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Das S, Chandukishore T, Ulaganathan N, Dhodduraj K, Gorantla SS, Chandna T, Gupta LK, Sahoo A, Atheena PV, Raval R, Anjana PA, DasuVeeranki V, Prabhu AA. Sustainable biorefinery approach by utilizing xylose fraction of lignocellulosic biomass. Int J Biol Macromol 2024; 266:131290. [PMID: 38569993 DOI: 10.1016/j.ijbiomac.2024.131290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/20/2024] [Accepted: 03/29/2024] [Indexed: 04/05/2024]
Abstract
Lignocellulosic biomass (LCB) has been a lucrative feedstock for developing biochemical products due to its rich organic content, low carbon footprint and abundant accessibility. The recalcitrant nature of this feedstock is a foremost bottleneck. It needs suitable pretreatment techniques to achieve a high yield of sugar fractions such as glucose and xylose with low inhibitory components. Cellulosic sugars are commonly used for the bio-manufacturing process, and the xylose sugar, which is predominant in the hemicellulosic fraction, is rejected as most cell factories lack the five‑carbon metabolic pathways. In the present review, more emphasis was placed on the efficient pretreatment techniques developed for disintegrating LCB and enhancing xylose sugars. Further, the transformation of the xylose to value-added products through chemo-catalytic routes was highlighted. In addition, the review also recapitulates the sustainable production of biochemicals by native xylose assimilating microbes and engineering the metabolic pathway to ameliorate biomanufacturing using xylose as the sole carbon source. Overall, this review will give an edge on the bioprocessing of microbial metabolism for the efficient utilization of xylose in the LCB.
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Affiliation(s)
- Satwika Das
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - T Chandukishore
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Nivedhitha Ulaganathan
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Kawinharsun Dhodduraj
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Sai Susmita Gorantla
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Teena Chandna
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Laxmi Kumari Gupta
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Ansuman Sahoo
- Biochemical Engineering Laboratory, Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - P V Atheena
- Department of Biotechnology, Manipal Institute of Technology, Manipal 576104, Karnataka, India
| | - Ritu Raval
- Department of Biotechnology, Manipal Institute of Technology, Manipal 576104, Karnataka, India
| | - P A Anjana
- Department of Chemical Engineering, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Venkata DasuVeeranki
- Biochemical Engineering Laboratory, Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ashish A Prabhu
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India.
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Ma XY, Coleman B, Prabhu P, Wen F. Segmentation and evaluation of pathway module efficiency: Quantitative approach to monitor and overcome evolving bottlenecks in xylose to ethanol pathway. BIORESOURCE TECHNOLOGY 2024; 395:130377. [PMID: 38278451 DOI: 10.1016/j.biortech.2024.130377] [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: 12/05/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Engineering microbes that can efficiently ferment xylose to ethanol is critical to the development of renewable fuels from lignocellulosic biomass. To accelerate the strain optimization process, a method termed Segmentation and Evaluation of Pathway Module Efficiency (SEPME) was developed to enable rapid and iterative identification and removal of metabolic bottlenecks. Using SEPME, the overall pathway was segmented into two modules: the upstream xylose assimilation pathway and the downstream pentose phosphate pathway, glycolysis, and fermentation. The efficiencies of both modules were then quantified to identify the rate controlling module, followed by analyses of control coefficients, reaction rates, and byproduct concentrations to narrow down targets within the module. SEPME analysis revealed that as the strain was engineered with increasing xylose-to-ethanol yields, the bottlenecks shifted within a module and across the two modules. Guided by SEPME, these bottlenecks were removed one by one, and a strain approaching the theoretical ethanol yield was obtained.
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Affiliation(s)
- Xiao Yin Ma
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States; Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Bryan Coleman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States; Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Ponnandy Prabhu
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States; Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, MI 48109, United States.
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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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Galhardo JP, Piffer AP, Fiamenghi MB, Borelli G, da Silva DRM, Vasconcelos AA, Carazzolle MF, Pereira GAG, José J. Wide distribution of D-xylose dehydrogenase in yeasts reveals a new element in the D-xylose metabolism for bioethanol production. FEMS Yeast Res 2023; 23:foad003. [PMID: 36731871 DOI: 10.1093/femsyr/foad003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/03/2023] [Accepted: 02/01/2023] [Indexed: 02/04/2023] Open
Abstract
D-xylose utilization by yeasts is an essential feature for improving second-generation ethanol production. However, industrial yeast strains are incapable of consuming D-xylose. Previous analyzes of D-xylose-consuming or fermenting yeast species reveal that the genomic features associated with this phenotype are complex and still not fully understood. Here we present a previously neglected yeast enzyme related to D-xylose metabolism, D-xylose dehydrogenase (XylDH), which is found in at least 105 yeast genomes. By analyzing the XylDH gene family, we brought evidence of gene evolution marked by purifying selection on codons and positive selection evidence in D-xylose-consuming and fermenting species, suggesting the importance of XylDH for D-xylose-related phenotypes in yeasts. Furthermore, although we found no putative metabolic pathway for XylDH in yeast genomes, namely the absence of three bacterial known pathways for this enzyme, we also provide its expression profile on D-xylose media following D-xylose reductase for two yeasts with publicly available transcriptomes. Based on these results, we suggest that XylDH plays an important role in D-xylose usage by yeasts, likely being involved in a cofactor regeneration system by reducing cofactor imbalance in the D-xylose reductase pathway.
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Affiliation(s)
- Juliana P Galhardo
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - André P Piffer
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Mateus B Fiamenghi
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Guilherme Borelli
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Duguay R M da Silva
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Adrielle A Vasconcelos
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Marcelo F Carazzolle
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Gonçalo A G Pereira
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Juliana José
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
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Stovicek V, Dato L, Almqvist H, Schöpping M, Chekina K, Pedersen LE, Koza A, Figueira D, Tjosås F, Ferreira BS, Forster J, Lidén G, Borodina I. Rational and evolutionary engineering of Saccharomyces cerevisiae for production of dicarboxylic acids from lignocellulosic biomass and exploring genetic mechanisms of the yeast tolerance to the biomass hydrolysate. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:22. [PMID: 35219341 PMCID: PMC8882276 DOI: 10.1186/s13068-022-02121-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/12/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Lignosulfonates are significant wood chemicals with a $700 million market, produced by sulfite pulping of wood. During the pulping process, spent sulfite liquor (SSL) is generated, which in addition to lignosulfonates contains hemicellulose-derived sugars-in case of hardwoods primarily the pentose sugar xylose. The pentoses are currently underutilized. If they could be converted into value-added chemicals, overall economic profitability of the process would increase. SSLs are typically very inhibitory to microorganisms, which presents a challenge for a biotechnological process. The aim of the present work was to develop a robust yeast strain able to convert xylose in SSL to carboxylic acids. RESULTS The industrial strain Ethanol Red of the yeast Saccharomyces cerevisiae was engineered for efficient utilization of xylose in a Eucalyptus globulus lignosulfonate stream at low pH using CRISPR/Cas genome editing and adaptive laboratory evolution. The engineered strain grew in synthetic medium with xylose as sole carbon source with maximum specific growth rate (µmax) of 0.28 1/h. Selected evolved strains utilized all carbon sources in the SSL at pH 3.5 and grew with µmax between 0.05 and 0.1 1/h depending on a nitrogen source supplement. Putative genetic determinants of the increased tolerance to the SSL were revealed by whole genome sequencing of the evolved strains. In particular, four top-candidate genes (SNG1, FIT3, FZF1 and CBP3) were identified along with other gene candidates with predicted important roles, based on the type and distribution of the mutations across different strains and especially the best performing ones. The developed strains were further engineered for production of dicarboxylic acids (succinic and malic acid) via overexpression of the reductive branch of the tricarboxylic acid cycle (TCA). The production strain produced 0.2 mol and 0.12 mol of malic acid and succinic acid, respectively, per mol of xylose present in the SSL. CONCLUSIONS The combined metabolic engineering and adaptive evolution approach provided a robust SSL-tolerant industrial strain that converts fermentable carbon content of the SSL feedstock into malic and succinic acids at low pH.in production yields reaching 0.1 mol and 0.065 mol per mol of total consumed carbon sources.. Moreover, our work suggests potential genetic background of the tolerance to the SSL stream pointing out potential gene targets for improving the tolerance to inhibitory industrial feedstocks.
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Affiliation(s)
- Vratislav Stovicek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Laura Dato
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.,River Stone Biotech ApS, Fruebjergvej 3, 2100, Copenhagen, Denmark
| | - Henrik Almqvist
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Marie Schöpping
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden.,Chr. Hansen A/S, Boge Alle 10-12, 2970, Hørsholm, Denmark.,Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Ksenia Chekina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Anna Koza
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.,Chr. Hansen A/S, Boge Alle 10-12, 2970, Hørsholm, Denmark
| | - Diogo Figueira
- Biotrend S.A., Biocant Park Núcleo 04, Lote 2, 3060-197, Cantanhede, Portugal
| | - Freddy Tjosås
- Borregaard ApS, Hjalmar Wessels vei 6, 1721, Sarpsborg, Norway
| | | | - Jochen Forster
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.
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Bae JH, Kim MJ, Sung BH, Jin YS, Sohn JH. Directed evolution and secretory expression of xylose isomerase for improved utilisation of xylose in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:223. [PMID: 34823570 PMCID: PMC8613937 DOI: 10.1186/s13068-021-02073-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Xylose contained in lignocellulosic biomass is an attractive carbon substrate for economically viable conversion to bioethanol. Extensive research has been conducted on xylose fermentation using recombinant Saccharomyces cerevisiae expressing xylose isomerase (XI) and xylose reductase/xylitol dehydrogenase (XR/XDH) pathways along with the introduction of a xylose transporter and amplification of the downstream pathway. However, the low utilization of xylose in the presence of glucose, due to the varying preference for cellular uptake, is a lingering challenge. Studies so far have mainly focused on xylose utilization inside the cells, but there have been little trials on the conversion of xylose to xylulose by cell before uptake. We hypothesized that the extracellular conversion of xylose to xylulose before uptake would facilitate better utilization of xylose even in the presence of glucose. To verify this, XI from Piromyces sp. was engineered and hyper-secreted in S. cerevisiae for the extracellular conversion of xylose to xylulose. RESULTS The optimal pH of XI was lowered from 7.0 to 5.0 by directed evolution to ensure its high activity under the acidic conditions used for yeast fermentation, and hyper-secretion of an engineered XI-76 mutant (E56A and I252M) was accomplished by employing target protein-specific translational fusion partners. The purified XI-76 showed twofold higher activity than that of the wild type at pH 5. The secretory expression of XI-76 in the previously developed xylose utilizing yeast strain, SR8 increased xylose consumption and ethanol production by approximately 7-20% and 15-20% in xylose fermentation and glucose and xylose co-fermentation, respectively. CONCLUSIONS Isomerisation of xylose to xylulose before uptake using extracellular XI was found to be effective in xylose fermentation or glucose/xylose co-fermentation. This suggested that glucose competed less with xylulose than with xylose for uptake by the cell. Consequently, the engineered XI secretion system constructed in this study can pave the way for simultaneous utilization of C5/C6 sugars from the sustainable lignocellulosic biomass.
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Affiliation(s)
- Jung-Hoon Bae
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Mi-Jin Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jung-Hoon Sohn
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
- Cellapy Bio Inc., Bio-Venture Center 211, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Palermo GCDL, Coutouné N, Bueno JGR, Maciel LF, dos Santos LV. Exploring metal ion metabolisms to improve xylose fermentation in Saccharomyces cerevisiae. Microb Biotechnol 2021; 14:2101-2115. [PMID: 34313008 PMCID: PMC8449651 DOI: 10.1111/1751-7915.13887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/25/2021] [Indexed: 01/22/2023] Open
Abstract
The development of high-performance xylose-fermenting yeast is essential to achieve feasible conversion of biomass-derived sugars in lignocellulose-based biorefineries. However, engineered C5-strains of Saccharomyces cerevisiae still present low xylose consumption rates under anaerobic conditions. Here, we explore alternative metabolisms involved in metal homeostasis, which positively affect C5 fermentation and analyse the non-obvious regulatory network connection of both metabolisms using time-course transcriptome analysis. Our results indicated the vacuolar Fe2+ /Mn2+ transporter CCC1, and the protein involved in heavy metal ion homeostasis BSD2, as promising new targets for rational metabolic engineering strategies, enhancing xylose consumption in nine and 2.3-fold compared with control. Notably, intracellular metal concentration levels were affected differently by mutations and the results were compared with positive controls isu1Δ, a Fe-S cluster scaffold protein, and ssk2Δ, a component of HOG pathway. Temporal expression profiles indicate a metabolic remodelling in response to xylose, demonstrating changes in the main sugar sensing signalling pathways.
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Affiliation(s)
- Gisele Cristina de Lima Palermo
- Brazilian Biorenewable National Laboratory (LNBR)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSão Paulo13083‐100Brazil
- Genetics and Molecular Biology Graduate ProgramInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSão PauloBrazil
| | - Natalia Coutouné
- Brazilian Biorenewable National Laboratory (LNBR)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSão Paulo13083‐100Brazil
- Genetics and Molecular Biology Graduate ProgramInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSão PauloBrazil
| | - João Gabriel Ribeiro Bueno
- Brazilian Biorenewable National Laboratory (LNBR)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSão Paulo13083‐100Brazil
- Genetics and Molecular Biology Graduate ProgramInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSão PauloBrazil
| | - Lucas Ferreira Maciel
- Brazilian Biorenewable National Laboratory (LNBR)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSão Paulo13083‐100Brazil
| | - Leandro Vieira dos Santos
- Brazilian Biorenewable National Laboratory (LNBR)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSão Paulo13083‐100Brazil
- Genetics and Molecular Biology Graduate ProgramInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSão PauloBrazil
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A novel D-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae. Sci Rep 2021; 11:4766. [PMID: 33637780 PMCID: PMC7910561 DOI: 10.1038/s41598-021-83937-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/09/2021] [Indexed: 11/25/2022] Open
Abstract
Carbohydrate rich substrates such as lignocellulosic hydrolysates remain one of the primary sources of potentially renewable fuel and bulk chemicals. The pentose sugar d-xylose is often present in significant amounts along with hexoses. Saccharomyces cerevisiae can acquire the ability to metabolize d-xylose through expression of heterologous d-xylose isomerase (XI). This enzyme is notoriously difficult to express in S. cerevisiae and only fourteen XIs have been reported to be active so far. We cloned a new d-xylose isomerase derived from microorganisms in the gut of the wood-feeding beetle Odontotaenius disjunctus. Although somewhat homologous to the XI from Piromyces sp. E2, the new gene was identified as bacterial in origin and the host as a Parabacteroides sp. Expression of the new XI in S. cerevisiae resulted in faster aerobic growth than the XI from Piromyces on d-xylose media. The d-xylose isomerization rate conferred by the new XI was also 72% higher, while absolute xylitol production was identical in both strains. Interestingly, increasing concentrations of xylitol (up to 8 g L−1) appeared not to inhibit d-xylose consumption. The newly described XI displayed 2.6 times higher specific activity, 37% lower KM for d-xylose, and exhibited higher activity over a broader temperature range, retaining 51% of maximal activity at 30 °C compared with only 29% activity for the Piromyces XI.
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Cunha JT, Soares PO, Baptista SL, Costa CE, Domingues L. Engineered Saccharomyces cerevisiae for lignocellulosic valorization: a review and perspectives on bioethanol production. Bioengineered 2020; 11:883-903. [PMID: 32799606 PMCID: PMC8291843 DOI: 10.1080/21655979.2020.1801178] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The biorefinery concept, consisting in using renewable biomass with economical and energy goals, appeared in response to the ongoing exhaustion of fossil reserves. Bioethanol is the most prominent biofuel and has been considered one of the top chemicals to be obtained from biomass. Saccharomyces cerevisiae, the preferred microorganism for ethanol production, has been the target of extensive genetic modifications to improve the production of this alcohol from renewable biomasses. Additionally, S. cerevisiae strains from harsh industrial environments have been exploited due to their robust traits and improved fermentative capacity. Nevertheless, there is still not an optimized strain capable of turning second generation bioprocesses economically viable. Considering this, and aiming to facilitate and guide the future development of effective S. cerevisiae strains, this work reviews genetic engineering strategies envisioning improvements in 2nd generation bioethanol production, with special focus in process-related traits, xylose consumption, and consolidated bioprocessing. Altogether, the genetic toolbox described proves S. cerevisiae to be a key microorganism for the establishment of a bioeconomy, not only for the production of lignocellulosic bioethanol, but also having potential as a cell factory platform for overall valorization of renewable biomasses.
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Affiliation(s)
- Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Pedro O Soares
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Sara L Baptista
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Carlos E Costa
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
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10
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Diwan B, Gupta P. A Deuteromycete Isolate Geotrichum candidum as Oleaginous Cell Factory for Medium-Chain Fatty Acid-Rich Oils. Curr Microbiol 2020; 77:3738-3749. [PMID: 32778944 DOI: 10.1007/s00284-020-02155-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 07/29/2020] [Indexed: 10/23/2022]
Abstract
Single cell oils (SCO) are oils derived from microorganisms which have potential to hyperaccumulate intracellular lipids (called oleaginous) under some essential nutrient (nitrogen, phosphorous or sometimes sulphur) starvation and an excess of carbon. The present work investigates the influence of these key parameters (for triggering oleaginicity), i.e. carbon (C) and nitrogen (N) on oleaginous behaviour of an oleaginous isolate, with the objective of improving the lipid content and obtaining oils of applicative interest. Eleven yeasts were isolated from rotten fruits and a unique yeast from rotten apple was screened on the basis of its ~ 20% (of dry mass) lipid content (LC), trademark of oleaginicity under nitrogen-stressed culture conditions. Subsequent investigation on influence of C, N and w/w ratio of carbon source concentration (Cs) to nitrogen source concentration (Ns) was conducted on this isolate. The isolate was identified as a Deuteromycete-Geotrichum candidum. 4.8 g/l was found to be minimum N concentration and glucose as suitable C source for optimum balance between biomass and lipid content. The highest LC of 73.6% (172.5% higher compared to 27% LC at Cs/Ns 80/4.8) was obtained at Cs/Ns 150/4.8 with a lipid coefficient of 8.7 (g lipid/100 g substrate). While remarkably higher production economy (lipid coefficient of 28.45) was noted at Cs/Ns 100/4.8 with significant LC of 54.4% (~ 100% higher than at Cs/Ns 80/4.8). The derived oils were predominantly rich in medium-chain fatty acids (MCFA)-caprylic acid, rare in plant oils. G. candidum is a previously referred oleaginous species; however, for the first time this study illustrates its detailed oleaginous behaviour and lipid compositional characteristics with varying nutritional parameters. The work is a progressive contribution towards current and upcoming researches in field of SCOs. Compositional characteristics of derived oils, make it an important candidate for potential medical and nutritional applications in future.
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Affiliation(s)
- Batul Diwan
- Department of Biotechnology, National Institute of Technology, Raipur, India
| | - Pratima Gupta
- Department of Biotechnology, National Institute of Technology, Raipur, India.
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11
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Jeong D, Oh EJ, Ko JK, Nam JO, Park HS, Jin YS, Lee EJ, Kim SR. Metabolic engineering considerations for the heterologous expression of xylose-catabolic pathways in Saccharomyces cerevisiae. PLoS One 2020; 15:e0236294. [PMID: 32716960 PMCID: PMC7384654 DOI: 10.1371/journal.pone.0236294] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/01/2020] [Indexed: 11/18/2022] Open
Abstract
Xylose, the second most abundant sugar in lignocellulosic biomass hydrolysates, can be fermented by Saccharomyces cerevisiae expressing one of two heterologous xylose pathways: a xylose oxidoreductase pathway and a xylose isomerase pathway. Depending on the type of the pathway, its optimization strategies and the fermentation efficiencies vary significantly. In the present study, we constructed two isogenic strains expressing either the oxidoreductase pathway (XYL123) or the isomerase pathway (XI-XYL3), and delved into simple and reproducible ways to improve the resulting strains. First, the strains were subjected to the deletion of PHO13, overexpression of TAL1, and adaptive evolution, but those individual approaches were only effective in the XYL123 strain but not in the XI-XYL3 strain. Among other optimization strategies of the XI-XYL3 strain, we found that increasing the copy number of the xylose isomerase gene (xylA) is the most promising but yet preliminary strategy for the improvement. These results suggest that the oxidoreductase pathway might provide a simpler metabolic engineering strategy than the isomerase pathway for the development of efficient xylose-fermenting strains under the conditions tested in the present study.
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Affiliation(s)
- Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Eun Joong Oh
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Ju-Ock Nam
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Eun Jung Lee
- Department of Chemical Engineering, School of Applied Chemical Engineering, Kyungpook National University, Daegu, Republic of Korea
- * E-mail: (EJL); (SRK)
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
- * E-mail: (EJL); (SRK)
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Combining Xylose Reductase from Spathaspora arborariae with Xylitol Dehydrogenase from Spathaspora passalidarum to Promote Xylose Consumption and Fermentation into Xylitol by Saccharomyces cerevisiae. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6030072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In recent years, many novel xylose-fermenting yeasts belonging to the new genus Spathaspora have been isolated from the gut of wood-feeding insects and/or wood-decaying substrates. We have cloned and expressed, in Saccharomyces cerevisiae, a Spathaspora arborariae xylose reductase gene (SaXYL1) that accepts both NADH and NADPH as co-substrates, as well as a Spathaspora passalidarum NADPH-dependent xylose reductase (SpXYL1.1 gene) and the SpXYL2.2 gene encoding for a NAD+-dependent xylitol dehydrogenase. These enzymes were co-expressed in a S. cerevisiae strain over-expressing the native XKS1 gene encoding xylulokinase, as well as being deleted in the alkaline phosphatase encoded by the PHO13 gene. The S. cerevisiae strains expressing the Spathaspora enzymes consumed xylose, and xylitol was the major fermentation product. Higher specific growth rates, xylose consumption and xylitol volumetric productivities were obtained by the co-expression of the SaXYL1 and SpXYL2.2 genes, when compared with the co-expression of the NADPH-dependent SpXYL1.1 xylose reductase. During glucose-xylose co-fermentation by the strain with co-expression of the SaXYL1 and SpXYL2.2 genes, both ethanol and xylitol were produced efficiently. Our results open up the possibility of using the advantageous Saccharomyces yeasts for xylitol production, a commodity with wide commercial applications in pharmaceuticals, nutraceuticals, food and beverage industries.
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Robak K, Balcerek M. Current state-of-the-art in ethanol production from lignocellulosic feedstocks. Microbiol Res 2020; 240:126534. [PMID: 32683278 DOI: 10.1016/j.micres.2020.126534] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 01/08/2023]
Abstract
The renewable lignocellulosic biomass is a sustainable feedstock for the production of bioethanol, which shows the potential to replace fossil fuels. Due to the recalcitrant structure of plant cell wall made of cellulose, hemicellulose, and lignin, the biomass conversion process requires the use of efficient pretreatment process before enzymatic hydrolysis and fermentation to degrade the crystallinity of cellulose fibres and to remove lignin from biomass. Proper pretreatment techniques, economical production of cellulolytic enzymes, and effective fermentation of glucose and xylose in the presence of inhibitors are key challenges for the viable production of bioethanol. Although new strains capable of fermenting xylose are being designed, they are often not resistant to toxic compounds in hydrolysates. This paper provides an in-depth review of lignocellulosic bioethanol production via biochemical route, focusing on the most widely used pretreatment technologies and key operational conditions of enzymatic hydrolysis and fermentation considering sugar/ethanol yields. In addition, this review examines the relevant detoxification strategies for the removal of toxic substances and the importance of immobilization. The review also indicates potential usage of engineered microorganisms to improve glucose and xylose fermentation, cellulolytic enzymes production, and response to stress conditions.
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Affiliation(s)
- Katarzyna Robak
- Lodz University of Technology, Faculty of Biotechnology and Food Sciences, Institute of Fermentation Technology and Microbiology, Wólczańska 171/173, 90-924 Łódź, Poland.
| | - Maria Balcerek
- Lodz University of Technology, Faculty of Biotechnology and Food Sciences, Institute of Fermentation Technology and Microbiology, Wólczańska 171/173, 90-924 Łódź, Poland
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Promdonkoy P, Siripong W, Downes JJ, Tanapongpipat S, Runguphan W. Systematic improvement of isobutanol production from D-xylose in engineered Saccharomyces cerevisiae. AMB Express 2019; 9:160. [PMID: 31599368 PMCID: PMC6787123 DOI: 10.1186/s13568-019-0885-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/24/2019] [Indexed: 11/11/2022] Open
Abstract
As the importance of reducing carbon emissions as a means to limit the serious effects of global climate change becomes apparent, synthetic biologists and metabolic engineers are looking to develop renewable sources for transportation fuels and petroleum-derived chemicals. In recent years, microbial production of high-energy fuels has emerged as an attractive alternative to the traditional production of transportation fuels. In particular, the Baker’s yeast Saccharomyces cerevisiae, a highly versatile microbial chassis, has been engineered to produce a wide array of biofuels. Nevertheless, a key limitation of S. cerevisiae is its inability to utilize xylose, the second most abundant sugar in lignocellulosic biomass, for both growth and chemical production. Therefore, the development of a robust S. cerevisiae strain that is able to use xylose is of great importance. Here, we engineered S. cerevisiae to efficiently utilize xylose as a carbon source and produce the advanced biofuel isobutanol. Specifically, we screened xylose reductase (XR) and xylose dehydrogenase (XDH) variants from different xylose-metabolizing yeast strains to identify the XR–XDH combination with the highest activity. Overexpression of the selected XR–XDH variants, a xylose-specific sugar transporter, xylulokinase, and isobutanol pathway enzymes in conjunction with the deletions of PHO13 and GRE3 resulted in an engineered strain that is capable of producing isobutanol at a titer of 48.4 ± 2.0 mg/L (yield of 7.0 mg/g d-xylose). This is a 36-fold increase from the previous report by Brat and Boles and, to our knowledge, is the highest isobutanol yield from d-xylose in a microbial system. We hope that our work will set the stage for an economic route for the production of advanced biofuel isobutanol and enable efficient utilization of lignocellulosic biomass.
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Zhang Y, Lane S, Chen JM, Hammer SK, Luttinger J, Yang L, Jin YS, Avalos JL. Xylose utilization stimulates mitochondrial production of isobutanol and 2-methyl-1-butanol in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:223. [PMID: 31548865 PMCID: PMC6753614 DOI: 10.1186/s13068-019-1560-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/31/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Branched-chain higher alcohols (BCHAs), including isobutanol and 2-methyl-1-butanol, are promising advanced biofuels, superior to ethanol due to their higher energy density and better compatibility with existing gasoline infrastructure. Compartmentalizing the isobutanol biosynthetic pathway in yeast mitochondria is an effective way to produce BCHAs from glucose. However, to improve the sustainability of biofuel production, there is great interest in developing strains and processes to utilize lignocellulosic biomass, including its hemicellulose component, which is mostly composed of the pentose xylose. RESULTS In this work, we rewired the xylose isomerase assimilation and mitochondrial isobutanol production pathways in the budding yeast Saccharomyces cerevisiae. We then increased the flux through these pathways by making gene deletions of BAT1, ALD6, and PHO13, to develop a strain (YZy197) that produces as much as 4 g/L of BCHAs (3.10 ± 0.18 g isobutanol/L and 0.91 ± 0.02 g 2-methyl-1-butanol/L) from xylose. This represents approximately a 28-fold improvement on the highest isobutanol titers obtained from xylose previously reported in yeast and the first report of 2-methyl-1-butanol produced from xylose. The yield of total BCHAs is 57.2 ± 5.2 mg/g xylose, corresponding to ~ 14% of the maximum theoretical yield. Respirometry experiments show that xylose increases mitochondrial activity by as much as 7.3-fold compared to glucose. CONCLUSIONS The enhanced levels of mitochondrial BCHA production achieved, even without disrupting ethanol byproduct formation, arise mostly from xylose activation of mitochondrial activity and are correlated with slow rates of sugar consumption.
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Affiliation(s)
- Yanfei Zhang
- Department of Chemical and Biological Engineering, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ 08544 USA
| | - Stephan Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Jhong-Min Chen
- Department of Chemical and Biological Engineering, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ 08544 USA
| | - Sarah K. Hammer
- Department of Chemical and Biological Engineering, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ 08544 USA
| | - Jake Luttinger
- Department of Chemical and Biological Engineering, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ 08544 USA
| | - Lifeng Yang
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
- Department of Chemistry, Princeton University, Princeton, NJ USA
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - José L. Avalos
- Department of Chemical and Biological Engineering, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ 08544 USA
- Andlinger Center for Energy and the Environment, Princeton, NJ USA
- Department of Molecular Biology, Princeton University, Princeton, NJ USA
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16
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Overcoming the thermodynamic equilibrium of an isomerization reaction through oxidoreductive reactions for biotransformation. Nat Commun 2019; 10:1356. [PMID: 30902987 PMCID: PMC6430769 DOI: 10.1038/s41467-019-09288-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 02/21/2019] [Indexed: 01/22/2023] Open
Abstract
Isomerases perform biotransformations without cofactors but often cause an undesirable mixture of substrate and product due to unfavorable thermodynamic equilibria. We demonstrate the feasibility of using an engineered yeast strain harboring oxidoreductase reactions to overcome the thermodynamic limit of an isomerization reaction. Specifically, a yeast strain capable of consuming lactose intracellularly is engineered to produce tagatose from lactose through three layers of manipulations. First, GAL1 coding for galactose kinase is deleted to eliminate galactose utilization. Second, heterologous xylose reductase (XR) and galactitol dehydrogenase (GDH) are introduced into the ∆gal1 strain. Third, the expression levels of XR and GDH are adjusted to maximize tagatose production. The resulting engineered yeast produces 37.69 g/L of tagatose from lactose with a tagatose and galactose ratio of 9:1 in the reaction broth. These results suggest that in vivo oxidoreaductase reactions can be employed to replace isomerases in vitro for biotransformation. A desired product cannot be obtained at higher concentration than its equilibrium concentration when isomerases are used for biotransformation. Here, the authors engineer in vivo oxidoreductive reactions in yeast to overcome the equilibrium limitation of in vitro isomerases-based tagatose production.
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17
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Myers KS, Riley NM, MacGilvray ME, Sato TK, McGee M, Heilberger J, Coon JJ, Gasch AP. Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast. PLoS Genet 2019; 15:e1008037. [PMID: 30856163 PMCID: PMC6428351 DOI: 10.1371/journal.pgen.1008037] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/21/2019] [Accepted: 02/20/2019] [Indexed: 01/08/2023] Open
Abstract
Microbes can be metabolically engineered to produce biofuels and biochemicals, but rerouting metabolic flux toward products is a major hurdle without a systems-level understanding of how cellular flux is controlled. To understand flux rerouting, we investigated a panel of Saccharomyces cerevisiae strains with progressive improvements in anaerobic fermentation of xylose, a sugar abundant in sustainable plant biomass used for biofuel production. We combined comparative transcriptomics, proteomics, and phosphoproteomics with network analysis to understand the physiology of improved anaerobic xylose fermentation. Our results show that upstream regulatory changes produce a suite of physiological effects that collectively impact the phenotype. Evolved strains show an unusual co-activation of Protein Kinase A (PKA) and Snf1, thus combining responses seen during feast on glucose and famine on non-preferred sugars. Surprisingly, these regulatory changes were required to mount the hypoxic response when cells were grown on xylose, revealing a previously unknown connection between sugar source and anaerobic response. Network analysis identified several downstream transcription factors that play a significant, but on their own minor, role in anaerobic xylose fermentation, consistent with the combinatorial effects of small-impact changes. We also discovered that different routes of PKA activation produce distinct phenotypes: deletion of the RAS/PKA inhibitor IRA2 promotes xylose growth and metabolism, whereas deletion of PKA inhibitor BCY1 decouples growth from metabolism to enable robust fermentation without division. Comparing phosphoproteomic changes across ira2Δ and bcy1Δ strains implicated regulatory changes linked to xylose-dependent growth versus metabolism. Together, our results present a picture of the metabolic logic behind anaerobic xylose flux and suggest that widespread cellular remodeling, rather than individual metabolic changes, is an important goal for metabolic engineering.
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Affiliation(s)
- Kevin S. Myers
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Nicholas M. Riley
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Matthew E. MacGilvray
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Trey K. Sato
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mick McGee
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Justin Heilberger
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Audrey P. Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, United States of America
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18
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Cunha JT, Soares PO, Romaní A, Thevelein JM, Domingues L. Xylose fermentation efficiency of industrial Saccharomyces cerevisiae yeast with separate or combined xylose reductase/xylitol dehydrogenase and xylose isomerase pathways. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:20. [PMID: 30705706 PMCID: PMC6348659 DOI: 10.1186/s13068-019-1360-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/18/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Xylose isomerase (XI) and xylose reductase/xylitol dehydrogenase (XR/XDH) pathways have been extensively used to confer xylose assimilation capacity to Saccharomyces cerevisiae and tackle one of the major bottlenecks in the attainment of economically viable lignocellulosic ethanol production. Nevertheless, there is a lack of studies comparing the efficiency of those pathways both separately and combined. In this work, the XI and/or XR/XDH pathways were introduced into two robust industrial S. cerevisiae strains, evaluated in synthetic media and corn cob hemicellulosic hydrolysate and the results were correlated with the differential enzyme activities found in the xylose-pathway engineered strains. RESULTS The sole expression of XI was found to increase the fermentative capacity of both strains in synthetic media at 30 °C and 40 °C: decreasing xylitol accumulation and improving xylose consumption and ethanol production. Similar results were observed in fermentations of detoxified hydrolysate. However, in the presence of lignocellulosic-derived inhibitors, a positive synergistic effect resulted from the expression of both XI and XR/XDH, possibly caused by a cofactor equilibrium between the XDH and furan detoxifying enzymes, increasing the ethanol yield by more than 38%. CONCLUSIONS This study clearly shows an advantage of using the XI from Clostridium phytofermentans to attain high ethanol productivities and yields from xylose. Furthermore, and for the first time, the simultaneous utilization of XR/XDH and XI pathways was compared to the single expression of XR/XDH or XI and was found to improve ethanol production from non-detoxified hemicellulosic hydrolysates. These results extend the knowledge regarding S. cerevisiae xylose assimilation metabolism and pave the way for the construction of more efficient strains for use in lignocellulosic industrial processes.
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Affiliation(s)
- Joana T. Cunha
- CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Pedro O. Soares
- CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Aloia Romaní
- CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
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Lane S, Dong J, Jin YS. Value-added biotransformation of cellulosic sugars by engineered Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2018; 260:380-394. [PMID: 29655899 DOI: 10.1016/j.biortech.2018.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 05/26/2023]
Abstract
The substantial research efforts into lignocellulosic biofuels have generated an abundance of valuable knowledge and technologies for metabolic engineering. In particular, these investments have led to a vast growth in proficiency of engineering the yeast Saccharomyces cerevisiae for consuming lignocellulosic sugars, enabling the simultaneous assimilation of multiple carbon sources, and producing a large variety of value-added products by introduction of heterologous metabolic pathways. While microbial conversion of cellulosic sugars into large-volume low-value biofuels is not currently economically feasible, there may still be opportunities to produce other value-added chemicals as regulation of cellulosic sugar metabolism is quite different from glucose metabolism. This review summarizes these recent advances with an emphasis on employing engineered yeast for the bioconversion of lignocellulosic sugars into a variety of non-ethanol value-added products.
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Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jia Dong
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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20
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Ko JK, Jung JH, Altpeter F, Kannan B, Kim HE, Kim KH, Alper HS, Um Y, Lee SM. Largely enhanced bioethanol production through the combined use of lignin-modified sugarcane and xylose fermenting yeast strain. BIORESOURCE TECHNOLOGY 2018; 256:312-320. [PMID: 29455099 DOI: 10.1016/j.biortech.2018.01.123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 05/26/2023]
Abstract
The recalcitrant structure of lignocellulosic biomass is a major barrier in efficient biomass-to-ethanol bioconversion processes. The combination of feedstock engineering via modification in the lignin synthesis pathway of sugarcane and co-fermentation of xylose and glucose with a recombinant xylose utilizing yeast strain produced 148% more ethanol compared to that of the wild type biomass and control strain. The lignin reduced biomass led to a substantially increased release of fermentable sugars (glucose and xylose). The engineered yeast strain efficiently co-utilized glucose and xylose for fermentation, elevating ethanol yields. In this study, it was experimentally demonstrated that the combined efforts of engineering both feedstock and microorganisms largely enhances the bioconversion of lignocellulosic feedstock to bioethanol. This strategy will significantly improve the economic feasibility of lignocellulosic biofuels production.
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Affiliation(s)
- Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Je Hyeong Jung
- Center for Natural Products Convergence Research, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea
| | - Fredy Altpeter
- Agronomy Department, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, IFAS, PO Box 110300, Gainesville, FL 32611, USA
| | - Baskaran Kannan
- Agronomy Department, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, IFAS, PO Box 110300, Gainesville, FL 32611, USA
| | - Ha Eun Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Clean Energy and Chemical Engineering, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Clean Energy and Chemical Engineering, Korea University of Science and Technology, Daejeon 34113, Republic of Korea.
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21
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Diwan B, Parkhey P, Gupta P. From agro-industrial wastes to single cell oils: a step towards prospective biorefinery. Folia Microbiol (Praha) 2018; 63:547-568. [DOI: 10.1007/s12223-018-0602-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
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22
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HamediRad M, Lian J, Li H, Zhao H. RNAi assisted genome evolution unveils yeast mutants with improved xylose utilization. Biotechnol Bioeng 2018; 115:1552-1560. [DOI: 10.1002/bit.26570] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/28/2018] [Accepted: 02/08/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Mohammad HamediRad
- Department of Chemical and Biomolecular EngineeringCarl R. Woese Institute for Genomic BiologyUrbanaIllinois
| | - Jiazhang Lian
- Department of Chemical and Biomolecular EngineeringCarl R. Woese Institute for Genomic BiologyUrbanaIllinois
- College of Chemical and Biological EngineeringZhejiang UniversityHangzhouChina
| | - Hejun Li
- Department of Agricultural and Biological EngineeringUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
| | - Huimin Zhao
- Department of Chemical and Biomolecular EngineeringCarl R. Woese Institute for Genomic BiologyUrbanaIllinois
- Departments of Chemistry Biochemistry and BioengineeringUniversity of Illinois at UrbanaUrbanaIllinois
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23
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Lamb CDC, Silva BMZD, de Souza D, Fornasier F, Riça LB, Schneider RDCDS. Bioethanol production from rice hull and evaluation of the final solid residue. CHEM ENG COMMUN 2018. [DOI: 10.1080/00986445.2017.1422495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Christiano de C. Lamb
- Environmental Technology Postgraduation Program, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | | | - Diego de Souza
- Environmental Technology Postgraduation Program, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | - Franccesca Fornasier
- Department of Chemistry and Physics, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | - Larissa Brixner Riça
- Department of Chemistry and Physics, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | - Rosana de Cassia de Souza Schneider
- Environmental Technology Postgraduation Program, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
- Department of Chemistry and Physics, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
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24
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Cheng C, Tang RQ, Xiong L, Hector RE, Bai FW, Zhao XQ. Association of improved oxidative stress tolerance and alleviation of glucose repression with superior xylose-utilization capability by a natural isolate of Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:28. [PMID: 29441126 PMCID: PMC5798184 DOI: 10.1186/s13068-018-1018-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Saccharomyces cerevisiae wild strains generally have poor xylose-utilization capability, which is a major barrier for efficient bioconversion of lignocellulosic biomass. Laboratory adaption is commonly used to enhance xylose utilization of recombinant S. cerevisiae. Apparently, yeast cells could remodel the metabolic network for xylose metabolism. However, it still remains unclear why natural isolates of S. cerevisiae poorly utilize xylose. Here, we analyzed a unique S. cerevisiae natural isolate YB-2625 which has superior xylose metabolism capability in the presence of mixed-sugar. Comparative transcriptomic analysis was performed using S. cerevisiae YB-2625 grown in a mixture of glucose and xylose, and the model yeast strain S288C served as a control. Global gene transcription was compared at both the early mixed-sugar utilization stage and the latter xylose-utilization stage. RESULTS Genes involved in endogenous xylose-assimilation (XYL2 and XKS1), gluconeogenesis, and TCA cycle showed higher transcription levels in S. cerevisiae YB-2625 at the xylose-utilization stage, when compared to the reference strain. On the other hand, transcription factor encoding genes involved in regulation of glucose repression (MIG1, MIG2, and MIG3) as well as HXK2 displayed decreased transcriptional levels in YB-2625, suggesting the alleviation of glucose repression of S. cerevisiae YB-2625. Notably, genes encoding antioxidant enzymes (CTT1, CTA1, SOD2, and PRX1) showed higher transcription levels in S. cerevisiae YB-2625 in the xylose-utilization stage than that of the reference strain. Consistently, catalase activity of YB-2625 was 1.9-fold higher than that of S. cerevisiae S288C during the xylose-utilization stage. As a result, intracellular reactive oxygen species levels of S. cerevisiae YB-2625 were 43.3 and 58.6% lower than that of S288C at both sugar utilization stages. Overexpression of CTT1 and PRX1 in the recombinant strain S. cerevisiae YRH396 deriving from S. cerevisiae YB-2625 increased cell growth when xylose was used as the sole carbon source, leading to 13.5 and 18.1%, respectively, more xylose consumption. CONCLUSIONS Enhanced oxidative stress tolerance and relief of glucose repression are proposed to be two major mechanisms for superior xylose utilization by S. cerevisiae YB-2625. The present study provides insights into the innate regulatory mechanisms underlying xylose utilization in wild-type S. cerevisiae, which benefits the rapid development of robust yeast strains for lignocellulosic biorefineries.
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Affiliation(s)
- Cheng Cheng
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Rui-Qi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Liang Xiong
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Ronald E. Hector
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL USA
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
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25
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Xylose transport in yeast for lignocellulosic ethanol production: Current status. J Biosci Bioeng 2017; 125:259-267. [PMID: 29196106 DOI: 10.1016/j.jbiosc.2017.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/07/2017] [Accepted: 10/10/2017] [Indexed: 01/07/2023]
Abstract
Lignocellulosic ethanol has been considered as an alternative transportation fuel. Utilization of hemicellulosic fraction in lignocelluloses is crucial in economical production of lignocellulosic ethanol. However, this fraction has not efficiently been utilized by traditional yeast Saccharomyces cerevisiae. Genetically modified S. cerevisiae, which can utilize xylose, has several limitations including low ethanol yield, redox imbalance, and undesired metabolite formation similar to native xylose utilizing yeasts. Besides, xylose uptake is a major issue, where sugar transport system plays an important role. These genetically modified and wild-type yeast strains have further been engineered for improved xylose uptake. Various techniques have been employed to facilitate the xylose transportation in these strains. The present review is focused on the sugar transport machineries, mechanisms of xylose transport, limitations and how to deal with xylose transport for xylose assimilation in yeast cells. The recent advances in different techniques to facilitate the xylose transportation have also been discussed.
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26
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Cadete RM, Rosa CA. The yeasts of the genus Spathaspora
: potential candidates for second-generation biofuel production. Yeast 2017; 35:191-199. [DOI: 10.1002/yea.3279] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/26/2017] [Accepted: 08/16/2017] [Indexed: 11/08/2022] Open
Affiliation(s)
- Raquel M. Cadete
- Departamento de Microbiologia, ICB, C.P. 486; Universidade Federal de Minas Gerais; Belo Horizonte MG 31270-901 Brazil
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486; Universidade Federal de Minas Gerais; Belo Horizonte MG 31270-901 Brazil
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27
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Kwak S, Jin YS. Production of fuels and chemicals from xylose by engineered Saccharomyces cerevisiae: a review and perspective. Microb Cell Fact 2017; 16:82. [PMID: 28494761 PMCID: PMC5425999 DOI: 10.1186/s12934-017-0694-9] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 05/02/2017] [Indexed: 02/06/2023] Open
Abstract
Efficient xylose utilization is one of the most important pre-requisites for developing an economic microbial conversion process of terrestrial lignocellulosic biomass into biofuels and biochemicals. A robust ethanol producing yeast Saccharomyces cerevisiae has been engineered with heterologous xylose assimilation pathways. A two-step oxidoreductase pathway consisting of NAD(P)H-linked xylose reductase and NAD+-linked xylitol dehydrogenase, and one-step isomerase pathway using xylose isomerase have been employed to enable xylose assimilation in engineered S. cerevisiae. However, the resulting engineered yeast exhibited inefficient and slow xylose fermentation. In order to improve the yield and productivity of xylose fermentation, expression levels of xylose assimilation pathway enzymes and their kinetic properties have been optimized, and additional optimizations of endogenous or heterologous metabolisms have been achieved. These efforts have led to the development of engineered yeast strains ready for the commercialization of cellulosic bioethanol. Interestingly, xylose metabolism by engineered yeast was preferably respiratory rather than fermentative as in glucose metabolism, suggesting that xylose can serve as a desirable carbon source capable of bypassing metabolic barriers exerted by glucose repression. Accordingly, engineered yeasts showed superior production of valuable metabolites derived from cytosolic acetyl-CoA and pyruvate, such as 1-hexadecanol and lactic acid, when the xylose assimilation pathway and target synthetic pathways were optimized in an adequate manner. While xylose has been regarded as a sugar to be utilized because it is present in cellulosic hydrolysates, potential benefits of using xylose instead of glucose for yeast-based biotechnological processes need to be realized.
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Affiliation(s)
- Suryang Kwak
- Department of Food Science and Human Nutrition and Carl R. Woose Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition and Carl R. Woose Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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28
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Dos Santos LV, Carazzolle MF, Nagamatsu ST, Sampaio NMV, Almeida LD, Pirolla RAS, Borelli G, Corrêa TLR, Argueso JL, Pereira GAG. Unraveling the genetic basis of xylose consumption in engineered Saccharomyces cerevisiae strains. Sci Rep 2016; 6:38676. [PMID: 28000736 PMCID: PMC5175268 DOI: 10.1038/srep38676] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/11/2016] [Indexed: 11/21/2022] Open
Abstract
The development of biocatalysts capable of fermenting xylose, a five-carbon sugar abundant in lignocellulosic biomass, is a key step to achieve a viable production of second-generation ethanol. In this work, a robust industrial strain of Saccharomyces cerevisiae was modified by the addition of essential genes for pentose metabolism. Subsequently, taken through cycles of adaptive evolution with selection for optimal xylose utilization, strains could efficiently convert xylose to ethanol with a yield of about 0.46 g ethanol/g xylose. Though evolved independently, two strains carried shared mutations: amplification of the xylose isomerase gene and inactivation of ISU1, a gene encoding a scaffold protein involved in the assembly of iron-sulfur clusters. In addition, one of evolved strains carried a mutation in SSK2, a member of MAPKKK signaling pathway. In validation experiments, mutating ISU1 or SSK2 improved the ability to metabolize xylose of yeast cells without adaptive evolution, suggesting that these genes are key players in a regulatory network for xylose fermentation. Furthermore, addition of iron ion to the growth media improved xylose fermentation even by non-evolved cells. Our results provide promising new targets for metabolic engineering of C5-yeasts and point to iron as a potential new additive for improvement of second-generation ethanol production.
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Affiliation(s)
- Leandro Vieira Dos Santos
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil.,GranBio/BioCelere, Campinas, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Sheila Tiemi Nagamatsu
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Nádia Maria Vieira Sampaio
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins-CO, 80523-1618, USA
| | | | | | - Guilherme Borelli
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins-CO, 80523-1618, USA
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil.,GranBio/BioCelere, Campinas, Brazil
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29
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Ko JK, Um Y, Lee SM. Effect of manganese ions on ethanol fermentation by xylose isomerase expressing Saccharomyces cerevisiae under acetic acid stress. BIORESOURCE TECHNOLOGY 2016; 222:422-430. [PMID: 27744166 DOI: 10.1016/j.biortech.2016.09.130] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 06/06/2023]
Abstract
The efficient fermentation of lignocellulosic hydrolysates in the presence of inhibitors is highly desirable for bioethanol production. Among the inhibitors, acetic acid released during the pretreatment of lignocellulose negatively affects the fermentation performance of biofuel producing organisms. In this study, we evaluated the inhibitory effects of acetic acid on glucose and xylose fermentation by a high performance engineered strain of xylose utilizing Saccharomyces cerevisiae, SXA-R2P-E, harboring a xylose isomerase based pathway. The presence of acetic acid severely decreased the xylose fermentation performance of this strain. However, the acetic acid stress was alleviated by metal ion supplementation resulting in a 52% increased ethanol production rate under 2g/L of acetic acid stress. This study shows the inhibitory effect of acetic acid on an engineered isomerase-based xylose utilizing strain and suggests a simple but effective method to improve the co-fermentation performance under acetic acid stress for efficient bioethanol production.
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Affiliation(s)
- Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Clean Energy and Chemical Engineering, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Clean Energy and Chemical Engineering, Korea University of Science and Technology, Daejeon 34113, Republic of Korea.
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30
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Zhang GC, Kong II, Wei N, Peng D, Turner TL, Sung BH, Sohn JH, Jin YS. Optimization of an acetate reduction pathway for producing cellulosic ethanol by engineered yeast. Biotechnol Bioeng 2016; 113:2587-2596. [DOI: 10.1002/bit.26021] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/24/2016] [Accepted: 05/27/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Guo-Chang Zhang
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - In Iok Kong
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - Na Wei
- Department of Civil and Environmental Engineering and Earth Sciences; University of Notre Dame; South Bend Indiana
| | - Dairong Peng
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - Timothy L. Turner
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - Bong Hyun Sung
- Bioenergy and Biochemical Research Center; Korea Research Institute of Bioscience and Biotechnology; Daejeon Korea
| | - Jung-Hoon Sohn
- Bioenergy and Biochemical Research Center; Korea Research Institute of Bioscience and Biotechnology; Daejeon Korea
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois
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31
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Activation of an Otherwise Silent Xylose Metabolic Pathway in Shewanella oneidensis. Appl Environ Microbiol 2016; 82:3996-4005. [PMID: 27107127 DOI: 10.1128/aem.00881-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 04/21/2016] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Shewanella oneidensis is unable to metabolize the sugar xylose as a carbon and energy source. In the present study, an otherwise silent xylose catabolic pathway was activated in S. oneidensis by following an adaptive evolution strategy. Genome-wide scans indicated that the S. oneidensis genome encoded two proteins similar to the xylose oxido-reductase pathway enzymes xylose reductase (SO_0900) and xylulokinase (SO_4230), and purified SO_0900 and SO_4230 displayed xylose reductase and xylulokinase activities, respectively. The S. oneidensis genome was missing, however, an Escherichia coli XylE-like xylose transporter. After 12 monthly transfers in minimal growth medium containing successively higher xylose concentrations, an S. oneidensis mutant (termed strain XM1) was isolated for the acquired ability to grow aerobically on xylose as a carbon and energy source. Whole-genome sequencing indicated that strain XM1 contained a mutation in an unknown membrane protein (SO_1396) resulting in a glutamine-to-histidine conversion at amino acid position 207. Homology modeling demonstrated that the Q207H mutation in SO_1396 was located at the homologous xylose docking site in XylE. The expansion of the S. oneidensis metabolic repertoire to xylose expands the electron donors whose oxidation may be coupled to the myriad of terminal electron-accepting processes catalyzed by S. oneidensis Since xylose is a lignocellulose degradation product, this study expands the potential substrates to include lignocellulosic biomass. IMPORTANCE The activation of an otherwise silent xylose metabolic system in Shewanella oneidensis is a powerful example of how accidental mutations allow microorganisms to adaptively evolve. The expansion of the S. oneidensis metabolic repertoire to xylose expands the electron donors whose oxidation may be coupled to the myriad of terminal electron-accepting processes catalyzed by S. oneidensis Since xylose is a lignocellulose degradation product, this study expands the potential substrates to include lignocellulosic biomass.
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