 5725-5736. 10.1128/MCB.01375-06.

Aiking H, Tempest DW: Growth and physiology of Candida utilis NCYC 321 in potassium-limited chemostat culture. Arch Microbiol. 1976, 108 (1): 117-124. 10.1007/BF00425101.

Rodriguez-Navarro A: Potassium transport in fungi and plants. Biochim Biophys Acta. 2000, 1469 (1): 1-30.

Serrano R: Transport across yeast vacuolar and plasma membranes. The molecular and cellular biology of the yeast Saccharomyces: genome dynamics, protein synthesis, and energetics. Edited by: Broach JR, Jones EW, Pringle JR. 1991, 523-585. NY: Cold Spring Harbor Laboratory Press

Yenush L, Mulet JM, Arino J, Serrano R: The Ppz protein phosphatases are key regulators of K+ and pH homeostasis: implications for salt tolerance, cell wall integrity and cell cycle progression. EMBO J. 2002, 21 (5): 920-929. 10.1093/emboj/21.5.920.

Macpherson N, Shabala L, Rooney H, Jarman MG, Davies JM: Plasma membrane H+ and K+ transporters are involved in the weak-acid preservative response of disparate food spoilage yeasts. Microbiology. 2005, 151: 1995-2003. 10.1099/mic.0.27502-0.

Rodriguez-Navarro A, Ramos J: Dual system for potassium transport in Saccharomyces cerevisiae. J Bacteriol. 1984, 159 (3): 940-945.

Kosman DJ: Molecular mechanisms of iron uptake in fungi. Mol Microbiol. 2003, 47 (5): 1185-1197. 10.1046/j.1365-2958.2003.03368.x.

Chen OS, Crisp RJ, Valachovic M, Bard M, Winge DR, Kaplan J: Transcription of the yeast iron regulon does not respond directly to iron but rather to iron-sulfur cluster biosynthesis. J Biol Chem. 2004, 279 (28): 29513-29518. 10.1074/jbc.M403209200.

Rutherford JC, Ojeda L, Balk J, Muhlenhoff U, Lill R, Winge DR: Activation of the iron regulon by the yeast Aft1/Aft2 transcription factors depends on mitochondrial but not cytosolic iron-sulfur protein biogenesis. J Biol Chem. 2005, 280 (11): 10135-10140. 10.1074/jbc.M413731200.

Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G: Engineering yeast transcription machinery for improved ethanol tolerance and production. Science. 2006, 314 (5805): 1565-1568. 10.1126/science.1131969.

Cardona F, Carrasco P, Perez-Ortin JE, del Olmo M, Aranda A: A novel approach for the improvement of stress resistance in wine yeasts. Int J Food Microbiol. 2007, 114 (1): 83-91. 10.1016/j.ijfoodmicro.2006.10.043.

Camacho M, Ramos J, Rodríguez-Navarro A: Potassium Requirements of Saccharomyces cerevisiae. Curr Microbiol. 1981, 6: 295-299. 10.1007/BF01566880.

Eide DJ, Clark S, Nair TM, Gehl M, Gribskov M, Guerinot ML, Harper JF: Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae. Genome Biol. 2005, 6 (9): R77- 10.1186/gb-2005-6-9-r77.

Thông tin
Thông tin xuất bản

Microbial Cell Factories

Tập 9 Số 1

Thông tin tác giả