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Bae JH, Kim MJ, Sung BH, Jin YS, Sohn JH. Directed evolution and secretory expression of xylose isomerase for improved utilisation of xylose in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:223. [PMID: 34823570 PMCID: PMC8613937 DOI: 10.1186/s13068-021-02073-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Xylose contained in lignocellulosic biomass is an attractive carbon substrate for economically viable conversion to bioethanol. Extensive research has been conducted on xylose fermentation using recombinant Saccharomyces cerevisiae expressing xylose isomerase (XI) and xylose reductase/xylitol dehydrogenase (XR/XDH) pathways along with the introduction of a xylose transporter and amplification of the downstream pathway. However, the low utilization of xylose in the presence of glucose, due to the varying preference for cellular uptake, is a lingering challenge. Studies so far have mainly focused on xylose utilization inside the cells, but there have been little trials on the conversion of xylose to xylulose by cell before uptake. We hypothesized that the extracellular conversion of xylose to xylulose before uptake would facilitate better utilization of xylose even in the presence of glucose. To verify this, XI from Piromyces sp. was engineered and hyper-secreted in S. cerevisiae for the extracellular conversion of xylose to xylulose. RESULTS The optimal pH of XI was lowered from 7.0 to 5.0 by directed evolution to ensure its high activity under the acidic conditions used for yeast fermentation, and hyper-secretion of an engineered XI-76 mutant (E56A and I252M) was accomplished by employing target protein-specific translational fusion partners. The purified XI-76 showed twofold higher activity than that of the wild type at pH 5. The secretory expression of XI-76 in the previously developed xylose utilizing yeast strain, SR8 increased xylose consumption and ethanol production by approximately 7-20% and 15-20% in xylose fermentation and glucose and xylose co-fermentation, respectively. CONCLUSIONS Isomerisation of xylose to xylulose before uptake using extracellular XI was found to be effective in xylose fermentation or glucose/xylose co-fermentation. This suggested that glucose competed less with xylulose than with xylose for uptake by the cell. Consequently, the engineered XI secretion system constructed in this study can pave the way for simultaneous utilization of C5/C6 sugars from the sustainable lignocellulosic biomass.
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Affiliation(s)
- Jung-Hoon Bae
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Mi-Jin Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jung-Hoon Sohn
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
- Cellapy Bio Inc., Bio-Venture Center 211, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Cunha JT, Soares PO, Baptista SL, Costa CE, Domingues L. Engineered Saccharomyces cerevisiae for lignocellulosic valorization: a review and perspectives on bioethanol production. Bioengineered 2020; 11:883-903. [PMID: 32799606 PMCID: PMC8291843 DOI: 10.1080/21655979.2020.1801178] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The biorefinery concept, consisting in using renewable biomass with economical and energy goals, appeared in response to the ongoing exhaustion of fossil reserves. Bioethanol is the most prominent biofuel and has been considered one of the top chemicals to be obtained from biomass. Saccharomyces cerevisiae, the preferred microorganism for ethanol production, has been the target of extensive genetic modifications to improve the production of this alcohol from renewable biomasses. Additionally, S. cerevisiae strains from harsh industrial environments have been exploited due to their robust traits and improved fermentative capacity. Nevertheless, there is still not an optimized strain capable of turning second generation bioprocesses economically viable. Considering this, and aiming to facilitate and guide the future development of effective S. cerevisiae strains, this work reviews genetic engineering strategies envisioning improvements in 2nd generation bioethanol production, with special focus in process-related traits, xylose consumption, and consolidated bioprocessing. Altogether, the genetic toolbox described proves S. cerevisiae to be a key microorganism for the establishment of a bioeconomy, not only for the production of lignocellulosic bioethanol, but also having potential as a cell factory platform for overall valorization of renewable biomasses.
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Affiliation(s)
- Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Pedro O Soares
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Sara L Baptista
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Carlos E Costa
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
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The biotechnological potential of the yeast Dekkera bruxellensis. World J Microbiol Biotechnol 2019; 35:103. [PMID: 31236799 DOI: 10.1007/s11274-019-2678-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 06/15/2019] [Indexed: 10/26/2022]
Abstract
Dekkera bruxellensis is an industrial yeast mainly regarded as a contaminant species in fermentation processes. In winemaking, it is associated with off-flavours that cause wine spoilage, while in bioethanol production this yeast is linked to a reduction of industrial productivity by competing with Saccharomyces cerevisiae for the substrate. In spite of that, this point of view is gradually changing, mostly because D. bruxellensis is also able to produce important metabolites, such as ethanol, acetate, fusel alcohols, esters and others. This dual role is likely due to the fact that this yeast presents a set of metabolic traits that might be either industrially attractive or detrimental, depending on how they are faced and explored. Therefore, a proper industrial application for D. bruxellensis depends on the correct assembly of its central metabolic puzzle. In this sense, researchers have addressed issues regarding the physiological and genetic aspects of D. bruxellensis, which have brought to light much of our current knowledge on this yeast. In this review, we shall outline what is presently understood about the main metabolic features of D. bruxellensis and how they might be managed to improve its current or future industrial applications (except for winemaking, in which it is solely regarded as a contaminant). Moreover, we will discuss the advantages and challenges that must be overcome in order to take advantage of the full biotechnological potential of this yeast.
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The production of ethanol from lignocellulosic biomass by Kluyveromyces marxianus CICC 1727-5 and Spathaspora passalidarum ATCC MYA-4345. Appl Microbiol Biotechnol 2019; 103:2845-2855. [DOI: 10.1007/s00253-019-09625-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 11/18/2018] [Accepted: 12/16/2018] [Indexed: 11/25/2022]
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Gao M, Ploessl D, Shao Z. Enhancing the Co-utilization of Biomass-Derived Mixed Sugars by Yeasts. Front Microbiol 2019; 9:3264. [PMID: 30723464 PMCID: PMC6349770 DOI: 10.3389/fmicb.2018.03264] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/14/2018] [Indexed: 12/11/2022] Open
Abstract
Plant biomass is a promising carbon source for producing value-added chemicals, including transportation biofuels, polymer precursors, and various additives. Most engineered microbial hosts and a select group of wild-type species can metabolize mixed sugars including oligosaccharides, hexoses, and pentoses that are hydrolyzed from plant biomass. However, most of these microorganisms consume glucose preferentially to non-glucose sugars through mechanisms generally defined as carbon catabolite repression. The current lack of simultaneous mixed-sugar utilization limits achievable titers, yields, and productivities. Therefore, the development of microbial platforms capable of fermenting mixed sugars simultaneously from biomass hydrolysates is essential for economical industry-scale production, particularly for compounds with marginal profits. This review aims to summarize recent discoveries and breakthroughs in the engineering of yeast cell factories for improved mixed-sugar co-utilization based on various metabolic engineering approaches. Emphasis is placed on enhanced non-glucose utilization, discovery of novel sugar transporters free from glucose repression, native xylose-utilizing microbes, consolidated bioprocessing (CBP), improved cellulase secretion, and creation of microbial consortia for improving mixed-sugar utilization. Perspectives on the future development of biorenewables industry are provided in the end.
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Affiliation(s)
- Meirong Gao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States
| | - Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States.,The Ames Laboratory, Iowa State University, Ames, IA, United States.,The Interdisciplinary Microbiology Program, Biorenewables Research Laboratory, Iowa State University, Ames, IA, United States
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Cunha JT, Soares PO, Romaní A, Thevelein JM, Domingues L. Xylose fermentation efficiency of industrial Saccharomyces cerevisiae yeast with separate or combined xylose reductase/xylitol dehydrogenase and xylose isomerase pathways. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:20. [PMID: 30705706 PMCID: PMC6348659 DOI: 10.1186/s13068-019-1360-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/18/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Xylose isomerase (XI) and xylose reductase/xylitol dehydrogenase (XR/XDH) pathways have been extensively used to confer xylose assimilation capacity to Saccharomyces cerevisiae and tackle one of the major bottlenecks in the attainment of economically viable lignocellulosic ethanol production. Nevertheless, there is a lack of studies comparing the efficiency of those pathways both separately and combined. In this work, the XI and/or XR/XDH pathways were introduced into two robust industrial S. cerevisiae strains, evaluated in synthetic media and corn cob hemicellulosic hydrolysate and the results were correlated with the differential enzyme activities found in the xylose-pathway engineered strains. RESULTS The sole expression of XI was found to increase the fermentative capacity of both strains in synthetic media at 30 °C and 40 °C: decreasing xylitol accumulation and improving xylose consumption and ethanol production. Similar results were observed in fermentations of detoxified hydrolysate. However, in the presence of lignocellulosic-derived inhibitors, a positive synergistic effect resulted from the expression of both XI and XR/XDH, possibly caused by a cofactor equilibrium between the XDH and furan detoxifying enzymes, increasing the ethanol yield by more than 38%. CONCLUSIONS This study clearly shows an advantage of using the XI from Clostridium phytofermentans to attain high ethanol productivities and yields from xylose. Furthermore, and for the first time, the simultaneous utilization of XR/XDH and XI pathways was compared to the single expression of XR/XDH or XI and was found to improve ethanol production from non-detoxified hemicellulosic hydrolysates. These results extend the knowledge regarding S. cerevisiae xylose assimilation metabolism and pave the way for the construction of more efficient strains for use in lignocellulosic industrial processes.
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Affiliation(s)
- Joana T. Cunha
- CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Pedro O. Soares
- CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Aloia Romaní
- CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
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Bioethanol a Microbial Biofuel Metabolite; New Insights of Yeasts Metabolic Engineering. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation4010016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Wang C, Li Y, Qiu C, Wang S, Ma J, Shen Y, Zhang Q, Du B, Ding Y, Bao X. Identification of Important Amino Acids in Gal2p for Improving the L-arabinose Transport and Metabolism in Saccharomyces cerevisiae. Front Microbiol 2017; 8:1391. [PMID: 28785254 PMCID: PMC5519586 DOI: 10.3389/fmicb.2017.01391] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/10/2017] [Indexed: 11/29/2022] Open
Abstract
Efficient and cost-effective bioethanol production from lignocellulosic materials requires co-fermentation of the main hydrolyzed sugars, including glucose, xylose, and L-arabinose. Saccharomyces cerevisiae is a glucose-fermenting yeast that is traditionally used for ethanol production. Fermentation of L-arabinose is also possible after metabolic engineering. Transport into the cell is the first and rate-limiting step for L-arabinose metabolism. The galactose permease, Gal2p, is a non-specific, endogenous monosaccharide transporter that has been shown to transport L-arabinose. However, Gal2p-mediated transport of L-arabinose occurs at a low efficiency. In this study, homologous modeling and L-arabinose docking were used to predict amino acids in Gal2p that are crucial for L-arabinose transport. Nine amino acid residues in Gal2p were identified and were the focus for site-directed mutagenesis. In the Gal2p transport-deficient chassis cells, the capacity for L-arabinose transport of the different Gal2p mutants was compared by testing growth rates using L-arabinose as the sole carbon source. Almost all the tested mutations affected L-arabinose transport capacity. Among them, F85 is a unique site. The F85S, F85G, F85C, and F85T point mutations significantly increased L-arabinose transport activities, while, the F85E and F85R mutations decreased L-arabinose transport activities compared to the Gal2p-expressing wild-type strain. These results verified F85 as a key residue in L-arabinose transport. The F85S mutation, having the most significant effect, elevated the exponential growth rate by 40%. The F85S mutation also improved xylose transport efficiency and weakened the glucose transport preference. Overall, enhancing the L-arabinose transport capacity further improved the L-arabinose metabolism of engineered S. cerevisiae.
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Affiliation(s)
- Chengqiang Wang
- College of Life Sciences/Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural UniversityTai'an, China.,The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China
| | - Yanwei Li
- The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China
| | - Chenxi Qiu
- College of Life Sciences/Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural UniversityTai'an, China.,The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China
| | - Shihao Wang
- College of Life Sciences/Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural UniversityTai'an, China.,The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China
| | - Jinjin Ma
- College of Life Sciences/Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural UniversityTai'an, China
| | - Yu Shen
- The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China
| | - Qingzhu Zhang
- The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China
| | - Binghai Du
- College of Life Sciences/Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural UniversityTai'an, China
| | - Yanqin Ding
- College of Life Sciences/Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural UniversityTai'an, China
| | - Xiaoming Bao
- The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China.,College of Bioengineering, Qilu University of TechnologyJinan, China
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