Abstract
Global gene expression was analyzed in Saccharomyces cerevisiae T2 cells grown in the presence of hardwood spent sulphite liquor (HW SSL) and each of the three main inhibitors in HW SSL, acetic acid, hydroxymethyfurfural (HMF) and furfural, using a S. cerevisiae DNA oligonucleotide microarray. The objective was to compare the gene expression profiles of T2 cells in response to the individual inhibitors against that elicited in response to HW SSL. Acetic acid mainly affected the expression of genes related to the uptake systems of the yeast as well as energy generation and metabolism. Furfural and HMF mainly affected the transcription of genes involved in the redox balance of the cell. On the other hand, the effect of HW SSL on S. cerevisiae T2 cells was distinct and considerably more diverse as compared to the effect of individual inhibitors found in lignocellulosic hydrolysates. This is not surprising as HW SSL contains a complex mixture of inhibitors which may act synergistically. HW SSL elicited significant changes in expression of genes involved in diverse and multiple effects on several aspects of the cellular structure and function. A notable response to HW SSL was decreased expression of the ribosomal protein genes in T2 cells. In addition, HW SSL decreased the expression of genes functioning in the synthesis and transport of proteins as well as metabolism of carbohydrates, lipids, vitamins and vacuolar proteins. Furthermore, the expression of genes involved in multidrug resistance, iron transport and pheromone response was increased, suggesting that T2 cells grown in the presence of HW SSL may have activated pheromone response and/or activated pleiotropic drug response. Some of the largest changes in gene expression were observed in the presence of HW SSL and the affected genes are involved in mating, iron transport, stress response and phospholipid metabolism. A total of 59 out of the 400 genes differentially expressed in the presence of HW SSL, acetic acid, HMF and furfural, belonged to the category of poorly characterized genes. The results indicate that transcriptional responses to individual lignocellulosic inhibitors gave a different picture and may not be representative of how the cells would respond to the presence of all the inhibitors in lignocellulosic hydrolysates such as HW SSL.
Similar content being viewed by others
References
Agarwal S, Sharma S, Agrawal V, Roy N (2005) Caloric restriction augments ROS defense in S. cerevisiae, by a Sir2p independent mechanism. Free Radic Res 39:55–62
Allen SA, Clark W, McCaffery JM, Cai Z, Lanctot A, Slininger PJ, Liu ZL, Gorsich SW (2010) Furfural induces reactive oxygen species accumulation and cellular damage in Saccharomyces cerevisiae. Biotechnol Biofuels 3:2. doi:10.1186/1754-6834-3-2
Almeida B, Ohlmeier S, Almeida AJ, Madeo F, Leão C, Rodrigues F (2009) Yeast protein expression profile during acetic acid-induced apoptosis indicates causal involvement of the TOR pathway. Proteomics 9:720–732
Amartey S, Jeffries T (1996) An improvement in Pichia stipitis fermentation of acid-hydrolysed hemicellulose achieved by overliming (calcium hydroxide treatment) and strain adaptation. World J Microbiol Biotechnol 12:281–283
Bajwa PK, Shireen T, D’Aoust F, Pinel D, Martin VJJ, Trevors JT, Lee H (2009) Mutants of the pentose-fermenting yeast Pichia stipitis with improved tolerance to inhibitors in hardwood spent sulphite liquor. Biotechnol Bioeng 104:892–900
Bajwa PK, Pinel D, Martin VJJ, Trevors JT, Lee H (2010) Strain improvement of the pentose-fermenting yeast Pichia stipitis by genome shuffling. J Microbiol Methods 81:179–186
Cheadle C, Vawter MP, Freed WJ, Becker KG (2003) Analysis of microarray data using Z score transformation. J Mol Diagn 5:73–81
Ding MZ, Wang X, Liu W, Cheng JS, Yang Y, Yuan YJ (2012) Proteomic research reveals the stress response and detoxification of yeast to combined inhibitors. PLoS ONE 7(8):e43474
Fernandes AR, Mira NP, Vargas RC, Canelhas I, Sá-Correia I (2005) Saccharomyces cerevisiae adaptation to weak acids involves the transcription factor Haa1p and Haa1p-regulated genes. Biochem Biophys Res Commun 337(1):95–103
Giannattasio S, Guaragnella N, Corte-Real M, Passarella S, Marra E (2005) Acid stress adaptation protects Saccharomyces cerevisiae from acetic acid-induced programmed cell death. Gene 354:93–98
Goranov AI, Cook M, Ricicova M, Ben-Ari G, Gonzalez C, Hansen C, Tyers M, Amon A (2009) The rate of cell growth is governed by cell cycle stage. Gene Dev 23:1408–1422
Gorsich SW, Dien BS, Nichols NN, Slininger PJ, Liu ZL, Skory CD (2006) Tolerance to furfural-induced stress is associated with pentose phosphate pathway genes ZWF1, GND1, RPE1, and TKL1 in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 71:339–349
Haemmerli SD, Leisola MS, Sanglard D, Fiechter A (1987) Oxidation of benzo(a)pyrene by extracellular ligninases of Phanerochaete chrysosporium. Veratryl alcohol and stability of ligninase. J Biol Chem 261:6900–6903
Han K, Hong J, Lim HC (1993) Relieving effects of glycine and methionine from acetic acid inhibition in Escherichia coli fermentation. Biotechnol Bioeng 41:316–324
Heer D, Sauer U (2008) Identification of furfural as the key toxin in lignocellulosic hydrolysates and evolution of a tolerant yeast strain. Microb Biotechnol 1:497–506
Heer D, Heine D, Sauer U (2009) Resistance of Saccharomyces cerevisiae to high concentrations of furfural is based on NADPH-dependent reduction by at least two oxireductases. Appl Environ Microbiol 75:7631–7638
Kitagawa E, Momose Y, Iwahashi H (2003) Correlation of the structures of agricultural fungicides to gene expression in Saccharomyces cerevisiae upon exposure to toxic doses. Environ Sci Technol 37:2788–2793
Kobayashi N, McEntee K (1990) Evidence for a heat shock transcription factor-independent mechanism for heat shock induction of transcription in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 87:6550–6554
Kobayashi N, Mcclanahan TK, Simon JR, Treger JM, McEntee K (1996) Structure and functional analysis of the multistress response gene DDR2 from Saccharomyces cerevisiae. Biochem Biophys Res Commun 229:540–547
Larroy C, Pares X, Biosca JA (2002) Characterization of a Saccharomyces cerevisiae NADP(H)-dependent alcohol dehydrogenase (ADHVII), a member of the cinnamyl alcohol dehydrogenase family. Eur J Biochem 269:5738–5745
Li B-Z, Yuan YJ (2010) Transcriptome shifts in response to furfural and acetic acid in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 86:1915–1924
Lin F-M, Qiao B, Yuan Y-J (2009) Comparative proteomic analysis of tolerance and adaptation of ethanologenic Saccharomyces cerevisiae to furfural, a lignocellulosic inhibitory compound. Appl Environ Microbiol 75:3765–3766
Liu ZL, Slininger PJ (2006) Transcriptome dynamics of ethanologenic yeast in response to 5-hydroxymethylfurfural stress related to biomass conversion to ethanol. In: Marzal A, Reviriego MI, Navarro C, de Lope F, Møller AP (eds) Recent research developments in multidisciplinary applied microbiology, understanding and exploiting microbes and their interactions—biological, physical, chemical and engineering aspects. Wiley, New York, pp 679–684
Ma M, Liu ZL (2010) Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae. BMC Genomics 11:660. doi:10.1186/1471-2164-11-660
Mira NP, Palma M, Guerreiro J, Sá-Correia I (2010) Genome-wide identification of Saccharomyces cerevisiae genes required for tolerance to acetic acid. Microb Cell Factories 9:79–91
Nigam JN (2001) Development of xylose-fermenting yeast Pichia stipitis for ethanol production through adaptation on hardwood hemicellulose acid prehydrolysate. J Appl Microbiol 90:208–215
Petersson A, Almeida JR, Modig T, Karhumma K, Hahn-Hägerdal B, Gorwa-Grauslund MF (2006) A 5-hydroxymethylfurfural reducing enzyme encoded by the Saccharomyces cerevisiae ADH6 gene conveys HMF tolerance. Yeast 23:455–464
Pinel D, D’Aoust F, del Cardayré SB, Bajwa PK, Lee H, Martin VJJ (2011) Genome shuffling of Saccharomyces cerevisiae through recursive population mating leads to improved tolerance to spent sulfite liquor. Appl Environ Microbiol 77:4736–4743
Richardson TL, Harner N, Bajwa PK, Trevors JT, Lee H (2011) Approaches to deal with toxic inhibitors during fermentation of lignocellulosic substrates. In: Zhu JY, Zhang X, Pan XJ (eds) Sustainable production of fuels, chemicals, and fibers from forest biomass, ACS symposium series, vol 1067, Chap. 7. American Chemical Society Publication, Washington, DC, pp 171–202
Roe AJ, O’Byrne C, McLaggan D, Booth IR (2002) Inhibition of Escherichia coli growth by acetic acid: a problem with methionine biosynthesis and homocysteine toxicity. Microbiology 148:2215–2222
Rohde JR, Cardenas ME (2003) The tor pathway regulates gene expression by linking nutrient sensing to histone acetylation. Mol Cell Biol 23:629–635
Taherzadeh MJ, Gustafsson L, Niklasson C, Liden G (2000) Physiological effects of 5-hydroxymethylfurfural on Saccharomyces cerevisiae. Appl Microbiol Biotechnol 53:701–708
Teixeira MC, Fernandes AR, Mira NP, Becker JD, Sá-Correia I (2006a) Early transcriptional response of Saccharomyces cerevisiae to stress imposed by the herbicide 2,4-dichlorophenoxyacetic acid. FEMS Yeast Res 6:230–248
Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Nuno P, Mira NP, Alenquer M, Freitas AT, Oliveira AL, Sá-Correia I (2006b) The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res 34:D446–D451
Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q (2010) The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 38:W214–W220
Warner JR (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 24:437–440
Acknowledgments
This research was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada. We thank J. Strmen (formerly of Tembec) for providing the S. cerevisiae T2 strain and HW SSL.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Bajwa, P.K., Ho, CY., Chan, CK. et al. Transcriptional profiling of Saccharomyces cerevisiae T2 cells upon exposure to hardwood spent sulphite liquor: comparison to acetic acid, furfural and hydroxymethylfurfural. Antonie van Leeuwenhoek 103, 1281–1295 (2013). https://doi.org/10.1007/s10482-013-9909-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10482-013-9909-1