Abstract
Enzyme cost is a major impediment to second-generation (2G) cellulosic ethanol production. One strategy to reduce enzyme cost is to engineer enzyme production capacity in a fermentative microorganism to enable consolidated bio-processing (CBP). Ideally, a strain with a high secretory phenotype, high fermentative capacity as well as an innate robustness to bioethanol-specific stressors, including tolerance to products formed during pre-treatment and fermentation of lignocellulosic substrates should be used. Saccharomyces cerevisiae is a robust fermentative yeast but has limitations as a potential CBP host, such as low heterologous protein secretion titers. In this study, we evaluated natural S. cerevisiae isolate strains for superior secretion activity and other industrially relevant characteristics needed during the process of lignocellulosic ethanol production. Individual cellulases namely Saccharomycopsis fibuligera Cel3A (β-glucosidase), Talaromyces emersonii Cel7A (cellobiohydrolase), and Trichoderma reesei Cel5A (endoglucanase) were utilized as reporter proteins. Natural strain YI13 was identified to have a high secretory phenotype, demonstrating a 3.7- and 3.5-fold higher Cel7A and Cel5A activity, respectively, compared to the reference strain S288c. YI13 also demonstrated other industrially relevant characteristics such as growth vigor, high ethanol titer, multi-tolerance to high temperatures (37 and 40 °C), ethanol (10 % w/v), and towards various concentrations of a cocktail of inhibitory compounds commonly found in lignocellulose hydrolysates. This study accentuates the value of natural S. cerevisiae isolate strains to serve as potential robust and highly productive chassis organisms for CBP strain development.
Similar content being viewed by others
References
Ali N, Athar MA, Khan YH, Idrees M, Ahmad D (2014) Regulation and improvement of cellulase production: recent advances. Nat Resour 5:857–863
Basso LC, De Amorim HV, De Oliveira AJ, Lopes ML (2008) Yeast selection for fuel ethanol production in Brazil. FEMS Yeast Res 8:1155–1163
Blaauw D (2015) Crossbreeding of natural Saccharomyces cerevisiae strains for enhanced bio-ethanol production. Master dissertation. Stellenbosch University, South Africa
Bull VH, Thiede B (2012) Proteome analysis of tunicamycin-induced ER stress. Electrophoresis 33:1814–1123
Carreto L, Eiriz MF, Gomes AC, Pereira PM, Schuller D, Santos MA (2008) Comparative genomics of wild type yeast strains unveils important genome diversity. BMC Genomics 9:17
Cavalieri D, Townsend JP, Hartl DL (2000) Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proc Natl Acad Sci U S A 97:12369–12374
Cho KM, Yoo YJ, Kang HS (1999) δ-integration of endo/exo-glucanase and β-glucosidase genes into the yeast chromosomes for direct conversion of cellulose to ethanol. Enzym Microb Technol 25:23–30
Da Silva-Filho EA, Brito dos Santos SK, Resende ADM, De Morais JOF, De Morais MA, Ardaillon Simões D (2005) Yeast population dynamics of industrial fuel-ethanol fermentation process assessed by PCR-fingerprinting. Antonie Van Leeuwenhoek 88:13–23
De Baetselier A, Vasavada A, Dohet P, Ha-Thi V, De Beukelaer M, Erpicum T, De Clerck L, Hanotier J, Rosenberg S (1991) Fermentation of a yeast producing Aspergillus niger glucose oxidase: scale-up, purification and characterization of the recombinant enzyme. Nat Biotechnol 9:559–561
Demeke MM, Dumortier F, Li Y, Broeckx T, Foulquié-Moreno MR, Thevelein JM (2013) Combining inhibitor tolerance and D-xylose fermentation in industrial Saccharomyces cerevisiae for efficient lignocellulose-based bioethanol production. Biotechnol Biofuels 6:120
Den Haan R, Rose SH, Lynd LR, Van Zyl WH (2007) Hydrolysis and fermentation of amorphous cellulose by recombinant Saccharomyces cerevisiae. Metab Eng 9:87–94
Den Haan R, Kroukamp H, Van Zyl J-HD, Van Zyl WH (2013) Cellobiohydrolase secretion by yeast: current state and prospects for improvement. Process Biochem 48:1–12
Den Haan R, Van Rensburg E, Rose SH, Görgens JF, Van Zyl WH (2015) Progress and challenges in the engineering of non-cellulolytic microorganisms for consolidated bioprocessing. Curr Opin Biotechnol 33:32–38
Dumortier H, Lacotte S, Pastorin G, Marega R, Wu W, Bonifazi D, Briand J-P, Prato M, Muller S, Bianco A (2006) Functionalized carbon nanotubes are non-cytotoxic and preserve the functionality of primary immune cells. Nano Lett 6:1522–1528
Favaro L, Basaglia M, Trento A, Van Rensburg E, García-Aparicio M, Van Zyl WH, Casella S (2013) Exploring grape marc as trove for new thermotolerant and inhibitor-tolerant Saccharomyces cerevisiae strains for second-generation bioethanol production. Biotechnol Biofuels 6:168
Favaro L, Viktor MJ, Rose SH, Viljoen-Bloom M, Van Zyl WH, Basaglia M, Cagnin L, Casella S (2015) Consolidated bioprocessing of starchy substrates into ethanol by industrial Saccharomyces cerevisiae strains secreting fungal amylases. Biotechnol Bioeng 112:1751–1760
Fay JC, McCullough HL, Sniegowski PD, Eisen MB (2004) Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biol 5:26
Gasser B, Saloheimo M, Rinas U, Dragosits M, Rodríguez-Carmona E, Baumann K, Giuliani M, Parrilli E, Branduardi P, Lang C, Porro D, Ferrer P, Tutino ML, Mattanovich D, Villaverde A (2008) Protein folding and conformational stress in microbial cells producing recombinant proteins: a host comparative overview. Microb Cell Factories 7:11
Gurgu L, Lafraya Á, Polaina J, Marín-Navarro J (2011) Fermentation of cellobiose to ethanol by industrial Saccharomyces strains carrying the β-glucosidase gene (BGL1) from Saccharomycopsis fibuligera. Bioresource Technol 102:5229–5236
Harkness TAA, Arnason TG (2014) A simplified method for measuring secreted invertase activity in Saccharomyces cerevisiae. Biochem Pharmacol (Los Angel) 3:151
Hoffman EP, Brown RH, Kunkel LM (1987) Dystrophin: the protein product of the Duchenne muscular dystrophy locus. Cell 51:919–928
Hubmann G, Foulquié-moreno MR, Nevoigt E, Duitama J, Meurens N, Pais TM, Mathé L, Thi H, Nguyen T, Swinnen S (2013) Quantitative trait analysis of yeast biodiversity yields novel gene tools for metabolic engineering. Metab Eng 17:68–81
Idiris A, Tohda H, Kumagai H, Takegawa K (2010) Engineering of protein secretion in yeast: strategies and impact on protein production. Appl Microbiol Biotechnol 86:403–417
Ilmén M, Den Haan R, Brevnova E, McBride J, Wiswall E, Froehlich A, Koivula A, Voutilainen SP, Siika-Aho M, La Grange DC, Thorngren N, Ahlgren S, Mellon M, Deleault K, Rajgarhia V, Van Zyl WH, Penttilä M (2011) High level secretion of cellobiohydrolases by Saccharomyces cerevisiae. Biotechnol Biofuels 4:30
Jin M, Sarks C, Gunawan C, Bice BD, Simonett SP, Avanasi Narasimhan R, Willis LB, Dale BE, Balan V, Sato TK (2013) Phenotypic selection of a wild Saccharomyces cerevisiae strain for simultaneous saccharification and co-fermentation of AFEX™ pretreated corn Stover. Biotechnol Biofuels 6:108
Kanik-Ennulat C, Montalvo E, Neff N (1995) Sodium orthovanadate-resistant mutants of Saccharomyces cerevisiae show defects in golgi-mediated protein glycosylation, sporulation and detergent resistance. Genetics 140:933–943
Koppram R, Albers E, Olsson L (2012) Evolutionary engineering strategies to enhance tolerance of xylose utilizing recombinant yeast to inhibitors derived from spruce biomass. Biotechnol Biofuels 5:32
Kricka W, Fitzpatrick J, Bond U (2015) Challenges for the production of bioethanol from biomass using recombinant yeasts. Adv Appl Microbiol 92:89–125
Kroukamp H (2015) Improving the protein secretion capacity of Saccharomyces cerevisiae with strain engineering. Doctoral Dissertation. Stellenbosch University, South Africa
Kroukamp H, Den Haan R, Van Wyk N, Van Zyl WH (2013) Overexpression of native PSE1 and SOD1 in Saccharomyces cerevisiae improved heterologous cellulase secretion. Appl Energy 102:150–156
Kvitek DJ, Will JL, Gasch AP (2008) Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PLoS Genet 4:e1000223
La Grange DC, Den Haan R, Van Zyl WH (2010) Engineering cellulolytic ability into bioprocessing organisms. Appl Microbiol Biotechnol 87:1195–1208
Lambertz C, Garvey M, Klinger J, Heesel D, Klose H, Fischer R, Commandeur U (2014) Challenges and advances in the heterologous expression of cellulolytic enzymes: a review. Biotechnol Biofuels 7:135
Liu Z (2012) Doctoral Dissertation. In: Metabolic engineering of recombinant protein productions by Saccharomyces cerevisiae. Chalmers University, Sweden
Liu Z, Österlund T, Hou J, Petranovic D, Nielsen J (2013) Anaerobic α-amylase production and secretion with fumarate as the final electron acceptor in Saccharomyces cerevisiae. Appl Environ Microbiol 79:2962–2967
Martin C, Jönsson LJ (2003) Comparison of the resistance of industrial and laboratory strains of Saccharomyces and Zygosaccharomyces to lignocellulose-derived fermentation inhibitors. Enzym Microb Technol 32:386–395
Mattanovich D, Gasser B, Hohenblum H, Sauer M (2004) Stress in recombinant protein producing yeasts. J Biotechnol 113:121–135
McBride JEE, Deleault KM, Lynd LR, Pronk JT (2007) Recombinant yeast strains expressing tethered cellulase enzymes. Patent PCT/US2007/085390
Meinander N, Zacchi G, Hahn-Hägerdal B (1996) A heterologous reductase affects the redox balance of recombinant Saccharomyces cerevisiae. Microbiology 142:165–172
Mukherjee V, Steensels J, Lievens B, Van de Voorde I, Verplaetse A, Aerts G, Willems KA, Thevelein JM, Verstrepen KJ, Ruyters S (2014) Phenotypic evaluation of natural and industrial Saccharomyces yeasts for different traits desirable in industrial bioethanol production. Appl Microbiol Biotechnol 98:9483–9498
Njokweni AP, Rose SH, Van Zyl WH (2012) Fungal β-glucosidase expression in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 39:1445–1452
Olson DG, McBride JE, Shaw AJ, Lynd LR (2012) Recent progress in consolidated bioprocessing. Curr Opin Biotechnol 23:396–405
Pretorius IS (2000) Tailoring wine yeast for the new millennium: novel approaches to the ancient art of winemaking. Yeast 16:675–729
Ruyters S, Mukherjee V, Verstrepen KJ, Thevelein JM, Willems KA, Lievens B (2014) Assessing the potential of wild yeasts for bioethanol production. J Ind Microbiol Biotechnol 42:39–48
Sambrook J, Russel DB (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
Schuller D, Casal M (2007) The genetic structure of fermentative vineyard-associated Saccharomyces cerevisiae populations revealed by microsatellite analysis. Antonie Van Leeuwenhoek 91:137–150
Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, Johansson M, Jaschob D, Graczyk B, Shulman NJ, Wakefield J, Cooper SJ, Fields S, Noble WS, Muller EGD, Davis TN, Dunham MJ, Maccoss MJ, Akey JM (2013) Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Genome Res 23:1496–1504
Steensels J, Snoek T, Meersman E, Nicolino MP, Voordeckers K, Verstrepen KJ (2014) Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol Rev 38:947–995
Swinnen S, Thevelein JM, Nevoigt E (2012) Genetic mapping of quantitative phenotypic traits in Saccharomyces cerevisiae. FEMS Yeast Res 12:215–227
Teste MA, Duquenne M, François JM, Parrou J-L (2009) Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae. BMC Mol Biol 10:99
Van Zyl JHD, Den Haan R, Van Zyl WH (2014) Over-expression of native Saccharomyces cerevisiae exocytic SNARE genes increased heterologous cellulase secretion. Appl Microbiol Biotechnol 98:5567–5578
Warringer J, Zörgö E, Cubillos FA, Zia A, Gjuvsland A, Simpson JT, Forsmark A, Durbin R, Omholt SW, Louis EJ, Liti G, Moses A, Blomberg A (2011) Trait variation in yeast is defined by population history. PLoS Genet 7:e1002111
Van Der Westhuizen TJ, Augustyn OPH, Pretorius IS (2000) Geographical distribution of indigenous Saccharomyces cerevisiae strains isolated from vineyards in the coastal regions of the western cape in South Africa. S Afr J Enol Vitic 21:3–9
Van Rooyen R, Hahn-Hägerdal B, La Grange DC, Van Zyl WH (2005) Construction of cellobiose-growing and fermenting Saccharomyces cerevisiae strains. J Biotechnol 120:284–295
Yamada R, Tanaka T, Ogino C, Kondo A (2010) Gene copy number and polyploidy on products formation in yeast. Appl Microbiol Biotechnol 88:849–857
Zakrzewska A, van Eikenhorst G, Burggraaff JE, Vis DJ, Hoefsloot H, Delneri D, Oliver SG, Brul S, Smits GJ (2011) Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness. Mol Biol Cell 22:4435–4446
Acknowledgments
The authors would like to thank the National Research Foundation (NRF) for financial support to the Chair of Energy Research: Biofuels and other clean alternative fuels (grant number UID 86423 awarded to WHvZ). The authors would like to thank Dr. Neil Jolly from ARC Infruitec-Nietvoorbij, Stellenbosch South Africa for making the natural S. cerevisiae strains available for this study.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
This article does not contain any studies with human participants or animals performed by any of the authors.
Conflict of interest
The authors declare that they have no conflict of interest.
Electronic supplementary material
ESM 1
(PDF 657 kb)
Rights and permissions
About this article
Cite this article
Davison, S.A., den Haan, R. & van Zyl, W.H. Heterologous expression of cellulase genes in natural Saccharomyces cerevisiae strains. Appl Microbiol Biotechnol 100, 8241–8254 (2016). https://doi.org/10.1007/s00253-016-7735-x
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-016-7735-x