Engineering Saccharomyces pastorianus for the co-utilisation of xylose and cellulose from biomass

Microbial Cell Factories

Volumn 14, Issue 1, 2015, Pages

  Kricka, William ^a   James, Tharappel C ^a   Fitzpatrick, James ^a   Bond, Ursula ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

Author keywords

Biomass; Co utilisation of xylose and cellulose; S. pastorianus; Spent grain fermentations

Indexed keywords

BETA GLUCOSIDASE; BETA GLUCOSIDASE 1; CELLOBIOHYDROLASE 2; CELLULASE; CELLULOSE; CELLULOSE 1,4 BETA CELLOBIOSIDASE; GLUCAN SYNTHASE; GLUCAN SYNTHASE 2; HEMICELLULOSE; LIGNOCELLULOSE; NICOTINAMIDE ADENINE DINUCLEOTIDE; OXIDOREDUCTASE; RECOMBINANT ENZYME; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; UNCLASSIFIED DRUG; XYLITOL; XYLITOL DEHYDROGENASE; XYLOSE; XYLOSE ISOMERASE; XYLOSE REDUCTASE; XYLULOSE KINASE;

ALCOHOL PRODUCTION; ARTICLE; BIOENGINEERING; BIOMASS; BIOMASS FERMENTATION; CARBOHYDRATE METABOLISM; CATABOLISM; CELL DENSITY; CELL GROWTH; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME SYNTHESIS; FUNGAL CELL CULTURE; FUNGAL GENE; FUNGAL STRAIN; GENE EXPRESSION; GENE OVEREXPRESSION; GENETIC CODE; GLUCOSE INTAKE; GRASS; GROWTH INHIBITION; HYDROLYSIS; HYPOCREA JECORINA; INDUSTRIAL WASTE; MACROPUS GIGANTEUS; MISCANTHUS SINENSIS; NONHUMAN; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES PASTORIANUS; TETRAPLOIDY; XDH1 GENE; XKS1 GENE; XYL1 GENE; YEAST; BACTERIUM; GENETIC ENGINEERING; GENETICS; METABOLISM; PROCEDURES; SACCHAROMYCES;

HYPOCREA JECORINA; MISCANTHUS SINENSIS; SACCHAROMYCES PASTORIANUS;

BACTERIA; BIOMASS; CELLULOSE; GENETIC ENGINEERING; SACCHAROMYCES; XYLOSE;

EID: 84928807849     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-015-0242-4     Document Type: Article

References (64)

1. Lennartsson PR, Erlandsson P, Taherzadeh MJ. Integration of the first and second generation bioethanol processes and the importance of by-products. Bioresour Technol. 2014;165:3-8.
2. Kricka W, Fitzpatrick J, Bond U. Metabolic engineering of yeasts by heterologous enzyme production for degradation of cellulose and hemicellulose from biomass: a perspective. Front Microbiol. 2014;5:174.
3. Mosier N, Wyman C, Dale B, Elander R, Lee YY, Holtzapple M, et al. Features of promising technologies for pretreatment of lignocellulosic biomass. Bioresour Technol. 2005;96:673-86.
4. Chandel AK, Singh OV. Weedy lignocellulosic feedstock and microbial metabolic engineering: advancing the generation of 'Biofuel'. Appl Microbiol Biotechnol. 2011;89:1289-303.
5. Ruel K, Nishiyama Y, Joseleau JP. Crystalline and amorphous cellulose in the secondary walls of Arabidopsis. Plant Sci. 2012;193-194:48-61.
6. Peng F, Peng P, Xu F, Sun RC. Fractional purification and bioconversion of hemicelluloses. Biotechnol Adv. 2012;30:879-903.
7. Madhavan A, Srivastava A, Kondo A, Bisaria VS. Bioconversion of lignocellulose-derived sugars to ethanol by engineered Saccharomyces cerevisiae. Crit Rev Biotechnol. 2012;32:22-48.
8. Weng JK, Li X, Bonawitz ND, Chapple C. Emerging strategies of lignin engineering and degradation for cellulosic biofuel production. Curr Opin Biotechnol. 2008;19:166-72.
9. Chiaramonti D, Prussi M, Ferrero S, Oriani L, Ottonello P, Torre P, et al. Review of pretreatment processes for lignocellulosic ethanol production, and development of an innovative method. Biomass and Bioenergy. 2012;46:25-35.
10. Hou X. Anaerobic xylose fermentation by Spathaspora passalidarum. Appl Microbiol Biotechnol. 2012;94:205-14.
11. Urbina H, Frank R, Blackwell M. Scheffersomyces cryptocercus: a new xylose-fermenting yeast associated with the gut of wood roaches and new combinations in the Sugiyamaella yeast clade. Mycologia. 2013;105:650-60.
12. Wanlapa L, Ancharida A, Motofumi S, Moriya O, Somboon T. Diversity and Fermentation Products of Xylose-Utilizing Yeasts Isolated from Buffalo Feces in Thailand. Microb Environ. 2013;28:354-60.
13. Zhang G, Lin Y, He P, Li L, Wang Q, Ma Y. Characterization of the sugar alcohol-producing yeast Pichia anomala. J Ind Microbiol Biotechnol. 2014;41:41-8.
14. Nakatani Y, Yamada R, Ogino C, Kondo A. Synergetic effect of yeast cell-surface expression of cellulase and expansin-like protein on direct ethanol production from cellulose. Microb Cell Fact. 2013;12:66.
15. Wenger J, Schwartz K, Sherlock G. Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae. PLoS genetics 2010, 6. 13;6(5):e1000942. doi: 10.1371/journal.pgen.1000942.
16. Schwartz K, Wenger JW, Dunn B, Sherlock G. APJ1 and GRE3 homologs work in concert to allow growth in xylose in a natural Saccharomyces sensu stricto hybrid yeast. Genetics. 2012;191:621-32.
17. Bera AK, Ho NW, Khan A, Sedlak M. A genetic overhaul of Saccharomyces cerevisiae 424A(LNH-ST) to improve xylose fermentation. J Ind Microbiol Biotechnol. 2011;38:617-26.
18. Matsushika A, Inoue H, Murakami K, Takimura O, Sawayama S. Bioethanol production performance of five recombinant strains of laboratory and industrial xylose-fermenting Saccharomyces cerevisiae. Bioresour Technol. 2009;100:2392-8.
19. Kato H, Matsuda F, Yamada R, Nagata K, Shirai T, Hasunuma T, et al. Cocktail delta-integration of xylose assimilation genes for efficient ethanol production from xylose in Saccharomyces cerevisiae. J Biosci Bioeng. 2013;116:333-6.
20. Karhumaa K, Fromanger R, Hahn-Hagerdal B, Gorwa-Grauslund MF. High activity of xylose reductase and xylitol dehydrogenase improves xylose fermentation by recombinant Saccharomyces cerevisiae. Appl Microbiol Biotechnol. 2007;73:1039-46.
21. Hector RE, Dien BS, Cotta MA, Mertens JA. Growth and fermentation of D-xylose by Saccharomyces cerevisiae expressing a novel D-xylose isomerase originating from the bacterium Prevotella ruminicola TC2-24. Biotechnol Biofuels. 2013;6:84.
22. de Figueiredo VL, de Mello VM, Reis VC, Bon EP, Goncalves Torres FA, Neves BC, et al. Functional expression of Burkholderia cenocepacia xylose isomerase in yeast increases ethanol production from a glucose-xylose blend. Bioresour Technol. 2013;128:792-6.
23. Tanino T, Hotta A, Ito T, Ishii J, Yamada R, Hasunuma T, et al. Construction of a xylose-metabolizing yeast by genome integration of xylose isomerase gene and investigation of the effect of xylitol on fermentation. Appl Microbiol Biotechnol. 2010;88:1215-21.
24. Walfridsson M, Bao X, Anderlund M, Lilius G, Bulow L, Hahn-Hagerdal B. Ethanolic fermentation of xylose with Saccharomyces cerevisiae harboring the Thermus thermophilus xylA gene, which expresses an active xylose (glucose) isomerase. Appl Environ Microbiol. 1996;62:4648-51.
25. Kuyper M, Winkler AA, van Dijken JP, Pronk JT. Minimal metabolic engineering of Saccharomyces cerevisiae for efficient anaerobic xylose fermentation: a proof of principle. FEMS Yeast Res. 2004;4:655-64.
26. Xiong M, Chen G, Barford J. Alteration of xylose reductase coenzyme preference to improve ethanol production by Saccharomyces cerevisiae from high xylose concentrations. Bioresour Technol. 2011;102:9206-15.
27. Ma TY, Lin TH, Hsu TC, Huang CF, Guo GL, Hwang WS. An improved method of xylose utilization by recombinant Saccharomyces cerevisiae. J Ind Microbiol Biotechnol. 2012;39:1477-86.
28. Diao L, Liu Y, Qian F, Yang J, Jiang Y, Yang S. Construction of fast xylose-fermenting yeast based on industrial ethanol-producing diploid Saccharomyces cerevisiae by rational design and adaptive evolution. BMC Biotechnol. 2013;13:110.
29. Lee SM, Jellison T, Alper HS. Directed evolution of xylose isomerase for improved xylose catabolism and fermentation in the yeast Saccharomyces cerevisiae. Appl Environ Microbiol. 2012;78:5708-16.
30. Demeke MM, Dietz H, Li Y, Foulquie-Moreno MR, Mutturi S, Deprez S, et al. Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering. Biotechnol Biofuels. 2013;6:89.
31. Baek SH, Kim S, Lee K, Lee JK, Hahn JS. Cellulosic ethanol production by combination of cellulase-displaying yeast cells. Enzyme Microb Technol. 2012;51:366-72.
32. Kim S, Baek SH, Lee K, Hahn JS. Cellulosic ethanol production using a yeast consortium displaying a minicellulosome and beta-glucosidase. Microb Cell Fact. 2013;12:14.
33. Yamada R, Taniguchi N, Tanaka T, Ogino C, Fukuda H, Kondo A. Direct ethanol production from cellulosic materials using a diploid strain of Saccharomyces cerevisiae with optimized cellulase expression. Biotechnol Biofuels. 2011;4:8.
34. Yanase S, Yamada R, Kaneko S, Noda H, Hasunuma T, Tanaka T, et al. Ethanol production from cellulosic materials using cellulase-expressing yeast. Biotechnol J. 2010;5:449-55.
35. Fitzpatrick J, Kricka W, James TC, Bond U. Expression of three Trichoderma reesei cellulase genes in Saccharomyces pastorianus for the development of a two-step process of hydrolysis and fermentation of cellulose. J Appl Microbiol. 2014;117:96-108.
36. Den Haan R, Rose SH, Lynd LR, van Zyl WH. Hydrolysis and fermentation of amorphous cellulose by recombinant Saccharomyces cerevisiae. Metab Eng. 2007;9:87-94.
37. Goyal G, Tsai SL, Madan B, DaSilva NA, Chen W. Simultaneous cell growth and ethanol production from cellulose by an engineered yeast consortium displaying a functional mini-cellulosome. Microb Cell Fact. 2011;10:89.
38. Fujita Y, Ito J, Ueda M, Fukuda H, Kondo A. Synergistic saccharification, and direct fermentation to ethanol, of amorphous cellulose by use of an engineered yeast strain codisplaying three types of cellulolytic enzyme. Appl Environ Microbiol. 2004;70:1207-12.
39. Wen F, Sun J, Zhao H. Yeast surface display of trifunctional minicellulosomes for simultaneous saccharification and fermentation of cellulose to ethanol. Appl Environ Microbiol. 2010;76:1251-60.
40. Saitoh S, Hasunuma T, Tanaka T, Kondo A. Co-fermentation of cellobiose and xylose using beta-glucosidase displaying diploid industrial yeast strain OC-2. Appl Microbiol Biotechnol. 2010;87:1975-82.
41. Ha SJ, Galazka JM, Kim SR, Choi JH, Yang X, Seo JH, et al. Engineered Saccharomyces cerevisiae capable of simultaneous cellobiose and xylose fermentation. Proc Natl Acad Sci U S A. 2011;108:504-9.
42. Saitoh S, Tanaka T, Kondo A. Co-fermentation of cellulose/xylan using engineered industrial yeast strain OC-2 displaying both beta-glucosidase and beta-xylosidase. Appl Microbiol Biotechnol. 2011;91:1553-9.
43. Bond U. The Genomes of Lager Yeasts. In: Laskin AI, Sariaslani S, Gadd GM, editors. Adv Appl Microbiol, vol. 69. Burlington: Academic Press; 2009. p. 159-82.
44. Libkind D, Hittinger CT, Valerio E, Goncalves C, Dover J, Johnston M, et al. Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proc Natl Acad Sci U S A. 2011;108:14539-44.
45. Monerawela C, James TC, Wolfe KH, Bond U. Loss of lager specific genes and subtelomeric regions define two different Saccharomyces cerevisiae lineages for Saccharomyces pastorianus Group I and II strains. FEMS Yeast Res. 2015;15:1-11.
46. Bettiga M, Hahn-Hagerdal B, Gorwa-Grauslund MF. Comparing the xylose reductase/xylitol dehydrogenase and xylose isomerase pathways in arabinose and xylose fermenting Saccharomyces cerevisiae strains. Biotechnol Biofuels. 2008;1:16.
47. Karhumaa K, Garcia Sanchez R, Hahn-Hagerdal B, Gorwa-Grauslund MF. Comparison of the xylose reductase-xylitol dehydrogenase and the xylose isomerase pathways for xylose fermentation by recombinant Saccharomyces cerevisiae. Microb Cell Fact. 2007;6:5.
48. Bajwa PK, Ho CY, Chan CK, Martin VJ, Trevors JT, Lee H. Transcriptional profiling of Saccharomyces cerevisiae T2 cells upon exposure to hardwood spent sulphite liquor: comparison to acetic acid, furfural and hydroxymethylfurfural. Antonie Van Leeuwenhoek. 2013;103:1281-95.
49. Hasunuma T, Sanda T, Yamada R, Yoshimura K, Ishii J, Kondo A. Metabolic pathway engineering based on metabolomics confers acetic and formic acid tolerance to a recombinant xylose-fermenting strain of Saccharomyces cerevisiae. Microb Cell Fact. 2011;10:2.
50. Hasunuma T, Ismail KS, Nambu Y, Kondo A. Co-expression of TAL1 and ADH1 in recombinant xylose-fermenting Saccharomyces cerevisiae improves ethanol production from lignocellulosic hydrolysates in the presence of furfural. J Biosci Bioeng. 2014;117:165-9.
51. Li BZ, Yuan YJ. Transcriptome shifts in response to furfural and acetic acid in Saccharomyces cerevisiae. Appl Microbiol Biotechnol. 2010;86:1915-24.
52. Zhuang J, Liu Y, Wu Z, Sun Y, Lin L. Hydrolysis of wheat straw hemicellulose and detoxification of the hydrolysate for xylitol production. Bio-Resources. 2009;4:674-86.
53. Chandel AK, Kapoor RK, Singh A, Kuhad RC. Detoxification of sugarcane bagasse hydrolysate improves ethanol production by Candida shehatae NCIM 3501. Bioresour Technol. 2007;98:1947-50.
54. Grzenia DL, Wickramasinghe SR, Schell DJ. Fermentation of reactive-membrane-extracted and ammonium-hydroxide-conditioned dilute-acid-pretreated corn stover. Appl Biochem Biotechnol. 2012;166:470-8.
55. Koppram R, Albers E, Olsson L. Evolutionary engineering strategies to enhance tolerance of xylose utilizing recombinant yeast to inhibitors derived from spruce biomass. Biotechnol Biofuels. 2012;5:32.
56. Heer D, Sauer U. Identification of furfural as a key toxin in lignocellulosic hydrolysates and evolution of a tolerant yeast strain. Microb Biotechnol. 2008;1:497-506.
57. Wallace-Salinas V, Gorwa-Grauslund MF. Adaptive evolution of an industrial strain of Saccharomyces cerevisiae for combined tolerance to inhibitors and temperature. Biotechnol Biofuels. 2013;6:151.
58. Almario MP, Reyes LH, Kao KC. Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass. Biotechnol Bioeng. 2013;110:2616-23.
59. James TC, Usher J, Campbell S, Bond U. Lager yeasts possess dynamic genomes that undergo rearrangements and gene amplification in response to stress. Curr Genet. 2008;53:139-52.
60. Ekberg J, Rautio J, Mattinen L, Vidgren V, Londesborough J, Gibson BR. Adaptive evolution of the lager brewing yeast Saccharomyces pastorianus for improved growth under hyperosmotic conditions and its influence on fermentation performance. FEMS Yeast Res. 2013;13:335-49.
61. Wei N, Quarterman J, Kim SR, Cate JH, Jin YS. Enhanced biofuel production through coupled acetic acid and xylose consumption by engineered yeast. Nat Commun. 2013;4:2580.
62. Richardson SM, Wheelan SJ, Yarrington RM, Boeke JD. GeneDesign: rapid, automated design of multikilobase synthetic genes. Genome Res. 2006;16:550-6.
63. Jansen G, Wu C, Schade B, Thomas DY, Whiteway M. Drag&Drop cloning in yeast. Gene. 2005;344:43-51.
64. Taxis C, Knop M. System of centromeric, episomal, and integrative vectors based on drug resistance markers for Saccharomyces cerevisiae. Biotechniques. 2006;40:73-8.