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Huang M, Cui X, Zhang P, Jin Z, Li H, Liu J, Jiang Z. Engineered Saccharomyces cerevisiae harbors xylose isomerase and xylose transporter improves co-fermentation of xylose and glucose for ethanol production. Prep Biochem Biotechnol 2024; 54:1058-1067. [PMID: 38349751 DOI: 10.1080/10826068.2024.2315479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Saccharomyces cerevisiae cannot assimilate xylose, second to glucose derived from lignocellulosic biomass. Here, the engineered S. cerevisiae strains INVSc-XI and INVSc-XI/XT were constructed using xylA and Xltr1p to co-utilize xylose and glucose, achieving economic viability and sustainable production of fuels. The xylose utilization rate of INVSc-XI/XT was 2.3-fold higher than that of INVSc-XI, indicating that overexpressing Xltr1p could further enhance xylose utilization. In mixed sugar media, a small amount of glucose enhanced the consumption of xylose by INVSc-XI/XT. Transcriptome analysis showed that glucose increased the upregulation of acetate of coenzyme A synthetase (ACS), alcohol dehydrogenase (ADH), and transketolase (TKL) gene expression in INVSc-XI/XT, further promoting xylose utilization and ethanol yield. The highest ethanol titer of 2.91 g/L with a yield of 0.29 g/g at 96 h by INVSc-XI/XT was 56.9% and 63.0% of the theoretical ethanol yield from glucose and xylose, respectively. These results showed overexpression of xylA and Xltr1p is a promising strategy for improving xylose and glucose conversion to ethanol. Although the ability of strain INVSc-XI/XT to produce ethanol was not very satisfactory, glucose was discovered to influence xylose utilization in strain INVSc-XI/XT. Altering the glucose concentration is a promising strategy to improve the xylose and glucose co-utilization.
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Affiliation(s)
- Mengtian Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, P.R. China
- College of Life Science and Technology, Hubei Engineering University, Xiaogan, P.R. China
| | - Xinxin Cui
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, P.R. China
| | - Peining Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, P.R. China
| | - Zhuocheng Jin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, P.R. China
| | - Huanan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, P.R. China
| | - Jiashu Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, P.R. China
| | - Zhengbing Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, P.R. China
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Bolzico BC, Racca S, Khawam JN, Leonardi RJ, Tomassi AH, Benzzo MT, Comelli RN. Exploring xylose metabolism in non-conventional yeasts: kinetic characterization and product accumulation under different aeration conditions. J Ind Microbiol Biotechnol 2024; 51:kuae023. [PMID: 38936832 PMCID: PMC11247345 DOI: 10.1093/jimb/kuae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/26/2024] [Indexed: 06/29/2024]
Abstract
d-Xylose is a metabolizable carbon source for several non-Saccharomyces species, but not for native strains of S. cerevisiae. For the potential application of xylose-assimilating yeasts in biotechnological processes, a deeper understanding of pentose catabolism is needed. This work aimed to investigate the traits behind xylose utilization in diverse yeast species. The performance of 9 selected xylose-metabolizing yeast strains was evaluated and compared across 3 oxygenation conditions. Oxygenation diversely impacted growth, xylose consumption, and product accumulation. Xylose utilization by ethanol-producing species such as Spathaspora passalidarum and Scheffersomyces stipitis was less affected by oxygen restriction compared with other xylitol-accumulating species such as Meyerozyma guilliermondii, Naganishia liquefaciens, and Yamadazyma sp., for which increased aeration stimulated xylose assimilation considerably. Spathaspora passalidarum exhibited superior conversion of xylose to ethanol and showed the fastest growth and xylose consumption in all 3 conditions. By performing assays under identical conditions for all selected yeasts, we minimize bias in comparisons, providing valuable insight into xylose metabolism and facilitating the development of robust bioprocesses. ONE-SENTENCE SUMMARY This work aims to expand the knowledge of xylose utilization in different yeast species, with a focus on how oxygenation impacts xylose assimilation.
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Affiliation(s)
- Bruna C Bolzico
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
| | - Sofia Racca
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
| | - Jorge N Khawam
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
| | - Rodrigo J Leonardi
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
| | - Ariel H Tomassi
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
| | - Maria T Benzzo
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
| | - Raul N Comelli
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
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3
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Topaloğlu A, Esen Ö, Turanlı-Yıldız B, Arslan M, Çakar ZP. From Saccharomyces cerevisiae to Ethanol: Unlocking the Power of Evolutionary Engineering in Metabolic Engineering Applications. J Fungi (Basel) 2023; 9:984. [PMID: 37888240 PMCID: PMC10607480 DOI: 10.3390/jof9100984] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Increased human population and the rapid decline of fossil fuels resulted in a global tendency to look for alternative fuel sources. Environmental concerns about fossil fuel combustion led to a sharp move towards renewable and environmentally friendly biofuels. Ethanol has been the primary fossil fuel alternative due to its low carbon emission rates, high octane content and comparatively facile microbial production processes. In parallel to the increased use of bioethanol in various fields such as transportation, heating and power generation, improvements in ethanol production processes turned out to be a global hot topic. Ethanol is by far the leading yeast output amongst a broad spectrum of bio-based industries. Thus, as a well-known platform microorganism and native ethanol producer, baker's yeast Saccharomyces cerevisiae has been the primary subject of interest for both academic and industrial perspectives in terms of enhanced ethanol production processes. Metabolic engineering strategies have been primarily adopted for direct manipulation of genes of interest responsible in mainstreams of ethanol metabolism. To overcome limitations of rational metabolic engineering, an alternative bottom-up strategy called inverse metabolic engineering has been widely used. In this context, evolutionary engineering, also known as adaptive laboratory evolution (ALE), which is based on random mutagenesis and systematic selection, is a powerful strategy to improve bioethanol production of S. cerevisiae. In this review, we focus on key examples of metabolic and evolutionary engineering for improved first- and second-generation S. cerevisiae bioethanol production processes. We delve into the current state of the field and show that metabolic and evolutionary engineering strategies are intertwined and many metabolically engineered strains for bioethanol production can be further improved by powerful evolutionary engineering strategies. We also discuss potential future directions that involve recent advancements in directed genome evolution, including CRISPR-Cas9 technology.
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Affiliation(s)
- Alican Topaloğlu
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Türkiye; (A.T.); (Ö.E.)
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
| | - Ömer Esen
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Türkiye; (A.T.); (Ö.E.)
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
| | - Burcu Turanlı-Yıldız
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
| | - Mevlüt Arslan
- Department of Genetics, Faculty of Veterinary Medicine, Van Yüzüncü Yıl University, Van 65000, Türkiye;
| | - Zeynep Petek Çakar
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Türkiye; (A.T.); (Ö.E.)
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
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Trivedi VD, Sullivan SF, Choudhury D, Endalur Gopinarayanan V, Hart T, Nair NU. Integration of metabolism and regulation reveals rapid adaptability to growth on non-native substrates. Cell Chem Biol 2023; 30:1135-1143.e5. [PMID: 37421944 PMCID: PMC10529486 DOI: 10.1016/j.chembiol.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/18/2023] [Accepted: 06/08/2023] [Indexed: 07/10/2023]
Abstract
Engineering synthetic heterotrophy is a key to the efficient bio-based valorization of renewable and waste substrates. Among these, engineering hemicellulosic pentose utilization has been well-explored in Saccharomyces cerevisiae (yeast) over several decades-yet the answer to what makes their utilization inherently recalcitrant remains elusive. Through implementation of a semi-synthetic regulon, we find that harmonizing cellular and engineering objectives are a key to obtaining highest growth rates and yields with minimal metabolic engineering effort. Concurrently, results indicate that "extrinsic" factors-specifically, upstream genes that direct flux of pentoses into central carbon metabolism-are rate-limiting. We also reveal that yeast metabolism is innately highly adaptable to rapid growth on non-native substrates and that systems metabolic engineering (i.e., functional genomics, network modeling, etc.) is largely unnecessary. Overall, this work provides an alternate, novel, holistic (and yet minimalistic) approach based on integrating non-native metabolic genes with a native regulon system.
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Affiliation(s)
- Vikas D Trivedi
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Sean F Sullivan
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Debika Choudhury
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | | | - Taylor Hart
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Nikhil U Nair
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA.
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Baptista SL, Romaní A, Cunha JT, Domingues L. Multi-feedstock biorefinery concept: Valorization of winery wastes by engineered yeast. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 326:116623. [PMID: 36368200 DOI: 10.1016/j.jenvman.2022.116623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
The wine industry produces significant amounts of by-products and residues that are not properly managed, posing an environmental problem. Grape must surplus, vine shoots, and wine lees have the potential to be used as renewable resources for the production of energy and chemicals. Metabolic engineering efforts have established Saccharomyces cerevisiae as an efficient microbial cell factory for biorefineries. Current biorefineries designed for producing multiple products often rely on just one feedstock, but the bioeconomy would clearly benefit if these biorefineries could efficiently convert multiple feedstocks. Moreover, to reduce the environmental impact of fossil fuel consumption and maximize production economics, a biorefinery should be capable to supplement the manufacture of biofuel with the production of high-value products. This study proposes an integrated approach for the valorization of diverse wastes resulting from winemaking processes through the biosynthesis of xylitol and ethanol. Using genetically modified S. cerevisiae strains, the xylose-rich hemicellulosic fraction of hydrothermally pretreated vine shoots was converted into xylitol, and the cellulosic fraction was used to produce bioethanol. In addition, grape must, enriched in sugars, was efficiently used as a low-cost source for yeast propagation. The production of xylitol was optimized, in a Simultaneous Saccharification and Fermentation process configuration, by adjusting the inoculum size and enzyme loading. Furthermore, a yeast strain displaying cellulases in the cell surface was applied for the production of bioethanol from the glucan-rich cellulosic. With the addition of grape must and/or wine lees, high ethanol concentrations were reached, which are crucial for the economic feasibility of distillation. This integrated multi-feedstock valorization provides a synergistic alternative for converting a range of winery wastes and by-products into biofuel and an added-value chemical while decreasing waste released to the environment.
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Affiliation(s)
- Sara L Baptista
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Aloia Romaní
- Department of Chemical Engineering, Faculty of Science, University of Vigo (Campus Ourense), As Lagoas, 32004, Ourense, Spain
| | - Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal.
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6
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Coimbra L, Malan K, Fagúndez A, Guigou M, Lareo C, Fernández B, Pratto M, Batista S. Fermentation of D-xylose to Ethanol by Saccharomyces cerevisiae CAT-1 Recombinant Strains. BIOENERGY RESEARCH 2023; 16:1001-1012. [PMID: 36248719 PMCID: PMC9540035 DOI: 10.1007/s12155-022-10514-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/27/2022] [Indexed: 05/09/2023]
Abstract
Ethanol production by the D-xylose fermentation of lignocellulosic biomass would augment environmental sustainability by increasing the yield of biofuel obtained per cultivated area. A set of recombinant strains derived from the industrial strain Saccharomyces cerevisiae CAT-1 was developed for this purpose. First, two recombinant strains were obtained by the chromosomal insertion of genes involved in the assimilation and transport of D-xylose (Gal2-N376F). Strain CAT-1-XRT was developed with heterologous genes for D-xylose metabolism from the oxo-reductive pathway of Scheffersomyces stipitis (XYL1-K270R, XYL2); and strain CAT-1-XIT, with D-xylose isomerase (xylA gene, XI) from Streptomyces coelicolor. Moreover, both recombinant strains contained extra copies of homologous genes for xylulose kinase (XK) and transaldolase (TAL1). Furthermore, plasmid (pRS42K::XI) was constructed with xylA from Piromyces sp. transferred to CAT-1, CAT-1-XRT, and CAT-1-XIT, followed by an evolution protocol. After 10 subcultures, CAT-1-XIT (pRS42K::XI) consumed 74% of D-xylose, producing 12.6 g/L ethanol (0.31 g ethanol/g D-xylose). The results of this study show that CAT-1-XIT (pRS42K::XI) is a promising recombinant strain for the efficient utilization of D-xylose to produce ethanol from lignocellulosic materials.
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Affiliation(s)
- Lucía Coimbra
- Laboratorio de Microbiología Molecular, Departamento BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
| | - Karen Malan
- Laboratorio de Microbiología Molecular, Departamento BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
| | - Alejandra Fagúndez
- Laboratorio de Microbiología Molecular, Departamento BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
| | - Mairan Guigou
- Departamento de Bioingeniería, Facultad de Ingeniería, Instituto de Ingeniería Química, Universidad de La República. Julio Herrera Y Reissig 565, 11300 Montevideo, CP Uruguay
| | - Claudia Lareo
- Departamento de Bioingeniería, Facultad de Ingeniería, Instituto de Ingeniería Química, Universidad de La República. Julio Herrera Y Reissig 565, 11300 Montevideo, CP Uruguay
| | - Belén Fernández
- Laboratorio de Microbiología Molecular, Departamento BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
| | - Martín Pratto
- Departamento de Bioingeniería, Facultad de Ingeniería, Instituto de Ingeniería Química, Universidad de La República. Julio Herrera Y Reissig 565, 11300 Montevideo, CP Uruguay
| | - Silvia Batista
- Laboratorio de Microbiología Molecular, Departamento BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
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Wang H, Cao L, Li Q, Wijayawardene NN, Zhao J, Cheng M, Li QR, Li X, Promputtha I, Kang YQ. Overexpressing GRE3 in Saccharomyces cerevisiae enables high ethanol production from different lignocellulose hydrolysates. Front Microbiol 2022; 13:1085114. [PMID: 36601405 PMCID: PMC9807136 DOI: 10.3389/fmicb.2022.1085114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
The efficiently renewable bioethanol can help to alleviate energy crisis and environmental pollution. Genetically modified strains for efficient use of xylose and developing lignocellulosic hydrolysates play an essential role in facilitating cellulosic ethanol production. Here we present a promising strain GRE3OE via GRE3 overexpressed in a previously reported Saccharomyces cerevisiae strain WXY70. A comprehensive evaluation of the fermentation level of GRE3OE in alkaline-distilled sweet sorghum bagasse, sorghum straw and xylose mother liquor hydrolysate. Under simulated corn stover hydrolysate, GRE3OE produced 53.39 g/L ethanol within 48 h. GRE3OE produced about 0.498 g/g total sugar in sorghum straw hydrolysate solution. Moreover, GRE3OE consumed more xylose than WXY70 in the high-concentration xylose mother liquor. Taken together, GRE3OE could be a candidate strain for industrial ethanol development, which is due to its remarkable fermentation efficiency during different lignocellulosic hydrolysates.
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Affiliation(s)
- Haijie Wang
- Key Laboratory of Medical Microbiology and Parasitology & Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China
| | - Limin Cao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Qi Li
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Nalin N. Wijayawardene
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China,Section of Genetics, Institute for Research and Development in Health and Social Care, Battaramulla, Sri Lanka,National Institute of Fundamental Studies, Kandy, Sri Lanka
| | - Jian Zhao
- State key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min Cheng
- Key Laboratory of Medical Microbiology and Parasitology & Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China,Department of Hospital Infection Management, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Qi-Rui Li
- Key Laboratory of Medical Microbiology and Parasitology & Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaobin Li
- Chishui Riverside Jiangi-Flavour Baijiu Research Center, Guizhou Sunveen Liquor Co., Ltd, Guiyang, China
| | - Itthayakorn Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand,Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Ying-Qian Kang
- Key Laboratory of Medical Microbiology and Parasitology & Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China,*Correspondence: Ying-Qian Kang,
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Bioethanol Production from Lignocellulosic Biomass-Challenges and Solutions. Molecules 2022; 27:molecules27248717. [PMID: 36557852 PMCID: PMC9785513 DOI: 10.3390/molecules27248717] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Regarding the limited resources for fossil fuels and increasing global energy demands, greenhouse gas emissions, and climate change, there is a need to find alternative energy sources that are sustainable, environmentally friendly, renewable, and economically viable. In the last several decades, interest in second-generation bioethanol production from non-food lignocellulosic biomass in the form of organic residues rapidly increased because of its abundance, renewability, and low cost. Bioethanol production fits into the strategy of a circular economy and zero waste plans, and using ethanol as an alternative fuel gives the world economy a chance to become independent of the petrochemical industry, providing energy security and environmental safety. However, the conversion of biomass into ethanol is a challenging and multi-stage process because of the variation in the biochemical composition of biomass and the recalcitrance of lignin, the aromatic component of lignocellulose. Therefore, the commercial production of cellulosic ethanol has not yet become well-received commercially, being hampered by high research and production costs, and substantial effort is needed to make it more widespread and profitable. This review summarises the state of the art in bioethanol production from lignocellulosic biomass, highlights the most challenging steps of the process, including pretreatment stages required to fragment biomass components and further enzymatic hydrolysis and fermentation, presents the most recent technological advances to overcome the challenges and high costs, and discusses future perspectives of second-generation biorefineries.
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Cheng C, Wang WB, Sun ML, Tang RQ, Bai L, Alper HS, Zhao XQ. Deletion of NGG1 in a recombinant Saccharomyces cerevisiae improved xylose utilization and affected transcription of genes related to amino acid metabolism. Front Microbiol 2022; 13:960114. [PMID: 36160216 PMCID: PMC9493327 DOI: 10.3389/fmicb.2022.960114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Production of biofuels and biochemicals from xylose using yeast cell factory is of great interest for lignocellulosic biorefinery. Our previous studies revealed that a natural yeast isolate Saccharomyces cerevisiae YB-2625 has superior xylose-fermenting ability. Through integrative omics analysis, NGG1, which encodes a transcription regulator as well as a subunit of chromatin modifying histone acetyltransferase complexes was revealed to regulate xylose metabolism. Deletion of NGG1 in S. cerevisiae YRH396h, which is the haploid version of the recombinant yeast using S. cerevisiae YB-2625 as the host strain, improved xylose consumption by 28.6%. Comparative transcriptome analysis revealed that NGG1 deletion down-regulated genes related to mitochondrial function, TCA cycle, ATP biosynthesis, respiration, as well as NADH generation. In addition, the NGG1 deletion mutant also showed transcriptional changes in amino acid biosynthesis genes. Further analysis of intracellular amino acid content confirmed the effect of NGG1 on amino acid accumulation during xylose utilization. Our results indicated that NGG1 is one of the core nodes for coordinated regulation of carbon and nitrogen metabolism in the recombinant S. cerevisiae. This work reveals novel function of Ngg1p in yeast metabolism and provides basis for developing robust yeast strains to produce ethanol and biochemicals using lignocellulosic biomass.
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Affiliation(s)
- Cheng Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Meng-Lin Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui-Qi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Long Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Xin-Qing Zhao,
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Shahbaz A, Hussain N, Saleem MZ, Saeed MU, Bilal M, Iqbal HM. Nanoparticles as stimulants for efficient generation of biofuels and renewables. FUEL 2022; 319:123724. [DOI: 10.1016/j.fuel.2022.123724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Li B, Liu N, Zhao X. Response mechanisms of Saccharomyces cerevisiae to the stress factors present in lignocellulose hydrolysate and strategies for constructing robust strains. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:28. [PMID: 35292082 PMCID: PMC8922928 DOI: 10.1186/s13068-022-02127-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/01/2022] [Indexed: 11/19/2022]
Abstract
Bioconversion of lignocellulosic biomass to biofuels such as bioethanol and high value-added products has attracted great interest in recent decades due to the carbon neutral nature of biomass feedstock. However, there are still many key technical difficulties for the industrial application of biomass bioconversion processes. One of the challenges associated with the microorganism Saccharomyces cerevisiae that is usually used for bioethanol production refers to the inhibition of the yeast by various stress factors. These inhibitive effects seriously restrict the growth and fermentation performance of the strains, resulting in reduced bioethanol production efficiency. Therefore, improving the stress response ability of the strains is of great significance for industrial production of bioethanol. In this article, the response mechanisms of S. cerevisiae to various hydrolysate-derived stress factors including organic acids, furan aldehydes, and phenolic compounds have been reviewed. Organic acids mainly stimulate cells to induce intracellular acidification, furan aldehydes mainly break the intracellular redox balance, and phenolic compounds have a greater effect on membrane homeostasis. These damages lead to inadequate intracellular energy supply and dysregulation of transcription and translation processes, and then activate a series of stress responses. The regulation mechanisms of S. cerevisiae in response to these stress factors are discussed with regard to the cell wall/membrane, energy, amino acids, transcriptional and translational, and redox regulation. The reported key target genes and transcription factors that contribute to the improvement of the strain performance are summarized. Furthermore, the genetic engineering strategies of constructing multilevel defense and eliminating stress effects are discussed in order to provide technical strategies for robust strain construction. It is recommended that robust S. cerevisiae can be constructed with the intervention of metabolic regulation based on the specific stress responses. Rational design with multilevel gene control and intensification of key enzymes can provide good strategies for construction of robust strains.
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Affiliation(s)
- Bo Li
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China.,Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Nan Liu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China.,Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xuebing Zhao
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China. .,Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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12
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Saravanan A, Senthil Kumar P, Jeevanantham S, Karishma S, Vo DVN. Recent advances and sustainable development of biofuels production from lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2022; 344:126203. [PMID: 34710606 DOI: 10.1016/j.biortech.2021.126203] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/16/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Many countries in the world are facing the demand for non-renewable fossil fuels because of overpopulation and economic boom. To reduce environmental pollution and zero carbon emission, the conversion of biomass into biofuels has paid better attention and is considered to be an innovative approach. A diverse raw material has been utilized as feedstock for the production of biofuel, depending on the availability of biomass, cost-effectiveness, and their geographic location. Among the different raw materials, lignocellulosic biomass has fascinated many researchers around the world. The current review discovers the potential application of lignocellulosic biomass for the production of biofuels. Various pretreatment methods have been widely used to increase the hydrolysis rate and accessibility of biomass. This review highlights recent advances in pretreatment methodologies for the enhanced production of biofuels. Detailed descriptions of the mechanism of biomass processing pathway, optimization, and modeling study have been discussed.
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Affiliation(s)
- A Saravanan
- Department of Energy and Environmental Engineering, Saveetha School of Engineering, SIMATS, Chennai 602105, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai 603110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai 603110, India.
| | - S Jeevanantham
- Department of Biotechnology, Rajalakshmi Engineering College, Chennai 602105, India
| | - S Karishma
- Department of Biotechnology, Rajalakshmi Engineering College, Chennai 602105, India
| | - Dai-Viet N Vo
- Institute of Environmental Sciences, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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13
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Gutmann F, Jann C, Pereira F, Johansson A, Steinmetz LM, Patil KR. CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:41. [PMID: 33568224 PMCID: PMC7874482 DOI: 10.1186/s13068-021-01880-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/07/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Baker's yeast is a widely used eukaryotic cell factory, producing a diverse range of compounds including biofuels and fine chemicals. The use of lignocellulose as feedstock offers the opportunity to run these processes in an environmentally sustainable way. However, the required hydrolysis pretreatment of lignocellulosic material releases toxic compounds that hamper yeast growth and consequently productivity. RESULTS Here, we employ CRISPR interference in S. cerevisiae to identify genes modulating fermentative growth in plant hydrolysate and in presence of lignocellulosic toxins. We find that at least one-third of hydrolysate-associated gene functions are explained by effects of known toxic compounds, such as the decreased growth of YAP1 or HAA1, or increased growth of DOT6 knock-down strains in hydrolysate. CONCLUSION Our study confirms previously known genetic elements and uncovers new targets towards designing more robust yeast strains for the utilization of lignocellulose hydrolysate as sustainable feedstock, and, more broadly, paves the way for applying CRISPRi screens to improve industrial fermentation processes.
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Affiliation(s)
- Friederike Gutmann
- European Molecular Biology Laboratory (EMBL), Structural and Cell Biology Unit, 69117, Heidelberg, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Cosimo Jann
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117, Heidelberg, Germany.
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.
| | - Filipa Pereira
- European Molecular Biology Laboratory (EMBL), Structural and Cell Biology Unit, 69117, Heidelberg, Germany.
| | - Andreas Johansson
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117, Heidelberg, Germany
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Genome Technology Center, Palo Alto, CA, 94304, USA
| | - Kiran R Patil
- European Molecular Biology Laboratory (EMBL), Structural and Cell Biology Unit, 69117, Heidelberg, Germany.
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK.
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14
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Baptista SL, Costa CE, Cunha JT, Soares PO, Domingues L. Metabolic engineering of Saccharomyces cerevisiae for the production of top value chemicals from biorefinery carbohydrates. Biotechnol Adv 2021; 47:107697. [PMID: 33508428 DOI: 10.1016/j.biotechadv.2021.107697] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/16/2022]
Abstract
The implementation of biorefineries for a cost-effective and sustainable production of energy and chemicals from renewable carbon sources plays a fundamental role in the transition to a circular economy. The US Department of Energy identified a group of key target compounds that can be produced from biorefinery carbohydrates. In 2010, this list was revised and included organic acids (lactic, succinic, levulinic and 3-hydroxypropionic acids), sugar alcohols (xylitol and sorbitol), furans and derivatives (hydroxymethylfurfural, furfural and furandicarboxylic acid), biohydrocarbons (isoprene), and glycerol and its derivatives. The use of substrates like lignocellulosic biomass that impose harsh culture conditions drives the quest for the selection of suitable robust microorganisms. The yeast Saccharomyces cerevisiae, widely utilized in industrial processes, has been extensively engineered to produce high-value chemicals. For its robustness, ease of handling, genetic toolbox and fitness in an industrial context, S. cerevisiae is an ideal platform for the founding of sustainable bioprocesses. Taking these into account, this review focuses on metabolic engineering strategies that have been applied to S. cerevisiae for converting renewable resources into the previously identified chemical targets. The heterogeneity of each chemical and its manufacturing process leads to inevitable differences between the development stages of each process. Currently, 8 of 11 of these top value chemicals have been already reported to be produced by recombinant S. cerevisiae. While some of them are still in an early proof-of-concept stage, others, like xylitol or lactic acid, are already being produced from lignocellulosic biomass. Furthermore, the constant advances in genome-editing tools, e.g. CRISPR/Cas9, coupled with the application of innovative process concepts such as consolidated bioprocessing, will contribute for the establishment of S. cerevisiae-based biorefineries.
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Affiliation(s)
- 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
| | - 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
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal.
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15
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Abstract
In order to exploit a fast-growing Paulownia hardwood as an energy crop, a xylose-enriched hydrolysate was obtained in this work to increase the ethanol concentration using the hemicellulosic fraction, besides the already widely studied cellulosic fraction. For that, Paulownia elongata x fortunei was submitted to autohydrolysis treatment (210 °C or S0 of 4.08) for the xylan solubilization, mainly as xylooligosaccharides. Afterwards, sequential stages of acid hydrolysis, concentration, and detoxification were evaluated to obtain fermentable sugars. Thus, detoxified and non-detoxified hydrolysates (diluted or not) were fermented for ethanol production using a natural xylose-consuming yeast, Scheffersomyces stipitis CECT 1922, and an industrial Saccharomyces cerevisiae MEC1133 strain, metabolic engineered strain with the xylose reductase/xylitol dehydrogenase pathway. Results from fermentation assays showed that the engineered S. cerevisiae strain produced up to 14.2 g/L of ethanol (corresponding to 0.33 g/g of ethanol yield) using the non-detoxified hydrolysate. Nevertheless, the yeast S. stipitis reached similar values of ethanol, but only in the detoxified hydrolysate. Hence, the fermentation data prove the suitability and robustness of the engineered strain to ferment non-detoxified liquor, and the appropriateness of detoxification of liquor for the use of less robust yeast. In addition, the success of hemicellulose-to-ethanol production obtained in this work shows the Paulownia biomass as a suitable renewable source for ethanol production following a suitable fractionation process within a biorefinery approach.
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16
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Adegboye MF, Ojuederie OB, Talia PM, Babalola OO. Bioprospecting of microbial strains for biofuel production: metabolic engineering, applications, and challenges. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:5. [PMID: 33407786 PMCID: PMC7788794 DOI: 10.1186/s13068-020-01853-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/09/2020] [Indexed: 05/17/2023]
Abstract
The issues of global warming, coupled with fossil fuel depletion, have undoubtedly led to renewed interest in other sources of commercial fuels. The search for renewable fuels has motivated research into the biological degradation of lignocellulosic biomass feedstock to produce biofuels such as bioethanol, biodiesel, and biohydrogen. The model strain for biofuel production needs the capability to utilize a high amount of substrate, transportation of sugar through fast and deregulated pathways, ability to tolerate inhibitory compounds and end products, and increased metabolic fluxes to produce an improved fermentation product. Engineering microbes might be a great approach to produce biofuel from lignocellulosic biomass by exploiting metabolic pathways economically. Metabolic engineering is an advanced technology for the construction of highly effective microbial cell factories and a key component for the next-generation bioeconomy. It has been extensively used to redirect the biosynthetic pathway to produce desired products in several native or engineered hosts. A wide range of novel compounds has been manufactured through engineering metabolic pathways or endogenous metabolism optimizations by metabolic engineers. This review is focused on the potential utilization of engineered strains to produce biofuel and gives prospects for improvement in metabolic engineering for new strain development using advanced technologies.
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Affiliation(s)
- Mobolaji Felicia Adegboye
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa
| | - Omena Bernard Ojuederie
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa
- Department of Biological Sciences, Faculty of Science, Kings University, Ode-Omu, PMB 555, Osun State, Nigeria
| | - Paola M Talia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA CICVyA, CNIA, INTA Castelar, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, 1686) Hurlingham, Provincia de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Buenos Aires, Provincia de Buenos Aires, Argentina
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa.
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17
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Qin L, Dong S, Yu J, Ning X, Xu K, Zhang SJ, Xu L, Li BZ, Li J, Yuan YJ, Li C. Stress-driven dynamic regulation of multiple tolerance genes improves robustness and productive capacity of Saccharomyces cerevisiae in industrial lignocellulose fermentation. Metab Eng 2020; 61:160-170. [DOI: 10.1016/j.ymben.2020.06.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 12/20/2022]
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19
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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: 39] [Impact Index Per Article: 7.8] [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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20
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Cunha JT, Romaní A, Inokuma K, Johansson B, Hasunuma T, Kondo A, Domingues L. Consolidated bioprocessing of corn cob-derived hemicellulose: engineered industrial Saccharomyces cerevisiae as efficient whole cell biocatalysts. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:138. [PMID: 32782474 PMCID: PMC7414751 DOI: 10.1186/s13068-020-01780-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/29/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Consolidated bioprocessing, which combines saccharolytic and fermentative abilities in a single microorganism, is receiving increased attention to decrease environmental and economic costs in lignocellulosic biorefineries. Nevertheless, the economic viability of lignocellulosic ethanol is also dependent of an efficient utilization of the hemicellulosic fraction, which contains xylose as a major component in concentrations that can reach up to 40% of the total biomass in hardwoods and agricultural residues. This major bottleneck is mainly due to the necessity of chemical/enzymatic treatments to hydrolyze hemicellulose into fermentable sugars and to the fact that xylose is not readily consumed by Saccharomyces cerevisiae-the most used organism for large-scale ethanol production. In this work, industrial S. cerevisiae strains, presenting robust traits such as thermotolerance and improved resistance to inhibitors, were evaluated as hosts for the cell-surface display of hemicellulolytic enzymes and optimized xylose assimilation, aiming at the development of whole-cell biocatalysts for consolidated bioprocessing of corn cob-derived hemicellulose. RESULTS These modifications allowed the direct production of ethanol from non-detoxified hemicellulosic liquor obtained by hydrothermal pretreatment of corn cob, reaching an ethanol titer of 11.1 g/L corresponding to a yield of 0.328 g/g of potential xylose and glucose, without the need for external hydrolytic catalysts. Also, consolidated bioprocessing of pretreated corn cob was found to be more efficient for hemicellulosic ethanol production than simultaneous saccharification and fermentation with addition of commercial hemicellulases. CONCLUSIONS These results show the potential of industrial S. cerevisiae strains for the design of whole-cell biocatalysts and paves the way for the development of more efficient consolidated bioprocesses for lignocellulosic biomass valorization, further decreasing environmental and economic costs.
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Affiliation(s)
- Joana T. Cunha
- CEB–Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Aloia Romaní
- CEB–Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Kentaro Inokuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501 Japan
| | - Björn Johansson
- Center of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501 Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501 Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501 Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501 Japan
| | - Lucília Domingues
- CEB–Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
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21
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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] [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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22
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Del Río PG, Gomes-Dias JS, Rocha CMR, Romaní A, Garrote G, Domingues L. Recent trends on seaweed fractionation for liquid biofuels production. BIORESOURCE TECHNOLOGY 2020; 299:122613. [PMID: 31870706 DOI: 10.1016/j.biortech.2019.122613] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 05/18/2023]
Abstract
Concerns about fossil fuels depletion has led to seek for new sources of energy. The use of marine biomass (seaweed) to produce biofuels presents widely recognized advantages over terrestrial biomasses such as higher production ratio, higher photosynthetic efficiency or carbon-neutral emissions. In here, interesting seaweed sources as a whole or as a residue from seaweed processing industries for biofuel production were identified and their diverse composition and availability compiled. In addition, the pretreatments used for seaweed fractionation were thoroughly revised as this step is pivotal in a seaweed biorefinery for integral biomass valorization and for enabling biomass-to-biofuel economic feasibility processes. Traditional and emerging technologies were revised, with particular emphasis on green technologies, relating pretreatment not only with the type of biomass but also with the final target product(s) and yields. Current hurdles of marine biomass-to-biofuel processes were pinpointed and discussed and future perspectives on the development of these processes given.
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Affiliation(s)
- Pablo G Del Río
- Department of Chemical Engineering, Faculty of Science, University of Vigo Campus Ourense, As Lagoas, 32004 Ourense, Spain
| | - Joana S Gomes-Dias
- CEB-Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Cristina M R Rocha
- CEB-Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Aloia Romaní
- CEB-Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal.
| | - Gil Garrote
- Department of Chemical Engineering, Faculty of Science, University of Vigo Campus Ourense, As Lagoas, 32004 Ourense, Spain
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
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23
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Hoang Nguyen Tran P, Ko JK, Gong G, Um Y, Lee SM. Improved simultaneous co-fermentation of glucose and xylose by Saccharomyces cerevisiae for efficient lignocellulosic biorefinery. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:12. [PMID: 31993090 PMCID: PMC6975041 DOI: 10.1186/s13068-019-1641-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/19/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Lignocellulosic biorefinery offers economical and sustainable production of fuels and chemicals. Saccharomyces cerevisiae, a promising industrial host for biorefinery, has been intensively developed to expand its product profile. However, the sequential and slow conversion of xylose into target products remains one of the main challenges for realizing efficient industrial lignocellulosic biorefinery. RESULTS In this study, we developed a powerful mixed-sugar co-fermenting strain of S. cerevisiae, XUSEA, with improved xylose conversion capacity during simultaneous glucose/xylose co-fermentation. To reinforce xylose catabolism, the overexpression target in the pentose phosphate pathway was selected using a DNA assembler method and overexpressed increasing xylose consumption and ethanol production by twofold. The performance of the newly engineered strain with improved xylose catabolism was further boosted by elevating fermentation temperature and thus significantly reduced the co-fermentation time by half. Through combined efforts of reinforcing the pathway of xylose catabolism and elevating the fermentation temperature, XUSEA achieved simultaneous co-fermentation of lignocellulosic hydrolysates, composed of 39.6 g L-1 glucose and 23.1 g L-1 xylose, within 24 h producing 30.1 g L-1 ethanol with a yield of 0.48 g g-1. CONCLUSIONS Owing to its superior co-fermentation performance and ability for further engineering, XUSEA has potential as a platform in a lignocellulosic biorefinery toward realizing a more economical and sustainable process for large-scale bioethanol production.
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Affiliation(s)
- Phuong Hoang Nguyen Tran
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
- Green School, Korea University, Seoul, 02841 Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
- Green School, Korea University, Seoul, 02841 Republic of Korea
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Smekenov I, Bakhtambayeva M, Bissenbayev K, Saparbayev M, Taipakova S, Bissenbaev AK. Heterologous secretory expression of β-glucosidase from Thermoascus aurantiacus in industrial Saccharomyces cerevisiae strains. Braz J Microbiol 2019; 51:107-123. [PMID: 31776864 DOI: 10.1007/s42770-019-00192-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 11/14/2019] [Indexed: 10/25/2022] Open
Abstract
The use of plant biomass for biofuel production will require efficient utilization of the sugars in lignocellulose, primarily cellobiose, because it is the major soluble by-product of cellulose and acts as a strong inhibitor, especially for cellobiohydrolase, which plays a key role in cellulose hydrolysis. Commonly used ethanologenic yeast Saccharomyces cerevisiae is unable to utilize cellobiose; accordingly, genetic engineering efforts have been made to transfer β-glucosidase genes enabling cellobiose utilization. Nonetheless, laboratory yeast strains have been employed for most of this research, and such strains may be difficult to use in industrial processes because of their generally weaker resistance to stressors and worse fermenting abilities. The purpose of this study was to engineer industrial yeast strains to ferment cellobiose after stable integration of tabgl1 gene that encodes a β-glucosidase from Thermoascus aurantiacus (TaBgl1). The recombinant S. cerevisiae strains obtained in this study secrete TaBgl1, which can hydrolyze cellobiose and produce ethanol. This study clearly indicates that the extent of glycosylation of secreted TaBgl1 depends from the yeast strains used and is greatly influenced by carbon sources (cellobiose or glucose). The recombinant yeast strains showed high osmotolerance and resistance to various concentrations of ethanol and furfural and to high temperatures. Therefore, these yeast strains are suitable for ethanol production processes with saccharified lignocellulose.
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Affiliation(s)
- Izat Smekenov
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Marzhan Bakhtambayeva
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Kudaybergen Bissenbayev
- Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Nazarbayev Intellectual School, Almaty, Kazakhstan, 050044
| | - Murat Saparbayev
- Gustave Roussy Cancer Campus, CNRS UMR8200, Université Paris-Sud, F-94805, Villejuif Cedex, France
| | - Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Amangeldy K Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040. .,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.
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de Andrade Silva CA, Oka ML, Fonseca GG. Physiology of yeast strains isolated from Brazilian biomes in a minimal medium using fructose as the sole carbon source reveals potential biotechnological applications. 3 Biotech 2019; 9:191. [PMID: 31065491 DOI: 10.1007/s13205-019-1721-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 04/17/2019] [Indexed: 01/06/2023] Open
Abstract
The aim of this study was to evaluate the kinetic parameters and the production of metabolites of 13 novel yeasts isolated from a distillery and fruits, and Saccharomyces cerevisiae CAT-1, cultivated in fructose-based medium. The yeasts with the highest µ max were obtained from must, Pichia kudriavzevii BB2, P. kudriavzevii BB1, and S. cerevisiae BB9 (0.47-0.49 h-1). S. cerevisiae CAT-1 (3.02 g gDCM-1 h-1), S. cerevisiae BB9 (3.01 g gDCM-1 h-1), and Candida glabrata Recol 41 (2.52 g gDCM-1 h-1) stood out in terms of µ S. C. parapsilosis Recol 29, and Rhodotorula mucilaginosa Recol 03 strains showed the highest Y X/S (0.30 and 0.28 gDCM g-1, respectively). C. glabrata Recol 10 and S. cerevisiae BB9 strains stood out for their higher substrate conversion rates into ethanol (0.44 and 0.41 gEth gS-1, respectively). R. mucilaginosa Recol 03 presented the poorest performance in substrate consumption (0.87 g gDCM-1 h-1), while the strains isolated from must and C. glabrata Recol 10 showed the highest ethanol production and the C. parapsilosis Recol 29 showed the highest biomass conversion.
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Sun XB, Cao JW, Wang JK, Lin HZ, Gao DY, Qian GY, Park YD, Chen ZF, Wang Q. SpyTag/SpyCatcher molecular cyclization confers protein stability and resilience to aggregation. N Biotechnol 2019; 49:28-36. [DOI: 10.1016/j.nbt.2018.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 12/14/2018] [Accepted: 12/15/2018] [Indexed: 01/02/2023]
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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: 81] [Impact Index Per Article: 13.5] [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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Cunha JT, Romaní A, Costa CE, Sá-Correia I, Domingues L. Molecular and physiological basis of Saccharomyces cerevisiae tolerance to adverse lignocellulose-based process conditions. Appl Microbiol Biotechnol 2018; 103:159-175. [PMID: 30397768 DOI: 10.1007/s00253-018-9478-3] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/27/2022]
Abstract
Lignocellulose-based biorefineries have been gaining increasing attention to substitute current petroleum-based refineries. Biomass processing requires a pretreatment step to break lignocellulosic biomass recalcitrant structure, which results in the release of a broad range of microbial inhibitors, mainly weak acids, furans, and phenolic compounds. Saccharomyces cerevisiae is the most commonly used organism for ethanol production; however, it can be severely distressed by these lignocellulose-derived inhibitors, in addition to other challenging conditions, such as pentose sugar utilization and the high temperatures required for an efficient simultaneous saccharification and fermentation step. Therefore, a better understanding of the yeast response and adaptation towards the presence of these multiple stresses is of crucial importance to design strategies to improve yeast robustness and bioconversion capacity from lignocellulosic biomass. This review includes an overview of the main inhibitors derived from diverse raw material resultants from different biomass pretreatments, and describes the main mechanisms of yeast response to their presence, as well as to the presence of stresses imposed by xylose utilization and high-temperature conditions, with a special emphasis on the synergistic effect of multiple inhibitors/stressors. Furthermore, successful cases of tolerance improvement of S. cerevisiae are highlighted, in particular those associated with other process-related physiologically relevant conditions. Decoding the overall yeast response mechanisms will pave the way for the integrated development of sustainable yeast cell-based biorefineries.
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Affiliation(s)
- Joana T Cunha
- Centre of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal
| | - Aloia Romaní
- Centre of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal
| | - Carlos E Costa
- Centre of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Lucília Domingues
- Centre of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal.
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Baptista SL, Cunha JT, Romaní A, Domingues L. Xylitol production from lignocellulosic whole slurry corn cob by engineered industrial Saccharomyces cerevisiae PE-2. BIORESOURCE TECHNOLOGY 2018; 267:481-491. [PMID: 30041142 DOI: 10.1016/j.biortech.2018.07.068] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
In this work, the industrial Saccharomyces cerevisiae PE-2 strain, presenting innate capacity for xylitol accumulation, was engineered for xylitol production by overexpression of the endogenous GRE3 gene and expression of different xylose reductases from Pichia stipitis. The best-performing GRE3-overexpressing strain was capable to produce 148.5 g/L of xylitol from high xylose-containing media, with a 0.95 g/g yield, and maintained close to maximum theoretical yields (0.89 g/g) when tested in non-detoxified corn cob hydrolysates. Furthermore, a successful integrated strategy was developed for the production of xylitol from whole slurry corn cob in a presaccharification and simultaneous saccharification and fermentation process (15% solid loading and 36 FPU) reaching xylitol yield of 0.93 g/g and a productivity of 0.54 g/L·h. This novel approach results in an intensified valorization of lignocellulosic biomass for xylitol production in a fully integrated process and represents an advance towards a circular economy.
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Affiliation(s)
- Sara L Baptista
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Joana T Cunha
- 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
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
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Zhou J, Zhu P, Hu X, Lu H, Yu Y. Improved secretory expression of lignocellulolytic enzymes in Kluyveromyces marxianus by promoter and signal sequence engineering. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:235. [PMID: 30279722 PMCID: PMC6116501 DOI: 10.1186/s13068-018-1232-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/20/2018] [Indexed: 06/05/2023]
Abstract
BACKGROUND Taking into account its thermotolerance, high growth rate, and broad substrate spectrum, Kluyveromyces marxianus can be considered an ideal consolidated bioprocessing (CBP). A major obstacle to ethanol production using K. marxianus is the low production of lignocellulolytic enzymes, which reduces the cellulose hydrolysis and ethanol production. Thus, further improvement of enzyme expression and secretion is essential. RESULTS To improve the expression of lignocellulolytic enzymes, the inulinase promoter and signal sequence from K. marxianus was optimized through mutagenesis. A T(-361)A mutation inside the promoter, a deletion of AT-rich region inside 5'UTR (UTR∆A), and a P10L substitution in the signal sequence increased the secretory expression of the feruloyl esterase Est1E by up to sixfold. T(-361)A and UTR∆A increased the mRNA expression, while the P10L substitution extended the hydrophobic core of signal sequence and promoted secretion of mature protein. P10L and T(-361)A mutations increased secretory expressions of other types of lignocellulolytic enzymes by up to threefold, including endo-1,4-β-glucanase RuCelA, endo-1,4-β-endoxylanase Xyn-CDBFV, and endo-1,4-β-mannanase MAN330. During the fed-batch fermentation of strains carrying optimized modules, the peak activities of RuCelA, Xyn-CDBFV, MAN330, and Est1E reached 24 U/mL, 25,600 U/mL, 10,200 U/mL, and 1220 U/mL, respectively. Importantly, higher yield of enzymes by optimized promoter and signal sequence were achieved in all tested carbon sources, including the major end products of lignocellulose saccharification and fermentation, with growth on xylose resulting in the highest production. CONCLUSIONS The engineered promoter and signal sequence presented increased secretory expressions of different lignocellulolytic enzymes in K. marxianus by means of various carbon resources. Activities of lignocellulolytic enzymes in fed-batch fermentation were the highest activities reported for K. marxianus so far. Our engineered modules are valuable in producing lignocellulolytic enzymes by K. marxianus and in constructing efficient CBP strains for cellulosic ethanol production.
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Affiliation(s)
- Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Peixia Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Xiaoyue Hu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, 200237 China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
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Cunha JT, Costa CE, Ferraz L, Romaní A, Johansson B, Sá-Correia I, Domingues L. HAA1 and PRS3 overexpression boosts yeast tolerance towards acetic acid improving xylose or glucose consumption: unravelling the underlying mechanisms. Appl Microbiol Biotechnol 2018; 102:4589-4600. [PMID: 29607452 DOI: 10.1007/s00253-018-8955-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/12/2018] [Accepted: 03/18/2018] [Indexed: 11/28/2022]
Abstract
Acetic acid tolerance and xylose consumption are desirable traits for yeast strains used in industrial biotechnological processes. In this work, overexpression of a weak acid stress transcriptional activator encoded by the gene HAA1 and a phosphoribosyl pyrophosphate synthetase encoded by PRS3 in a recombinant industrial Saccharomyces cerevisiae strain containing a xylose metabolic pathway was evaluated in the presence of acetic acid in xylose- or glucose-containing media. HAA1 or PRS3 overexpression resulted in superior yeast growth and higher sugar consumption capacities in the presence of 4 g/L acetic acid, and a positive synergistic effect resulted from the simultaneous overexpression of both genes. Overexpressing these genes also improved yeast adaptation to a non-detoxified hardwood hydrolysate with a high acetic acid content. Furthermore, the overexpression of HAA1 and/or PRS3 was found to increase the robustness of yeast cell wall when challenged with acetic acid stress, suggesting the involvement of the modulation of the cell wall integrity pathway. This study clearly shows HAA1 and/or, for the first time, PRS3 overexpression to play an important role in the improvement of industrial yeast tolerance towards acetic acid. The results expand the molecular toolbox and add to the current understanding of the mechanisms involved in higher acetic acid tolerance, paving the way for the further development of more efficient industrial processes.
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Affiliation(s)
- Joana T Cunha
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Carlos E Costa
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Luís Ferraz
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Aloia Romaní
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Björn Johansson
- Center of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Lucília Domingues
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Cruz ML, Resende MMD, Ribeiro EJ. Evaluation of process conditions in the performance of yeast on alcoholic fermentation. CHEM ENG COMMUN 2018. [DOI: 10.1080/00986445.2017.1423061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Mariana Lopes Cruz
- Faculty of Chemical Engineering, Uberlândia Federal University, Uberlândia, Minas Gerais, Brazil
| | - Miriam Maria de Resende
- Faculty of Chemical Engineering, Uberlândia Federal University, Uberlândia, Minas Gerais, Brazil
| | - Eloízio Júlio Ribeiro
- Faculty of Chemical Engineering, Uberlândia Federal University, Uberlândia, Minas Gerais, Brazil
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Cunha M, Romaní A, Carvalho M, Domingues L. Boosting bioethanol production from Eucalyptus wood by whey incorporation. BIORESOURCE TECHNOLOGY 2018; 250:256-264. [PMID: 29174903 DOI: 10.1016/j.biortech.2017.11.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 06/07/2023]
Abstract
The mixture of Eucalyptus globulus wood (EGW) and cheese whey powder (CWP) was proposed for intensification of simultaneous saccharification and fermentation (SSF) at high temperature and solid loadings using the industrial Saccharomyces cerevisiae Ethanol Red® strain. High ethanol concentration (93 g/L), corresponding to 94% ethanol yield, was obtained at 35 °C from 37% of solid mixture using cellulase and β-galactosidase enzymes (24.2 FPU/g and 20.0 U/g, respectively). The use of CWP mixed with pretreated EGW increased the ethanol concentration in 1.5-fold, in comparison with SSF experiments without CWP for both Ethanol Red® and CEN.PK113-7D strains. Moreover, 1.4-fold higher ethanol concentration was obtained with Ethanol Red®, in comparison with CEN.PK113-7D strain. Ethanol Red® strain was genetically engineered for β-galactosidase production in order to advance towards a fully integrated process. This work shows the feasibility of attaining high ethanol concentrations in second generation bioprocesses by a multi-waste valorization approach.
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Affiliation(s)
- Manuel Cunha
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Aloia Romaní
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Margarida Carvalho
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal.
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Tran Nguyen Hoang P, Ko JK, Gong G, Um Y, Lee SM. Genomic and phenotypic characterization of a refactored xylose-utilizing Saccharomyces cerevisiae strain for lignocellulosic biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:268. [PMID: 30288173 PMCID: PMC6162923 DOI: 10.1186/s13068-018-1269-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/21/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Engineered strains of Saccharomyces cerevisiae have significantly improved the prospects of biorefinery by improving the bioconversion yields in lignocellulosic bioethanol production and expanding the product profiles to include advanced biofuels and chemicals. However, the lignocellulosic biorefinery concept has not been fully applied using engineered strains in which either xylose utilization or advanced biofuel/chemical production pathways have been upgraded separately. Specifically, high-performance xylose-fermenting strains have rarely been employed as advanced biofuel and chemical production platforms and require further engineering to expand their product profiles. RESULTS In this study, we refactored a high-performance xylose-fermenting S. cerevisiae that could potentially serve as a platform strain for advanced biofuels and biochemical production. Through combinatorial CRISPR-Cas9-mediated rational and evolutionary engineering, we obtained a newly refactored isomerase-based xylose-fermenting strain, XUSE, that demonstrated efficient conversion of xylose into ethanol with a high yield of 0.43 g/g. In addition, XUSE exhibited the simultaneous fermentation of glucose and xylose with negligible glucose inhibition, indicating the potential of this isomerase-based xylose-utilizing strain for lignocellulosic biorefinery. The genomic and transcriptomic analysis of XUSE revealed beneficial mutations and changes in gene expression that are responsible for the enhanced xylose fermentation performance of XUSE. CONCLUSIONS In this study, we developed a high-performance xylose-fermenting S. cerevisiae strain, XUSE, with high ethanol yield and negligible glucose inhibition. Understanding the genomic and transcriptomic characteristics of XUSE revealed isomerase-based engineering strategies for improved xylose fermentation in S. cerevisiae. With high xylose fermentation performance and room for further engineering, XUSE could serve as a promising platform strain for lignocellulosic biorefinery.
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Affiliation(s)
- Phuong Tran Nguyen Hoang
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
- Green School, Korea University, Seoul, 02841 Republic of Korea
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Influence of genetic background of engineered xylose-fermenting industrial Saccharomyces cerevisiae strains for ethanol production from lignocellulosic hydrolysates. J Ind Microbiol Biotechnol 2017; 44:1575-1588. [PMID: 28891041 DOI: 10.1007/s10295-017-1979-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
An industrial ethanol-producing Saccharomyces cerevisiae strain with genes of fungal oxido-reductive pathway needed for xylose fermentation integrated into its genome (YRH1415) was used to obtain haploids and diploid isogenic strains. The isogenic strains were more effective in metabolizing xylose than YRH1415 strain and able to co-ferment glucose and xylose in the presence of high concentrations of inhibitors resulting from the hydrolysis of lignocellulosic biomass (switchgrass). The rate of xylose consumption did not appear to be affected by the ploidy of strains or the presence of two copies of the xylose fermentation genes but by heterozygosity of alleles for xylose metabolism in YRH1415. Furthermore, inhibitor tolerance was influenced by the heterozygous genome of the industrial strain, which also showed a marked influenced on tolerance to increasing concentrations of toxic compounds, such as furfural. In this work, selection of haploid derivatives was found to be a useful strategy to develop efficient xylose-fermenting industrial yeast strains.
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Metabolic engineering of a haploid strain derived from a triploid industrial yeast for producing cellulosic ethanol. Metab Eng 2017; 40:176-185. [DOI: 10.1016/j.ymben.2017.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/06/2017] [Accepted: 02/14/2017] [Indexed: 12/25/2022]
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Costa CE, Romaní A, Cunha JT, Johansson B, Domingues L. Integrated approach for selecting efficient Saccharomyces cerevisiae for industrial lignocellulosic fermentations: Importance of yeast chassis linked to process conditions. BIORESOURCE TECHNOLOGY 2017; 227:24-34. [PMID: 28013133 DOI: 10.1016/j.biortech.2016.12.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/02/2016] [Accepted: 12/04/2016] [Indexed: 05/22/2023]
Abstract
In this work, four robust yeast chassis isolated from industrial environments were engineered with the same xylose metabolic pathway. The recombinant strains were physiologically characterized in synthetic xylose and xylose-glucose medium, on non-detoxified hemicellulosic hydrolysates of fast-growing hardwoods (Eucalyptus and Paulownia) and agricultural residues (corn cob and wheat straw) and on Eucalyptus hydrolysate at different temperatures. Results show that the co-consumption of xylose-glucose was dependent on the yeast background. Moreover, heterogeneous results were obtained among different hydrolysates and temperatures for each individual strain pointing to the importance of designing from the very beginning a tailor-made yeast considering the specific raw material and process.
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Affiliation(s)
- Carlos E Costa
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Aloia Romaní
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Björn Johansson
- CBMA - Center of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.
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Li H, Shen Y, Wu M, Hou J, Jiao C, Li Z, Liu X, Bao X. Engineering a wild-type diploid Saccharomyces cerevisiae strain for second-generation bioethanol production. BIORESOUR BIOPROCESS 2016; 3:51. [PMID: 27942436 PMCID: PMC5122614 DOI: 10.1186/s40643-016-0126-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 11/11/2016] [Indexed: 11/24/2022] Open
Abstract
Background The cost-effective production of second-generation bioethanol, which is made from lignocellulosic materials, has to face the following two problems: co-fermenting xylose with glucose and enhancing the strain’s tolerance to lignocellulosic inhibitors. Based on our previous study, the wild-type diploid Saccharomyces cerevisiae strain BSIF with robustness and good xylose metabolism genetic background was used as a chassis for constructing efficient xylose-fermenting industrial strains. The performance of the resulting strains in the fermentation of media with sugars and hydrolysates was investigated. Results The following two novel heterologous genes were integrated into the genome of the chassis cell: the mutant MGT05196N360F, which encodes a xylose-specific, glucose-insensitive transporter and is derived from the Meyerozyma guilliermondii transporter gene MGT05196, and Ru-xylA (where Ru represents the rumen), which encodes a xylose isomerase (XI) with higher activity in S. cerevisiae. Additionally, endogenous modifications were also performed, including the overproduction of the xylulokinase Xks1p and the non-oxidative PPP (pentose phosphate pathway), and the inactivation of the aldose reductase Gre3p and the alkaline phosphatase Pho13p. These rationally designed genetic modifications, combined with alternating adaptive evolutions in xylose and SECS liquor (the leach liquor of steam-exploding corn stover), resulted in a final strain, LF1, with excellent xylose fermentation and enhanced inhibitor resistance. The specific xylose consumption rate of LF1 reached as high as 1.089 g g−1 h−1 with xylose as the sole carbon source. Moreover, its highly synchronized utilization of xylose and glucose was particularly significant; 77.6% of xylose was consumed along with glucose within 12 h, and the ethanol yield was 0.475 g g−1, which is more than 93% of the theoretical yield. Additionally, LF1 performed well in fermentations with two different lignocellulosic hydrolysates. Conclusion The strain LF1 co-ferments glucose and xylose efficiently and synchronously. This result highlights the great potential of LF1 for the practical production of second-generation bioethanol. Electronic supplementary material The online version of this article (doi:10.1186/s40643-016-0126-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongxing Li
- State Key Laboratory of Microbial Technology, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China.,Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Jinan, 250353 China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
| | - Meiling Wu
- State Key Laboratory of Microbial Technology, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
| | - Chunlei Jiao
- State Key Laboratory of Microbial Technology, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
| | - Zailu Li
- Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Jinan, 250353 China
| | - Xinli Liu
- Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Jinan, 250353 China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China.,Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Jinan, 250353 China
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Rai AK, Kumari R, Sanjukta S, Sahoo D. Production of bioactive protein hydrolysate using the yeasts isolated from soft chhurpi. BIORESOURCE TECHNOLOGY 2016; 219:239-245. [PMID: 27494105 DOI: 10.1016/j.biortech.2016.07.129] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
The aim of this work was to study the production of bioactive protein hydrolysates using yeasts isolated from chhurpi. For this, a total of 125 proteolytic yeasts were isolated and molecular identification was carried out by analysis of the restriction digestion pattern generated by digesting the PCR amplified internal transcribed spacer region and 5.8S rRNA gene (ITS1-5.8S-ITS2) using three endonucleases (HaeIII, CfoI and HinfI). The results obtained showed that different proteolytic yeasts were dominant in marketed products (Kluyveromyces marxianus and Issatchenkia orientalis) and samples from production centers (Trichosporon asahii, Saccharomyces cerevisiae and Exophiala dermatitidis). Proteolytic strains in individual groups showed their ability to hydrolyze milk protein and enhance antioxidant property. Among the isolates, fermentation using K. marxianus YMP45 and S. cerevisiae YAM14 resulted in higher antioxidant activity. This is the first report on application of yeast isolated from fermented food of North-East India for the production of bioactive protein hydrolysate.
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Affiliation(s)
- Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Sikkim Centre, Tadong 737102, Sikkim, India.
| | - Reena Kumari
- Institute of Bioresources and Sustainable Development, Sikkim Centre, Tadong 737102, Sikkim, India
| | - Samurailatpam Sanjukta
- Institute of Bioresources and Sustainable Development, Sikkim Centre, Tadong 737102, Sikkim, India
| | - Dinabandhu Sahoo
- Institute of Bioresources and Sustainable Development, Imphal 795001, Manipur, India
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Romaní A, Tomaz PD, Garrote G, Teixeira JA, Domingues L. Combined alkali and hydrothermal pretreatments for oat straw valorization within a biorefinery concept. BIORESOURCE TECHNOLOGY 2016; 220:323-332. [PMID: 27591518 DOI: 10.1016/j.biortech.2016.08.077] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/18/2016] [Accepted: 08/20/2016] [Indexed: 05/16/2023]
Abstract
The aim of this work was the evaluation of lime pretreatment combined or not with previous step of autohydrolysis for oat straw valorization. Under selected conditions of lime pretreatment, 96% of glucan and 77% of xylan were recovered and 42% of delignification was achieved. Xylose fermentation to ethanol by metabolic engineered Saccharomyces cerevisiae (MEC1133) strain improved the ethanol production by 22% achieving 41g/L. Alternatively, first step of autohydrolysis (S0=4.22) allowed a high oligosaccharides recovery (68%) and subsequent lime pretreatment attained a 57% of delignification and 99% of glucan to glucose conversion. Oat straw processed by autohydrolysis and lime pretreatment reached the maximal ethanol concentration (50g/L). Both strategies led to oat straw valorization into bioethanol, oligosaccharides and lignin indicating that these pretreatments are adequate as a first stage within an oat straw biorefinery.
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Affiliation(s)
- Aloia Romaní
- CEB-Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; Department of Chemical Engineering, Faculty of Science, University of Vigo (Campus Ourense), As Lagoas, 32004 Ourense, Spain
| | - Pablo D Tomaz
- Department of Chemical Engineering, Faculty of Science, University of Vigo (Campus Ourense), As Lagoas, 32004 Ourense, Spain
| | - Gil Garrote
- Department of Chemical Engineering, Faculty of Science, University of Vigo (Campus Ourense), As Lagoas, 32004 Ourense, Spain; CITI-Tecnopole, San Ciprián das Viñas, 32901 Ourense, Spain
| | - José A Teixeira
- CEB-Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal.
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41
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Gomes D, Domingues L, Gama M. Valorizing recycled paper sludge by a bioethanol production process with cellulase recycling. BIORESOURCE TECHNOLOGY 2016; 216:637-644. [PMID: 27289054 DOI: 10.1016/j.biortech.2016.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 06/06/2023]
Abstract
The feasibility of cellulase recycling in the scope of bioethanol production from recycled paper sludge (RPS), an inexpensive byproduct with around 39% of carbohydrates, is analyzed. RPS was easily converted and fermented by enzymes and cells, respectively. Final enzyme partition between solid and liquid phases was investigated, the solid-bound enzymes being efficiently recovered by alkaline washing. RPS hydrolysis and fermentation was conducted over four rounds, recycling the cellulases present in both fractions. A great overall enzyme stability was observed: 71, 64 and 100% of the initial Cel7A, Cel7B and β-glucosidase activities, respectively, were recovered. Even with only 30% of fresh enzymes added on the subsequent rounds, solid conversions of 92, 83 and 71% were achieved for the round 2, 3 and 4, respectively. This strategy enabled an enzyme saving around 53-60%, while can equally contribute to a 40% reduction in RPS disposal costs.
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Affiliation(s)
- Daniel Gomes
- Centre of Biological Engineering - University of Minho, Campus de Gualtar - 4710-057 Braga, Portugal
| | - Lucília Domingues
- Centre of Biological Engineering - University of Minho, Campus de Gualtar - 4710-057 Braga, Portugal.
| | - Miguel Gama
- Centre of Biological Engineering - University of Minho, Campus de Gualtar - 4710-057 Braga, Portugal
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42
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Ko JK, Um Y, Woo HM, Kim KH, Lee SM. Ethanol production from lignocellulosic hydrolysates using engineered Saccharomyces cerevisiae harboring xylose isomerase-based pathway. BIORESOURCE TECHNOLOGY 2016; 209:290-6. [PMID: 26990396 DOI: 10.1016/j.biortech.2016.02.124] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 05/12/2023]
Abstract
The efficient co-fermentation of glucose and xylose is necessary for the economically feasible bioethanol production from lignocellulosic biomass. Even with xylose utilizing Saccharomyces cerevisiae, the efficiency of the lignocellulosic ethanol production remains suboptimal mainly due to the low conversion yield of xylose to ethanol. In this study, we evaluated the co-fermentation performances of SXA-R2P-E, a recently engineered isomerase-based xylose utilizing strain, in mixed sugars and in lignocellulosic hydrolysates. In a high-sugar fermentation with 70g/L of glucose and 40g/L of xylose, SXA-R2P-E produced 50g/L of ethanol with an yield of 0.43gethanol/gsugars at 72h. From dilute acid-pretreated hydrolysates of rice straw and hardwood (oak), the strain produced 18-21g/L of ethanol with among the highest yield of 0.43-0.46gethanol/gsugars ever reported. This study shows a highly promising potential of a xylose isomerase-expressing strain as an industrially relevant ethanol producer from lignocellulosic hydrolysates.
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Affiliation(s)
- Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Han Min Woo
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.
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Pereira F, Azevedo F, Parachin NS, Hahn-Hägerdal B, Gorwa-Grauslund MF, Johansson B. Yeast Pathway Kit: A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation. ACS Synth Biol 2016; 5:386-94. [PMID: 26916955 DOI: 10.1021/acssynbio.5b00250] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have developed the Yeast Pathway Kit (YPK) for rational and random metabolic pathway assembly in Saccharomyces cerevisiae using reusable and redistributable genetic elements. Genetic elements are cloned in a suicide vector in a rapid process that omits PCR product purification. Single-gene expression cassettes are assembled in vivo using genetic elements that are both promoters and terminators (TP). Cassettes sharing genetic elements are assembled by recombination into multigene pathways. A wide selection of prefabricated TP elements makes assembly both rapid and inexpensive. An innovative software tool automatically produces detailed self-contained executable documentation in the form of pydna code in the narrative Jupyter notebook format to facilitate planning and sharing YPK projects. A d-xylose catabolic pathway was created using YPK with four or eight genes that resulted in one of the highest growth rates reported on d-xylose (0.18 h(-1)) for recombinant S. cerevisiae without adaptation. The two-step assembly of single-gene expression cassettes into multigene pathways may improve the yield of correct pathways at the cost of adding overall complexity, which is offset by the supplied software tool.
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Affiliation(s)
- Filipa Pereira
- CBMA—Centre
of Molecular and Environmental Biology, Department
of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Flávio Azevedo
- CBMA—Centre
of Molecular and Environmental Biology, Department
of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Nadia Skorupa Parachin
- Division
of Applied Microbiology, Department of Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Bärbel Hahn-Hägerdal
- Division
of Applied Microbiology, Department of Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Marie F. Gorwa-Grauslund
- Division
of Applied Microbiology, Department of Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Björn Johansson
- CBMA—Centre
of Molecular and Environmental Biology, Department
of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
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Ochoa MP, Estrada V, Di Maggio J, Hoch PM. Dynamic global sensitivity analysis in bioreactor networks for bioethanol production. BIORESOURCE TECHNOLOGY 2016; 200:666-679. [PMID: 26556401 DOI: 10.1016/j.biortech.2015.10.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/17/2015] [Accepted: 10/20/2015] [Indexed: 06/05/2023]
Abstract
Dynamic global sensitivity analysis (GSA) was performed for three different dynamic bioreactor models of increasing complexity: a fermenter for bioethanol production, a bioreactors network, where two types of bioreactors were considered: aerobic for biomass production and anaerobic for bioethanol production and a co-fermenter bioreactor, to identify the parameters that most contribute to uncertainty in model outputs. Sobol's method was used to calculate time profiles for sensitivity indices. Numerical results have shown the time-variant influence of uncertain parameters on model variables. Most influential model parameters have been determined. For the model of the bioethanol fermenter, μmax (maximum growth rate) and Ks (half-saturation constant) are the parameters with largest contribution to model variables uncertainty; in the bioreactors network, the most influential parameter is μmax,1 (maximum growth rate in bioreactor 1); whereas λ (glucose-to-total sugars concentration ratio in the feed) is the most influential parameter over all model variables in the co-fermentation bioreactor.
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Affiliation(s)
- M P Ochoa
- Planta Piloto de Ingeniería Química, CONICET, 8000 Bahía Blanca, Argentina; Universidad Nacional del Sur, Departamento de Ingeniería Química, 8000 Bahía Blanca, Argentina
| | - V Estrada
- Planta Piloto de Ingeniería Química, CONICET, 8000 Bahía Blanca, Argentina; Universidad Nacional del Sur, Departamento de Ingeniería Química, 8000 Bahía Blanca, Argentina.
| | - J Di Maggio
- Planta Piloto de Ingeniería Química, CONICET, 8000 Bahía Blanca, Argentina; Universidad Nacional del Sur, Departamento de Ingeniería Química, 8000 Bahía Blanca, Argentina
| | - P M Hoch
- Planta Piloto de Ingeniería Química, CONICET, 8000 Bahía Blanca, Argentina; Universidad Nacional del Sur, Departamento de Ingeniería Química, 8000 Bahía Blanca, Argentina
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45
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Nijland JG, Vos E, Shin HY, de Waal PP, Klaassen P, Driessen AJM. Improving pentose fermentation by preventing ubiquitination of hexose transporters in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:158. [PMID: 27468310 PMCID: PMC4962381 DOI: 10.1186/s13068-016-0573-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/14/2016] [Indexed: 05/12/2023]
Abstract
BACKGROUND Engineering of the yeast Saccharomyces cerevisiae for improved utilization of pentose sugars is vital for cost-efficient cellulosic bioethanol production. Although endogenous hexose transporters (Hxt) can be engineered into specific pentose transporters, they remain subjected to glucose-regulated protein degradation. Therefore, in the absence of glucose or when the glucose is exhausted from the medium, some Hxt proteins with high xylose transport capacity are rapidly degraded and removed from the cytoplasmic membrane. Thus, turnover of such Hxt proteins may lead to poor growth on solely xylose. RESULTS The low affinity hexose transporters Hxt1, Hxt36 (Hxt3 variant), and Hxt5 are subjected to catabolite degradation as evidenced by a loss of GFP fused hexose transporters from the membrane upon glucose depletion. Catabolite degradation occurs through ubiquitination, which is a major signaling pathway for turnover. Therefore, N-terminal lysine residues of the aforementioned Hxt proteins predicted to be the target of ubiquitination, were replaced for arginine residues. The mutagenesis resulted in improved membrane localization when cells were grown on solely xylose concomitantly with markedly stimulated growth on xylose. The mutagenesis also improved the late stages of sugar fermentation when cells are grown on both glucose and xylose. CONCLUSIONS Substitution of N-terminal lysine residues in the endogenous hexose transporters Hxt1 and Hxt36 that are subjected to catabolite degradation results in improved retention at the cytoplasmic membrane in the absence of glucose and causes improved xylose fermentation upon the depletion of glucose and when cells are grown in d-xylose alone.
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Affiliation(s)
- Jeroen G. Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
| | - Erwin Vos
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
| | - Hyun Yong Shin
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
| | - Paul P. de Waal
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Paul Klaassen
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Arnold J. M. Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
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Cunha JT, Aguiar TQ, Romaní A, Oliveira C, Domingues L. Contribution of PRS3, RPB4 and ZWF1 to the resistance of industrial Saccharomyces cerevisiae CCUG53310 and PE-2 strains to lignocellulosic hydrolysate-derived inhibitors. BIORESOURCE TECHNOLOGY 2015; 191:7-16. [PMID: 25974617 DOI: 10.1016/j.biortech.2015.05.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 04/30/2015] [Accepted: 05/02/2015] [Indexed: 05/13/2023]
Abstract
PRS3, RPB4 and ZWF1 were previously identified as key genes for yeast tolerance to lignocellulose-derived inhibitors. To better understand their contribution to yeast resistance to the multiple stresses occurring during lignocellulosic hydrolysate fermentations, we overexpressed these genes in two industrial Saccharomyces cerevisiae strains, CCUG53310 and PE-2, and evaluated their impact on the fermentation of Eucalyptus globulus wood and corn cob hydrolysates. PRS3 overexpression improved the fermentation rate (up to 32%) and productivity (up to 48%) in different hydrolysates. ZWF1 and RPB4 overexpression did not improve the fermentation performance, but their increased expression in the presence of acetic acid, furfural and hydroxymethylfurfural was found to contribute to yeast adaptation to these inhibitors. This study expands our understanding about the molecular mechanisms involved in industrial yeast tolerance to the stresses occurring during lignocellulosic bioethanol production and highlights the importance of selecting appropriate strain backgrounds/hydrolysates combinations when addressing further improvement of these processes.
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Affiliation(s)
- Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Tatiana Q Aguiar
- 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
| | - Carla Oliveira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
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Cao YD, He YC, Li H, Kai GY, Xu JH, Yu HL. Efficient biosynthesis of rare natural product scopolamine using E. coli cells expressing a S14P/K97A mutant of hyoscyamine 6β-hydroxylase AaH6H. J Biotechnol 2015; 211:123-9. [PMID: 26239231 DOI: 10.1016/j.jbiotec.2015.07.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 07/23/2015] [Accepted: 07/27/2015] [Indexed: 11/30/2022]
Abstract
Hyoscyamine 6β-hydroxylase (H6H, EC 1.14.11.11), an α-ketoglutarate dependent dioxygenase catalyzes the hydroxylation of (-)-hyoscyamine and the subsequent epoxidation of 6β-hydroxyhyoscyamine to form scopolamine, a valuable natural alkaloid. In this study, random mutagenesis and site-directed saturation mutagenesis were used to enhance the hydroxylation activity of H6H from Anisodus acutangulus (AaH6H). A double mutant, AaH6HM1 (S14P/K97A), showed a 3.4-fold improved hydroxylation activity compared with the wild-type enzyme, and the in vivo epoxidation activity was also improved by 2.3 times. After 34h cultivation of Escherichia coli cells harboring Aah6hm1 in a 5-L bioreactor with a working volume of 3L, scopolamine was produced via a single-enzyme-mediated two-step transformation from 500mgL(-1) (-)-hyoscyamine in 97% conversion, and 1.068g of the product were isolated, corresponding to a space-time yield of 251mgL(-1)d(-1). This study shows that the protein engineering of some key enzymes is a promising and effective way for improving the production of rare natural products such as scopolamine.
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Affiliation(s)
- Yue-De Cao
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Yu-Cai He
- Laboratory of Biocatalysis and Bioprocessing, College of Pharmaceutical Engineering and Life Sciences, Changzhou University, Changzhou 213164, PR China
| | - Hao Li
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Guo-Yin Kai
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, PR China
| | - Jian-He Xu
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China; Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, PR China
| | - Hui-Lei Yu
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China; Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, PR China.
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Gomes D, Rodrigues AC, Domingues L, Gama M. Cellulase recycling in biorefineries—is it possible? Appl Microbiol Biotechnol 2015; 99:4131-43. [DOI: 10.1007/s00253-015-6535-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/09/2015] [Accepted: 03/11/2015] [Indexed: 11/28/2022]
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