Genomic adaptation of saccharomyces cerevisiae to inhibitors for lignocellulosic biomass conversion to ethanol

Applied Mycology

Volumn , Issue , 2009, Pages 136-155

  Liu, Zonglin Lewis ^a   Song, Mingzhou ^b  

^a NATIONAL CENTER FOR AGRICULTURAL UTILIZATION RESEARCH   (United States)

^b New Mexico State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84890255747     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (89)

1. Antal, M.J., Mok, W.S.L. and Richards, G.N. (1990) Mechanism of formation of 5-(hydroxymethyl)-2-furaldehyde from D-fructose and sucrose. Carbohydrate Research 199, 91-109.
2. Antal, M.J., Leesomboon, T., Mok, W.S. and Richards, G.N. (1991) Mechanism of formation of 2-furaldehyde from D-xylose. Carbohydrate Research 217, 71-85.
3. Badiee, A., Eiken, H.G., Steen, V.M. and Lovlie, R. (2003) Evaluation of five different cDNA labeling methods for microarrays using spike controls. BMC Biotechnology 3, 23.
4. Baker, S.C., Bauer, S.R., Beyer, R.P., Brenton, J.D., Bromley, B., Burrill, J. et al. (2005) The external RNA controls consortium: a progress report. Nature Methods 2, 731-734.
5. Bammler, T., Beyer, R.P., Bhattacharya, S., Boorman, G.A., Boyles, A., Bradford, B.U. et al. (2005) Standardizing global gene expression analysis between laboratories and across platforms. Nature Methods 2, 351-356.
6. Banerjee, N., Bhatnagar, R. and Viswanathan, L. (1981) Development of resistance in Saccharomyces cerevisiae against inhibitory effects of Browning reaction products. Enzyme and Microbial Technology 3, 24-28.
7. Bothast, R. and Saha, B. (1997) Ethanol production from agricultural biomass substrate. Advances in Applied Microbiology 44, 261-286.
8. Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C. et al. (2001) Minimum information about a microarray experiment (MIAME) -toward standards for microarray data. Nature Genetics 29, 365-371.
9. Brejning, J., Jespersen, L, and Arneborg, N. (2003) Genome-wide transcriptional changes during the lag phase of Saccharomyces cerevisiae. Archives of Microbiology 179, 278-294.
10. Causton, H.C., Ren, B., Koh, S.S., Harbison, C.T., Kanin, E., Jennings, E.G., Lee, T.I., True, H.L., Lander, E.S. and Young, R.A. (2001) Remodeling of yeast genome expression in response to environmental changes. Molecular Biology of the Cell 12, 323-337.
11. Chen, D., Toone, M.W., Mata, J., Lyne, R., Burns, G., Kivinen, K., Brazma, A., Jones, N. and Bahler, J. (2003) Global transcriptional responses of fission yeast to environmental stress. Molecular Biology of the Cell 14, 214-229.
12. Chung, I.S. and Lee, Y.Y. (1985) Ethanol fermentation of crude acid hydrolyzate of cellulose using high-level yeast inocula. Biotechnology and Bioengineering 27, 308-315.
13. Churchill, G.A. (2004) Using ANOVA to analyze microarray data. BioTechniques 37, 173-177.
14. Dallas, P.B., Gottardo, N.G., Firth, M.J., Beesley, A.H., Hoffmann, K., Terry, P.A., Freitas, J.R., Boag, J.M., Cummings, A.J. and Kees, U.R. (2005) Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -how well do they correlate?. BMC Genomics 6, 59.
15. Devantier, R., Pedersen, S. and Olsson, L. (2005) Transcription analysis of S. cerevisiae in VHG fermentation. Industrial Biotechnology 1, 51-63.
16. Devaux, F., Carvajal, E., Moye-Rowley, S. and Jacq, C. (2002) Genome-wide studies on the nuclear PDR3-controlled response to mitochondrial dysfunction in yeast. FEBS Letters 515(1-3), 25-28.
17. Dunlop, A.P. (1948) Furfural formation and behavior. Industrial Engineering and Chemistry 40, 204-209.
18. Erasmus, D., van der Merwe, G. and van Vuure, H (2003) Genome-wide expression analysis: metabolic adaptation of Saccharomyces cerevisiae to high sugar stress. Yeast Research 3, 375-399.
19. Etienne, W., Meyer, M.H., Peppers, J. and Meyer Jr, R.A. (2005) Comparison of mRNA gene expression by RT-PCR and DNA microarray. BioTechniques 36, 618-626.
20. External RNA Controls Consortium(2005). Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics 6, 150.
21. Fisk, D.G., Ball, C.A., Dolinski, K., Engel, S.R., Hong, E.L., Issel-Tarver, L., Schwartz, K., Sethuraman, A., Botstein, D. and Cherry, J.M. (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23, 857-865.
22. Gasch, A. and Werner-Washburne, M, (2002) The genomics of yeast response to environmental stress and starvation. Functional and Integrated Genomics 2, 181-192.
23. Gasch, A.P., Spellman, P.T., Kao, C.M., Carmel-Harel, O., Eisen, M.B., Storz, G., Botstein, D. and Brown, P.O. (2000) Genomic expression program in the response of yeast cells to environmental changes. Molecular Biology of the Cell 11, 4241-4257.
24. Gorsich, S.W., Dien, B.S., Nichols, N.N., Slininger, P.J., Liu, Z.L. and Skory, C.D. (2005) Tolerance to furfural-induced stress is associated with pentose phosphate pathway genes ZWF1, GND1, RPE1, and TKL1 in Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 71, 339-349.
25. Hähn-Hägerdal, B., Wahlbom, F., Gárdony, M., Van Zyl, W., Otero, R. and Jönsson, L. (2001) Metabolic engineering of Saccharomyces cerevisiae for xylose utilization. Advances in Biochemical Engineering and Biotechnology 73, 53-84.
26. Haugen, A.C., Kelley, R., Collins, J.B., Tucker, C.J., Deng, C., Afshari, C.A., Brown, J.M., Ideker, T. and van Houten, B. (2004) Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biology 5(12), R95.
27. Ho, N., Chen, Z. and Brainard, A. (1998) Genetically engineered Saccharomyces yeast capable of effective cofermentation of glucose and xylose. Applied and Environmental Microbiology 64, 1852-1859.
28. Irizarry, R.A., Warren, D., Spencer, F., Kim, I.F., Biswal, S., Frank, B.C. et al. (2005) Multiplelaboratory comparison of microarray platforms. Nature Methods 2, 345-350.
29. James, T.C., Campbell, S., Donnelly, D. and Bond, U. (2003) Transcription profile of brewery yeast under fermentation conditions. Journal of Applied Microbiology 94, 432-448.
30. Jeffries, T. and Shi, Q. (1999) Genetic engineering for improved fermentation by yeasts. Advances in Biochemical Engineering and Biotechnology 65, 117-161.
31. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M. and Hirakawa, M. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Research 34, D354-D357.
32. Kang, S. and Okada, H. (1973) Alcohol dehydrogenase of Cephalosporium sp. induced by furfural alcohol. Journal of Fermentation Technology 51, 118-124.
33. Kerr, M.K. and Churchill, G.A. (2001) Statistical design and the analysis of gene expression microarray data. Genetic Research 77, 123-128.
34. Khan, Q. and Hadi, S. (1994) Inactivation and repair of bacteriophage lambda by furfural. Biochemistry and Molecular Biology International 32, 379-385.
35. Klinke, H.B., Thomsen, A.B. and Ahring, B.K. (2004) Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass. Applied Microbiology and Biotechnology 66, 10-26.
36. Kuyper, M., Toirkens, M.J., Diderich, J.A., Winkler, A.A., van Dijken, J.P. and Pronk, J.T. (2005) Evolutionary engineering of mixed-sugar utilization by a xylose-fermenting Saccharomyces cerevisiae strain. FEMS Yeast Research 5, 925-934.
37. Lage, J.M., Hamann, S., Gribanov, O., Leamon, J.H., Pejovic, T. and Lizardi, P.M. (2002) Microgel assessment of nucleic acid integrity and labeling quality in microarray experiments. BioTechniques 32, 312-314.
38. Larkin, J.E., Frank, B.C., Gavras, H., Sultana, R. and Quackenbush, J. (2005) Independence and reproducibility across microarray platforms. Nature Methods 2, 337-344.
39. Larroy, C., Fernadez, M.R., Gonzalez, E., Pares, X. and Biosca, J.A. (2002) Characterization of the Saccharomyces cerevisiae YMR318C (ADH6) gene product as a broad specificity NADPH-dependent alcohol dehydrogenase: relevance in aldehyde reduction. Biochemical Journal 361, 163-172.
40. Larsson, S., Palmqvist, E., Hähn-Hägerdal, B., Tengborg, C., Stenberg, K., Zacchi, G. and Nilvebrant, N. (1999) The generation of inhibitors during dilute acid hydrolysis of softwood. Enzyme and Microbial Technology 24, 151-159.
41. Lee, J., Godon, C., Lagniel, G., Spector, D., Garin, J., Labarre, J. and Toledano, M.B. (1999) Yap1 and Skn7 control two specialized oxidative stress response regulons in yeast. Journal of Biological Chemistry 274(23), 16040-16046.
42. Lee, T., Rinaldi, N., Robert, F., Odom, D., Bar-Joseph, Z., Gerber, G. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 298(5594), 763-764.
43. Leonard, R.H. and Hajny, G.J. (1945) Fermentation of wood sugars to ethyl alcohol. Industrial Engineering and Chemistry 37, 390-395.
44. Lewkowski, J. (2001) Synthesis, chemistry and applications of 5-hydroxymethylfurfural and its derivatives. Arkivoc 1, 17-54.
45. Liu, Z.L. (2006) Genomic adaptation of ethanologenic yeast to biomass conversion inhibitors. Applied Microbiology and Biotechnology 73, 27-36.
46. Liu, Z.L. and Blaschek, H.P. (2009) Biomass conversion inhibitors and in situ detoxification. In: Vertès, A.A., Blaschek, H.P., Yukawa, H. and Qureshi, N. (eds)Biomass to Biofuels. John Wiley & Sons, Chichester, UK In press.
47. Liu, Z.L. and Sinha, S. (2006) Transcriptional regulatory analysis reveals PDR3 and GCR1 as regulators of significantly induced genes by 5-hydroxymethylfurfrual stress involved in bioethanol conversion for ethanologenic yeast Saccharomyces cerevisiae. Microarray Gene Expression Data Society Meeting 9, 119.
48. Liu, Z.L. and Slininger, P.J. (2005) Development of genetically engineered stress-tolerant ethanologenic yeasts using integrated functional genomics for effective biomass conversion to ethanol. In: Outlaw, J., Collins, K. and Duffield, J. (eds)Agriculture as a Producer and Consumer of Energy. CAB International, Wallingford, UK,pp. 283-294.
49. Liu, Z.L. and Slininger, P.J. (2006) Transcriptome dynamics of ethanologenic yeast in response to 5-hydroxymethylfurfural stress related to biomass conversion to ethanol. In: Mendez-Vilas, A. (ed.)Modern Multidisciplinary Applied Microbiology: Exploiting Microbes and Their Interactions. Wiley-VCH, Weinheim, Germany,pp. 679-684.
50. Liu, Z.L. and Slininger, P.J. (2007) Universal external RNA controls for microbial gene expression analysis using microarray and qRT-PCR. Journal of Microbiological Methods 68, 486-496.
51. Liu, Z.L, Slininger, P.J., Dien, B.S,, Berhow, M.A., Kurtzman, C.P. and Gorsich, S.W. (2004) Adaptive response of yeasts to furfural and 5-hydroxymethylfurfural and new chemical evidence for HMF conversion to 2,5-bis-hydroxymethylfuran. Journal of Industrial and Microbiological Biotechnology 31, 345-352.
52. Liu, Z.L., Slininger, P.J. and Gorsich, S.W. (2005) Enhanced biotransformation of furfural and 5-hydroxy methylfurfural by newly developed ethanologenic yeast strains. Applied Biochemistry and Biotechnology 121-124, 451-460.
53. Liu, Z.L., Slininger, P.J. and Andersh, B.J. (2006) Induction of pleiotropic drug resistance gene expression indicates important roles of PDR to cope with furfural and 5-hydroxymethylfurufral stress in ethanologenic yeast. In: 27th Symposium on Biotechnology and Fuels Chemistry, Denver, Colorado, 1-4 May 2005,p. 169.
54. Liu, Z.L., Saha, B.C. and Slininger, P.J. (2008a) Lignocellulosic biomass conversion to ethanol by Saccharomyces. In: Wall, J., Harwood, C. and Demain, A. (eds)Bioenergy. ASM Press, Washington, DC.
55. Liu, Z.L., Moon, J., Andersh, B.J., Slininger, P.J. and Weber, S. (2008b) Multiple gene-mediated aldehyde reduction is a mechanism of in situ detoxification of furfural and HMF by ethanologenic yeast Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 81(4), 743-753.
56. Lucau-Danila, A., Lelandais, G., Kozovska, Z., Tanty, V., Delaveau, T., Devaux, F. and Jacq, C. (2005) Early expression of yeast genes affected by chemical stress. Molecular Cell Biology 25, 1860-1868.
57. Luo, C., Brink, D. and Blanch, H. (2002) Identification of potential fermentation inhibitors in conversion of hybrid poplar hydrolyzate to ethanol. Biomass and Bioenergy 22, 125-138.
58. Martin, C. and Jonsson, L. (2003) Comparison of the resistance of industrial and laboratory strains of Saccharomyces and Zygosaccharomyces to lignocellulose-derived fermentation inhibitors. Enzyme and Microbial Technology 32, 386-395.
59. Martin, C., Marcelo, M., Almazan, O. and Jonsson, L.J. (2007) Adaptation of a recombinant xylose-utilizing Saccharomyces cerevisiae strain to a sugarcane bagasse hydrolysate with high content of fermentation inhibitors. Bioresource Technology 98, 1767-1773.
60. Martinez, A., Rodriguez, M.E., York, S.W., Preston, J.F. and Ingram, L.O. (2000) Effect of Ca(OH)2 treatments ('Overliming') on the composition and toxicity of bagasse hemicellulose hydrolyzates. Biotechnology and Bioengineering 69, 526-536.
61. Modig, T., Liden, G. and Taherzadeh, M. (2002) Inhibition effects of furfural on alcohol dehydrogenase, aldehyde dehydrogenase and pyruvate dehydrogenase. Biochemical Journal 363, 769-776.
62. Mohsenzadeh, M., Saupe-Thies, W., Sterier, G., Schroeder, T., Francella, F., Ruoff, P. and Rensing, L. (1998) Temperature adaptation of house keeping and heat shock gene expression in Neurospora crassa. Fungal Genetics and Biology 25, 31-43.
63. Morimoto, S. and Murakami, M. (1967) Studies on fermentation products from aldehyde by microorganisms: the fermentative production of furfural alcohol from furfural by yeasts (part I). Journal of Fermentation Technology 45, 442-446.
64. Mussatto, S.I. and Roberto, I.C. (2004) Alternatives for detoxification of dilute-acid lignocellulosic hydrolyzates for use in fermentative processes: a review. Bioresource Technology 93, 1-10.
65. Nemirovskii, V. and Kostenko, V. (1991) Transformation of yeast growth inhibitors which occurs during biochemical processing of wood hydrolysates. Gidroliz Lesokhimm Prom-st 1, 16-17.
66. Nemirovskii, V., Gusarova, L., Rakhmilevich, Y., Sizov, A. and Kostenko, V. (1989) Pathways of furfurol and oxymethyl furfurol conversion in the process of fodder yeast cultivation. Biotekhnologiya 5, 285-289.
67. Nigam, J. (2001) Ethanol production from wheat straw hemicellulose hydrolysate by Pichia stipitis. Journal of Biotechnology 87, 17-27.
68. Nilsson, A., Gorwa-Grauslund, M.F., Hähn-Hägerdal, B. and Liden, G. (2005) Cofactor dependence in furan reduction by Saccharomyces cerevisiae in fermentation of acidhydrolyzed lignocellulose. Applied and Environmental Microbiology 71, 7866-7871.
69. Olsson, L. and Hähn-Hägerdal, B. (1996) Fermentation of lignocellulosic hydrolysates for ethanol production. Enzyme and Microbial Technology 18, 312-331.
70. Ostergaard, S., Olsson, L. and Nielsen, J. (2000) Metabolic engineering of Saccharomyces cerevisiae. Microbiology and Molecular Biology Reviews 64, 34-50.
71. Outlaw, J., Collins, K.J. and Duffield, J.A. (2005) Agriculture as a Producer and Consumer of Energy. CABI Publishing, Wallingford, UK, 345 pp.
72. Palmqvist, E. and Hähn-Hägerdal, B. (2000) Fermentation of lignocellulosic hydrolysates II: inhibitors and mechanisms of inhibition. Bioresource Technology 74, 25-33.
73. Palmqvist, E., Almeida, J. and Hähn-Hägerdal, B. (1999) Influence of furfural on anaerobic glycolytic kinetics of Saccharomyces cerevisiae in batch culture. Biotechnology and Bioengineering 62, 447-454.
74. Peterson, J., Umayam, L.A., Dickinson, T., Hickey, E.K. and White, O. (2001) The comprehensive microbial resource. Nucleic Acids Research 29, 123-125.
75. Petersson, A., Almeida, J.R.M., Modig, T., Karhumaa, K., Hähn-Hägerdal, B., Gorwa-Grauslund, M.F. and Liden, G. (2006) A 5-hyfroxymethyl furfural reducing enzyme encoded by the Saccharomyces cerevisiae ADH6 gene conveys HMF tolerance. Yeast 23, 455-464.
76. Saha, B. (2003) Hemicellulose bioconversion. Journal of Industrial Microbiology and Biotechnology 30, 279-291.
77. Sanchez, B. and Bautista, J. (1988) Effects of furfural and 5-hydroxymethylfurfrual on the fermentation of Saccharomyces cerevisiae and biomass production from Candida guilliermondii. Enzyme and Microbial Technology 10, 315-318.
78. Schena, M., Shalon, D., Davis, R.W. and Brown, P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470.
79. Sonderegger, M. and Sauer, U. (2003) Evolutionary engineering of Saccharomyces cerevisiae for anaerobic growth on xylose. Applied and Environmental Microbiology 69, 1990-1998.
80. Song, M. and Liu, Z.L. (2007) A linear discrete dynamic system model for temporal gene interaction and regulatory network influence in response to bioethanol conversion inhibitor HMF for ethanologenic yeast. Lecture Notes in Bioinformatics 4532, 77-95.
81. Taherzadeh, M., Gustafsson, L. and Niklasson, C. (2000a) Physiological effects of 5-hydroxymethylfurfural on Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 53, 701-708.
82. Taherzadeh, M., Niklasson, C. and Liden, G. (2000b) On-line control of fed-batch fermentation of dilute-acid hydrolysates. Biotechnology and Bioengineering 69, 330-338.
83. Teixeira, M., Monteirom C.P., Jain, P., Tenreiro, S., Fernandes, A.R., Mira, N.P., Alenquer, M., Freitas, A.T., Oliveira, A.L. and Sá-Correia, I. (2006) The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Research 34, D446-D451.
84. The Gene Ontology Consortium (2000) Nature Genetics 25, 25-29. Villa, G.P., Bartroli, R., Lopez, R., Guerra, M., Enrique, M., Penas, M., Rodriquez, E., Redondo, D., Iglesias, I. and Diaz, M. (1992) Microbial transformation of furfural to furfuryl alcohol by Saccharomyces cerevisiae. Acta Biotechnologia 12, 509-512.
85. Wahlbom, C.F. and Hähn-Hägerdal, B. (2002) Furfural, 5-hydroxymethylfurfrual, and acetone act as external electron acceptors during anaerobic fermentation of xylose in recombinant Saccharomyces cerevisiae. Biotechnology and Bioengineering 78, 172-178.
86. Wheals, A.E., Basso, L.C., Alves, D.M. and Amorim, H.V. (1999) Fuel ethanol after 25 years. Trends in Biotechnology 17, 482-487.
87. YEAst Search for Transcriptional Regulators and Consensus Tracking (YEASTRACT)(2006) http://www.yeastract.com (accessed 12 September 2006).
88. Zaldivar, J., Nielsen, J. and Olsson, L. (2001) Fuel ethanol production from lignocellulose: a challenge for metabolic engineering and process integration. Applied Microbiology and Biotechnology 56, 17-34.
89. Zhang, W., Needham, D.L., Coffin, M., Rooker, A., Hurban, P., Tanzer, M.M. and Shuster, J.R. (2003) Microarray analysis of the metabolic response of Saccharomyces cerevisiae to organic solvent dimethyl sulfoxide. Journal of Industrial Microbiology and Biotechnology 30, 57-69.