Towards efficient bioethanol production from agricultural and forestry residues: Exploration of unique natural microorganisms in combination with advanced strain engineering

Bioresource Technology

Volumn 215, Issue , 2016, Pages 84-91

  Zhao, Xinqing ^a   Xiong, Liang ^b   Zhang, Mingming ^b   Bai, Fengwu ^a,b  

^a Shanghai Jiao Tong University   (China)

^b DALIAN UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Agricultural residues; Cellulase; Fuel ethanol; Saccharomyces cerevisiae; Stress tolerance; Xylose

Indexed keywords

AGRICULTURAL WASTES; AGRICULTURE; ETHANOL; ETHANOL FUELS; FORESTRY; FOSSIL FUELS; FUELS; MICROORGANISMS; SUGARS; TIMBER; WASTE UTILIZATION; XYLOSE; YEAST;

BIO-ETHANOL PRODUCTION; BIOFUELS PRODUCTION; CELLULASE; CELLULASE PRODUCTION; FUEL ETHANOL; LIGNOCELLULOSIC FEEDSTOCKS; STRAIN ENGINEERING; STRESS TOLERANCE;

BIOETHANOL;

BIOETHANOL; BIOFUEL; CARBOHYDRATE; CELLULASE; FOSSIL FUEL; GLUCOSE; LIGNOCELLULOSE; XYLOSE; ALCOHOL; INDUSTRIAL WASTE; LIGNIN;

AGRICULTURAL TECHNOLOGY; BACTERIUM; BIOENGINEERING; BIOFUEL; EFFICIENCY MEASUREMENT; ENVIRONMENTAL STRESS; ETHANOL; INDUSTRIAL WASTE; MICROORGANISM; PLANT RESIDUE; SUGAR; TOLERANCE; WASTE TECHNOLOGY;

ALCOHOL PRODUCTION; ARTICLE; BIOMASS; FERMENTATION; FORESTRY; GENETIC ENGINEERING; HYDROLYSIS; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; STRESS; AGRICULTURE; BIOSYNTHESIS; BIOTECHNOLOGY; INDUSTRIAL WASTE; METABOLIC ENGINEERING; METABOLISM; MICROBIOLOGY; PROCEDURES;

SACCHAROMYCES CEREVISIAE;

AGRICULTURE; BIOFUELS; BIOTECHNOLOGY; CELLULASE; ETHANOL; FERMENTATION; FORESTRY; INDUSTRIAL MICROBIOLOGY; INDUSTRIAL WASTE; LIGNIN; METABOLIC ENGINEERING; SACCHAROMYCES CEREVISIAE;

EID: 84975270811     PISSN: 09608524     EISSN: 18732976     Source Type: Journal    
DOI: 10.1016/j.biortech.2016.03.158     Document Type: Article

References (71)

1. An J., Kwon H., Kim E., Lee Y.M., Ko H.J., Park H., Choi I.G., Kim S., Kim K.H., Kim W., Choi W. Tolerance to acetic acid is improved by mutations of the TATA-binding protein gene. Environ. Microbiol. 2015, 17:656-669.
2. Arfi Y., Shamshoum M., Rogachev I., Peleg Y., Bayer E.A. Integration of bacterial lytic polysaccharide monooxygenases into designer cellulosomes promotes enhanced cellulose degradation. Proc. Natl. Acad. Sci. USA 2014, 111:9109-9114.
3. Assareh R., Shahbani Zahiri H., Akbari Noghabi K., Aminzadeh S., Bakhshi Khaniki G. Characterization of the newly isolated Geobacillus sp. T1, the efficient cellulase-producer on untreated barley and wheat straws. Bioresour. Technol. 2012, 120:99-105.
4. Becker J., Wittmann C. Advanced biotechnology: metabolically engineered cells for the bio-based production of chemicals and fuels, materials, and health-care products. Angew. Chem. Int. Ed. Engl. 2015, 54:3328-3350.
5. Chen Y., Sheng J., Jiang T., Stevens J., Feng X., Wei N. Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae. Biotechnol. Biofuels 2016, 9:9.
6. Corrêa T.L., Dos Santos L.V., Pereira G.A. AA9 and AA10: from enigmatic to essential enzymes. Appl. Microbiol. Biotechnol. 2016, 100:9-16.
7. Demeke M.M., Dietz H., Li Y., Foulquie-Moreno M.R., Mutturi S., Deprez S., Den Abt T., Bonini B.M., Liden G., Dumortier F., Verplaetse A., Boles E., Thevelein J.M. 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.
8. Du B., Sharma L.N., Becker C., Chen S.F., Mowery R.A., van Walsum G.P., Chambliss C.K. Effect of varying feedstock-pretreatment chemistry combinations on the formation and accumulation of potentially inhibitory degradation products in biomass hydrolysates. Biotechnol. Bioeng. 2010, 107:430-440.
9. Du J., Yuan Y., Si T., Lian J., Zhao H. Customized optimization of metabolic pathways by combinatorial transcriptional engineering. Nucleic Acids Res. 2012, 40:e142.
10. Erdei B., Franko B., Galbe M., Zacchi G. Glucose and xylose co-fermentation of pretreated wheat straw using mutants of S. cerevisiae TMB3400. J. Biotechnol. 2013, 164:50-58.
11. Falkoski D.L., Guimarães V.M., de Almeida M.N., Alfenas A.C., Colodette J.L., de Rezende S.T. Chrysoporthe cubensis: a new source of cellulases and hemicellulases to application in biomass saccharification processes. Bioresour. Technol. 2013, 130:296-305.
12. Fang H., Xia L. High activity cellulase production by recombinant Trichoderma reesei ZU-02 with the enhanced cellobiohydrolase production. Bioresour. Technol. 2013, 144:693-697.
13. Gao L., Gao F., Zhang D., Zhang C., Wu G., Chen S. Purification and characterization of a new β-glucosidase from Penicillium piceum and its application in enzymatic degradation of delignified corn stover. Bioresour. Technol. 2013, 147:658-661.
14. Georgelis N., Nikolaidis N., Cosgrove D.J. Bacterial expansins and related proteins from the world of microbes. Appl. Microbiol. Biotechnol. 2015, 99:3807-3823.
15. Goldbeck R., Ramos M.M., Pereira G.A., Maugeri-Filho F. Cellulase production from a new strain Acremonium strictum isolated from the Brazilian biome using different substrates. Bioresour. Technol. 2013, 128:797-803.
16. Häkkinen M., Valkonen M.J., Westerholm-Parvinen A., Aro N., Arvas M., Vitikainen M., Penttilä M., Saloheimo M., Pakula T.M. Screening of candidate regulators for cellulase and hemicellulase production in Trichoderma reesei and identification of a factor essential for cellulase production. Biotechnol. Biofuels 2014, 7:14.
17. 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.
18. Hasunuma T., Ishii J., Kondo A. Rational design and evolutional fine tuning of Saccharomyces cerevisiae for biomass breakdown. Curr. Opin. Chem. Biol. 2015, 29:1-9.
19. He Y., Zhang J., Bao J. Acceleration of biodetoxification on dilute acid pretreated lignocellulose feedstock by aeration and the consequent ethanol fermentation evaluation. Biotechnol. Biofuels 2016, 9:19.
20. Ho D.P., Ngo H.H., Guo W. A mini review on renewable sources for biofuel. Bioresour. Technol. 2014, 169:742-749.
21. Hou J., Shen Y., Jiao C., Ge R., Zhang X., Bao X. Characterization and evolution of xylose isomerase screened from the bovine rumen metagenome in Saccharomyces cerevisiae. J. Biosci. Bioeng. 2015, 121:160-165.
22. Jin M., Gunawan C., Balan V., Lau M.W., Dale B.E. Simultaneous saccharification and co-fermentation (SSCF) of AFEX(TM) pretreated corn stover for ethanol production using commercial enzymes and Saccharomyces cerevisiae 424A(LNH-ST). Bioresour. Technol. 2012, 110:587-594.
23. Jin M., Sarks C., Gunawan C., Bice B.D., Simonett S.P., Avanasi Narasimhan R., Willis L.B., Dale B.E., Balan V., Sato T.K. Phenotypic selection of a wild Saccharomyces cerevisiae strain for simultaneous saccharification and co-fermentation of AFEX pretreated corn stover. Biotechnol. Biofuels 2013, 6:108.
24. Jönsson L.J., Martín C. Pretreatment of lignocellulose: Formation of inhibitory by-products and strategies for minimizing their effects. Bioresour. Technol. 2016, 199:103-112.
25. Kim S.R., Park Y.C., Jin Y.S., Seo J.H. Strain engineering of Saccharomyces cerevisiae for enhanced xylose metabolism. Biotechnol. Adv. 2013, 31:851-861.
26. Kim I.J., Lee H.J., Chop I.G., Kim K.H. Synergistic proteins for the enhanced enzymatic hydrolysis of cellulose by cellulase. Appl. Microbiol. Biotechnol. 2014, 98:8469-8480.
27. Kim S.K., Jin Y.S., Choi I.G., Park Y.C., Seo J.H. Enhanced tolerance of Saccharomyces cerevisiae to multiple lignocellulose-derived inhibitors through modulation of spermidine contents. Metab. Eng. 2015, 29:46-55.
28. Ko J.K., Um Y., Woo H.M., Kim K.H., Lee S.M. Ethanol production from lignocellulosic hydrolysates using engineered Saccharomyces cerevisiae harboring xylose isomerase-based pathway. Bioresour. Technol. 2016, 209:290-296.
29. 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.
30. Koppram R., Tomás-Pejó E., Xiros C., Olsson L. Lignocellulosic ethanol production at high-gravity: challenges and perspectives. Trends Biotechnol. 2014, 32:46-53.
31. Latimer L.N., Lee M.E., Medina-Cleghorn D., Kohnz R.A., Nomura D.K., Dueber J.E. Employing a combinatorial expression approach to characterize xylose utilization in Saccharomyces cerevisiae. Metab. Eng. 2014, 25:20-29.
32. Lee S.M., Jellison T., Alper H.S. Systematic and evolutionary engineering of a xylose isomerase-based pathway in Saccharomyces cerevisiae for efficient conversion yields. Biotechnol. Biofuels 2014, 7:122.
33. Lee Y., Nasution O., Choi E., Choi I.G., Kim W., Choi W. Transcriptome analysis of acetic-acid-treated yeast cells identifies a large set of genes whose overexpression or deletion enhances acetic acid tolerance. Appl. Microbiol. Biotechnol. 2015, 99:6391-6403.
34. Li Y.C., Mitsumasu K., Gou Z.X., Gou M., Tang Y.Q., Li G.Y., Wu X.L., Akamatsu T., Taguchi H., Kida K. Xylose fermentation efficiency and inhibitor tolerance of the recombinant industrial Saccharomyces cerevisiae strain NAPX37. Appl. Microbiol. Biotechnol. 2016, 100:1531-1542.
35. Liu G., Qin Y., Li Z., Qu Y. Development of highly efficient, low-cost lignocellulolytic enzyme systems in the post-genomic era. Biotechnol. Adv. 2013, 31:962-975.
36. Liu Y., Zhang G., Sun H., Sun X., Jiang N., Rasool A., Lin Z., Li C. Enhanced pathway efficiency of Saccharomyces cerevisiae by introducing thermo-tolerant devices. Bioresour. Technol. 2014, 170:38-44.
37. Liu Z.H., Qin L., Zhu J.Q., Li B.Z., Yuan Y.J. Simultaneous saccharification and fermentation of steam-exploded corn stover at high glucan loading and high temperature. Biotechnol. Biofuels 2014, 7:67.
38. Lu Y., Wang Y., Xu G., Chu J., Zhuang Y., Zhang S. Influence of high solid concentration on enzymatic hydrolysis and fermentation of steam-exploded corn stover biomass. Appl. Biochem. Biotechnol. 2010, 160:360-369.
39. Ma C., Wei X.W., Sun C.H., Zhang F., Xu J.R., Zhao X.Q., Bai F.W. Improvement of acetic acid tolerance of Saccharomyces cerevisiae using a zinc-finger-based artificial transcription factor and identification of novel genes involved in acetic acid tolerance. Appl. Microbiol. Biotechnol. 2015, 99:2441-2449.
40. Mahajan C., Basotra N., Singh S., Di Falco M., Tsang A., Chadha B.S. Malbranchea cinnamomea: A thermophilic fungal source of catalytically efficient lignocellulolytic glycosyl hydrolases and metal dependent enzymes. Bioresour. Technol. 2016, 200:55-63.
41. Meijnen J.P., Randazzo P., Foulquié-Moreno M.R., van den Brink J., Vandecruys P., Stojiljkovic M., Dumortier F., Zalar P., Boekhout T., Gunde-Cimerman N., Kokošar J., Štajdohar M., Curk T., Petrovič U., Thevelein J.M. Polygenic analysis and targeted improvement of the complex trait of high acetic acid tolerance in the yeast Saccharomyces cerevisiae. Biotechnol. Biofuels 2016, 9:5.
42. Nielsen F., Tomás-Pejó E., Olsson L., Wallberg O. Short-term adaptation during propagation improves the performance of xylose-fermenting Saccharomyces cerevisiae in simultaneous saccharification and co-fermentation. Biotechnol. Biofuels 2015, 8:219.
43. Parawira W., Tekere M. Biotechnological strategies to overcome inhibitors in lignocellulose hydrolysates for ethanol production: review. Crit. Rev. Biotechnol. 2011, 31:20-31.
44. Parreiras L.S., Breuer R.J., Avanasi Narasimhan R., Higbee A.J., La Reau A., Tremaine M., Qin L., Willis L.B., Bice B.D., Bonfert B.L., Pinhancos R.C., Balloon A.J., Uppugundla N., Liu T., Li C., Tanjore D., Ong I.M., Li H., Pohlmann E.L., Serate J., Withers S.T., Simmons B.A., Hodge D.B., Westphall M.S., Coon J.J., Dale B.E., Balan V., Keating D.H., Zhang Y., Landick R., Gasch A.P., Sato T.K. Engineering and two-stage evolution of a lignocellulosic hydrolysate-tolerant Saccharomyces cerevisiae strain for anaerobic fermentation of xylose from AFEX pretreated corn stover. PLoS ONE 2014, 9:e107499.
45. Peng B., Shen Y., Li X., Chen X., Hou J., Bao X. Improvement of xylose fermentation in respiratory-deficient xylose-fermenting Saccharomyces cerevisiae. Metab. Eng. 2012, 14(1):9-18.
46. Pereira F.B., Romaní A., Ruiz H.A., Teixeira J.A., Domingues L. Industrial robust yeast isolates with great potential for fermentation of lignocellulosic biomass. Bioresour. Technol. 2014, 161:192-199.
47. Qin L., Liu Z.H., Li B.Z., Dale B.E., Yuan Y.J. Mass balance and transformation of corn stover by pretreatment with different dilute organic acids. Bioresour. Technol. 2012, 112:319-326.
48. Qureshi A.S., Zhang J., Bao J. High ethanol fermentation performance of the dry dilute acid pretreated corn stover by an evolutionarily adapted Saccharomyces cerevisiae strain. Bioresour. Technol. 2015, 189:399-404.
49. Shen Y., Chen X., Peng B., Chen L., Hou J., Bao X. An efficient xylose-fermenting recombinant Saccharomyces cerevisiae strain obtained through adaptive evolution and its global transcription profile. Appl. Microbiol. Biotechnol. 2012, 96:1079-1091.
50. Shi S., Liang Y., Zhang M.M., Ang E.L., Zhao H. A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae. Metab. Eng. 2016, 33:19-27.
51. Silva J.P.A., Mussatto S.I., Roberto I.C. The influence of initial xylose concentration, agitation, and aeration on ethanol production by Pichia stipitis from rice straw hemicellulosic hydrolysate. Appl. Biochem. Biotechnol. 2010, 162:1306-1315.
52. Tiwari R., Singh S., Nain P.K., Rana S., Sharma A., Pranaw K., Nain L. Harnessing the hydrolytic potential of phytopathogenic fungus Phoma exigua ITCC 2049 for saccharification of lignocellulosic biomass. Bioresour. Technol. 2013, 150:228-234.
53. Toquero C., Bolado S. Effect of four pretreatments on enzymatic hydrolysis and ethanol fermentation of wheat straw. Influence of inhibitors and washing. Bioresour. Technol. 2014, 157:68-76.
54. Tsai C.S., Kong I.I., Lesmana A., Million G., Zhang G.C., Kim S.R., Jin Y.S. Rapid and marker-free refactoring of xylose-fermenting yeast strains with Cas9/CRISPR. Biotechnol. Bioeng. 2015, 112:2406-2411.
55. Wallace-Salinas V., Brink D.P., Ahrén D., Gorwa-Grauslund M.F. Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress. BMC Genomics 2015, 16:514.
56. Wang M., Zhao Q., Yang J., Jiang B., Wang F., Liu K., Fang X. A mitogen-activated protein kinase Tmk3 participates in high osmolarity resistance, cell wall integrity maintenance and cellulase production regulation in Trichoderma reesei. PLoS ONE 2013, 8:e72189.
57. Wang X., Bai X., Chen D.F., Chen F.Z., Li B.Z., Yuan Y.J. Increasing proline and myo-inositol improves tolerance of Saccharomyces cerevisiae to the mixture of multiple lignocellulose-derived inhibitors. Biotechnol. Biofuels 2015, 8:142.
58. Wei N., Oh E.J., Million G., Cate J.H., Jin Y.S. Simultaneous utilization of cellobiose, xylose, and acetic acid from lignocellulosic biomass for biofuel production by an engineered yeast platform. ACS Synth. Biol. 2015, 4:707-713.
59. 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, 102:9206-9215.
60. Xu H., Kim S., Sorek H., Lee Y., Jeong D., Kim J., Oh E.J., Yun E.J., Wemmer D.E., Kim K.H., Kim S.R., Jin Y.S. PHO13 deletion-induced transcriptional activation prevents sedoheptulose accumulation during xylose metabolism in engineered Saccharomyces cerevisiae. Metab. Eng. 2016, 34:88-96.
61. Zakaria M.R., Hirata S., Fujimoto S., Ibrahim I., Hassan M.A. Soluble inhibitors generated during hydrothermal pretreatment of oil palm mesocarp fiber suppressed the catalytic activity of Acremonium cellulase. Bioresour. Technol. 2016, 200:541-547.
62. Zhang J., Zhong Y., Zhao X., Wang T. Development of the cellulolytic fungus Trichoderma reesei strain with enhanced beta-glucosidase and filter paper activity using strong artificial cellobiohydrolase 1 promoter. Bioresour. Technol. 2010, 101:9815-9818.
63. Zhang W., Kou Y., Xu J., Cao Y., Zhao G., Shao J., Wang H., Wang Z., Bao X., Chen G., Liu W. Two major facilitator superfamily sugar transporters from Trichoderma reesei and their roles in induction of cellulase biosynthesis. J. Biol. Chem. 2013, 288:32861-32872.
64. Zhang M.M., Zhao X.Q., Cheng C., Bai F.W. Improved growth and ethanol fermentation of Saccharomyces cerevisiae in the presence of acetic acid by overexpression of SET5 and PPR1. Biotechnol. J. 2015, 10:1903-1911.
65. Zhao X.Q., Zi L.H., Bai F.W., Lin H.L., Hao X.M., Yue G.J., Ho N.W.Y. Bioethanol from lignocellulosic biomass. Biotechnology in China III: Biofuels and Bioenergy, Advances in Biochemical Engineering/Biotechnology 2012, vol. 128:25-51. Springer, Berlin Heidelberg.
66. Zheng D., Wu X.C., Tao X.L., Wang P.M., Li P., Chi X.Q., Li Y.D., Yan Q.F., Zhao Y.H. Screening and construction of Saccharomyces cerevisiae strains with improved multi-tolerance and bioethanol fermentation performance. Bioresour. Technol. 2011, 102:3020-3027.
67. Zheng D., Liu T.Z., Chen J., Zhang K., Li O., Zhu L., Zhao Y.H., Wu X.C., Wang P.M. Comparative functional genomics to reveal the molecular basis of phenotypic diversities and guide the genetic breeding of industrial yeast strains. Appl. Microbiol. Biotechnol. 2013, 97:2067-2076.
68. Zhong Y., Wang X., Yu H., Liang S., Wang T. Application of T-DNA insertional mutagenesis for improving cellulase production in the filamentous fungus Trichoderma reesei. Bioresour. Technol. 2012, 110:572-577.
69. Zhu J.Y., Pan X.J., Wang G.S., Gleisner R. Sulfite pretreatment (SPORL) for robust enzymatic saccharification of spruce and red pine. Bioresour. Technol. 2009, 100:2411-2418.
70. Zhu J.Q., Qin L., Li B.Z., Yuan Y.J. Simultaneous saccharification and co-fermentation of aqueous ammonia pretreated corn stover with an engineered Saccharomyces cerevisiae SyBE005. Bioresour. Technol. 2014, 169:9-18.
71. Zhu J.Q., Qin L., Li W.C., Zhang J., Bao J., Huang Y.D., Li B.Z., Yuan Y.J. Simultaneous saccharification and co-fermentation of dry diluted acid pretreated corn stover at high dry matter loading: overcoming the inhibitors by non-tolerant yeast. Bioresour. Technol. 2015, 198:39-46.