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Barros KO, Mader M, Krause DJ, Pangilinan J, Andreopoulos B, Lipzen A, Mondo SJ, Grigoriev IV, Rosa CA, Sato TK, Hittinger CT. Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:20. [PMID: 38321504 PMCID: PMC10848558 DOI: 10.1186/s13068-024-02467-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/28/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND Cost-effective production of biofuels from lignocellulose requires the fermentation of D-xylose. Many yeast species within and closely related to the genera Spathaspora and Scheffersomyces (both of the order Serinales) natively assimilate and ferment xylose. Other species consume xylose inefficiently, leading to extracellular accumulation of xylitol. Xylitol excretion is thought to be due to the different cofactor requirements of the first two steps of xylose metabolism. Xylose reductase (XR) generally uses NADPH to reduce xylose to xylitol, while xylitol dehydrogenase (XDH) generally uses NAD+ to oxidize xylitol to xylulose, creating an imbalanced redox pathway. This imbalance is thought to be particularly consequential in hypoxic or anoxic environments. RESULTS We screened the growth of xylose-fermenting yeast species in high and moderate aeration and identified both ethanol producers and xylitol producers. Selected species were further characterized for their XR and XDH cofactor preferences by enzyme assays and gene expression patterns by RNA-Seq. Our data revealed that xylose metabolism is more redox balanced in some species, but it is strongly affected by oxygen levels. Under high aeration, most species switched from ethanol production to xylitol accumulation, despite the availability of ample oxygen to accept electrons from NADH. This switch was followed by decreases in enzyme activity and the expression of genes related to xylose metabolism, suggesting that bottlenecks in xylose fermentation are not always due to cofactor preferences. Finally, we expressed XYL genes from multiple Scheffersomyces species in a strain of Saccharomyces cerevisiae. Recombinant S. cerevisiae expressing XYL1 from Scheffersomyces xylosifermentans, which encodes an XR without a cofactor preference, showed improved anaerobic growth on xylose as the primary carbon source compared to S. cerevisiae strain expressing XYL genes from Scheffersomyces stipitis. CONCLUSION Collectively, our data do not support the hypothesis that xylitol accumulation occurs primarily due to differences in cofactor preferences between xylose reductase and xylitol dehydrogenase; instead, gene expression plays a major role in response to oxygen levels. We have also identified the yeast Sc. xylosifermentans as a potential source for genes that can be engineered into S. cerevisiae to improve xylose fermentation and biofuel production.
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Affiliation(s)
- Katharina O Barros
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Megan Mader
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Krause
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bill Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Computer Science, San Jose State University, One Washington Square, San Jose, CA, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen J Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Plant and Microbial Department, University of California Berkeley, Berkeley, CA, USA
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
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Zhang J, Yuan Y, Wang Z, Chen T. Metabolic engineering of Halomonas bluephagenesis for high-level mevalonate production from glucose and acetate mixture. Metab Eng 2023; 79:203-213. [PMID: 37657641 DOI: 10.1016/j.ymben.2023.08.005] [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] [Received: 07/11/2023] [Revised: 08/14/2023] [Accepted: 08/27/2023] [Indexed: 09/03/2023]
Abstract
Mevalonate (MVA) plays a crucial role as a building block for the biosynthesis of isoprenoids. In this study, we engineered Halomonas bluephagenesis to efficiently produce MVA. Firstly, by screening MVA synthetases from eight different species, the two efficient candidate modules, specifically NADPH-dependent mvaESEfa from Enterococcus faecalis and NADH-dependent mvaESLca from Lactobacillus casei, were integrated into the chromosome, leading to the construction of the H. bluephagenesis MVA11. Through the synergetic utilization of glucose and acetate as mixed carbon sources, MVA11 produced 11.2 g/L MVA with a yield of 0.45 g/g (glucose + acetic acid) in the shake flask. Subsequently, 10 beneficial genes out of 50 targets that could promote MVA production were identified using CRISPR interference. The simultaneous repression of rpoN (encoding RNA polymerase sigma-54 factor) and IldD (encoding L-lactate dehydrogenase) increased MVA titer (13.3 g/L) by 19.23% and yield (0.53 g/g (glucose + acetic acid)) by 17.78%, respectively. Furthermore, introducing the non-oxidative glycolysis (NOG) pathway into MVA11 enhanced MVA yield by 12.20%. Ultimately, by combining these strategies, the resultant H. bluephagenesis MVA13/pli-63 produced 13.9 g/L MVA in the shake flask, and the yield increased to 0.56 g/g (glucose + acetic acid), which was the highest reported so far. Under open fed-batch fermentation conditions, H. bluephagenesis MVA13/pli-63 produced 121 g/L of MVA with a yield of 0.42 g/g (glucose + acetic acid), representing the highest reported titer and yield in the bioreactor to date. This study demonstrates that H. bluephagenesis is one of the most favorable chassis for MVA production.
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Affiliation(s)
- Jing Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, 300072, China
| | - Yue Yuan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, 300072, China
| | - Zhiwen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, 300072, China
| | - Tao Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, 300072, China.
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3
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Nielsen JR, Weusthuis RA, Huang WE. Growth-coupled enzyme engineering through manipulation of redox cofactor regeneration. Biotechnol Adv 2023; 63:108102. [PMID: 36681133 DOI: 10.1016/j.biotechadv.2023.108102] [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: 09/01/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023]
Abstract
Enzymes need to be efficient, robust, and highly specific for their effective use in commercial bioproduction. These properties can be introduced using various enzyme engineering techniques, with random mutagenesis and directed evolution (DE) often being chosen when there is a lack of structural information -or mechanistic understanding- of the enzyme. The screening or selection step of DE is the limiting part of this process, since it must ideally be (ultra)-high throughput, specifically target the catalytic activity of the enzyme and have an accurately quantifiable metric for said activity. Growth-coupling selection strategies involve coupling a desired enzyme activity to cellular metabolism and therefore growth, where growth (rate) becomes the output metric. Redox cofactors (NAD+/NADH and NADP+/NADPH) have recently been identified as promising target molecules for growth coupling, owing to their essentiality for cellular metabolism and ubiquitous nature. Redox cofactor oxidation or reduction can be disrupted through metabolic engineering and the use of specific culturing conditions, rendering the cell inviable unless a 'rescue' reaction complements the imposed metabolic deficiency. Using this principle, enzyme variants displaying improved cofactor oxidation or reduction rates can be selected for through an increased growth rate of the cell. In recent years, several E. coli strains have been developed that are deficient in the oxidation or reduction of NAD+/NADH and NADP+/NADPH pairs, and of non-canonical redox cofactor pairs NMN+/NMNH and NCD+/NCDH, which provides researchers with a versatile toolbox of enzyme engineering platforms. A range of redox cofactor dependent enzymes have since been engineered using a variety of these strains, demonstrating the power of using this growth-coupling technique for enzyme engineering. This review aims to summarize the metabolic engineering involved in creating strains auxotrophic for the reduced or oxidized state of redox cofactors, and the resulting successes in using them for enzyme engineering. Perspectives on the unique features and potential future applications of this technique are also presented.
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Affiliation(s)
- Jochem R Nielsen
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom.
| | - Ruud A Weusthuis
- Department of Bioprocess Engineering, Wageningen University & Research, Wageningen 6700AA, the Netherlands.
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom.
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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: 1] [Impact Index Per Article: 1.0] [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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Theodosiou E, Tüllinghoff A, Toepel J, Bühler B. Exploitation of Hetero- and Phototrophic Metabolic Modules for Redox-Intensive Whole-Cell Biocatalysis. Front Bioeng Biotechnol 2022; 10:855715. [PMID: 35497353 PMCID: PMC9043136 DOI: 10.3389/fbioe.2022.855715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
The successful realization of a sustainable manufacturing bioprocess and the maximization of its production potential and capacity are the main concerns of a bioprocess engineer. A main step towards this endeavor is the development of an efficient biocatalyst. Isolated enzyme(s), microbial cells, or (immobilized) formulations thereof can serve as biocatalysts. Living cells feature, beside active enzymes, metabolic modules that can be exploited to support energy-dependent and multi-step enzyme-catalyzed reactions. Metabolism can sustainably supply necessary cofactors or cosubstrates at the expense of readily available and cheap resources, rendering external addition of costly cosubstrates unnecessary. However, for the development of an efficient whole-cell biocatalyst, in depth comprehension of metabolic modules and their interconnection with cell growth, maintenance, and product formation is indispensable. In order to maximize the flux through biosynthetic reactions and pathways to an industrially relevant product and respective key performance indices (i.e., titer, yield, and productivity), existing metabolic modules can be redesigned and/or novel artificial ones established. This review focuses on whole-cell bioconversions that are coupled to heterotrophic or phototrophic metabolism and discusses metabolic engineering efforts aiming at 1) increasing regeneration and supply of redox equivalents, such as NAD(P/H), 2) blocking competing fluxes, and 3) increasing the availability of metabolites serving as (co)substrates of desired biosynthetic routes.
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Affiliation(s)
- Eleni Theodosiou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Adrian Tüllinghoff
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Jörg Toepel
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
- *Correspondence: Bruno Bühler,
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Narisetty V, Cox R, Bommareddy R, Agrawal D, Ahmad E, Pant KK, Chandel AK, Bhatia SK, Kumar D, Binod P, Gupta VK, Kumar V. Valorisation of xylose to renewable fuels and chemicals, an essential step in augmenting the commercial viability of lignocellulosic biorefineries. SUSTAINABLE ENERGY & FUELS 2021; 6:29-65. [PMID: 35028420 PMCID: PMC8691124 DOI: 10.1039/d1se00927c] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/25/2021] [Indexed: 05/30/2023]
Abstract
Biologists and engineers are making tremendous efforts in contributing to a sustainable and green society. To that end, there is growing interest in waste management and valorisation. Lignocellulosic biomass (LCB) is the most abundant material on the earth and an inevitable waste predominantly originating from agricultural residues, forest biomass and municipal solid waste streams. LCB serves as the renewable feedstock for clean and sustainable processes and products with low carbon emission. Cellulose and hemicellulose constitute the polymeric structure of LCB, which on depolymerisation liberates oligomeric or monomeric glucose and xylose, respectively. The preferential utilization of glucose and/or absence of the xylose metabolic pathway in microbial systems cause xylose valorization to be alienated and abandoned, a major bottleneck in the commercial viability of LCB-based biorefineries. Xylose is the second most abundant sugar in LCB, but a non-conventional industrial substrate unlike glucose. The current review seeks to summarize the recent developments in the biological conversion of xylose into a myriad of sustainable products and associated challenges. The review discusses the microbiology, genetics, and biochemistry of xylose metabolism with hurdles requiring debottlenecking for efficient xylose assimilation. It further describes the product formation by microbial cell factories which can assimilate xylose naturally and rewiring of metabolic networks to ameliorate xylose-based bioproduction in native as well as non-native strains. The review also includes a case study that provides an argument on a suitable pathway for optimal cell growth and succinic acid (SA) production from xylose through elementary flux mode analysis. Finally, a product portfolio from xylose bioconversion has been evaluated along with significant developments made through enzyme, metabolic and process engineering approaches, to maximize the product titers and yield, eventually empowering LCB-based biorefineries. Towards the end, the review is wrapped up with current challenges, concluding remarks, and prospects with an argument for intense future research into xylose-based biorefineries.
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Affiliation(s)
- Vivek Narisetty
- School of Water, Energy and Environment, Cranfield University Cranfield MK43 0AL UK +44 (0)1234754786
| | - Rylan Cox
- School of Water, Energy and Environment, Cranfield University Cranfield MK43 0AL UK +44 (0)1234754786
- School of Aerospace, Transport and Manufacturing, Cranfield University Cranfield MK43 0AL UK
| | - Rajesh Bommareddy
- Department of Applied Sciences, Northumbria University Newcastle upon Tyne NE1 8ST UK
| | - Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR- Indian Institute of Petroleum Mohkampur Dehradun 248005 India
| | - Ejaz Ahmad
- Department of Chemical Engineering, Indian Institute of Technology (ISM) Dhanbad 826004 India
| | - Kamal Kumar Pant
- Department of Chemical Engineering, Indian Institute of Technology Delhi New Delhi 110016 India
| | - Anuj Kumar Chandel
- Department of Biotechnology, Engineering School of Lorena (EEL), University of São Paulo Lorena 12.602.810 Brazil
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University Seoul 05029 Republic of Korea
| | - Dinesh Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences Solan 173229 Himachal Pradesh India
| | - Parmeswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Thiruvananthapuram 695 019 Kerala India
| | | | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University Cranfield MK43 0AL UK +44 (0)1234754786
- Department of Chemical Engineering, Indian Institute of Technology Delhi New Delhi 110016 India
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Narisetty V, Castro E, Durgapal S, Coulon F, Jacob S, Kumar D, Kumar Awasthi M, Kishore Pant K, Parameswaran B, Kumar V. High level xylitol production by Pichia fermentans using non-detoxified xylose-rich sugarcane bagasse and olive pits hydrolysates. BIORESOURCE TECHNOLOGY 2021; 342:126005. [PMID: 34592613 PMCID: PMC8651628 DOI: 10.1016/j.biortech.2021.126005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/16/2021] [Accepted: 09/19/2021] [Indexed: 05/22/2023]
Abstract
Hemicellulosic sugars, the overlooked fraction of lignocellulosic residues can serve as potential and cost-effective raw material that can be exploited for xylitol production. Xylitol is a top platform chemical with applications in food and pharmaceutical industries. Sugarcane bagasse (SCB) and olive pits (OP) are the major waste streams from sugar and olive oil industries, respectively. The current study evaluated the potential of Pichia fermentans for manufacturing of xylitol from SCB and OP hydrolysates through co-fermentation strategy. The highest xylitol accumulation was noticed with a glucose and xylose ratio of 1:10 followed by feeding with xylose alone. The fed-batch cultivation using pure xylose, SCB, and OP hydrolysates, resulted in xylitol accumulation of 102.5, 86.6 and 71.9 g/L with conversion yield of 0.78, 0.75 and 0.74 g/g, respectively. The non-pathogenic behaviour and ability to accumulate high xylitol levels from agro-industrial residues demonstrates the potential of P. fermentans as microbial cell factory.
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Affiliation(s)
- Vivek Narisetty
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Eulogio Castro
- Department of Chemical, Environmental and Materials Engineering, Universidad de Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - Sumit Durgapal
- Department of Pharmaceutical Sciences, Kumaun University, Bhimtal, Nainital 263136, Uttarakhand, India
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Samuel Jacob
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu District, Tamil Nadu, 603203, India
| | - Dinesh Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences, Solan 173229, Himachal Pradesh, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Kamal Kishore Pant
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Binod Parameswaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala 695019, India
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK.
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Unraveling continuous 2G ethanol production from xylose using hemicellulose hydrolysate and immobilized superior recombinant yeast in fixed-bed bioreactor. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107963] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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9
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Zhu Y, Zhang J, Zhu L, Jia Z, Li Q, Xiao W, Cao L. Minimize the Xylitol Production in Saccharomyces cerevisiae by Balancing the Xylose Redox Metabolic Pathway. Front Bioeng Biotechnol 2021; 9:639595. [PMID: 33718341 PMCID: PMC7953151 DOI: 10.3389/fbioe.2021.639595] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/12/2021] [Indexed: 11/13/2022] Open
Abstract
Xylose is the second most abundant sugar in lignocellulose, but it cannot be used as carbon source by budding yeast Saccharomyces cerevisiae. Rational promoter elements engineering approaches were taken for efficient xylose fermentation in budding yeast. Among promoters surveyed, HXT7 exhibited the best performance. The HXT7 promoter is suppressed in the presence of glucose and derepressed by xylose, making it a promising candidate to drive xylose metabolism. However, simple ectopic expression of both key xylose metabolic genes XYL1 and XYL2 by the HXT7 promoter resulted in massive accumulation of the xylose metabolic byproduct xylitol. Through the HXT7-driven expression of a reported redox variant, XYL1-K270R, along with optimized expression of XYL2 and the downstream pentose phosphate pathway genes, a balanced xylose metabolism toward ethanol formation was achieved. Fermented in a culture medium containing 50 g/L xylose as the sole carbon source, xylose is nearly consumed, with less than 3 g/L xylitol, and more than 16 g/L ethanol production. Hence, the combination of an inducible promoter and redox balance of the xylose utilization pathway is an attractive approach to optimizing fuel production from lignocellulose.
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Affiliation(s)
- Yixuan Zhu
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Jingtao Zhang
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China.,China Center of Industrial Culture Collection, Beijing, China
| | - Lang Zhu
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Zefang Jia
- 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
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Wei Xiao
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China.,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Limin Cao
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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11
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Biorefinery: The Production of Isobutanol from Biomass Feedstocks. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10228222] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Environmental issues have prompted the vigorous development of biorefineries that use agricultural waste and other biomass feedstock as raw materials. However, most current biorefinery products are cellulosic ethanol. There is an urgent need for biorefineries to expand into new bioproducts. Isobutanol is an important bulk chemical with properties that are close to gasoline, making it a very promising biofuel. The use of microorganisms to produce isobutanol has been extensively studied, but there is still a considerable gap to achieving the industrial production of isobutanol from biomass. This review summarizes current metabolic engineering strategies that have been applied to biomass isobutanol production and recent advances in the production of isobutanol from different biomass feedstocks.
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Xie CY, Yang BX, Song QR, Xia ZY, Gou M, Tang YQ. Different transcriptional responses of haploid and diploid S. cerevisiae strains to changes in cofactor preference of XR. Microb Cell Fact 2020; 19:211. [PMID: 33187525 PMCID: PMC7666519 DOI: 10.1186/s12934-020-01474-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/07/2020] [Indexed: 01/27/2023] Open
Abstract
Background Xylitol accumulation is a major barrier for efficient ethanol production through heterologous xylose reductase-xylitol dehydrogenase (XR-XDH) pathway in recombinant Saccharomyces cerevisiae. Mutated NADH-preferring XR is usually employed to alleviate xylitol accumulation. However, it remains unclear how mutated XR affects the metabolic network for xylose metabolism. In this study, haploid and diploid strains were employed to investigate the transcriptional responses to changes in cofactor preference of XR through RNA-seq analysis during xylose fermentation. Results For the haploid strains, genes involved in xylose-assimilation (XYL1, XYL2, XKS1), glycolysis, and alcohol fermentation had higher transcript levels in response to mutated XR, which was consistent with the improved xylose consumption rate and ethanol yield. For the diploid strains, genes related to protein biosynthesis were upregulated while genes involved in glyoxylate shunt were downregulated in response to mutated XR, which might contribute to the improved yields of biomass and ethanol. When comparing the diploids with the haploids, genes involved in glycolysis and MAPK signaling pathway were significantly downregulated, while oxidative stress related transcription factors (TFs) were significantly upregulated, irrespective of the cofactor preference of XR. Conclusions Our results not only revealed the differences in transcriptional responses of the diploid and haploid strains to mutated XR, but also provided underlying basis for better understanding the differences in xylose metabolism between the diploid and haploid strains.
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Affiliation(s)
- Cai-Yun Xie
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Bai-Xue Yang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Qing-Ran Song
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Zi-Yuan Xia
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China.
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China.
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13
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Cunha JT, Soares PO, Baptista SL, Costa CE, Domingues L. Engineered Saccharomyces cerevisiae for lignocellulosic valorization: a review and perspectives on bioethanol production. Bioengineered 2020; 11:883-903. [PMID: 32799606 PMCID: PMC8291843 DOI: 10.1080/21655979.2020.1801178] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The biorefinery concept, consisting in using renewable biomass with economical and energy goals, appeared in response to the ongoing exhaustion of fossil reserves. Bioethanol is the most prominent biofuel and has been considered one of the top chemicals to be obtained from biomass. Saccharomyces cerevisiae, the preferred microorganism for ethanol production, has been the target of extensive genetic modifications to improve the production of this alcohol from renewable biomasses. Additionally, S. cerevisiae strains from harsh industrial environments have been exploited due to their robust traits and improved fermentative capacity. Nevertheless, there is still not an optimized strain capable of turning second generation bioprocesses economically viable. Considering this, and aiming to facilitate and guide the future development of effective S. cerevisiae strains, this work reviews genetic engineering strategies envisioning improvements in 2nd generation bioethanol production, with special focus in process-related traits, xylose consumption, and consolidated bioprocessing. Altogether, the genetic toolbox described proves S. cerevisiae to be a key microorganism for the establishment of a bioeconomy, not only for the production of lignocellulosic bioethanol, but also having potential as a cell factory platform for overall valorization of renewable biomasses.
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Affiliation(s)
- Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Pedro O Soares
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Sara L Baptista
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Carlos E Costa
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
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Yang BX, Xie CY, Xia ZY, Wu YJ, Li B, Tang YQ. The effect of xylose reductase genes on xylitol production by industrial Saccharomyces cerevisiae in fermentation of glucose and xylose. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.05.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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15
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Qu C, Chen L, Fu H, Wang J. Engineering Thermoanaerobacterium aotearoense SCUT27 with argR knockout for enhanced ethanol production from lignocellulosic hydrolysates. BIORESOURCE TECHNOLOGY 2020; 310:123435. [PMID: 32361198 DOI: 10.1016/j.biortech.2020.123435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
Although Thermoanaerobacterium aotearoense SCUT27 (SCUT27) could co-utilize glucose and xylose, the presence of glucose still repressed xylose catabolism. Arginine repressors (ArgRs) were involved in several key metabolic pathways and might be the global regulator. In SCUT27, three genes (V518_0585; V518_1870; V518_1864) were annotated as argR and only the deficiency of argR1864 could greatly improve the co-utilization of glucose and xylose, due to the enhanced activity of xylose isomerase, xylulokinase and the higher energy level. The metabolic flux of SCUT27/ΔargR1864 indicated that new carbon distribution had been re-established and the ethanol yield had increased by 82.95%, strains growth and acetate yield improved by ~35.91% without detectable lactate for the poor activity of lactate dehydrogenase. The improved concentration of ATP and NAD(H) in SCUT27/ΔargR1864 provided more energy to respond the stress, which enabled the mutant the better cell viability to utilize lignocellulosic hydrolysates for enhanced ethanol formation.
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Affiliation(s)
- Chunyun Qu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Lili Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Hongxin Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; The State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510641, China.
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Su B, Song D, Zhu H. Metabolic Engineering of Saccharomyces cerevisiae for Enhanced Carotenoid Production From Xylose-Glucose Mixtures. Front Bioeng Biotechnol 2020; 8:435. [PMID: 32478054 PMCID: PMC7240070 DOI: 10.3389/fbioe.2020.00435] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/15/2020] [Indexed: 01/31/2023] Open
Abstract
Co-utilization of xylose and glucose from lignocellulosic biomass is an economically feasible bioprocess for chemical production. Many strategies have been implemented for efficiently assimilating xylose which is one of the predominant sugars of lignocellulosic biomass. However, there were few reports about engineering Saccharomyces cerevisiae for carotenoid production from xylose-glucose mixtures. Herein, we developed a platform for facilitating carotenoid production in S. cerevisiae by fermentation of xylose-glucose mixtures. Firstly, a xylose assimilation pathway with mutant xylose reductase (XYL1m), xylitol dehydrogenase (XYL2), and xylulokinase (XK) was constructed for utilizing xylose. Then, introduction of phosphoketolase (PK) pathway, deletion of Pho13 and engineering yeast hexose transporter Gal2 were conducted to improve carotenoid yields. The final strain SC105 produced a 1.6-fold higher production from mixed sugars than that from glucose in flask culture. In fed-batch fermentation with continuous feeding of mixed sugars, carotenoid production represented a 2.6-fold higher. To the best of our knowledge, this is the first report that S. cerevisiae was engineered to utilize xylose-glucose mixtures for carotenoid production with a considerable high yield. The present study exhibits a promising advantage of xylose-glucose mixtures assimilating strain as an industrial carotenoid producer from lignocellulosic biomass.
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Affiliation(s)
- Buli Su
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Dandan Song
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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17
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Atzmüller D, Ullmann N, Zwirzitz A. Identification of genes involved in xylose metabolism of Meyerozyma guilliermondii and their genetic engineering for increased xylitol production. AMB Express 2020; 10:78. [PMID: 32314068 PMCID: PMC7171046 DOI: 10.1186/s13568-020-01012-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/09/2020] [Indexed: 11/16/2022] Open
Abstract
Meyerozyma guilliermondii, a non-conventional yeast that naturally assimilates xylose, is considered as a candidate for biotechnological production of the sugar alternative xylitol. Because the genes of the xylose metabolism were yet unknown, all efforts published so far to increase the xylitol yield of this yeast are limited to fermentation optimization. Hence, this study aimed to genetically engineer this organism for the first time with the objective to increase xylitol production. Therefore, the previously uncharacterized genes of M. guilliermondii ATCC 6260 encoding for xylose reductase (XR) and xylitol dehydrogenase (XDH) were identified by pathway investigations and sequence similarity analysis. Cloning and overexpression of the putative XR as well as knockout of the putative XDH genes generated strains with about threefold increased xylitol yield. Strains that combined both genetic modifications displayed fivefold increase in overall xylitol yield. Enzymatic activity assays with lysates of XR overexpressing and XDH knockout strains underlined the presumed functions of the respective genes. Furthermore, growth evaluation of the engineered strains on xylose as sole carbon source provides insights into xylose metabolism and its utilization for cell growth.![]()
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18
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The Xylose Metabolizing Yeast Spathaspora passalidarum is a Promising Genetic Treasure for Improving Bioethanol Production. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6010033] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Currently, the fermentation technology for recycling agriculture waste for generation of alternative renewable biofuels is getting more and more attention because of the environmental merits of biofuels for decreasing the rapid rise of greenhouse gas effects compared to petrochemical, keeping in mind the increase of petrol cost and the exhaustion of limited petroleum resources. One of widely used biofuels is bioethanol, and the use of yeasts for commercial fermentation of cellulosic and hemicellulosic agricultural biomasses is one of the growing biotechnological trends for bioethanol production. Effective fermentation and assimilation of xylose, the major pentose sugar element of plant cell walls and the second most abundant carbohydrate, is a bottleneck step towards a robust biofuel production from agricultural waste materials. Hence, several attempts were implemented to engineer the conventional Saccharomyces cerevisiae yeast to transport and ferment xylose because naturally it does not use xylose, using genetic materials of Pichia stipitis, the pioneer native xylose fermenting yeast. Recently, the nonconventional yeast Spathaspora passalidarum appeared as a founder member of a new small group of yeasts that, like Pichia stipitis, can utilize and ferment xylose. Therefore, the understanding of the molecular mechanisms regulating the xylose assimilation in such pentose fermenting yeasts will enable us to eliminate the obstacles in the biofuels pipeline, and to develop industrial strains by means of genetic engineering to increase the availability of renewable biofuel products from agricultural biomass. In this review, we will highlight the recent advances in the field of native xylose metabolizing yeasts, with special emphasis on S. passalidarum for improving bioethanol production.
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19
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Reshamwala SMS, Lali AM. Exploiting the NADPH pool for xylitol production using recombinant Saccharomyces cerevisiae. Biotechnol Prog 2020; 36:e2972. [PMID: 31990139 DOI: 10.1002/btpr.2972] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 12/29/2019] [Accepted: 01/22/2020] [Indexed: 01/28/2023]
Abstract
Xylitol is a five-carbon sugar alcohol that has a variety of uses in the food and pharmaceutical industries. In xylose assimilating yeasts, NAD(P)H-dependent xylose reductase (XR) catalyzes the reduction of xylose to xylitol. In the present study, XR with varying cofactor specificities was overexpressed in Saccharomyces cerevisiae to screen for efficient xylitol production. Xylose consumption and xylitol yields were higher when NADPH-dependent enzymes (Candida tropicalis XR and S. cerevisiae Gre3p aldose reductase) were expressed, indicating that heterologous enzymes can utilize the intracellular NADPH pool more efficiently than the NADH pool, where they may face competition from native enzymes. This was confirmed by overexpression of a NADH-preferring C. tropicalis XR mutant, which led to decreased xylose consumption and lower xylitol yield. To increase intracellular NADPH availability for xylitol production, the promoter of the ZWF1 gene, coding for the first enzyme of the NADPH-generating pentose phosphate pathway, was replaced with the constitutive GPD promoter in a strain expressing C. tropicalis XR. This change led to a ~12% increase in xylitol yield. Deletion of XYL2 and SOR1, whose gene products can use xylitol as substrate, did not further increase xylitol yield. Using wheat stalk hydrolysate as source of xylose, the constructed strain efficiently produced xylitol, demonstrating practical relevance of this approach.
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Affiliation(s)
| | - Arvind M Lali
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India.,Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, India
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20
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Zhao Z, Xian M, Liu M, Zhao G. Biochemical routes for uptake and conversion of xylose by microorganisms. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:21. [PMID: 32021652 PMCID: PMC6995148 DOI: 10.1186/s13068-020-1662-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/21/2020] [Indexed: 05/23/2023]
Abstract
Xylose is a major component of lignocellulose and the second most abundant sugar present in nature. Efficient utilization of xylose is required for the development of economically viable processes to produce biofuels and chemicals from biomass. However, there are still some bottlenecks in the bioconversion of xylose, including the fact that some microorganisms cannot assimilate xylose naturally and that the uptake and metabolism of xylose are inhibited by glucose, which is usually present with xylose in lignocellulose hydrolysate. To overcome these issues, numerous efforts have been made to discover, characterize, and engineer the transporters and enzymes involved in xylose utilization to relieve glucose inhibition and to develop recombinant microorganisms to produce fuels and chemicals from xylose. Here we describe a recent advancement focusing on xylose-utilizing pathways, biosynthesis of chemicals from xylose, and engineering strategies used to improve the conversion efficiency of xylose.
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Affiliation(s)
- Zhe Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Min Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
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21
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Geijer C, Faria-Oliveira F, Moreno AD, Stenberg S, Mazurkewich S, Olsson L. Genomic and transcriptomic analysis of Candida intermedia reveals the genetic determinants for its xylose-converting capacity. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:48. [PMID: 32190113 PMCID: PMC7068945 DOI: 10.1186/s13068-020-1663-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/21/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND An economically viable production of biofuels and biochemicals from lignocellulose requires microorganisms that can readily convert both the cellulosic and hemicellulosic fractions into product. The yeast Candida intermedia displays a high capacity for uptake and conversion of several lignocellulosic sugars including the abundant pentose d-xylose, an underutilized carbon source since most industrially relevant microorganisms cannot naturally ferment it. Thus, C. intermedia constitutes an important source of knowledge and genetic information that could be transferred to industrial microorganisms such as Saccharomyces cerevisiae to improve their capacity to ferment lignocellulose-derived xylose. RESULTS To understand the genetic determinants that underlie the metabolic properties of C. intermedia, we sequenced the genomes of both the in-house-isolated strain CBS 141442 and the reference strain PYCC 4715. De novo genome assembly and subsequent analysis revealed C. intermedia to be a haploid species belonging to the CTG clade of ascomycetous yeasts. The two strains have highly similar genome sizes and number of protein-encoding genes, but they differ on the chromosomal level due to numerous translocations of large and small genomic segments. The transcriptional profiles for CBS 141442 grown in medium with either high or low concentrations of glucose and xylose were determined through RNA-sequencing analysis, revealing distinct clusters of co-regulated genes in response to different specific growth rates, carbon sources and osmotic stress. Analysis of the genomic and transcriptomic data also identified multiple xylose reductases, one of which displayed dual NADH/NADPH co-factor specificity that likely plays an important role for co-factor recycling during xylose fermentation. CONCLUSIONS In the present study, we performed the first genomic and transcriptomic analysis of C. intermedia and identified several novel genes for conversion of xylose. Together the results provide insights into the mechanisms underlying saccharide utilization in C. intermedia and reveal potential target genes to aid in xylose fermentation in S. cerevisiae.
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Affiliation(s)
- Cecilia Geijer
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fábio Faria-Oliveira
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Antonio D. Moreno
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Present Address: Biofuels Unit, Department of Energy, CIEMAT, Madrid, Spain
| | - Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Scott Mazurkewich
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Hector RE, Mertens JA, Nichols NN. Development and characterization of vectors for tunable expression of both xylose-regulated and constitutive gene expression in Saccharomyces yeasts. N Biotechnol 2019; 53:16-23. [DOI: 10.1016/j.nbt.2019.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 10/26/2022]
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Ruchala J, Kurylenko OO, Dmytruk KV, Sibirny AA. Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts (Scheffersomyces stipitis, Ogataea polymorpha). J Ind Microbiol Biotechnol 2019; 47:109-132. [PMID: 31637550 PMCID: PMC6970964 DOI: 10.1007/s10295-019-02242-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022]
Abstract
This review summarizes progress in the construction of efficient yeast ethanol producers from glucose/sucrose and lignocellulose. Saccharomyces cerevisiae is the major industrial producer of first-generation ethanol. The different approaches to increase ethanol yield and productivity from glucose in S. cerevisiae are described. Construction of the producers of second-generation ethanol is described for S. cerevisiae, one of the best natural xylose fermenters, Scheffersomyces stipitis and the most thermotolerant yeast known Ogataea polymorpha. Each of these organisms has some advantages and drawbacks. S. cerevisiae is the primary industrial ethanol producer and is the most ethanol tolerant natural yeast known and, however, cannot metabolize xylose. S. stipitis can effectively ferment both glucose and xylose and, however, has low ethanol tolerance and requires oxygen for growth. O. polymorpha grows and ferments at high temperatures and, however, produces very low amounts of ethanol from xylose. Review describes how the mentioned drawbacks could be overcome.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Olena O Kurylenko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Kostyantyn V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland.
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Guirimand GGY, Bamba T, Matsuda M, Inokuma K, Morita K, Kitada Y, Kobayashi Y, Yukawa T, Sasaki K, Ogino C, Hasunuma T, Kondo A. Combined Cell Surface Display of β‐
d
‐Glucosidase (BGL), Maltose Transporter (MAL11), and Overexpression of Cytosolic Xylose Reductase (XR) in
Saccharomyces cerevisiae
Enhance Cellobiose/Xylose Coutilization for Xylitol Bioproduction from Lignocellulosic Biomass. Biotechnol J 2019; 14:e1800704. [DOI: 10.1002/biot.201800704] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 06/10/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Gregory G. Y. Guirimand
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Engineering Biology Research CenterKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Takahiro Bamba
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Mami Matsuda
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Kentaro Inokuma
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Engineering Biology Research CenterKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Kenta Morita
- Department of Chemical Science and Engineering, Graduate School of EngineeringKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Research Facility Center for Science and TechnologyKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Yuki Kitada
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Yuma Kobayashi
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Takahiro Yukawa
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Kengo Sasaki
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Engineering Biology Research CenterKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Chiaki Ogino
- Engineering Biology Research CenterKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Department of Chemical Science and Engineering, Graduate School of EngineeringKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Engineering Biology Research CenterKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Engineering Biology Research CenterKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Department of Chemical Science and Engineering, Graduate School of EngineeringKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Biomass Engineering ProgramRIKEN 1‐7‐22 Suehiro‐cho 230‐0045 Tsurumi‐ku, Yokohama Kanagawa Japan
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25
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Veras HCT, Campos CG, Nascimento IF, Abdelnur PV, Almeida JRM, Parachin NS. Metabolic flux analysis for metabolome data validation of naturally xylose-fermenting yeasts. BMC Biotechnol 2019; 19:58. [PMID: 31382948 PMCID: PMC6683545 DOI: 10.1186/s12896-019-0548-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/19/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Efficient xylose fermentation still demands knowledge regarding xylose catabolism. In this study, metabolic flux analysis (MFA) and metabolomics were used to improve our understanding of xylose metabolism. Thus, a stoichiometric model was constructed to simulate the intracellular carbon flux and used to validate the metabolome data collected within xylose catabolic pathways of non-Saccharomyces xylose utilizing yeasts. RESULTS A metabolic flux model was constructed using xylose fermentation data from yeasts Scheffersomyces stipitis, Spathaspora arborariae, and Spathaspora passalidarum. In total, 39 intracellular metabolic reactions rates were utilized validating the measurements of 11 intracellular metabolites, acquired by mass spectrometry. Among them, 80% of total metabolites were confirmed with a correlation above 90% when compared to the stoichiometric model. Among the intracellular metabolites, fructose-6-phosphate, glucose-6-phosphate, ribulose-5-phosphate, and malate are validated in the three studied yeasts. However, the metabolites phosphoenolpyruvate and pyruvate could not be confirmed in any yeast. Finally, the three yeasts had the metabolic fluxes from xylose to ethanol compared. Xylose catabolism occurs at twice-higher flux rates in S. stipitis than S. passalidarum and S. arborariae. Besides, S. passalidarum present 1.5 times high flux rate in the xylose reductase reaction NADH-dependent than other two yeasts. CONCLUSIONS This study demonstrated a novel strategy for metabolome data validation and brought insights about naturally xylose-fermenting yeasts. S. stipitis and S. passalidarum showed respectively three and twice higher flux rates of XR with NADH cofactor, reducing the xylitol production when compared to S. arborariae. Besides then, the higher flux rates directed to pentose phosphate pathway (PPP) and glycolysis pathways resulted in better ethanol production in S. stipitis and S. passalidarum when compared to S. arborariae.
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Affiliation(s)
- Henrique C. T. Veras
- Grupo Engenharia de Biocatalisadores, Universidade de Brasília - UnB , Campus Darcy Ribeiro, Instituto de Ciências Biológicas, Bloco K, 1° andar, Asa Norte, Brasilia, 70.790-900 Brazil
- Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA Agroenergia, Brasília-DF, Brazil
| | - Christiane G. Campos
- Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA Agroenergia, Brasília-DF, Brazil
- Instituto de Química, Universidade Federal de Goiás - UFG, Goiânia, Brazil
| | - Igor F. Nascimento
- Programa de Pós-Graduação em Administração, Universidade de Brasília - UnB, Brasília, Brazil
| | - Patrícia V. Abdelnur
- Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA Agroenergia, Brasília-DF, Brazil
- Instituto de Química, Universidade Federal de Goiás - UFG, Goiânia, Brazil
| | - João R. M. Almeida
- Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA Agroenergia, Brasília-DF, Brazil
- Programa de Pós-Graduação em Biologia Microbiana, Instituto de Biologia, Universidade de Brasília - UnB, Brasilia, Brazil
| | - Nádia S. Parachin
- Grupo Engenharia de Biocatalisadores, Universidade de Brasília - UnB , Campus Darcy Ribeiro, Instituto de Ciências Biológicas, Bloco K, 1° andar, Asa Norte, Brasilia, 70.790-900 Brazil
- Programa de Pós-Graduação em Biologia Microbiana, Instituto de Biologia, Universidade de Brasília - UnB, Brasilia, Brazil
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26
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Abstract
Production of fuels and chemicals from renewable lignocellulosic feedstocks is a promising alternative to petroleum-derived compounds. Due to the complexity of lignocellulosic feedstocks, microbial conversion of all potential substrates will require substantial metabolic engineering. Non-model microbes offer desirable physiological traits, but also increase the difficulty of heterologous pathway engineering and optimization. The development of modular design principles that allow metabolic pathways to be used in a variety of novel microbes with minimal strain-specific optimization will enable the rapid construction of microbes for commercial production of biofuels and bioproducts. In this review, we discuss variability of lignocellulosic feedstocks, pathways for catabolism of lignocellulose-derived compounds, challenges to heterologous engineering of catabolic pathways, and opportunities to apply modular pathway design. Implementation of these approaches will simplify the process of modifying non-model microbes to convert diverse lignocellulosic feedstocks.
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27
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Gao M, Ploessl D, Shao Z. Enhancing the Co-utilization of Biomass-Derived Mixed Sugars by Yeasts. Front Microbiol 2019; 9:3264. [PMID: 30723464 PMCID: PMC6349770 DOI: 10.3389/fmicb.2018.03264] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/14/2018] [Indexed: 12/11/2022] Open
Abstract
Plant biomass is a promising carbon source for producing value-added chemicals, including transportation biofuels, polymer precursors, and various additives. Most engineered microbial hosts and a select group of wild-type species can metabolize mixed sugars including oligosaccharides, hexoses, and pentoses that are hydrolyzed from plant biomass. However, most of these microorganisms consume glucose preferentially to non-glucose sugars through mechanisms generally defined as carbon catabolite repression. The current lack of simultaneous mixed-sugar utilization limits achievable titers, yields, and productivities. Therefore, the development of microbial platforms capable of fermenting mixed sugars simultaneously from biomass hydrolysates is essential for economical industry-scale production, particularly for compounds with marginal profits. This review aims to summarize recent discoveries and breakthroughs in the engineering of yeast cell factories for improved mixed-sugar co-utilization based on various metabolic engineering approaches. Emphasis is placed on enhanced non-glucose utilization, discovery of novel sugar transporters free from glucose repression, native xylose-utilizing microbes, consolidated bioprocessing (CBP), improved cellulase secretion, and creation of microbial consortia for improving mixed-sugar utilization. Perspectives on the future development of biorenewables industry are provided in the end.
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Affiliation(s)
- Meirong Gao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States
| | - Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States.,The Ames Laboratory, Iowa State University, Ames, IA, United States.,The Interdisciplinary Microbiology Program, Biorenewables Research Laboratory, Iowa State University, Ames, IA, United States
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28
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Quehenberger J, Reichenbach T, Baumann N, Rettenbacher L, Divne C, Spadiut O. Kinetics and Predicted Structure of a Novel Xylose Reductase from Chaetomium thermophilum. Int J Mol Sci 2019; 20:ijms20010185. [PMID: 30621365 PMCID: PMC6337131 DOI: 10.3390/ijms20010185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 12/29/2018] [Accepted: 01/01/2019] [Indexed: 11/16/2022] Open
Abstract
While in search of an enzyme for the conversion of xylose to xylitol at elevated temperatures, a xylose reductase (XR) gene was identified in the genome of the thermophilic fungus Chaetomium thermophilum. The gene was heterologously expressed in Escherichia coli as a His6-tagged fusion protein and characterized for function and structure. The enzyme exhibits dual cofactor specificity for NADPH and NADH and prefers D-xylose over other pentoses and investigated hexoses. A homology model based on a XR from Candida tenuis was generated and the architecture of the cofactor binding site was investigated in detail. Despite the outstanding thermophilicity of its host the enzyme is, however, not thermostable.
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Affiliation(s)
- Julian Quehenberger
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Faculty of Technical Chemistry, TU Wien, 1060 Vienna, Austria.
| | - Tom Reichenbach
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health, SE-100 44 Stockholm, Sweden.
| | - Niklas Baumann
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Faculty of Technical Chemistry, TU Wien, 1060 Vienna, Austria.
| | - Lukas Rettenbacher
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Faculty of Technical Chemistry, TU Wien, 1060 Vienna, Austria.
| | - Christina Divne
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health, SE-100 44 Stockholm, Sweden.
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Faculty of Technical Chemistry, TU Wien, 1060 Vienna, Austria.
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29
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Son HF, Lee SM, Kim KJ. Structural insight into D-xylose utilization by xylose reductase from Scheffersomyces stipitis. Sci Rep 2018; 8:17442. [PMID: 30487522 PMCID: PMC6261992 DOI: 10.1038/s41598-018-35703-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 11/09/2018] [Indexed: 11/09/2022] Open
Abstract
Lignocellulosic biomass, of which D-xylose accounts for approximately 35% of the total sugar, has attracted attention as a future energy source for biofuel. To elucidate molecular mechanism of D-xylose utilization, we determined the crystal structure of D-xylose reductase from Schefferzomyces stipitis (SsXR) at a 1.95 Å resolution. We also determined the SsXR structure in complex with the NADPH cofactor and revealed that the protein undergoes an open/closed conformation change upon NADPH binding. The substrate binding pocket of SsXR is somewhat hydrophobic, which seems to result in low binding affinity to the substrate. Phylogenetic tree analysis showed that AKR enzymes annotated with bacterial/archaeal XRs belonged to uncharacterized AKR families and might have no XR function, and yeast/fungi derived enzymes, which belong to the same group with SsXR, can be candidates for XR to increase xylose consumption.
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Affiliation(s)
- Hyeoncheol Francis Son
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea.
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea.
- KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.
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30
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Lian J, Mishra S, Zhao H. Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications. Metab Eng 2018; 50:85-108. [DOI: 10.1016/j.ymben.2018.04.011] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
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31
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Yaguchi A, Spagnuolo M, Blenner M. Engineering yeast for utilization of alternative feedstocks. Curr Opin Biotechnol 2018; 53:122-129. [DOI: 10.1016/j.copbio.2017.12.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/01/2017] [Accepted: 12/01/2017] [Indexed: 11/16/2022]
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32
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Lane S, Dong J, Jin YS. Value-added biotransformation of cellulosic sugars by engineered Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2018; 260:380-394. [PMID: 29655899 DOI: 10.1016/j.biortech.2018.04.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 05/26/2023]
Abstract
The substantial research efforts into lignocellulosic biofuels have generated an abundance of valuable knowledge and technologies for metabolic engineering. In particular, these investments have led to a vast growth in proficiency of engineering the yeast Saccharomyces cerevisiae for consuming lignocellulosic sugars, enabling the simultaneous assimilation of multiple carbon sources, and producing a large variety of value-added products by introduction of heterologous metabolic pathways. While microbial conversion of cellulosic sugars into large-volume low-value biofuels is not currently economically feasible, there may still be opportunities to produce other value-added chemicals as regulation of cellulosic sugar metabolism is quite different from glucose metabolism. This review summarizes these recent advances with an emphasis on employing engineered yeast for the bioconversion of lignocellulosic sugars into a variety of non-ethanol value-added products.
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Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jia Dong
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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33
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Guo J, Huang S, Chen Y, Guo X, Xiao D. Heterologous expression of Spathaspora passalidarum xylose reductase and xylitol dehydrogenase genes improved xylose fermentation ability of Aureobasidium pullulans. Microb Cell Fact 2018; 17:64. [PMID: 29712559 PMCID: PMC5925849 DOI: 10.1186/s12934-018-0911-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/24/2018] [Indexed: 11/16/2022] Open
Abstract
Background Aureobasidium pullulans is a yeast-like fungus that can ferment xylose to generate high-value-added products, such as pullulan, heavy oil, and melanin. The combinatorial expression of two xylose reductase (XR) genes and two xylitol dehydrogenase (XDH) genes from Spathaspora passalidarum and the heterologous expression of the Piromyces sp. xylose isomerase (XI) gene were induced in A. pullulans to increase the consumption capability of A. pullulans on xylose. Results The overexpression of XYL1.2 (encoding XR) and XYL2.2 (encoding XDH) was the most beneficial for xylose utilization, resulting in a 17.76% increase in consumed xylose compared with the parent strain, whereas the introduction of the Piromyces sp. XI pathway failed to enhance xylose utilization efficiency. Mutants with superior xylose fermentation performance exhibited increased intracellular reducing equivalents. The fermentation performance of all recombinant strains was not affected when glucose or sucrose was utilized as the carbon source. The strain with overexpression of XYL1.2 and XYL2.2 exhibited excellent fermentation performance with mimicked hydrolysate, and pullulan production increased by 97.72% compared with that of the parent strain. Conclusions The present work indicates that the P4 mutant (using the XR/XDH pathway) with overexpressed XYL1.2 and XYL2.2 exhibited the best xylose fermentation performance. The P4 strain showed the highest intracellular reducing equivalents and XR and XDH activity, with consequently improved pullulan productivity and reduced melanin production. This valuable development in aerobic fermentation by the P4 strain may provide guidance for the biotransformation of xylose to high-value products by A. pullulans through genetic approach. Electronic supplementary material The online version of this article (10.1186/s12934-018-0911-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Siyao Huang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Yefu Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Xuewu Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Dongguang Xiao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
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34
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Liu J, Li H, Zhao G, Caiyin Q, Qiao J. Redox cofactor engineering in industrial microorganisms: strategies, recent applications and future directions. J Ind Microbiol Biotechnol 2018; 45:313-327. [PMID: 29582241 DOI: 10.1007/s10295-018-2031-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/22/2018] [Indexed: 02/07/2023]
Abstract
NAD and NADP, a pivotal class of cofactors, which function as essential electron donors or acceptors in all biological organisms, drive considerable catabolic and anabolic reactions. Furthermore, they play critical roles in maintaining intracellular redox homeostasis. However, many metabolic engineering efforts in industrial microorganisms towards modification or introduction of metabolic pathways, especially those involving consumption, generation or transformation of NAD/NADP, often induce fluctuations in redox state, which dramatically impede cellular metabolism, resulting in decreased growth performance and biosynthetic capacity. Here, we comprehensively review the cofactor engineering strategies for solving the problematic redox imbalance in metabolism modification, as well as their features, suitabilities and recent applications. Some representative examples of in vitro biocatalysis are also described. In addition, we briefly discuss how tools and methods from the field of synthetic biology can be applied for cofactor engineering. Finally, future directions and challenges for development of cofactor redox engineering are presented.
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Affiliation(s)
- Jiaheng Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Huiling Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Guangrong Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Qinggele Caiyin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Jianjun Qiao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China.
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35
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You C, Huang R, Wei X, Zhu Z, Zhang YHP. Protein engineering of oxidoreductases utilizing nicotinamide-based coenzymes, with applications in synthetic biology. Synth Syst Biotechnol 2017; 2:208-218. [PMID: 29318201 PMCID: PMC5655348 DOI: 10.1016/j.synbio.2017.09.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/08/2017] [Accepted: 09/22/2017] [Indexed: 01/01/2023] Open
Abstract
Two natural nicotinamide-based coenzymes (NAD and NADP) are indispensably required by the vast majority of oxidoreductases for catabolism and anabolism, respectively. Most NAD(P)-dependent oxidoreductases prefer one coenzyme as an electron acceptor or donor to the other depending on their different metabolic roles. This coenzyme preference associated with coenzyme imbalance presents some challenges for the construction of high-efficiency in vivo and in vitro synthetic biology pathways. Changing the coenzyme preference of NAD(P)-dependent oxidoreductases is an important area of protein engineering, which is closely related to product-oriented synthetic biology projects. This review focuses on the methodology of nicotinamide-based coenzyme engineering, with its application in improving product yields and decreasing production costs. Biomimetic nicotinamide-containing coenzymes have been proposed to replace natural coenzymes because they are more stable and less costly than natural coenzymes. Recent advances in the switching of coenzyme preference from natural to biomimetic coenzymes are also covered in this review. Engineering coenzyme preferences from natural to biomimetic coenzymes has become an important direction for coenzyme engineering, especially for in vitro synthetic pathways and in vivo bioorthogonal redox pathways.
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Affiliation(s)
- Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Rui Huang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA 24061, USA
| | - Xinlei Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Yi-Heng Percival Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.,Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA 24061, USA
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36
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Jo JH, Park YC, Jin YS, Seo JH. Construction of efficient xylose-fermenting Saccharomyces cerevisiae through a synthetic isozyme system of xylose reductase from Scheffersomyces stipitis. BIORESOURCE TECHNOLOGY 2017; 241:88-94. [PMID: 28550778 DOI: 10.1016/j.biortech.2017.05.091] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/13/2017] [Accepted: 05/15/2017] [Indexed: 05/12/2023]
Abstract
Engineered Saccharomyces cerevisiae has been used for ethanol production from xylose, the abundant sugar in lignocellulosic hydrolyzates. Development of engineered S. cerevisiae able to utilize xylose effectively is crucial for economical and sustainable production of fuels. To this end, the xylose-metabolic genes (XYL1, XYL2 and XYL3) from Scheffersomyces stipitis have been introduced into S. cerevisiae. The resulting engineered S. cerevisiae strains, however, often exhibit undesirable phenotypes such as slow xylose assimilation and xylitol accumulation. This work was undertaken to construct an improved xylose-fermenting strain by developing a synthetic isozyme system of xylose reductase (XR). The DXS strain having both wild XR and mutant XR showed low xylitol accumulation and fast xylose consumption compared to the engineered strains expressing only one type of XRs, resulting in improved ethanol yield and productivity. These results suggest that the introduction of the XR-based synthetic isozyme system is a promising strategy to develop efficient xylose-fermenting strains.
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Affiliation(s)
- Jung-Hyun Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Cheol Park
- Department of Bio and Fermentation Convergence Technology and BK21 Plus Program, Kookmin University, Seoul 03084, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jin-Ho Seo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea.
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37
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Comparative assessment of fermentative capacity of different xylose-consuming yeasts. Microb Cell Fact 2017; 16:153. [PMID: 28903764 PMCID: PMC5598047 DOI: 10.1186/s12934-017-0766-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/07/2017] [Indexed: 12/03/2022] Open
Abstract
Background Understanding the effects of oxygen levels on yeast xylose metabolism would benefit ethanol production. In this work, xylose fermentative capacity of Scheffersomyces stipitis, Spathaspora passalidarum, Spathaspora arborariae and Candida tenuis was systematically compared under aerobic, oxygen-limited and anaerobic conditions. Results Fermentative performances of the four yeasts were greatly influenced by oxygen availability. S. stipitis and S. passalidarum showed the highest ethanol yields (above 0.44 g g−1) under oxygen limitation. However, S. passalidarum produced 1.5 times more ethanol than S. stipitis under anaerobiosis. While C. tenuis showed the lowest xylose consumption rate and incapacity to produce ethanol, S. arborariae showed an intermediate fermentative performance among the yeasts. NAD(P)H xylose reductase (XR) activity in crude cell extracts correlated with xylose consumption rates and ethanol production. Conclusions Overall, the present work demonstrates that the availability of oxygen influences the production of ethanol by yeasts and indicates that the NADH-dependent XR activity is a limiting step on the xylose metabolism. S. stipitis and S. passalidarum have the greatest potential for ethanol production from xylose. Both yeasts showed similar ethanol yields near theoretical under oxygen-limited condition. Besides that, S. passalidarum showed the best xylose consumption and ethanol production under anaerobiosis.
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Zhao C, Zhao Q, Li Y, Zhang Y. Engineering redox homeostasis to develop efficient alcohol-producing microbial cell factories. Microb Cell Fact 2017; 16:115. [PMID: 28646866 PMCID: PMC5483285 DOI: 10.1186/s12934-017-0728-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/16/2017] [Indexed: 12/11/2022] Open
Abstract
The biosynthetic pathways of most alcohols are linked to intracellular redox homeostasis, which is crucial for life. This crucial balance is primarily controlled by the generation of reducing equivalents, as well as the (reduction)-oxidation metabolic cycle and the thiol redox homeostasis system. As a main oxidation pathway of reducing equivalents, the biosynthesis of most alcohols includes redox reactions, which are dependent on cofactors such as NADH or NADPH. Thus, when engineering alcohol-producing strains, the availability of cofactors and redox homeostasis must be considered. In this review, recent advances on the engineering of cellular redox homeostasis systems to accelerate alcohol biosynthesis are summarized. Recent approaches include improving cofactor availability, manipulating the affinity of redox enzymes to specific cofactors, as well as globally controlling redox reactions, indicating the power of these approaches, and opening a path towards improving the production of a number of different industrially-relevant alcohols in the near future.
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Affiliation(s)
- Chunhua Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qiuwei Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road Chaoyang District, Beijing, 100101 China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road Chaoyang District, Beijing, 100101 China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road Chaoyang District, Beijing, 100101 China
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van Niel EWJ, Bergdahl B, Hahn-Hägerdal B. Close to the Edge: Growth Restrained by the NAD(P)H/ATP Formation Flux Ratio. Front Microbiol 2017; 8:1149. [PMID: 28690597 PMCID: PMC5479917 DOI: 10.3389/fmicb.2017.01149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/07/2017] [Indexed: 11/13/2022] Open
Abstract
Most fermentative microorganisms grow well-under anaerobic conditions managing a balanced redox and appropriate energy metabolism, but a few species do exist in which cells have to cope with inadequate energy recovery or capture and/or redox balancing. Two cases of these species, i.e., the metabolically engineered Saccharomyces cerevisiae enabling it to ferment xylose and Lactobacillus reuteri fermenting glucose via the phosphoketolase pathway, are here used to introduce a quantification parameter to capture what limits the growth rate of these microorganisms under anaerobic conditions. This dimensionless parameter, the cofactor formation flux ratio (RJ), is the ratio between the redox formation flux (JNADH+NADPH), and the energy carrier formation flux (JATP), which are mainly connected to the central carbon pathways. Data from metabolic flux analyses performed in previous and present studies were used to estimate the RJ-values. Even though both microorganisms possess different central pathways, a similar relationship between RJ and the specific growth rate (μ) was found. Furthermore, for both microorganisms external electron acceptors moderately reduced the RJ-value, thereby raising the μ accordingly. Based on the emerging profile of this relationship an interpretation is presented suggesting that this quantitative analysis can be applied beyond the two microbial species experimentally investigated in the current study to provide data for future targeted strain development strategies.
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Affiliation(s)
- Ed W J van Niel
- Division of Applied Microbiology, Lund UniversityLund, Sweden
| | - Basti Bergdahl
- Division of Applied Microbiology, Lund UniversityLund, Sweden
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Kwak S, Jin YS. Production of fuels and chemicals from xylose by engineered Saccharomyces cerevisiae: a review and perspective. Microb Cell Fact 2017; 16:82. [PMID: 28494761 PMCID: PMC5425999 DOI: 10.1186/s12934-017-0694-9] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 05/02/2017] [Indexed: 02/06/2023] Open
Abstract
Efficient xylose utilization is one of the most important pre-requisites for developing an economic microbial conversion process of terrestrial lignocellulosic biomass into biofuels and biochemicals. A robust ethanol producing yeast Saccharomyces cerevisiae has been engineered with heterologous xylose assimilation pathways. A two-step oxidoreductase pathway consisting of NAD(P)H-linked xylose reductase and NAD+-linked xylitol dehydrogenase, and one-step isomerase pathway using xylose isomerase have been employed to enable xylose assimilation in engineered S. cerevisiae. However, the resulting engineered yeast exhibited inefficient and slow xylose fermentation. In order to improve the yield and productivity of xylose fermentation, expression levels of xylose assimilation pathway enzymes and their kinetic properties have been optimized, and additional optimizations of endogenous or heterologous metabolisms have been achieved. These efforts have led to the development of engineered yeast strains ready for the commercialization of cellulosic bioethanol. Interestingly, xylose metabolism by engineered yeast was preferably respiratory rather than fermentative as in glucose metabolism, suggesting that xylose can serve as a desirable carbon source capable of bypassing metabolic barriers exerted by glucose repression. Accordingly, engineered yeasts showed superior production of valuable metabolites derived from cytosolic acetyl-CoA and pyruvate, such as 1-hexadecanol and lactic acid, when the xylose assimilation pathway and target synthetic pathways were optimized in an adequate manner. While xylose has been regarded as a sugar to be utilized because it is present in cellulosic hydrolysates, potential benefits of using xylose instead of glucose for yeast-based biotechnological processes need to be realized.
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Affiliation(s)
- Suryang Kwak
- Department of Food Science and Human Nutrition and Carl R. Woose Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition and Carl R. Woose Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Yamasaki-Yashiki S, Komeda H, Hoshino K, Asano Y. Characterization and gene cloning of l-xylulose reductase involved in l-arabinose catabolism from the pentose-fermenting fungus Rhizomucor pusillus. Biosci Biotechnol Biochem 2017; 81:1612-1618. [PMID: 28471330 DOI: 10.1080/09168451.2017.1320518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
l-Xylulose reductase (LXR) catalyzes the reduction of l-xylulose to xylitol in the fungal l-arabinose catabolic pathway. LXR (RpLXR) was purified from the pentose-fermenting zygomycetous fungus Rhizomucor pusillus NBRC 4578. The native RpLXR is a homotetramer composed of 29 kDa subunits and preferred NADPH as a coenzyme. The Km values were 8.71 mM for l-xylulose and 3.89 mM for dihydroxyacetone. The lxr3 (Rplxr3) gene encoding RpLXR consists of 792 bp and encodes a putative 263 amino acid protein (Mr = 28,341). The amino acid sequence of RpLXR showed high similarity to 3-oxoacyl-(acyl-carrier-protein) reductase. The Rplxr3 gene was expressed in Escherichia coli and the recombinant RpLXR exhibited properties similar to those of native RpLXR. Transcription of the Rplxr3 gene in R. pusillus NBRC 4578 was induced in the presence of l-arabinose and inhibited in the presence of d-glucose, d-xylose, and d-mannitol, indicating that RpLXR is involved in the l-arabinose catabolic pathway.
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Affiliation(s)
- Shino Yamasaki-Yashiki
- a Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , Imizu , Japan
| | - Hidenobu Komeda
- a Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , Imizu , Japan
| | - Kazuhiro Hoshino
- b Graduate school of Science and Engineering , University of Toyama , Toyama , Japan
| | - Yasuhisa Asano
- a Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , Imizu , Japan
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Zhang GC, Turner TL, Jin YS. Enhanced xylose fermentation by engineered yeast expressing NADH oxidase through high cell density inoculums. ACTA ACUST UNITED AC 2017; 44:387-395. [DOI: 10.1007/s10295-016-1899-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/25/2016] [Indexed: 12/22/2022]
Abstract
Abstract
Accumulation of reduced byproducts such as glycerol and xylitol during xylose fermentation by engineered Saccharomyces cerevisiae hampers the economic production of biofuels and chemicals from cellulosic hydrolysates. In particular, engineered S. cerevisiae expressing NADPH-linked xylose reductase (XR) and NAD+-linked xylitol dehydrogenase (XDH) produces substantial amounts of the reduced byproducts under anaerobic conditions due to the cofactor difference of XR and XDH. While the additional expression of a water-forming NADH oxidase (NoxE) from Lactococcus lactis in engineered S. cerevisiae with the XR/XDH pathway led to reduced glycerol and xylitol production and increased ethanol yields from xylose, volumetric ethanol productivities by the engineered yeast decreased because of growth defects from the overexpression of noxE. In this study, we introduced noxE into an engineered yeast strain (SR8) exhibiting near-optimal xylose fermentation capacity. To overcome the growth defect caused by the overexpression of noxE, we used a high cell density inoculum for xylose fermentation by the SR8 expressing noxE. The resulting strain, SR8N, not only showed a higher ethanol yield and lower byproduct yields, but also exhibited a high ethanol productivity during xylose fermentation. As noxE overexpression elicits a negligible growth defect on glucose conditions, the beneficial effects of noxE overexpression were substantial when a mixture of glucose and xylose was used. Consumption of glucose led to rapid cell growth and therefore enhanced the subsequent xylose fermentation. As a result, the SR8N strain produced more ethanol and fewer byproducts from a mixture of glucose and xylose than the parental SR8 strain without noxE overexpression. Our results suggest that the growth defects from noxE overexpression can be overcome in the case of fermenting lignocellulose-derived sugars such as glucose and xylose.
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Affiliation(s)
- Guo-Chang Zhang
- grid.35403.31 0000000419369991 Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign 1206 W. Gregory Drive 61801 Urbana IL USA
- grid.35403.31 0000000419369991 Department of Food Science and Human Nutrition University of Illinois at Urbana-Champaign 61801 Urbana IL USA
| | - Timothy L Turner
- grid.35403.31 0000000419369991 Department of Food Science and Human Nutrition University of Illinois at Urbana-Champaign 61801 Urbana IL USA
| | - Yong-Su Jin
- grid.35403.31 0000000419369991 Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign 1206 W. Gregory Drive 61801 Urbana IL USA
- grid.35403.31 0000000419369991 Department of Food Science and Human Nutrition University of Illinois at Urbana-Champaign 61801 Urbana IL USA
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Cahn JKB, Werlang CA, Baumschlager A, Brinkmann-Chen S, Mayo SL, Arnold FH. A General Tool for Engineering the NAD/NADP Cofactor Preference of Oxidoreductases. ACS Synth Biol 2017; 6:326-333. [PMID: 27648601 DOI: 10.1021/acssynbio.6b00188] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability to control enzymatic nicotinamide cofactor utilization is critical for engineering efficient metabolic pathways. However, the complex interactions that determine cofactor-binding preference render this engineering particularly challenging. Physics-based models have been insufficiently accurate and blind directed evolution methods too inefficient to be widely adopted. Building on a comprehensive survey of previous studies and our own prior engineering successes, we present a structure-guided, semirational strategy for reversing enzymatic nicotinamide cofactor specificity. This heuristic-based approach leverages the diversity and sensitivity of catalytically productive cofactor binding geometries to limit the problem to an experimentally tractable scale. We demonstrate the efficacy of this strategy by inverting the cofactor specificity of four structurally diverse NADP-dependent enzymes: glyoxylate reductase, cinnamyl alcohol dehydrogenase, xylose reductase, and iron-containing alcohol dehydrogenase. The analytical components of this approach have been fully automated and are available in the form of an easy-to-use web tool: Cofactor Specificity Reversal-Structural Analysis and Library Design (CSR-SALAD).
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Affiliation(s)
- Jackson K. B. Cahn
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Caroline A. Werlang
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Armin Baumschlager
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Sabine Brinkmann-Chen
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Stephen L. Mayo
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
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Guo W, Sheng J, Feng X. Synergizing 13C Metabolic Flux Analysis and Metabolic Engineering for Biochemical Production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 162:265-299. [PMID: 28424826 DOI: 10.1007/10_2017_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Metabolic engineering of industrial microorganisms to produce chemicals, fuels, and drugs has attracted increasing interest as it provides an environment-friendly and renewable route that does not depend on depleting petroleum sources. However, the microbial metabolism is so complex that metabolic engineering efforts often have difficulty in achieving a satisfactory yield, titer, or productivity of the target chemical. To overcome this challenge, 13C Metabolic Flux Analysis (13C-MFA) has been developed to investigate rigorously the cell metabolism and quantify the carbon flux distribution in central metabolic pathways. In the past decade, 13C-MFA has been widely used in academic labs and the biotechnology industry to pinpoint the key issues related to microbial-based chemical production and to guide the development of the appropriate metabolic engineering strategies for improving the biochemical production. In this chapter we introduce the basics of 13C-MFA and illustrate how 13C-MFA has been applied to synergize with metabolic engineering to identify and tackle the rate-limiting steps in biochemical production.
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Affiliation(s)
- Weihua Guo
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Jiayuan Sheng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Xueyang Feng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
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Kogje A, Ghosalkar A. Xylitol production by Saccharomyces cerevisiae overexpressing different xylose reductases using non-detoxified hemicellulosic hydrolysate of corncob. 3 Biotech 2016; 6:127. [PMID: 28330197 PMCID: PMC4909029 DOI: 10.1007/s13205-016-0444-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/25/2016] [Indexed: 02/03/2023] Open
Abstract
Xylitol production was compared in fed batch fermentation by Saccharomyces cerevisiae strains overexpressing xylose reductase (XR) genes from Candida tropicalis, Pichia stipitis, Neurospora crassa, and an endogenous gene GRE3. The gene encoding a xylose specific transporter (SUT1) from P. stipitis was cloned to improve xylose transport and fed batch fermentation was used with glucose as a cosubstrate to regenerate NADPH. Xylitol yield was near theoretical for all the strains in fed batch fermentation. The highest volumetric (0.28 gL-1 h-1) and specific (34 mgg-1 h-1) xylitol productivities were obtained by the strain overexpressing GRE3 gene, while the control strain showed 7.2 mgg-1 h-1 specific productivity. The recombinant strains carrying XR from C. tropicalis, P. stipitis, and N. crassa produced xylitol with lower specific productivity of 14.3, 6.8, and 6.3 mgg-1 h-1, respectively, than GRE3 overexpressing strain. The glucose fed as cosubstrate was converted to biomass and ethanol, while xylose was only converted to xylitol. The efficiency of ethanol production was in the range of 38-45 % of the theoretical maximum for all the strains. Xylitol production from the non-detoxified corncob hemicellulosic hydrolysate by recombinant S. cerevisiae was reported for the first time. Xylitol productivity was found to be equivalent in the synthetic xylose as well as hemicellulosic hydrolysate-based media showing no inhibition on the S. cerevisiae due to the inhibitors present in the hydrolysate. A systematic evaluation of heterologous XRs and endogenous GRE3 genes was performed, and the strain overexpressing the endogenous GRE3 gene showed the best xylitol productivity.
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Affiliation(s)
- Anushree Kogje
- Department of Technology, Savitribai Phule Pune University, Pune, Maharashtra 411007 India
- Division of Praj Industries Limited, Praj-Matrix - R & D Centre, 402/403/1098, Urawade, Pune, Maharashtra 412115 India
| | - Anand Ghosalkar
- Division of Praj Industries Limited, Praj-Matrix - R & D Centre, 402/403/1098, Urawade, Pune, Maharashtra 412115 India
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de Las Heras AM, Portugal-Nunes DJ, Rizza N, Sandström AG, Gorwa-Grauslund MF. Anaerobic poly-3-D-hydroxybutyrate production from xylose in recombinant Saccharomyces cerevisiae using a NADH-dependent acetoacetyl-CoA reductase. Microb Cell Fact 2016; 15:197. [PMID: 27863495 PMCID: PMC5116212 DOI: 10.1186/s12934-016-0598-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/10/2016] [Indexed: 11/19/2022] Open
Abstract
Background Poly-3-d-hydroxybutyrate (PHB) that is a promising precursor for bioplastic with similar physical properties as polypropylene, is naturally produced by several bacterial species. The bacterial pathway is comprised of the three enzymes β-ketothiolase, acetoacetyl-CoA reductase (AAR) and PHB synthase, which all together convert acetyl-CoA into PHB. Heterologous expression of the pathway genes from Cupriavidus necator has enabled PHB production in the yeast Saccharomyces cerevisiae from glucose as well as from xylose, after introduction of the fungal xylose utilization pathway from Scheffersomyces stipitis including xylose reductase (XR) and xylitol dehydrogenase (XDH). However PHB titers are still low. Results In this study the acetoacetyl-CoA reductase gene from C. necator (CnAAR), a NADPH-dependent enzyme, was replaced by the NADH-dependent AAR gene from Allochromatium vinosum (AvAAR) in recombinant xylose-utilizing S. cerevisiae and PHB production was compared. A. vinosum AAR was found to be active in S. cerevisiae and able to use both NADH and NADPH as cofactors. This resulted in improved PHB titers in S. cerevisiae when xylose was used as sole carbon source (5-fold in aerobic conditions and 8.4-fold under oxygen limited conditions) and PHB yields (4-fold in aerobic conditions and up to 5.6-fold under oxygen limited conditions). Moreover, the best strain was able to accumulate up to 14% of PHB per cell dry weight under fully anaerobic conditions. Conclusions This study reports a novel approach for boosting PHB accumulation in S. cerevisiae by replacement of the commonly used AAR from C. necator with the NADH-dependent alternative from A. vinosum. Additionally, to the best of our knowledge, it is the first demonstration of anaerobic PHB synthesis from xylose. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0598-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Diogo J Portugal-Nunes
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden
| | - Nathasha Rizza
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.,Vattenhallen Science Center, John Ericssons väg 1, 223 63, Lund, Sweden
| | - Anders G Sandström
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.,Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
| | - Marie F Gorwa-Grauslund
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.
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Characterization and evolution of xylose isomerase screened from the bovine rumen metagenome in Saccharomyces cerevisiae. J Biosci Bioeng 2016; 121:160-5. [DOI: 10.1016/j.jbiosc.2015.05.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/16/2015] [Accepted: 05/22/2015] [Indexed: 11/20/2022]
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Cadete RM, de las Heras AM, Sandström AG, Ferreira C, Gírio F, Gorwa-Grauslund MF, Rosa CA, Fonseca C. Exploring xylose metabolism in Spathaspora species: XYL1.2 from Spathaspora passalidarum as the key for efficient anaerobic xylose fermentation in metabolic engineered Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:167. [PMID: 27499810 PMCID: PMC4974763 DOI: 10.1186/s13068-016-0570-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 07/12/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND The production of ethanol and other fuels and chemicals from lignocellulosic materials is dependent of efficient xylose conversion. Xylose fermentation capacity in yeasts is usually linked to xylose reductase (XR) accepting NADH as cofactor. The XR from Scheffersomyces stipitis, which is able to use NADH as cofactor but still prefers NADPH, has been used to generate recombinant xylose-fermenting Saccharomyces cerevisiae. Novel xylose-fermenting yeasts species, as those from the Spathaspora clade, have been described and are potential sources of novel genes to improve xylose fermentation in S. cerevisiae. RESULTS Xylose fermentation by six strains from different Spathaspora species isolated in Brazil, plus the Sp. passalidarum type strain (CBS 10155(T)), was characterized under two oxygen-limited conditions. The best xylose-fermenting strains belong to the Sp. passalidarum species, and their highest ethanol titers, yields, and productivities were correlated to higher XR activity with NADH than with NADPH. Among the different Spathaspora species, Sp. passalidarum appears to be the sole harboring two XYL1 genes: XYL1.1, similar to the XYL1 found in other Spathaspora and yeast species and XYL1.2, with relatively higher expression level. XYL1.1p and XYL1.2p from Sp. passalidarum were expressed in S. cerevisiae TMB 3044 and XYL1.1p was confirmed to be strictly NADPH-dependent, while XYL1.2p to use both NADPH and NADH, with higher activity with the later. Recombinant S. cerevisiae strains expressing XYL1.1p did not show anaerobic growth in xylose medium. Under anaerobic xylose fermentation, S. cerevisiae TMB 3504, which expresses XYL1.2p from Sp. passalidarum, revealed significant higher ethanol yield and productivity than S. cerevisiae TMB 3422, which harbors XYL1p N272D from Sc. stipitis in the same isogenic background (0.40 vs 0.34 g gCDW (-1) and 0.33 vs 0.18 g gCDW (-1) h(-1), respectively). CONCLUSION This work explored a new clade of xylose-fermenting yeasts (Spathaspora species) towards the engineering of S. cerevisiae for improved xylose fermentation. The new S. cerevisiae TMB 3504 displays higher XR activity with NADH than with NADPH, with consequent improved ethanol yield and productivity and low xylitol production. This meaningful advance in anaerobic xylose fermentation by recombinant S. cerevisiae (using the XR/XDH pathway) paves the way for the development of novel industrial pentose-fermenting strains.
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Affiliation(s)
- Raquel M. Cadete
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901 Brazil
- Laboratório Nacional de Energia e Geologia, I.P., Unidade de Bioenergia, Estrada do Paço do Lumiar 22, 1649-038 Lisbon, Portugal
- Department of Applied Microbiology, Lund University, PO Box 124, 22100 Lund, Sweden
| | | | - Anders G. Sandström
- Department of Applied Microbiology, Lund University, PO Box 124, 22100 Lund, Sweden
- Novozymes A/S, Krogshøjvej 36, 2880 Bagsværd, Denmark
| | - Carla Ferreira
- Laboratório Nacional de Energia e Geologia, I.P., Unidade de Bioenergia, Estrada do Paço do Lumiar 22, 1649-038 Lisbon, Portugal
| | - Francisco Gírio
- Laboratório Nacional de Energia e Geologia, I.P., Unidade de Bioenergia, Estrada do Paço do Lumiar 22, 1649-038 Lisbon, Portugal
| | | | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901 Brazil
| | - César Fonseca
- Laboratório Nacional de Energia e Geologia, I.P., Unidade de Bioenergia, Estrada do Paço do Lumiar 22, 1649-038 Lisbon, Portugal
- Section for Sustainable Biotechnology, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450 Copenhagen SV, Denmark
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13C-Metabolic Flux Analysis: An Accurate Approach to Demystify Microbial Metabolism for Biochemical Production. Bioengineering (Basel) 2015; 3:bioengineering3010003. [PMID: 28952565 PMCID: PMC5597161 DOI: 10.3390/bioengineering3010003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/10/2015] [Accepted: 12/18/2015] [Indexed: 12/15/2022] Open
Abstract
Metabolic engineering of various industrial microorganisms to produce chemicals, fuels, and drugs has raised interest since it is environmentally friendly, sustainable, and independent of nonrenewable resources. However, microbial metabolism is so complex that only a few metabolic engineering efforts have been able to achieve a satisfactory yield, titer or productivity of the target chemicals for industrial commercialization. In order to overcome this challenge, 13C Metabolic Flux Analysis (13C-MFA) has been continuously developed and widely applied to rigorously investigate cell metabolism and quantify the carbon flux distribution in central metabolic pathways. In the past decade, many 13C-MFA studies have been performed in academic labs and biotechnology industries to pinpoint key issues related to microbe-based chemical production. Insightful information about the metabolic rewiring has been provided to guide the development of the appropriate metabolic engineering strategies for improving the biochemical production. In this review, we will introduce the basics of 13C-MFA and illustrate how 13C-MFA has been applied via integration with metabolic engineering to identify and tackle the rate-limiting steps in biochemical production for various host microorganisms
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Lee SM, Jellison T, Alper HS. Bioprospecting and evolving alternative xylose and arabinose pathway enzymes for use in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2015; 100:2487-98. [DOI: 10.1007/s00253-015-7211-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 11/05/2015] [Accepted: 12/01/2015] [Indexed: 10/22/2022]
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