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Vargas BDO, dos Santos JR, Pereira GAG, de Mello FDSB. An atlas of rational genetic engineering strategies for improved xylose metabolism in Saccharomyces cerevisiae. PeerJ 2023; 11:e16340. [PMID: 38047029 PMCID: PMC10691383 DOI: 10.7717/peerj.16340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/03/2023] [Indexed: 12/05/2023] Open
Abstract
Xylose is the second most abundant carbohydrate in nature, mostly present in lignocellulosic material, and representing an appealing feedstock for molecule manufacturing through biotechnological routes. However, Saccharomyces cerevisiae-a microbial cell widely used industrially for ethanol production-is unable to assimilate this sugar. Hence, in a world with raising environmental awareness, the efficient fermentation of pentoses is a crucial bottleneck to producing biofuels from renewable biomass resources. In this context, advances in the genetic mapping of S. cerevisiae have contributed to noteworthy progress in the understanding of xylose metabolism in yeast, as well as the identification of gene targets that enable the development of tailored strains for cellulosic ethanol production. Accordingly, this review focuses on the main strategies employed to understand the network of genes that are directly or indirectly related to this phenotype, and their respective contributions to xylose consumption in S. cerevisiae, especially for ethanol production. Altogether, the information in this work summarizes the most recent and relevant results from scientific investigations that endowed S. cerevisiae with an outstanding capability for commercial ethanol production from xylose.
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Affiliation(s)
- Beatriz de Oliveira Vargas
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Jade Ribeiro dos Santos
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
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Trivedi VD, Sullivan SF, Choudhury D, Endalur Gopinarayanan V, Hart T, Nair NU. Integration of metabolism and regulation reveals rapid adaptability to growth on non-native substrates. Cell Chem Biol 2023; 30:1135-1143.e5. [PMID: 37421944 PMCID: PMC10529486 DOI: 10.1016/j.chembiol.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/18/2023] [Accepted: 06/08/2023] [Indexed: 07/10/2023]
Abstract
Engineering synthetic heterotrophy is a key to the efficient bio-based valorization of renewable and waste substrates. Among these, engineering hemicellulosic pentose utilization has been well-explored in Saccharomyces cerevisiae (yeast) over several decades-yet the answer to what makes their utilization inherently recalcitrant remains elusive. Through implementation of a semi-synthetic regulon, we find that harmonizing cellular and engineering objectives are a key to obtaining highest growth rates and yields with minimal metabolic engineering effort. Concurrently, results indicate that "extrinsic" factors-specifically, upstream genes that direct flux of pentoses into central carbon metabolism-are rate-limiting. We also reveal that yeast metabolism is innately highly adaptable to rapid growth on non-native substrates and that systems metabolic engineering (i.e., functional genomics, network modeling, etc.) is largely unnecessary. Overall, this work provides an alternate, novel, holistic (and yet minimalistic) approach based on integrating non-native metabolic genes with a native regulon system.
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Affiliation(s)
- Vikas D Trivedi
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Sean F Sullivan
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Debika Choudhury
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | | | - Taylor Hart
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Nikhil U Nair
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA.
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Nijland JG, Zhang X, Driessen AJM. D-xylose accelerated death of pentose metabolizing Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:67. [PMID: 37069654 PMCID: PMC10111712 DOI: 10.1186/s13068-023-02320-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/10/2023] [Indexed: 04/19/2023]
Abstract
Rapid and effective consumption of D-xylose by Saccharomyces cerevisiae is essential for cost-efficient cellulosic bioethanol production. Hence, heterologous D-xylose metabolic pathways have been introduced into S. cerevisiae. An effective solution is based on a xylose isomerase in combination with the overexpression of the xylulose kinase (Xks1) and all genes of the non-oxidative branch of the pentose phosphate pathway. Although this strain is capable of consuming D-xylose, growth inhibition occurs at higher D-xylose concentrations, even abolishing growth completely at 8% D-xylose. The decreased growth rates are accompanied by significantly decreased ATP levels. A key ATP-utilizing step in D-xylose metabolism is the phosphorylation of D-xylulose by Xks1. Replacement of the constitutive promoter of XKS1 by the galactose tunable promoter Pgal10 allowed the controlled expression of this gene over a broad range. By decreasing the expression levels of XKS1, growth at high D-xylose concentrations could be restored concomitantly with increased ATP levels and high rates of xylose metabolism. These data show that in fermentations with high D-xylose concentrations, too high levels of Xks1 cause a major drain on the cellular ATP levels thereby reducing the growth rate, ultimately causing substrate accelerated death. Hence, expression levels of XKS1 in S. cerevisiae needs to be tailored for the specific growth conditions and robust D-xylose metabolism.
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Affiliation(s)
- Jeroen G Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Xiaohuan Zhang
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
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Althuri A, Venkata Mohan S. Emerging innovations for sustainable production of bioethanol and other mercantile products from circular economy perspective. BIORESOURCE TECHNOLOGY 2022; 363:128013. [PMID: 36155807 DOI: 10.1016/j.biortech.2022.128013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Biogenic municipal solid waste (BMSW) and food waste (FW) with high energy density are ready to tap renewable resources for industrial scale ethanol refinery foreseen for establishing bio-based society. Circular economy has occupied limelight in the domain of renewable energy and sustainable chemicals production. The present review highlights the importance of BMSW/FW as newer feed reserves that can cater as parent molecules for an array of high-visibility industrial products along with bioethanol upon implementing a judicious closed-cascade mass-flow mechanism enabling ultimate feed and waste stream valorisation. Though these organics are attractive resources their true potential for energy production has not been quantified yet owing to their heterogeneous composition and associated technical challenges thus pushing waste refinery and industrial symbiosis concepts to backseat. To accelerate this industrial vision, the novel bioprocessing strategies for enhanced and low-cost production of bioethanol from BMSW/FW along with other commercially imperative product portfolio have been discussed.
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Affiliation(s)
- Avanthi Althuri
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, Telangana, India; Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy-502284, Telangana, India
| | - S Venkata Mohan
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, Telangana, India.
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van Dijk M, Rugbjerg P, Nygård Y, Olsson L. RNA sequencing reveals metabolic and regulatory changes leading to more robust fermentation performance during short-term adaptation of Saccharomyces cerevisiae to lignocellulosic inhibitors. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:201. [PMID: 34654441 PMCID: PMC8518171 DOI: 10.1186/s13068-021-02049-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The limited tolerance of Saccharomyces cerevisiae to inhibitors is a major challenge in second-generation bioethanol production, and our understanding of the molecular mechanisms providing tolerance to inhibitor-rich lignocellulosic hydrolysates is incomplete. Short-term adaptation of the yeast in the presence of dilute hydrolysate can improve its robustness and productivity during subsequent fermentation. RESULTS We utilized RNA sequencing to investigate differential gene expression in the industrial yeast strain CR01 during short-term adaptation, mimicking industrial conditions for cell propagation. In this first transcriptomic study of short-term adaption of S. cerevisiae to lignocellulosic hydrolysate, we found that cultures respond by fine-tuned up- and down-regulation of a subset of general stress response genes. Furthermore, time-resolved RNA sequencing allowed for identification of genes that were differentially expressed at 2 or more sampling points, revealing the importance of oxidative stress response, thiamin and biotin biosynthesis. furan-aldehyde reductases and specific drug:H+ antiporters, as well as the down-regulation of certain transporter genes. CONCLUSIONS These findings provide a better understanding of the molecular mechanisms governing short-term adaptation of S. cerevisiae to lignocellulosic hydrolysate, and suggest new genetic targets for improving fermentation robustness.
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Affiliation(s)
- Marlous van Dijk
- Department of Biology and Bioengineering, Division of Industrial Biotechnology, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Peter Rugbjerg
- Department of Biology and Bioengineering, Division of Industrial Biotechnology, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Yvonne Nygård
- Department of Biology and Bioengineering, Division of Industrial Biotechnology, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Department of Biology and Bioengineering, Division of Industrial Biotechnology, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.
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Kwon DH, Kim SB, Park, JB, Ha SJ. Overexpression of Mutant Galactose Permease ( ScGal2_N376F) Effective for Utilization of Glucose/Xylose or Glucose/ Galactose Mixture by Engineered Kluyveromyces marxianus. J Microbiol Biotechnol 2020; 30:1944-1949. [PMID: 33046681 PMCID: PMC9728301 DOI: 10.4014/jmb.2008.08035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022]
Abstract
Mutant sugar transporter ScGAL2-N376F was overexpressed in Kluyveromyces marxianus for efficient utilization of xylose, which is one of the main components of cellulosic biomass. K. marxianus ScGal2_N376F, the ScGAL2-N376F-overexpressing strain, exhibited 47.04 g/l of xylose consumption and 26.55 g/l of xylitol production, as compared to the parental strain (24.68 g/l and 7.03 g/l, respectively) when xylose was used as the sole carbon source. When a mixture of glucose and xylose was used as the carbon source, xylose consumption and xylitol production rates were improved by 195% and 360%, respectively, by K. marxianus ScGal2_N376F. Moreover, the glucose consumption rate was improved by 27% as compared to that in the parental strain. Overexpression of both wild-type ScGAL2 and mutant ScGAL2-N376F showed 48% and 52% enhanced sugar consumption and ethanol production rates, respectively, when a mixture of glucose and galactose was used as the carbon source, which is the main component of marine biomass. As shown in this study, ScGAL2-N376F overexpression can be applied for the efficient production of biofuels or biochemicals from cellulosic or marine biomass.
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Affiliation(s)
- Deok-Ho Kwon
- Department of Bioengineering and Technology, Kangwon National University, Chuncheon 2434, Republic of Korea,Interdisciplinary Program in Biohealth-Machinery Convergence Engineering, Kangwon National University, Chuncheon 2441, Republic of Korea
| | - Saet-Byeol Kim
- Department of Bioengineering and Technology, Kangwon National University, Chuncheon 2434, Republic of Korea
| | - Jae-Bum Park,
- Department of Bioengineering and Technology, Kangwon National University, Chuncheon 2434, Republic of Korea
| | - Suk-Jin Ha
- Department of Bioengineering and Technology, Kangwon National University, Chuncheon 2434, Republic of Korea,Institute of Fermentation and Brewing, Kangwon National University, Chuncheon 4341, Republic of Korea,Interdisciplinary Program in Biohealth-Machinery Convergence Engineering, Kangwon National University, Chuncheon 2441, Republic of Korea,Corresponding author Phone: +82-33-250-6278 Fax: +82-33-243-6350 E-mail:
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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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Patiño MA, Ortiz JP, Velásquez M, Stambuk BU. d-Xylose consumption by nonrecombinant Saccharomyces cerevisiae: A review. Yeast 2019; 36:541-556. [PMID: 31254359 DOI: 10.1002/yea.3429] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/02/2019] [Accepted: 06/21/2019] [Indexed: 01/24/2023] Open
Abstract
Xylose is the second most abundant sugar in nature. Its efficient fermentation has been considered as a critical factor for a feasible conversion of renewable biomass resources into biofuels and other chemicals. The yeast Saccharomyces cerevisiae is of exceptional industrial importance due to its excellent capability to ferment sugars. However, although S. cerevisiae is able to ferment xylulose, it is considered unable to metabolize xylose, and thus, a lot of research has been directed to engineer this yeast with heterologous genes to allow xylose consumption and fermentation. The analysis of the natural genetic diversity of this yeast has also revealed some nonrecombinant S. cerevisiae strains that consume or even grow (modestly) on xylose. The genome of this yeast has all the genes required for xylose transport and metabolism through the xylose reductase, xylitol dehydrogenase, and xylulokinase pathway, but there seems to be problems in their kinetic properties and/or required expression. Self-cloning industrial S. cerevisiae strains overexpressing some of the endogenous genes have shown interesting results, and new strategies and approaches designed to improve these S. cerevisiae strains for ethanol production from xylose will also be presented in this review.
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Affiliation(s)
- Margareth Andrea Patiño
- Instituto de Biotecnología.,Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Pablo Ortiz
- Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - Mario Velásquez
- Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Boris U Stambuk
- Departamento de Bioquímica, Universidad Federal de Santa Catarina, Florianópolis, Brazil
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Developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for plant biomass degradation. Biotechnol Adv 2019; 37:107361. [PMID: 30825514 DOI: 10.1016/j.biotechadv.2019.02.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/11/2019] [Accepted: 02/23/2019] [Indexed: 12/26/2022]
Abstract
Fungal strain engineering is commonly used in many areas of biotechnology, including the production of plant biomass degrading enzymes. Its aim varies from the production of specific enzymes to overall increased enzyme production levels and modification of the composition of the enzyme set that is produced by the fungus. Strain engineering involves a diverse range of methodologies, including classical mutagenesis, genetic engineering and genome editing. In this review, the main approaches for strain engineering of filamentous fungi in the field of plant biomass degradation will be discussed, including recent and not yet implemented methods, such as CRISPR/Cas9 genome editing and adaptive evolution.
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Endalur Gopinarayanan V, Nair NU. Pentose Metabolism in Saccharomyces cerevisiae: The Need to Engineer Global Regulatory Systems. Biotechnol J 2019; 14:e1800364. [PMID: 30171750 PMCID: PMC6452637 DOI: 10.1002/biot.201800364] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/27/2018] [Indexed: 12/13/2022]
Abstract
Extending the host substrate range of industrially relevant microbes, such as Saccharomyces cerevisiae, has been a highly-active area of research since the conception of metabolic engineering. Yet, rational strategies that enable non-native substrate utilization in this yeast without the need for combinatorial and/or evolutionary techniques are underdeveloped. Herein, this review focuses on pentose metabolism in S. cerevisiae as a case study to highlight the challenges in this field. In the last three decades, work has focused on expressing exogenous pentose metabolizing enzymes as well as endogenous enzymes for effective pentose assimilation, growth, and biofuel production. The engineering strategies that are employed for pentose assimilation in this yeast are reviewed, and compared with metabolism and regulation of native sugar, galactose. In the case of galactose metabolism, multiple signals regulate and aid growth in the presence of the sugar. However, for pentoses that are non-native, it is unclear if similar growth and regulatory signals are activated. Such a comparative analysis aids in identifying missing links in xylose and arabinose utilization. While research on pentose metabolism have mostly concentrated on pathway level optimization, recent transcriptomics analyses highlight the need to consider more global regulatory, structural, and signaling components.
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Affiliation(s)
| | - Nikhil U Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, 02155, U.S.A
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Tran Nguyen Hoang P, Ko JK, Gong G, Um Y, Lee SM. Genomic and phenotypic characterization of a refactored xylose-utilizing Saccharomyces cerevisiae strain for lignocellulosic biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:268. [PMID: 30288173 PMCID: PMC6162923 DOI: 10.1186/s13068-018-1269-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/21/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Engineered strains of Saccharomyces cerevisiae have significantly improved the prospects of biorefinery by improving the bioconversion yields in lignocellulosic bioethanol production and expanding the product profiles to include advanced biofuels and chemicals. However, the lignocellulosic biorefinery concept has not been fully applied using engineered strains in which either xylose utilization or advanced biofuel/chemical production pathways have been upgraded separately. Specifically, high-performance xylose-fermenting strains have rarely been employed as advanced biofuel and chemical production platforms and require further engineering to expand their product profiles. RESULTS In this study, we refactored a high-performance xylose-fermenting S. cerevisiae that could potentially serve as a platform strain for advanced biofuels and biochemical production. Through combinatorial CRISPR-Cas9-mediated rational and evolutionary engineering, we obtained a newly refactored isomerase-based xylose-fermenting strain, XUSE, that demonstrated efficient conversion of xylose into ethanol with a high yield of 0.43 g/g. In addition, XUSE exhibited the simultaneous fermentation of glucose and xylose with negligible glucose inhibition, indicating the potential of this isomerase-based xylose-utilizing strain for lignocellulosic biorefinery. The genomic and transcriptomic analysis of XUSE revealed beneficial mutations and changes in gene expression that are responsible for the enhanced xylose fermentation performance of XUSE. CONCLUSIONS In this study, we developed a high-performance xylose-fermenting S. cerevisiae strain, XUSE, with high ethanol yield and negligible glucose inhibition. Understanding the genomic and transcriptomic characteristics of XUSE revealed isomerase-based engineering strategies for improved xylose fermentation in S. cerevisiae. With high xylose fermentation performance and room for further engineering, XUSE could serve as a promising platform strain for lignocellulosic biorefinery.
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Affiliation(s)
- Phuong Tran Nguyen Hoang
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
- Green School, Korea University, Seoul, 02841 Republic of Korea
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Zeng WY, Tang YQ, Gou M, Sun ZY, Xia ZY, Kida K. Comparative transcriptomes reveal novel evolutionary strategies adopted by Saccharomyces cerevisiae with improved xylose utilization capability. Appl Microbiol Biotechnol 2016; 101:1753-1767. [DOI: 10.1007/s00253-016-8046-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 11/28/2016] [Accepted: 12/01/2016] [Indexed: 10/20/2022]
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13
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Isolation and characterization of xylitol-assimilating mutants of recombinant Saccharomyces cerevisiae. J Biosci Bioeng 2016; 122:446-55. [DOI: 10.1016/j.jbiosc.2016.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/22/2016] [Accepted: 03/12/2016] [Indexed: 11/22/2022]
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14
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Pires RH, Cataldi TR, Franceschini LM, Labate MV, Fusco-Almeida AM, Labate CA, Palma MS, Soares Mendes-Giannini MJ. Metabolic profiles of planktonic and biofilm cells of Candida orthopsilosis. Future Microbiol 2016; 11:1299-1313. [PMID: 27662506 DOI: 10.2217/fmb-2016-0025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AIM This study aims to understand which Candida orthopsilosis protein aids fungus adaptation upon its switching from planktonic growth to biofilm. MATERIALS & METHODS Ion mobility separation within mass spectrometry analysis combination were used. RESULTS Proteins mapped for different biosynthetic pathways showed that selective ribosome autophagy might occur in biofilms. Glucose, used as a carbon source in the glycolytic flux, changed to glycogen and trehalose. CONCLUSION Candida orthopsilosis expresses proteins that combine a variety of mechanisms to provide yeasts with the means to adjust the catalytic properties of enzymes. Adjustment of the enzymes helps modulate the biosynthesis/degradation rates of the available nutrients, in order to control and coordinate the metabolic pathways that enable cells to express an adequate response to nutrient availability.
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Affiliation(s)
- Regina Helena Pires
- Department of Clinical Analysis, Clinical Mycology Laboratory, Faculdade de Ciências Farmacêuticas, UNESP - Univ Estadual Paulista Júlio de Mesquita Filho, FCFAr, Rodovia Araraquara-Jaú, km1, Araraquara 14801-902, SP, Brazil
| | - Thaís Regiani Cataldi
- Department of Genetics, ESALQ/USP - Univ de São Paulo, Laboratory Max Feffer Plant Genetics, Av. Pádua Dias 11, Caixa Postal 83, Piracicaba 13400-970, SP, Brazil
| | - Livia Maria Franceschini
- Department of Genetics, ESALQ/USP - Univ de São Paulo, Laboratory Max Feffer Plant Genetics, Av. Pádua Dias 11, Caixa Postal 83, Piracicaba 13400-970, SP, Brazil
| | - Mônica Veneziano Labate
- Department of Genetics, ESALQ/USP - Univ de São Paulo, Laboratory Max Feffer Plant Genetics, Av. Pádua Dias 11, Caixa Postal 83, Piracicaba 13400-970, SP, Brazil
| | - Ana Marisa Fusco-Almeida
- Department of Clinical Analysis, Clinical Mycology Laboratory, Faculdade de Ciências Farmacêuticas, UNESP - Univ Estadual Paulista Júlio de Mesquita Filho, FCFAr, Rodovia Araraquara-Jaú, km1, Araraquara 14801-902, SP, Brazil
| | - Carlos Alberto Labate
- Department of Genetics, ESALQ/USP - Univ de São Paulo, Laboratory Max Feffer Plant Genetics, Av. Pádua Dias 11, Caixa Postal 83, Piracicaba 13400-970, SP, Brazil
| | - Mario Sérgio Palma
- Department of Biology, Lab. Structural Biology & Zoochemistry, CEIS, Univ Estadual Paulista Júlio de Mesquita Filho, UNESP, Institute of Biosciences, Av. 24-A, 1515. Bela Vista, Rio Claro 13506-900, SP, Brazil
| | - Maria José Soares Mendes-Giannini
- Department of Clinical Analysis, Clinical Mycology Laboratory, Faculdade de Ciências Farmacêuticas, UNESP - Univ Estadual Paulista Júlio de Mesquita Filho, FCFAr, Rodovia Araraquara-Jaú, km1, Araraquara 14801-902, SP, Brazil
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Moysés DN, Reis VCB, de Almeida JRM, de Moraes LMP, Torres FAG. Xylose Fermentation by Saccharomyces cerevisiae: Challenges and Prospects. Int J Mol Sci 2016; 17:207. [PMID: 26927067 PMCID: PMC4813126 DOI: 10.3390/ijms17030207] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/23/2016] [Accepted: 01/27/2016] [Indexed: 12/17/2022] Open
Abstract
Many years have passed since the first genetically modified Saccharomyces cerevisiae strains capable of fermenting xylose were obtained with the promise of an environmentally sustainable solution for the conversion of the abundant lignocellulosic biomass to ethanol. Several challenges emerged from these first experiences, most of them related to solving redox imbalances, discovering new pathways for xylose utilization, modulation of the expression of genes of the non-oxidative pentose phosphate pathway, and reduction of xylitol formation. Strategies on evolutionary engineering were used to improve fermentation kinetics, but the resulting strains were still far from industrial application. Lignocellulosic hydrolysates proved to have different inhibitors derived from lignin and sugar degradation, along with significant amounts of acetic acid, intrinsically related with biomass deconstruction. This, associated with pH, temperature, high ethanol, and other stress fluctuations presented on large scale fermentations led the search for yeasts with more robust backgrounds, like industrial strains, as engineering targets. Some promising yeasts were obtained both from studies of stress tolerance genes and adaptation on hydrolysates. Since fermentation times on mixed-substrate hydrolysates were still not cost-effective, the more selective search for new or engineered sugar transporters for xylose are still the focus of many recent studies. These challenges, as well as under-appreciated process strategies, will be discussed in this review.
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Affiliation(s)
- Danuza Nogueira Moysés
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
- Petrobras Research and Development Center, Biotechnology Management, Rio de Janeiro, RJ 21941-915, Brazil.
| | | | - João Ricardo Moreira de Almeida
- Embrapa Agroenergia, Laboratório de Genética e Biotecnologia, Parque Estação Biológica s/n, Av. W3 Norte, Brasília, DF 70770-901, Brazil.
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16
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Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae. Sci Rep 2016; 6:19512. [PMID: 26781725 PMCID: PMC4726032 DOI: 10.1038/srep19512] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/09/2015] [Indexed: 12/24/2022] Open
Abstract
Enhancing xylose utilization has been a major focus in Saccharomyces cerevisiae strain-engineering efforts. The incentive for these studies arises from the need to use all sugars in the typical carbon mixtures that comprise standard renewable plant-biomass-based carbon sources. While major advances have been made in developing utilization pathways, the efficient import of five carbon sugars into the cell remains an important bottleneck in this endeavor. Here we use an engineered S. cerevisiae BY4742 strain, containing an established heterologous xylose utilization pathway, and imposed a laboratory evolution regime with xylose as the sole carbon source. We obtained several evolved strains with improved growth phenotypes and evaluated the best candidate using genome resequencing. We observed remarkably few single nucleotide polymorphisms in the evolved strain, among which we confirmed a single amino acid change in the hexose transporter HXT7 coding sequence to be responsible for the evolved phenotype. The mutant HXT7(F79S) shows improved xylose uptake rates (Vmax = 186.4 ± 20.1 nmol•min−1•mg−1) that allows the S. cerevisiae strain to show significant growth with xylose as the sole carbon source, as well as partial co-utilization of glucose and xylose in a mixed sugar cultivation.
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Shalley Sharma, Sonia Sharma, Surender Singh, Lata, Anju Arora. Improving Yeast Strains for Pentose Hexose Co-fermentation: Successes and Hurdles. SPRINGER PROCEEDINGS IN ENERGY 2016. [DOI: 10.1007/978-81-322-2773-1_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Qi X, Zha J, Liu GG, Zhang W, Li BZ, Yuan YJ. Heterologous xylose isomerase pathway and evolutionary engineering improve xylose utilization in Saccharomyces cerevisiae. Front Microbiol 2015; 6:1165. [PMID: 26539187 PMCID: PMC4612707 DOI: 10.3389/fmicb.2015.01165] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 10/08/2015] [Indexed: 12/24/2022] Open
Abstract
Xylose utilization is one key issue for the bioconversion of lignocelluloses. It is a promising approach to engineering heterologous pathway for xylose utilization in Saccharomyces cerevisiae. Here, we constructed a xylose-fermenting yeast SyBE001 through combinatorial fine-tuning the expression of XylA and endogenous XKS1. Additional overexpression of genes RKI1, RPE1, TKL1, and TAL1 in the non-oxidative pentose phosphate pathway (PPP) in SyBE001 increased the xylose consumption rate by 1.19-fold. By repetitive adaptation, the xylose utilization rate was further increased by ∼10-fold in the resultant strain SyBE003. Gene expression analysis identified a variety of genes with significantly changed expression in the PPP, glycolysis and the tricarboxylic acid cycle in SyBE003.
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Affiliation(s)
- Xin Qi
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Jian Zha
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Gao-Gang Liu
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Weiwen Zhang
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
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19
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Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures. Appl Microbiol Biotechnol 2015; 100:969-85. [DOI: 10.1007/s00253-015-7038-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 09/14/2015] [Accepted: 09/22/2015] [Indexed: 12/27/2022]
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20
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Challenges for the production of bioethanol from biomass using recombinant yeasts. ADVANCES IN APPLIED MICROBIOLOGY 2015; 92:89-125. [PMID: 26003934 DOI: 10.1016/bs.aambs.2015.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Lignocellulose biomass, one of the most abundant renewable resources on the planet, is an alternative sustainable energy source for the production of second-generation biofuels. Energy in the form of simple or complex carbohydrates can be extracted from lignocellulose biomass and fermented by microorganisms to produce bioethanol. Despite 40 years of active and cutting-edge research invested into the development of technologies to produce bioethanol from lignocellulosic biomass, the process remains commercially unviable. This review describes the achievements that have been made in generating microorganisms capable of utilizing both simple and complex sugars from lignocellulose biomass and the fermentation of these sugars into ethanol. We also provide a discussion on the current "roadblocks" standing in the way of making second-generation bioethanol a commercially viable alternative to fossil fuels.
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Wasylenko TM, Stephanopoulos G. Metabolomic and (13)C-metabolic flux analysis of a xylose-consuming Saccharomyces cerevisiae strain expressing xylose isomerase. Biotechnol Bioeng 2014; 112:470-83. [PMID: 25311863 DOI: 10.1002/bit.25447] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/11/2014] [Accepted: 08/27/2014] [Indexed: 11/09/2022]
Abstract
Over the past two decades, significant progress has been made in the engineering of xylose-consuming Saccharomyces cerevisiae strains for production of lignocellulosic biofuels. However, the ethanol productivities achieved on xylose are still significantly lower than those observed on glucose for reasons that are not well understood. We have undertaken an analysis of central carbon metabolite pool sizes and metabolic fluxes on glucose and on xylose under aerobic and anaerobic conditions in a strain capable of rapid xylose assimilation via xylose isomerase in order to investigate factors that may limit the rate of xylose fermentation. We find that during xylose utilization the flux through the non-oxidative Pentose Phosphate Pathway (PPP) is high but the flux through the oxidative PPP is low, highlighting an advantage of the strain employed in this study. Furthermore, xylose fails to elicit the full carbon catabolite repression response that is characteristic of glucose fermentation in S. cerevisiae. We present indirect evidence that the incomplete activation of the fermentation program on xylose results in a bottleneck in lower glycolysis, leading to inefficient re-oxidation of NADH produced in glycolysis.
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Affiliation(s)
- Thomas M Wasylenko
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, 02139, Massachussetts
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22
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Xylose and xylose/glucose co-fermentation by recombinant Saccharomyces cerevisiae strains expressing individual hexose transporters. Enzyme Microb Technol 2014; 63:13-20. [DOI: 10.1016/j.enzmictec.2014.05.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 01/16/2023]
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Bergdahl B, Gorwa-Grauslund MF, van Niel EWJ. Physiological effects of over-expressing compartment-specific components of the protein folding machinery in xylose-fermenting Saccharomyces cerevisiae. BMC Biotechnol 2014; 14:28. [PMID: 24758421 PMCID: PMC4021093 DOI: 10.1186/1472-6750-14-28] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Efficient utilization of both glucose and xylose is necessary for a competitive ethanol production from lignocellulosic materials. Although many advances have been made in the development of xylose-fermenting strains of Saccharomyces cerevisiae, the productivity remains much lower compared to glucose. Previous transcriptional analyses of recombinant xylose-fermenting strains have mainly focused on central carbon metabolism. Very little attention has been given to other fundamental cellular processes such as the folding of proteins. Analysis of previously measured transcript levels in a recombinant XR/XDH-strain showed a wide down-regulation of genes targeted by the unfolded protein response during xylose fermentation. Under anaerobic conditions the folding of proteins is directly connected with fumarate metabolism and requires two essential enzymes: FADH2-dependent fumarate reductase (FR) and Ero1p. In this study we tested whether these enzymes impair the protein folding process causing the very slow growth of recombinant yeast strains on xylose under anaerobic conditions. RESULTS Four strains over-expressing the cytosolic (FRD1) or mitochondrial (OSM1) FR genes and ERO1 in different combinations were constructed. The growth and fermentation performance was evaluated in defined medium as well as in a complex medium containing glucose and xylose. Over-expression of FRD1, alone or in combination with ERO1, did not have any significant effect on xylose fermentation in any medium used. Over-expression of OSM1, on the other hand, led to a diversion of carbon from glycerol to acetate and a decrease in growth rate by 39% in defined medium and by 25% in complex medium. Combined over-expression of OSM1 and ERO1 led to the same diversion of carbon from glycerol to acetate and had a stronger detrimental effect on the growth in complex medium. CONCLUSIONS Increasing the activities of the FR enzymes and Ero1p is not sufficient to increase the anaerobic growth on xylose. So additional components of the protein folding mechanism that were identified in transcription analysis of UPR related genes may also be limiting. This includes i) the transcription factor encoded by HAC1 ii) the activity of Pdi1p and iii) the requirement of free FAD during anaerobic growth.
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Affiliation(s)
- Basti Bergdahl
- Division of Applied Microbiology, Department of Chemistry, Lund University, P,O, Box 124, Lund SE-22100, Sweden.
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24
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Kricka W, Fitzpatrick J, Bond U. Metabolic engineering of yeasts by heterologous enzyme production for degradation of cellulose and hemicellulose from biomass: a perspective. Front Microbiol 2014; 5:174. [PMID: 24795706 PMCID: PMC4001029 DOI: 10.3389/fmicb.2014.00174] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/31/2014] [Indexed: 11/13/2022] Open
Abstract
This review focuses on current approaches to metabolic engineering of ethanologenic yeast species for the production of bioethanol from complex lignocellulose biomass sources. The experimental strategies for the degradation of the cellulose and xylose-components of lignocellulose are reviewed. Limitations to the current approaches are discussed and novel solutions proposed.
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Affiliation(s)
- William Kricka
- School of Genetics and Microbiology, Department of Microbiology, Trinity College Dublin Dublin, Ireland
| | - James Fitzpatrick
- School of Genetics and Microbiology, Department of Microbiology, Trinity College Dublin Dublin, Ireland
| | - Ursula Bond
- School of Genetics and Microbiology, Department of Microbiology, Trinity College Dublin Dublin, Ireland
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25
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Farwick A, Bruder S, Schadeweg V, Oreb M, Boles E. Engineering of yeast hexose transporters to transport D-xylose without inhibition by D-glucose. Proc Natl Acad Sci U S A 2014; 111:5159-64. [PMID: 24706835 PMCID: PMC3986176 DOI: 10.1073/pnas.1323464111] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All known D-xylose transporters are competitively inhibited by D-glucose, which is one of the major reasons hampering simultaneous fermentation of D-glucose and D-xylose, two primary sugars present in lignocellulosic biomass. We have set up a yeast growth-based screening system for mutant D-xylose transporters that are insensitive to the presence of D-glucose. All of the identified variants had a mutation at either a conserved asparagine residue in transmembrane helix 8 or a threonine residue in transmembrane helix 5. According to a homology model of the yeast hexose transporter Gal2 deduced from the crystal structure of the D-xylose transporter XylE from Escherichia coli, both residues are found in the same region of the protein and are positioned slightly to the extracellular side of the central sugar-binding pocket. Therefore, it is likely that alterations sterically prevent D-glucose but not D-xylose from entering the pocket. In contrast, changing amino acids that are supposed to directly interact with the C6 hydroxymethyl group of D-glucose negatively affected transport of both D-glucose and D-xylose. Determination of kinetic properties of the mutant transporters revealed that Gal2-N376F had the highest affinity for D-xylose, along with a moderate transport velocity, and had completely lost the ability to transport hexoses. These transporter versions should prove valuable for glucose-xylose cofermentation in lignocellulosic hydrolysates by Saccharomyces cerevisiae and other biotechnologically relevant organisms. Moreover, our data contribute to the mechanistic understanding of sugar transport because the decisive role of the conserved asparagine residue for determining sugar specificity has not been recognized before.
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Affiliation(s)
- Alexander Farwick
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Stefan Bruder
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Virginia Schadeweg
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Mislav Oreb
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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26
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Breunig JS, Hackett SR, Rabinowitz JD, Kruglyak L. Genetic basis of metabolome variation in yeast. PLoS Genet 2014; 10:e1004142. [PMID: 24603560 PMCID: PMC3945093 DOI: 10.1371/journal.pgen.1004142] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 12/06/2013] [Indexed: 12/17/2022] Open
Abstract
Metabolism, the conversion of nutrients into usable energy and biochemical building blocks, is an essential feature of all cells. The genetic factors responsible for inter-individual metabolic variability remain poorly understood. To investigate genetic causes of metabolome variation, we measured the concentrations of 74 metabolites across ~ 100 segregants from a Saccharomyces cerevisiae cross by liquid chromatography-tandem mass spectrometry. We found 52 quantitative trait loci for 34 metabolites. These included linkages due to overt changes in metabolic genes, e.g., linking pyrimidine intermediates to the deletion of ura3. They also included linkages not directly related to metabolic enzymes, such as those for five central carbon metabolites to ira2, a Ras/PKA pathway regulator, and for the metabolites, S-adenosyl-methionine and S-adenosyl-homocysteine to slt2, a MAP kinase involved in cell wall integrity. The variant of ira2 that elevates metabolite levels also increases glucose uptake and ethanol secretion. These results highlight specific examples of genetic variability, including in genes without prior known metabolic regulatory function, that impact yeast metabolism.
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Affiliation(s)
- Jeffrey S. Breunig
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Sean R. Hackett
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Joshua D. Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
| | - Leonid Kruglyak
- Departments of Human Genetics and Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, UCLA, Los Angeles, California, United States of America
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27
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Matsushika A, Goshima T, Hoshino T. Transcription analysis of recombinant industrial and laboratory Saccharomyces cerevisiae strains reveals the molecular basis for fermentation of glucose and xylose. Microb Cell Fact 2014; 13:16. [PMID: 24467867 PMCID: PMC3917370 DOI: 10.1186/1475-2859-13-16] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 01/24/2014] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND There has been much research on the bioconversion of xylose found in lignocellulosic biomass to ethanol by genetically engineered Saccharomyces cerevisiae. However, the rate of ethanol production from xylose in these xylose-utilizing yeast strains is quite low compared to their glucose fermentation. In this study, two diploid xylose-utilizing S. cerevisiae strains, the industrial strain MA-R4 and the laboratory strain MA-B4, were employed to investigate the differences between anaerobic fermentation of xylose and glucose, and general differences between recombinant yeast strains, through genome-wide transcription analysis. RESULTS In MA-R4, many genes related to ergosterol biosynthesis were expressed more highly with glucose than with xylose. Additionally, these ergosterol-related genes had higher transcript levels in MA-R4 than in MA-B4 during glucose fermentation. During xylose fermentation, several genes related to central metabolic pathways that typically increase during growth on non-fermentable carbon sources were expressed at higher levels in both strains. Xylose did not fully repress the genes encoding enzymes of the tricarboxylic acid and respiratory pathways, even under anaerobic conditions. In addition, several genes involved in spore wall metabolism and the uptake of ammonium, which are closely related to the starvation response, and many stress-responsive genes mediated by Msn2/4p, as well as trehalose synthase genes, increased in expression when fermenting with xylose, irrespective of the yeast strain. We further observed that transcript levels of genes involved in xylose metabolism, membrane transport functions, and ATP synthesis were higher in MA-R4 than in MA-B4 when strains were fermented with glucose or xylose. CONCLUSIONS Our transcriptomic approach revealed the molecular events underlying the response to xylose or glucose and differences between MA-R4 and MA-B4. Xylose-utilizing S. cerevisiae strains may recognize xylose as a non-fermentable carbon source, which induces a starvation response and adaptation to oxidative stress, resulting in the increased expression of stress-response genes.
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Affiliation(s)
- Akinori Matsushika
- Biomass Refinery Research Center (BRRC), National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.
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28
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Rewiring yeast sugar transporter preference through modifying a conserved protein motif. Proc Natl Acad Sci U S A 2013; 111:131-6. [PMID: 24344268 DOI: 10.1073/pnas.1311970111] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Utilization of exogenous sugars found in lignocellulosic biomass hydrolysates, such as xylose, must be improved before yeast can serve as an efficient biofuel and biochemical production platform. In particular, the first step in this process, the molecular transport of xylose into the cell, can serve as a significant flux bottleneck and is highly inhibited by other sugars. Here we demonstrate that sugar transport preference and kinetics can be rewired through the programming of a sequence motif of the general form G-G/F-XXX-G found in the first transmembrane span. By evaluating 46 different heterologously expressed transporters, we find that this motif is conserved among functional transporters and highly enriched in transporters that confer growth on xylose. Through saturation mutagenesis and subsequent rational mutagenesis, four transporter mutants unable to confer growth on glucose but able to sustain growth on xylose were engineered. Specifically, Candida intermedia gxs1 Phe(38)Ile(39)Met(40), Scheffersomyces stipitis rgt2 Phe(38) and Met(40), and Saccharomyces cerevisiae hxt7 Ile(39)Met(40)Met(340) all exhibit this phenotype. In these cases, primary hexose transporters were rewired into xylose transporters. These xylose transporters nevertheless remained inhibited by glucose. Furthermore, in the course of identifying this motif, novel wild-type transporters with superior monosaccharide growth profiles were discovered, namely S. stipitis RGT2 and Debaryomyces hansenii 2D01474. These findings build toward the engineering of efficient pentose utilization in yeast and provide a blueprint for reprogramming transporter properties.
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29
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Kim SR, Park YC, Jin YS, Seo JH. Strain engineering of Saccharomyces cerevisiae for enhanced xylose metabolism. Biotechnol Adv 2013; 31:851-61. [DOI: 10.1016/j.biotechadv.2013.03.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 02/23/2013] [Accepted: 03/04/2013] [Indexed: 12/27/2022]
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30
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Zha J, Shen M, Hu M, Song H, Yuan Y. Enhanced expression of genes involved in initial xylose metabolism and the oxidative pentose phosphate pathway in the improved xylose-utilizing Saccharomyces cerevisiae through evolutionary engineering. J Ind Microbiol Biotechnol 2013; 41:27-39. [PMID: 24113893 DOI: 10.1007/s10295-013-1350-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 09/17/2013] [Indexed: 01/03/2023]
Abstract
Fermentation of xylose in lignocellulosic hydrolysates by Saccharomyces cerevisiae has been achieved through heterologous expression of the xylose reductase (XR)-xylitol dehydrogenase (XDH) pathway. However, the fermentation efficiency is far from the requirement for industrial application due to high yield of the byproduct xylitol, low ethanol yield, and low xylose consumption rate. Through evolutionary engineering, an improved xylose-utilizing strain SyBE005 was obtained with 78.3 % lower xylitol production and a 2.6-fold higher specific ethanol production rate than those of the parent strain SyBE004, which expressed an engineered NADP(+)-preferring XDH. The transcriptional differences between SyBE005 and SyBE004 were investigated by quantitative RT-PCR. Genes including XYL1, XYL2, and XKS1 in the initial xylose metabolic pathway showed the highest up-regulation in SyBE005. The increased expression of XYL1 and XYL2 correlated with enhanced enzymatic activities of XR and XDH. In addition, the expression level of ZWF1 in the oxidative pentose phosphate pathway increased significantly in SyBE005, indicating an elevated demand for NADPH from XR. Genes involved in the TCA cycle (LAT1, CIT1, CIT2, KGD1, KGD, SDH2) and gluconeogenesis (ICL1, PYC1) were also up-regulated in SyBE005. Genomic analysis revealed that point mutations in transcriptional regulators CYC8 and PHD1 might be responsible for the altered expression. In addition, a mutation (Y89S) in ZWF1 was identified which might improve NADPH production in SyBE005. Our results suggest that increasing the expression of XYL1, XYL2, XKS1, and enhancing NADPH supply are promising strategies to improve xylose fermentation in recombinant S. cerevisiae.
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Affiliation(s)
- Jian Zha
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin, 300072, People's Republic of China
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31
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Ferreira D, Nobre A, Silva ML, Faria-Oliveira F, Tulha J, Ferreira C, Lucas C. XYLHencodes a xylose/H+symporter from the highly related yeast speciesDebaryomyces fabryiandDebaryomyces hansenii. FEMS Yeast Res 2013; 13:585-96. [DOI: 10.1111/1567-1364.12061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/21/2013] [Accepted: 06/22/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Danielly Ferreira
- Centre of Molecular and Environmental Biology (CBMA); Department of Biology; University of Minho; Braga; Portugal
| | - Alexandra Nobre
- Centre of Molecular and Environmental Biology (CBMA); Department of Biology; University of Minho; Braga; Portugal
| | - Marta Luisa Silva
- Centre of Molecular and Environmental Biology (CBMA); Department of Biology; University of Minho; Braga; Portugal
| | - Fábio Faria-Oliveira
- Centre of Molecular and Environmental Biology (CBMA); Department of Biology; University of Minho; Braga; Portugal
| | - Joana Tulha
- Centre of Molecular and Environmental Biology (CBMA); Department of Biology; University of Minho; Braga; Portugal
| | - Célia Ferreira
- Centre of Molecular and Environmental Biology (CBMA); Department of Biology; University of Minho; Braga; Portugal
| | - Cândida Lucas
- Centre of Molecular and Environmental Biology (CBMA); Department of Biology; University of Minho; Braga; Portugal
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32
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Kim SR, Kwee NR, Kim H, Jin YS. Feasibility of xylose fermentation by engineered Saccharomyces cerevisiae overexpressing endogenous aldose reductase (GRE3), xylitol dehydrogenase (XYL2), and xylulokinase (XYL3) from Scheffersomyces stipitis. FEMS Yeast Res 2013; 13:312-21. [PMID: 23398717 DOI: 10.1111/1567-1364.12036] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 02/04/2013] [Accepted: 02/05/2013] [Indexed: 11/27/2022] Open
Abstract
Saccharomyces cerevisiae has been engineered for producing ethanol from xylose, the second most abundant sugar in cellulosic biomass hydrolyzates. Heterologous expressions of xylose reductase (XYL1) and xylitol dehydrogenase (XYL2), or of xylose isomerase (xylA), either case of which being accompanied by overexpression of xylulokinase (XKS1 or XYL3), are known as the prevalent strategies for metabolic engineering of S. cerevisiae to ferment xylose. In this study, we propose an alternative strategy that employs overexpression of GRE3 coding for endogenous aldose reductase instead of XYL1 to construct efficient xylose-fermenting S. cerevisiae. Replacement of XYL1 with GRE3 has been regarded as an undesirable approach because NADPH-specific aldose reductase (GRE3) would aggravate redox balance with xylitol dehydrogenase (XYL2) using NAD(+) exclusively. Here, we demonstrate that engineered S. cerevisiae overexpressing GRE3, XYL2, and XYL3 can ferment xylose as well as a mixture of glucose and xylose with higher ethanol yields (0.29-0.41 g g(-1) sugars) and productivities (0.13-0.85 g L(-1) h(-1)) than those (0.23-0.39 g g(-1) sugars, 0.10-0.74 g L(-1) h(-1)) of an isogenic strain overexpressing XYL1, XYL2, and XYL3 under oxygen-limited conditions. We found that xylose fermentation efficiency of a strain overexpressing GRE3 was dramatically increased by high expression levels of XYL2. Our results suggest that optimized expression levels of GRE3, XYL2, and XYL3 could overcome redox imbalance during xylose fermentation by engineered S. cerevisiae under oxygen-limited conditions.
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Affiliation(s)
- Soo Rin Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
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Kim SR, Lee KS, Kong II, Lesmana A, Lee WH, Seo JH, Kweon DH, Jin YS. Construction of an efficient xylose-fermenting diploid Saccharomyces cerevisiae strain through mating of two engineered haploid strains capable of xylose assimilation. J Biotechnol 2013; 164:105-11. [PMID: 23376240 DOI: 10.1016/j.jbiotec.2012.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 12/07/2012] [Accepted: 12/27/2012] [Indexed: 12/17/2022]
Abstract
Saccharomyces cerevisiae can be engineered for xylose fermentation through introduction of wild type or mutant genes (XYL1/XYL1 (R276H), XYL2, and XYL3) coding for xylose metabolic enzymes from Scheffersomyces stipitis. The resulting engineered strains, however, often yielded undesirable phenotypes such as slow xylose assimilation and xylitol accumulation. In this study, we performed the mating of two engineered strains that exhibit suboptimal xylose-fermenting phenotypes in order to develop an improved xylose-fermenting diploid strain. Specifically, we obtained two engineered haploid strains (YSX3 and SX3). The YSX3 strain consumed xylose rapidly and produced a lot of xylitol. On the contrary, the SX3 strain consumed xylose slowly with little xylitol production. After converting the mating type of SX3 from alpha to a, the resulting strain (SX3-2) was mated with YSX3 to construct a heterozygous diploid strain (KSM). The KSM strain assimilated xylose (0.25gxyloseh(-1)gcells(-1)) as fast as YSX3 and accumulated a small amount of xylitol (0.03ggxylose(-1)) as low as SX3, resulting in an improved ethanol yield (0.27ggxylose(-1)). We found that the improvement in xylose fermentation by the KSM strain was not because of heterozygosity or genome duplication but because of the complementation of the two xylose-metabolic pathways. This result suggested that mating of suboptimal haploid strains is a promising strategy to develop engineered yeast strains with improved xylose fermenting capability.
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Affiliation(s)
- Soo Rin Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Zha J, Hu ML, Shen MH, Li BZ, Wang JY, Yuan YJ. Balance of XYL1 and XYL2 expression in different yeast chassis for improved xylose fermentation. Front Microbiol 2012; 3:355. [PMID: 23060871 PMCID: PMC3464680 DOI: 10.3389/fmicb.2012.00355] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 09/19/2012] [Indexed: 01/04/2023] Open
Abstract
Reducing xylitol formation is necessary in engineering xylose utilization in recombinant Saccharomyces cerevisiae for ethanol production through xylose reductase/xylitol dehydrogenase pathway. To balance the expression of XYL1 and mutant XYL2 encoding xylose reductase (XR) and NADP+-dependent xylitol dehydrogenase (XDH), respectively, we utilized a strategy combining chassis selection and direct fine-tuning of XYL1 and XYL2 expression in this study. A XYL1 gene under the control of various promoters of ADH1, truncated ADH1 and PGK1, and a mutated XYL2 with different copy numbers were constructed into different xylose-utilizing modules, which were then expressed in two yeast chassises W303a and L2612. The strategy enabled an improved L2612-derived recombinant strain with XYL1 controlled by promoter PGK1 and with two copies of XYL2. The strain exhibited a 21.3% lower xylitol yield and a 40.0% higher ethanol yield. The results demonstrate the feasibility of the combinatorial strategy for construction of an efficient xylose-fermenting S. cerevisiae.
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Affiliation(s)
- Jian Zha
- Key Laboratory of Systems Bioengineering (Tianjin University), Ministry of Education, Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, P. R. China
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Zhou H, Cheng JS, Wang BL, Fink GR, Stephanopoulos G. Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae. Metab Eng 2012; 14:611-22. [PMID: 22921355 DOI: 10.1016/j.ymben.2012.07.011] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 07/10/2012] [Accepted: 07/21/2012] [Indexed: 11/28/2022]
Abstract
Xylose is the main pentose and second most abundant sugar in lignocellulosic feedstocks. To improve xylose utilization, necessary for the cost-effective bioconversion of lignocellulose, several metabolic engineering approaches have been employed in the yeast Saccharomyces cerevisiae. In this study, we describe the rational metabolic engineering of a S. cerevisiae strain, including overexpression of the Piromyces xylose isomerase gene (XYLA), Pichia stipitis xylulose kinase (XYL3) and genes of the non-oxidative pentose phosphate pathway (PPP). This engineered strain (H131-A3) was used to initialize a three-stage process of evolutionary engineering, through first aerobic and anaerobic sequential batch cultivation followed by growth in a xylose-limited chemostat. The evolved strain H131-A3-AL(CS) displayed significantly increased anaerobic growth rate (0.203±0.006 h⁻¹) and xylose consumption rate (1.866 g g⁻¹ h⁻¹) along with high ethanol conversion yield (0.41 g/g). These figures exceed by a significant margin any other performance metrics on xylose utilization and ethanol production by S. cerevisiae reported to-date. Further inverse metabolic engineering based on functional complementation suggested that efficient xylose assimilation is attributed, in part, to the elevated expression level of xylose isomerase, which was accomplished through the multiple-copy integration of XYLA in the chromosome of the evolved strain.
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Affiliation(s)
- Hang Zhou
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Oreb M, Dietz H, Farwick A, Boles E. Novel strategies to improve co-fermentation of pentoses with D-glucose by recombinant yeast strains in lignocellulosic hydrolysates. Bioengineered 2012; 3:347-51. [PMID: 22892590 PMCID: PMC3489712 DOI: 10.4161/bioe.21444] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Economically feasible production of second-generation biofuels requires efficient co-fermentation of pentose and hexose sugars in lignocellulosic hydrolysates under very harsh conditions. Baker’s yeast is an excellent, traditionally used ethanol producer but is naturally not able to utilize pentoses. This is due to the lack of pentose-specific transporter proteins and enzymatic reactions. Thus, natural yeast strains must be modified by genetic engineering. Although the construction of various recombinant yeast strains able to ferment pentose sugars has been described during the last two decades, their rates of pentose utilization is still significantly lower than D-glucose fermentation. Moreover, pentoses are only fermented after D-glucose is exhausted, resulting in an uneconomical increase in the fermentation time. In this addendum, we discuss novel approaches to improve utilization of pentoses by development of specific transporters and substrate channeling in enzyme cascades.
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Affiliation(s)
- Mislav Oreb
- Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt am Main, Germany.
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Kumari R, Pramanik K. Improvement of multiple stress tolerance in yeast strain by sequential mutagenesis for enhanced bioethanol production. J Biosci Bioeng 2012; 114:622-9. [PMID: 22867797 DOI: 10.1016/j.jbiosc.2012.07.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 06/08/2012] [Accepted: 07/02/2012] [Indexed: 01/13/2023]
Abstract
The present work deals with the improvement of multiple stress tolerance in a glucose-xylose co-fermenting hybrid yeast strain RPR39 by sequential mutagenesis using ethyl methane sulfonate, N-methyl-N'-nitro-N-nitrosoguanidine, near and far ultraviolet radiations. The mutants were evaluated for their tolerance to ethanol, temperature and fermentation inhibitors. Among these mutants, mutant RPRT90 exhibited highest tolerance to 10% initial ethanol concentration, 2 g L(-1) furfural and 8 g L(-1) acetic acid. The mutant also showed good growth at high temperature (39-40°C). A study on the combined effect of multiple stresses during fermentation of glucose-xylose mixture (3:1 ratio) was performed using mutant RPRT90. Under the combined effect of thermal (39°C) and inhibitor stress (0.25 g L(-1) vanillin, 0.5 g L(-1) furfural and 4 g L(-1) acetic acid), the mutant produced ethanol with a yield of 0.379 g g(-1), while under combined effect of ethanol (7% v/v) and inhibitor stress the ethanol yield obtained was 0.43 g g(-1). Further, under the synergistic effect of sugar (250 g L(-1)), thermal (39°C), ethanol (7% v/v) and inhibitors stress, the strain produced a maximum of 47.93 g L(-1) ethanol by utilizing 162.42 g L(-1) of glucose-xylose mixture giving an ethanol yield of 0.295 g g(-1) and productivity of 0.57 g L(-1) h(-1). Under same condition the fusant RPR39 produced a maximum of 30.0 g L(-1) ethanol giving a yield and productivity of 0.21 g g(-1) and 0.42 g L(-1) h(-1) respectively. The molecular characterization of mutant showed considerable difference in its genetic profile from hybrid RPR39. Thus, sequential mutagenesis was found to be effective to improve the stress tolerance properties in yeast.
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Affiliation(s)
- Rajni Kumari
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela 769008, Orissa, India.
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Young EM, Comer AD, Huang H, Alper HS. A molecular transporter engineering approach to improving xylose catabolism in Saccharomyces cerevisiae. Metab Eng 2012; 14:401-11. [DOI: 10.1016/j.ymben.2012.03.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 02/14/2012] [Accepted: 03/09/2012] [Indexed: 01/11/2023]
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Bergdahl B, Heer D, Sauer U, Hahn-Hägerdal B, van Niel EWJ. Dynamic metabolomics differentiates between carbon and energy starvation in recombinant Saccharomyces cerevisiae fermenting xylose. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:34. [PMID: 22587303 PMCID: PMC3462113 DOI: 10.1186/1754-6834-5-34] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 04/23/2012] [Indexed: 05/15/2023]
Abstract
BACKGROUND The concerted effects of changes in gene expression due to changes in the environment are ultimately reflected in the metabolome. Dynamics of metabolite concentrations under a certain condition can therefore give a description of the cellular state with a high degree of functional information. We used this potential to evaluate the metabolic status of two recombinant strains of Saccharomyces cerevisiae during anaerobic batch fermentation of a glucose/xylose mixture. Two isogenic strains were studied, differing only in the pathways used for xylose assimilation: the oxidoreductive pathway with xylose reductase (XR) and xylitol dehydrogenase (XDH) or the isomerization pathway with xylose isomerase (XI). The isogenic relationship between the two strains ascertains that the observed responses are a result of the particular xylose pathway and not due to unknown changes in regulatory systems. An increased understanding of the physiological state of these strains is important for further development of efficient pentose-utilizing strains for bioethanol production. RESULTS Using LC-MS/MS we determined the dynamics in the concentrations of intracellular metabolites in central carbon metabolism, nine amino acids, the purine nucleotides and redox cofactors. The general response to the transition from glucose to xylose was increased concentrations of amino acids and TCA-cycle intermediates, and decreased concentrations of sugar phosphates and redox cofactors. The two strains investigated had significantly different uptake rates of xylose which led to an enhanced response in the XI-strain. Despite the difference in xylose uptake rate, the adenylate energy charge remained high and stable around 0.8 in both strains. In contrast to the adenylate pool, large changes were observed in the guanylate pool. CONCLUSIONS The low uptake of xylose by the XI-strain led to several distinguished responses: depletion of key metabolites in glycolysis and NADPH, a reduced GTP/GDP ratio and accumulation of PEP and aromatic amino acids. These changes are strong indicators of carbon starvation. The XR/XDH-strain displayed few such traits. The coexistence of these traits and a stable adenylate charge indicates that xylose supplies energy to the cells but does not suppress a response similar to carbon starvation. Particular signals may play a role in the latter, of which the GTP/GMP ratio could be a candidate as it decreased significantly in both strains.
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Affiliation(s)
- Basti Bergdahl
- Applied Microbiology, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | | | - Uwe Sauer
- ETH Zurich, Zurich, 8093, Switzerland
| | | | - Ed WJ van Niel
- Applied Microbiology, Lund University, PO Box 124, SE-221 00, Lund, Sweden
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Scalcinati G, Otero JM, Vleet JR, Jeffries TW, Olsson L, Nielsen J. Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption. FEMS Yeast Res 2012; 12:582-97. [DOI: 10.1111/j.1567-1364.2012.00808.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/01/2012] [Accepted: 04/02/2012] [Indexed: 01/04/2023] Open
Affiliation(s)
| | | | - Jennifer R.H. Vleet
- Department of Bacteriology; University of Wisconsin-Madison; Madison; WI; USA
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Fox JM, Levine SE, Blanch HW, Clark DS. An evaluation of cellulose saccharification and fermentation with an engineered Saccharomyces cerevisiae capable of cellobiose and xylose utilization. Biotechnol J 2012; 7:361-73. [DOI: 10.1002/biot.201100209] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Oud B, van Maris AJA, Daran JM, Pronk JT. Genome-wide analytical approaches for reverse metabolic engineering of industrially relevant phenotypes in yeast. FEMS Yeast Res 2012; 12:183-96. [PMID: 22152095 PMCID: PMC3615171 DOI: 10.1111/j.1567-1364.2011.00776.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 11/21/2011] [Accepted: 11/21/2011] [Indexed: 11/28/2022] Open
Abstract
Successful reverse engineering of mutants that have been obtained by nontargeted strain improvement has long presented a major challenge in yeast biotechnology. This paper reviews the use of genome-wide approaches for analysis of Saccharomyces cerevisiae strains originating from evolutionary engineering or random mutagenesis. On the basis of an evaluation of the strengths and weaknesses of different methods, we conclude that for the initial identification of relevant genetic changes, whole genome sequencing is superior to other analytical techniques, such as transcriptome, metabolome, proteome, or array-based genome analysis. Key advantages of this technique over gene expression analysis include the independency of genome sequences on experimental context and the possibility to directly and precisely reproduce the identified changes in naive strains. The predictive value of genome-wide analysis of strains with industrially relevant characteristics can be further improved by classical genetics or simultaneous analysis of strains derived from parallel, independent strain improvement lineages.
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Affiliation(s)
- Bart Oud
- Department of Biotechnology, Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
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Improving Biomass Sugar Utilization by Engineered Saccharomyces cerevisiae. MICROBIOLOGY MONOGRAPHS 2012. [DOI: 10.1007/978-3-642-21467-7_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Contador CA, Andrews BA, Liao JC, Asenjo JA. Identification of transcription factors perturbed by the synthesis of high levels of a foreign protein in yeast saccharomyces cerevisiae. Biotechnol Prog 2011; 27:925-36. [DOI: 10.1002/btpr.616] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 11/25/2010] [Indexed: 11/10/2022]
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Almeida JRM, Runquist D, Sànchez i Nogué V, Lidén G, Gorwa-Grauslund MF. Stress-related challenges in pentose fermentation to ethanol by the yeast Saccharomyces cerevisiae. Biotechnol J 2011; 6:286-99. [PMID: 21305697 DOI: 10.1002/biot.201000301] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 11/09/2022]
Abstract
Conversion of agricultural residues, energy crops and forest residues into bioethanol requires hydrolysis of the biomass and fermentation of the released sugars. During the hydrolysis of the hemicellulose fraction, substantial amounts of pentose sugars, in particular xylose, are released. Fermentation of these pentose sugars to ethanol by engineered Saccharomyces cerevisiae under industrial process conditions is the subject of this review. First, fermentation challenges originating from the main steps of ethanol production from lignocellulosic feedstocks are discussed, followed by genetic modifications that have been implemented in S. cerevisiae to obtain xylose and arabinose fermenting capacity per se. Finally, the fermentation of a real lignocellulosic medium is discussed in terms of inhibitory effects of furaldehydes, phenolics and weak acids and the presence of contaminating microbiota.
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Affiliation(s)
- João R M Almeida
- Applied Microbiology, Lund University, Lund, Sweden; EMBRAPA Agroenergy, PqEB, Brasilia, 70770-901 DF, Brazil
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Hasunuma T, Sanda T, Yamada R, Yoshimura K, Ishii J, Kondo A. Metabolic pathway engineering based on metabolomics confers acetic and formic acid tolerance to a recombinant xylose-fermenting strain of Saccharomyces cerevisiae. Microb Cell Fact 2011; 10:2. [PMID: 21219616 PMCID: PMC3025834 DOI: 10.1186/1475-2859-10-2] [Citation(s) in RCA: 199] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 01/10/2011] [Indexed: 12/29/2022] Open
Abstract
Background The development of novel yeast strains with increased tolerance toward inhibitors in lignocellulosic hydrolysates is highly desirable for the production of bio-ethanol. Weak organic acids such as acetic and formic acids are necessarily released during the pretreatment (i.e. solubilization and hydrolysis) of lignocelluloses, which negatively affect microbial growth and ethanol production. However, since the mode of toxicity is complicated, genetic engineering strategies addressing yeast tolerance to weak organic acids have been rare. Thus, enhanced basic research is expected to identify target genes for improved weak acid tolerance. Results In this study, the effect of acetic acid on xylose fermentation was analyzed by examining metabolite profiles in a recombinant xylose-fermenting strain of Saccharomyces cerevisiae. Metabolome analysis revealed that metabolites involved in the non-oxidative pentose phosphate pathway (PPP) [e.g. sedoheptulose-7-phosphate, ribulose-5-phosphate, ribose-5-phosphate and erythrose-4-phosphate] were significantly accumulated by the addition of acetate, indicating the possibility that acetic acid slows down the flux of the pathway. Accordingly, a gene encoding a PPP-related enzyme, transaldolase or transketolase, was overexpressed in the xylose-fermenting yeast, which successfully conferred increased ethanol productivity in the presence of acetic and formic acid. Conclusions Our metabolomic approach revealed one of the molecular events underlying the response to acetic acid and focuses attention on the non-oxidative PPP as a target for metabolic engineering. An important challenge for metabolic engineering is identification of gene targets that have material importance. This study has demonstrated that metabolomics is a powerful tool to develop rational strategies to confer tolerance to stress through genetic engineering.
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Affiliation(s)
- Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
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Madhavan A, Srivastava A, Kondo A, Bisaria VS. Bioconversion of lignocellulose-derived sugars to ethanol by engineered Saccharomyces cerevisiae. Crit Rev Biotechnol 2011; 32:22-48. [PMID: 21204601 DOI: 10.3109/07388551.2010.539551] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Lignocellulosic biomass from agricultural and agro-industrial residues represents one of the most important renewable resources that can be utilized for the biological production of ethanol. The yeast Saccharomyces cerevisiae is widely used for the commercial production of bioethanol from sucrose or starch-derived glucose. While glucose and other hexose sugars like galactose and mannose can be fermented to ethanol by S. cerevisiae, the major pentose sugars D-xylose and L-arabinose remain unutilized. Nevertheless, D-xylulose, the keto isomer of xylose, can be fermented slowly by the yeast and thus, the incorporation of functional routes for the conversion of xylose and arabinose to xylulose or xylulose-5-phosphate in Saccharomyces cerevisiae can help to improve the ethanol productivity and make the fermentation process more cost-effective. Other crucial bottlenecks in pentose fermentation include low activity of the pentose phosphate pathway enzymes and competitive inhibition of xylose and arabinose transport into the cell cytoplasm by glucose and other hexose sugars. Along with a brief introduction of the pretreatment of lignocellulose and detoxification of the hydrolysate, this review provides an updated overview of (a) the key steps involved in the uptake and metabolism of the hexose sugars: glucose, galactose, and mannose, together with the pentose sugars: xylose and arabinose, (b) various factors that play a major role in the efficient fermentation of pentose sugars along with hexose sugars, and (c) the approaches used to overcome the metabolic constraints in the production of bioethanol from lignocellulose-derived sugars by developing recombinant S. cerevisiae strains.
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Affiliation(s)
- Anjali Madhavan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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Watanabe T, Watanabe I, Yamamoto M, Ando A, Nakamura T. A UV-induced mutant of Pichia stipitis with increased ethanol production from xylose and selection of a spontaneous mutant with increased ethanol tolerance. BIORESOURCE TECHNOLOGY 2011; 102:1844-1848. [PMID: 20947339 DOI: 10.1016/j.biortech.2010.09.087] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 09/13/2010] [Accepted: 09/17/2010] [Indexed: 05/30/2023]
Abstract
In the fermentation process of lignocellulosic biomass (such as wood and rice straw), efficient conversion of pentose (mainly xylose) into ethanol is important. Mutants of Pichia stipitis NBRC1687 were obtained after UV mutagenesis and selection of large colonies on ethanol-containing medium. One mutant, PXF58, produced 4.3% ethanol from 11.4% xylose while the parent strain only produced 3.1%. The ethanol productivities of PXF58 from glucose and fructose were about were about 1.4-fold higher than those of the parent strain. After continuous cultivation of PXF58 in YNB (yeast nitrogen base) medium containing 2% xylose and 5-7% ethanol, an ethanol-tolerant mutant, PET41, was obtained. Strain PET41 was able to produce 4.4% ethanol when first supplied with xylose then with glucose. This isolate might be thus useful for two-phase fermentation in which xylan is saccharified by xylanase to produce xylose, and glucan is saccharified later by cellulase and β-glucosidase to produce glucose.
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Affiliation(s)
- Takashi Watanabe
- National Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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Parachin NS, Bengtsson O, Hahn-Hägerdal B, Gorwa-Grauslund MF. The deletion of YLR042c improves ethanolic xylose fermentation by recombinant Saccharomyces cerevisiae. Yeast 2010; 27:741-51. [PMID: 20641017 DOI: 10.1002/yea.1777] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In a recent study combining transcriptome analyses of a number of recombinant laboratory and industrial S. cerevisiae strains with improved xylose utilization and their respective control strains, the ORF YLR042c was identified as a downregulated gene and it was shown that the gene deletion improved aerobic growth on xylose in the tested strain background. In the present study, the influence of deleting YLR042c on xylose fermentation was investigated in two different xylose-fermenting strains: TMB3001, which expresses genes from the initial xylose catabolizing pathway, including heterologous xylose reductase (XR) and xylitol dehydrogenase (XDH) and endogenous xylulokinase (XK); and TMB3057, which, in addition to the initial xylose catabolizing pathway, overexpresses the endogenous genes encoding the non-oxidative pentose phosphate pathway enzymes. The deletion of YLR042c led to improved aerobic growth on xylose in both strain backgrounds. However, the effect was more significant in the strain with the poorer growth rate on xylose (TMB3001). Under anaerobic conditions, the deletion of YLR042c increased the specific xylose consumption rate and the ethanol and xylitol yields. In strain TMB3057, xylose consumption was also improved at low concentrations and during co-fermentation of xylose and glucose. The effect of the gene deletion and overexpression was also tested for different carbon sources. Altogether, these results suggest that YLR042c influences xylose and the assimilation of carbon sources other than glucose, and that the effect could be at the level of sugar transport or sugar signalling.
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Young E, Lee SM, Alper H. Optimizing pentose utilization in yeast: the need for novel tools and approaches. BIOTECHNOLOGY FOR BIOFUELS 2010; 3:24. [PMID: 21080929 PMCID: PMC2993683 DOI: 10.1186/1754-6834-3-24] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 11/16/2010] [Indexed: 05/04/2023]
Abstract
Hexose and pentose cofermentation is regarded as one of the chief obstacles impeding economical conversion of lignocellulosic biomass to biofuels. Over time, successful application of traditional metabolic engineering strategy has produced yeast strains capable of utilizing the pentose sugars (especially xylose and arabinose) as sole carbon sources, yet major difficulties still remain for engineering simultaneous, exogenous sugar metabolism. Beyond catabolic pathways, the focus must shift towards non-traditional aspects of cellular engineering such as host molecular transport capability, catabolite sensing and stress response mechanisms. This review highlights the need for an approach termed 'panmetabolic engineering', a new paradigm for integrating new carbon sources into host metabolic pathways. This approach will concurrently optimize the interdependent processes of transport and metabolism using novel combinatorial techniques and global cellular engineering. As a result, panmetabolic engineering is a whole pathway approach emphasizing better pathways, reduced glucose-induced repression and increased product tolerance. In this paper, recent publications are reviewed in light of this approach and their potential to expand metabolic engineering tools. Collectively, traditional approaches and panmetabolic engineering enable the reprogramming of extant biological complexity and incorporation of exogenous carbon catabolism.
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Affiliation(s)
- Eric Young
- Department of Chemical Engineering, The University of Texas at Austin, 1 University Station, C0400, Austin, Texas 78712, USA
| | - Sun-Mi Lee
- Department of Chemical Engineering, The University of Texas at Austin, 1 University Station, C0400, Austin, Texas 78712, USA
- Water Environment Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seongbuk-gu, Seoul 136-791, Korea
| | - Hal Alper
- Department of Chemical Engineering, The University of Texas at Austin, 1 University Station, C0400, Austin, Texas 78712, USA
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