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Kendrick EG, Bhatia R, Barbosa FC, Goldbeck R, Gallagher JA, Leak DJ. Enzymatic generation of short chain cello-oligosaccharides from Miscanthus using different pretreatments. Bioresour Technol 2022; 358:127399. [PMID: 35640812 DOI: 10.1016/j.biortech.2022.127399] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Enzyme combinations producing short-chain cello-oligosaccharides (COS) as major bio-products from cellulose of Miscanthus Mx2779 accessed through different pretreatment methods were compared. Over short hydrolysis times, processive endoglucanase TfCel9a produced a high percentage of cellotetraose and cellopentaose and is synergistic with endoglucanase CcCel9m for producing short oligomers from amorphous cellulose but had low activity on untreated Miscanthus. Hydrolysis of the latter improved when these were combined with a mutant cellobio/triohydrolase OsCelC7(-105) and a lytic polysaccharide monooxygenase TrCel61a, a combination which also produced the highest COS yields from phosphoric acid swollen cellulose. Steam explosion pretreatment of Miscanthus increased COS yields, with/without phosphoric acid swelling, while increased swelling time (from 20 to 45 min) also increased yields but decreased the need for TrCel61a. The highest COS yields (933 mg/g glucan) and most stable product profile were obtained using ionic liquid [C2mim][OAc] pretreatment and the three enzyme mixture TfCel9a, Cel9m and OsCel7a(-105).
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Affiliation(s)
| | - Rakesh Bhatia
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth SY23 3EE, UK; Department of Agronomy and Plant Breeding, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Fernando C Barbosa
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Rosana Goldbeck
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Joe A Gallagher
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth SY23 3EE, UK
| | - David J Leak
- Department of Biology & Biochemistry, University of Bath, Bath BA2 7AY, UK.
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Zhang Y, Xu Z, Lu M, Ding B, Chen S, Wen Z, Yu Y, Zhou L, Jin M. Rapid evolution and mechanism elucidation for efficient cellobiose-utilizing Saccharomyces cerevisiae through Synthetic Chromosome Rearrangement and Modification by LoxPsym-mediated Evolution. Bioresour Technol 2022; 356:127268. [PMID: 35533888 DOI: 10.1016/j.biortech.2022.127268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Lack of cellobiose utilization capability for many microorganisms results in carbon source waste in lignocellulosic biorefinery. In this study, genes for cellobiose transport and hydrolysis were introduced to Saccharomyces cerevisiae synV, a semi-synthetic yeast with an inducible SCRaMbLE (Synthetic Chromosome Rearrangement and Modification by LoxPsym-mediated Evolution) system incorporated into its chromosome V, endowing cellobiose utilization capability to this strain. Thereafter, two evolved strains with 98.1% and 79.2% improvement, respectively, in cellobiose utilization rate were obtained through induced SCRaMbLE. Further studies suggested that the enhanced cellobiose utilization capability directly correlated with copy number increases of introduced genes and some chromosome structural variations. In particular, it was experimentally demonstrated for the first time that deletion of redox stress related gene MXR1 and ATP conversion related gene ADK2 contributed to enhanced cellobiose conversion. Thereafter, the effectiveness of MXR1 and ADK2 deletions was demonstrated in artificial hydrolysate and rice straw hydrolysate, respectively.
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Affiliation(s)
- Yuwei Zhang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Boning Ding
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Sitong Chen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Yang Yu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Linlin Zhou
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China.
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Ylinen A, de Ruijter JC, Jouhten P, Penttilä M. PHB production from cellobiose with Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:124. [PMID: 35729556 PMCID: PMC9210708 DOI: 10.1186/s12934-022-01845-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
Replacement of petrochemical-based materials with microbially produced biodegradable alternatives calls for industrially attractive fermentation processes. Lignocellulosic materials offer non-edible alternatives for cultivated sugars, but require often use of expensive sugar releasing enzymes, such as β-glucosidases. These cellulose treatment costs could be reduced if microbial production hosts could use short cellodextrins such as cellobiose directly as their substrates. In this study, we demonstrate production of poly(hydroxybutyrate) (PHB) in yeast Saccharomyces cerevisiae using cellobiose as a sole carbon source. Yeast strains expressing PHB pathway genes from Cupriavidus necator and cellodextrin transporter gene CDT-1 from Neurospora crassa were complemented either with β-glucosidase gene GH1-1 from N. crassa or with cellobiose phosphorylase gene cbp from Ruminococcus flavefaciens. These cellobiose utilization routes either with Gh1-1 or Cbp enzymes differ in energetics and dynamics. However, both routes enabled higher PHB production per consumed sugar and higher PHB accumulation % of cell dry weight (CDW) than use of glucose as a carbon source. As expected, the strains with Gh1-1 consumed cellobiose faster than the strains with Cbp, both in flask and bioreactor batch cultures. In shake flasks, higher final PHB accumulation % of CDW was reached with Cbp route (10.0 ± 0.3%) than with Gh1-1 route (8.1 ± 0.2%). However, a higher PHB accumulation was achieved in better aerated and pH-controlled bioreactors, in comparison to shake flasks, and the relative performance of strains switched. In bioreactors, notable PHB accumulation levels per CDW of 13.4 ± 0.9% and 18.5 ± 3.9% were achieved with Cbp and Gh1-1 routes, respectively. The average molecular weights of accumulated PHB were similar using both routes; approximately 500 kDa and 450 kDa for strains expressing either cbp or GH1-1 genes, respectively. The formation of PHB with high molecular weights, combined with efficient cellobiose conversion, demonstrates a highly potential solution for improving attractiveness of sustainable polymer production using microbial cells.
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Affiliation(s)
- Anna Ylinen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland.
| | - Jorg C de Ruijter
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland
| | - Paula Jouhten
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland.,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 00076, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland.,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 00076, Espoo, Finland
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Choi HJ, Jin YS, Lee WH. Effects of Engineered Saccharomyces cerevisiae Fermenting Cellobiose through Low-Energy-Consuming Phosphorolytic Pathway in Simultaneous Saccharification and Fermentation. J Microbiol Biotechnol 2022; 32:117-125. [PMID: 34949751 PMCID: PMC9628822 DOI: 10.4014/jmb.2111.11047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/07/2021] [Indexed: 12/15/2022]
Abstract
Until recently, four types of cellobiose-fermenting Saccharomyces cerevisiae strains have been developed by introduction of a cellobiose metabolic pathway based on either intracellular β-glucosidase (GH1-1) or cellobiose phosphorylase (CBP), along with either an energy-consuming active cellodextrin transporter (CDT-1) or a non-energy-consuming passive cellodextrin facilitator (CDT-2). In this study, the ethanol production performance of two cellobiose-fermenting S. cerevisiae strains expressing mutant CDT-2 (N306I) with GH1-1 or CBP were compared with two cellobiose-fermenting S. cerevisiae strains expressing mutant CDT-1 (F213L) with GH1-1 or CBP in the simultaneous saccharification and fermentation (SSF) of cellulose under various conditions. It was found that, regardless of the SSF conditions, the phosphorolytic cellobiose-fermenting S. cerevisiae expressing mutant CDT-2 with CBP showed the best ethanol production among the four strains. In addition, during SSF contaminated by lactic acid bacteria, the phosphorolytic cellobiose-fermenting S. cerevisiae expressing mutant CDT-2 with CBP showed the highest ethanol production and the lowest lactate formation compared with those of other strains, such as the hydrolytic cellobiose-fermenting S. cerevisiae expressing mutant CDT-1 with GH1-1, and the glucose-fermenting S. cerevisiae with extracellular β-glucosidase. These results suggest that the cellobiose-fermenting yeast strain exhibiting low energy consumption can enhance the efficiency of the SSF of cellulosic biomass.
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Affiliation(s)
- Hyo-Jin Choi
- Department of Bioenergy Science and Technology, and Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Corresponding authors Y.S. Jin Phone: +217-333-7981 Fax: +217-333-0508 E-mail:
| | - Won-Heong Lee
- Department of Bioenergy Science and Technology, and Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea,Department of Food Science and Human Nutrition, and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,
W.H. Lee Phone: +82-62-530-2046 Fax: +82-62-530-2047 E-mail:
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Oh EJ, Jin YS. Engineering of Saccharomyces cerevisiae for efficient fermentation of cellulose. FEMS Yeast Res 2021; 20:5698803. [PMID: 31917414 DOI: 10.1093/femsyr/foz089] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/08/2020] [Indexed: 12/18/2022] Open
Abstract
Conversion of lignocellulosic biomass to biofuels using microbial fermentation is an attractive option to substitute petroleum-based production economically and sustainably. The substantial efforts to design yeast strains for biomass hydrolysis have led to industrially applicable biological routes. Saccharomyces cerevisiae is a robust microbial platform widely used in biofuel production, based on its amenability to systems and synthetic biology tools. The critical challenges for the efficient microbial conversion of lignocellulosic biomass by engineered S. cerevisiae include heterologous expression of cellulolytic enzymes, co-fermentation of hexose and pentose sugars, and robustness against various stresses. Scientists developed many engineering strategies for cellulolytic S. cerevisiae strains, bringing the application of consolidated bioprocess at an industrial scale. Recent advances in the development and implementation of engineered yeast strains capable of assimilating lignocellulose will be reviewed.
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Affiliation(s)
- Eun Joong Oh
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, 4001 Discovery Dr., CO 80303, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, 905 S. Goodwin Ave., IL 61801, USA.,1105 Carl R. Woese Institute for Genomic Biology, 1206 W. Gregory Dr. Urbana, IL 61801. USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr. Urbana, IL 61801, USA
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Bermejo PM, Raghavendran V, Gombert AK. Neither 1G nor 2G fuel ethanol: setting the ground for a sugarcane-based biorefinery using an iSUCCELL yeast platform. FEMS Yeast Res 2020; 20:5836716. [PMID: 32401320 DOI: 10.1093/femsyr/foaa027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/11/2020] [Indexed: 11/12/2022] Open
Abstract
First-generation (1G) fuel ethanol production in sugarcane-based biorefineries is an established economic enterprise in Brazil. Second-generation (2G) fuel ethanol from lignocellulosic materials, though extensively investigated, is currently facing severe difficulties to become economically viable. Some of the challenges inherent to these processes could be resolved by efficiently separating and partially hydrolysing the cellulosic fraction of the lignocellulosic materials into the disaccharide cellobiose. Here, we propose an alternative biorefinery, where the sucrose-rich stream from the 1G process is mixed with a cellobiose-rich stream in the fermentation step. The advantages of mixing are 3-fold: (i) decreased concentrations of metabolic inhibitors that are typically produced during pretreatment and hydrolysis of lignocellulosic materials; (ii) decreased cooling times after enzymatic hydrolysis prior to fermentation; and (iii) decreased availability of free glucose for contaminating microorganisms and undesired glucose repression effects. The iSUCCELL platform will be built upon the robust Saccharomyces cerevisiae strains currently present in 1G biorefineries, which offer competitive advantage in non-aseptic environments, and into which intracellular hydrolyses of sucrose and cellobiose will be engineered. It is expected that high yields of ethanol can be achieved in a process with cell recycling, lower contamination levels and decreased antibiotic use, when compared to current 2G technologies.
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Affiliation(s)
| | - Vijayendran Raghavendran
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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de Ruijter JC, Igarashi K, Penttilä M. The Lipomyces starkeyi gene Ls120451 encodes a cellobiose transporter that enables cellobiose fermentation in Saccharomyces cerevisiae. FEMS Yeast Res 2020; 20:foaa019. [PMID: 32310262 PMCID: PMC7204792 DOI: 10.1093/femsyr/foaa019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/17/2020] [Indexed: 12/14/2022] Open
Abstract
Processed lignocellulosic biomass is a source of mixed sugars that can be used for microbial fermentation into fuels or higher value products, like chemicals. Previously, the yeast Saccharomyces cerevisiae was engineered to utilize its cellodextrins through the heterologous expression of sugar transporters together with an intracellular expressed β-glucosidase. In this study, we screened a selection of eight (putative) cellodextrin transporters from different yeast and fungal hosts in order to extend the catalogue of available cellobiose transporters for cellobiose fermentation in S. cerevisiae. We confirmed that several in silico predicted cellodextrin transporters from Aspergillus niger were capable of transporting cellobiose with low affinity. In addition, we found a novel cellobiose transporter from the yeast Lipomyces starkeyi, encoded by the gene Ls120451. This transporter allowed efficient growth on cellobiose, while it also grew on glucose and lactose, but not cellotriose nor cellotetraose. We characterized the transporter more in-depth together with the transporter CdtG from Penicillium oxalicum. CdtG showed to be slightly more efficient in cellobiose consumption than Ls120451 at concentrations below 1.0 g/L. Ls120451 was more efficient in cellobiose consumption at higher concentrations and strains expressing this transporter grew slightly slower, but produced up to 30% more ethanol than CdtG.
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Affiliation(s)
- Jorg C de Ruijter
- VTT Technical Research Centre of Finland, Tietotie 2, FI-02150 Espoo, Finland
| | - Kiyohiko Igarashi
- VTT Technical Research Centre of Finland, Tietotie 2, FI-02150 Espoo, Finland
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yajoi, Bunkyo, Tokyo 113–8657, Japan
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Tietotie 2, FI-02150 Espoo, Finland
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Li J, Zhang Y, Li J, Sun T, Tian C. Metabolic engineering of the cellulolytic thermophilic fungus Myceliophthora thermophila to produce ethanol from cellobiose. Biotechnol Biofuels 2020; 13:23. [PMID: 32021654 PMCID: PMC6995234 DOI: 10.1186/s13068-020-1661-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/21/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Cellulosic biomass is a promising resource for bioethanol production. However, various sugars in plant biomass hydrolysates including cellodextrins, cellobiose, glucose, xylose, and arabinose, are poorly fermented by microbes. The commonly used ethanol-producing microbe Saccharomyces cerevisiae can usually only utilize glucose, although metabolically engineered strains that utilize xylose have been developed. Direct fermentation of cellobiose could avoid glucose repression during biomass fermentation, but applications of an engineered cellobiose-utilizing S. cerevisiae are still limited because of its long lag phase. Bioethanol production from biomass-derived sugars by a cellulolytic filamentous fungus would have many advantages for the biorefinery industry. RESULTS We selected Myceliophthora thermophila, a cellulolytic thermophilic filamentous fungus for metabolic engineering to produce ethanol from glucose and cellobiose. Ethanol production was increased by 57% from glucose but not cellobiose after introduction of ScADH1 into the wild-type (WT) strain. Further overexpression of a glucose transporter GLT-1 or the cellodextrin transport system (CDT-1/CDT-2) from N. crassa increased ethanol production by 131% from glucose or by 200% from cellobiose, respectively. Transcriptomic analysis of the engineered cellobiose-utilizing strain and WT when grown on cellobiose showed that genes involved in oxidation-reduction reactions and the stress response were downregulated, whereas those involved in protein biosynthesis were upregulated in this effective ethanol production strain. Turning down the expression of pyc gene results the final engineered strain with the ethanol production was further increased by 23%, reaching up to 11.3 g/L on cellobiose. CONCLUSIONS This is the first attempt to engineer the cellulolytic fungus M. thermophila to produce bioethanol from biomass-derived sugars such as glucose and cellobiose. The ethanol production can be improved about 4 times up to 11 grams per liter on cellobiose after a couple of genetic engineering. These results show that M. thermophila is a promising platform for bioethanol production from cellulosic materials in the future.
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Affiliation(s)
- Jinyang Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yongli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Tao Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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Wilken SE, Swift CL, Podolsky IA, Lankiewicz TS, Seppälä S, O'Malley MA. Linking ‘omics’ to function unlocks the biotech potential of non-model fungi. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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