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Lu M, Liu S, Liu J, Zhao L, Pei J. A sustainable and efficient strategy for bioconverting naringin to L-rhamnose, 2R-naringenin, and kaempferol. Food Chem 2024; 447:138942. [PMID: 38484542 DOI: 10.1016/j.foodchem.2024.138942] [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: 09/07/2023] [Revised: 02/01/2024] [Accepted: 03/02/2024] [Indexed: 04/10/2024]
Abstract
The development of a sustainable and efficient bioconversion strategy is crucial for the full-component utilization of naringin. In this study, an engineering Pichia pastoris co-culture system was developed to produce L-rhamnose and 2S/2R-naringenin. By optimizing transformation conditions, the co-culture system could completely convert naringin while fully consuming glucose. The production of 2S/2R-naringenin reached 59.5 mM with a molar conversion of 99.2%, and L-rhamnose reached 59.1 mM with a molar conversion of 98.5%. In addition, an engineering Escherichia coli co-culture system was developed to produce 2R-naringenin and kaempferol from 2S/2R-naringenin. Maximal kaempferol production reached 1050 mg/L with a corresponding molar conversion of 99.0%, and 996 mg/L 2R-naringenin was accumulated. Finally, a total of 17.4 g 2R-naringenin, 18.0 g kaempferol, and 26.1 g L-rhamnose were prepared from 100 g naringin. Thus, this study provides a novel strategy for the production of value-added compounds from naringin with an environmentally safe process.
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Affiliation(s)
- Mengfan Lu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Simin Liu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Jiamei Liu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Linguo Zhao
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China.
| | - Jianjun Pei
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China.
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2
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Qiu Y, Liu W, Wu M, Bao H, Sun X, Dou Q, Jia H, Liu W, Shen Y. Construction of an alternative NADPH regeneration pathway improves ethanol production in Saccharomyces cerevisiae with xylose metabolic pathway. Synth Syst Biotechnol 2024; 9:269-276. [PMID: 38469586 PMCID: PMC10926300 DOI: 10.1016/j.synbio.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
Full conversion of glucose and xylose from lignocellulosic hydrolysates is required for obtaining a high ethanol yield. However, glucose and xylose share flux in the pentose phosphate pathway (PPP) and glycolysis pathway (EMP), with glucose having a competitive advantage in the shared metabolic pathways. In this work, we knocked down ZWF1 to preclude glucose from entering the PPP. This reduced the [NADPH] level and disturbed growth on both glucose or xylose, confirming that the oxidative PPP, which begins with Zwf1p and ultimately leads to CO2 production, is the primary source of NADPH in both glucose and xylose. Upon glucose depletion, gluconeogenesis is necessary to generate glucose-6-phosphate, the substrate of Zwf1p. We re-established the NADPH regeneration pathway by replacing the endogenous NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene TDH3 with heterogenous NADP + -GAPDH genes GDH, gapB, and GDP1. Among the resulting strains, the strain BZP1 (zwf1Δ, tdh3::GDP1) exhibited a similar xylose consumption rate before glucose depletion, but a 1.6-fold increased xylose consumption rate following glucose depletion compared to the original strain BSGX001, and the ethanol yield for total consumed sugars of BZP1 was 13.5% higher than BSGX001. This suggested that using the EMP instead of PPP to generate NADPH reduces the wasteful metabolic cycle and excess CO2 release from oxidative PPP. Furthermore, we used a copper-repressing promoter to modulate the expression of ZWF1 and optimize the timing of turning off the ZWF1, therefore, to determine the competitive equilibrium between glucose-xylose co-metabolism. This strategy allowed fast growth in the early stage of fermentation and low waste in the following stages of fermentation.
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Affiliation(s)
- Yali Qiu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Wei Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Meiling Wu
- Advanced Medical Research Institute, Shandong University, Jinan, 250012, China
| | - Haodong Bao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xinhua Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Qin Dou
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Hongying Jia
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
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3
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Shin J, Liao S, Kuanyshev N, Xin Y, Kim C, Lu T, Jin YS. Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium. Nat Commun 2024; 15:781. [PMID: 38278783 PMCID: PMC10817915 DOI: 10.1038/s41467-024-45011-w] [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: 08/31/2022] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.
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Affiliation(s)
- Jonghyeok Shin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Siqi Liao
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nurzhan Kuanyshev
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yongping Xin
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chanwoo Kim
- 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
| | - Ting Lu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 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.
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4
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Trivellin C, Rugbjerg P, Olsson L. Performance and robustness analysis reveals phenotypic trade-offs in yeast. Life Sci Alliance 2024; 7:e202302215. [PMID: 37903627 PMCID: PMC10618107 DOI: 10.26508/lsa.202302215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023] Open
Abstract
To design strains that can function efficiently in complex industrial settings, it is crucial to consider their robustness, that is, the stability of their performance when faced with perturbations. In the present study, we cultivated 24 Saccharomyces cerevisiae strains under conditions that simulated perturbations encountered during lignocellulosic bioethanol production, and assessed the performance and robustness of multiple phenotypes simultaneously. The observed negative correlations confirmed a trade-off between performance and robustness of ethanol yield, biomass yield, and cell dry weight. Conversely, the specific growth rate performance positively correlated with the robustness, presumably because of evolutionary selection for robust, fast-growing cells. The Ethanol Red strain exhibited both high performance and robustness, making it a good candidate for bioproduction in the tested perturbation space. Our results experimentally map the robustness-performance trade-offs, previously demonstrated mainly by single-phenotype and computational studies.
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Affiliation(s)
- Cecilia Trivellin
- https://ror.org/040wg7k59 Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Peter Rugbjerg
- https://ror.org/040wg7k59 Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
- Enduro Genetics ApS, Copenhagen, Denmark
| | - Lisbeth Olsson
- https://ror.org/040wg7k59 Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
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5
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Zhang Y, Li M, Zhu R, Xin Y, Guo Z, Gu Z, Guo Z, Zhang L. Installing xylose assimilation and cellodextrin phosphorolysis pathways in obese Yarrowia lipolytica facilitates cost-effective lipid production from lignocellulosic hydrolysates. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:186. [PMID: 38031183 PMCID: PMC10688077 DOI: 10.1186/s13068-023-02434-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Yarrowia lipolytica, one of the most charming chassis cells in synthetic biology, is unable to use xylose and cellodextrins. RESULTS Herein, we present work to tackle for the first time the engineering of Y. lipolytica to produce lipids from cellodextrins and xylose by employing rational and combinatorial strategies. This includes constructing a cellodextrin-phosphorolytic Y. lipolytica by overexpressing Neurospora crassa cellodextrin transporter, Clostridium thermocellum cellobiose/cellodextrin phosphorylase and Saccharomyces cerevisiae phosphoglucomutase. The effect of glucose repression on xylose consumption was relieved by installing a xylose uptake facilitator combined with enhanced PPP pathway and increased cytoplasmic NADPH supply. Further enhancing lipid production and interrupting its consumption conferred the obese phenotype to the engineered yeast. The strain is able to co-ferment glucose, xylose and cellodextrins efficiently, achieving a similar μmax of 0.19 h-1, a qs of 0.34 g-s/g-DCW/h and a YX/S of 0.54 DCW-g/g-s on these substrates, and an accumulation of up to 40% of lipids on the sugar mixture and on wheat straw hydrolysate. CONCLUSIONS Therefore, engineering Y. lipolytica capable of assimilating xylose and cellodextrins is a vital step towards a simultaneous saccharification and fermentation (SSF) process of LC biomass, allowing improved substrate conversion rate and reduced production cost due to low demand of external glucosidase.
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Affiliation(s)
- Yiran Zhang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, People's Republic of China
| | - Moying Li
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Rui Zhu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Yu Xin
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Zitao Guo
- School of Food and Biological Engineering, Jiangsu University, Xuefu Road 301, Jingkou District, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Zhenghua Gu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Zhongpeng Guo
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China.
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China.
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, People's Republic of China.
| | - Liang Zhang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, People's Republic of China
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6
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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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7
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Saxena A, Hussain A, Parveen F, Ashfaque M. Current status of metabolic engineering of microorganisms for bioethanol production by effective utilization of pentose sugars of lignocellulosic biomass. Microbiol Res 2023; 276:127478. [PMID: 37625339 DOI: 10.1016/j.micres.2023.127478] [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: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Lignocellulosic biomass, consisting of homo- and heteropolymeric sugars, acts as a substrate for the generation of valuable biochemicals and biomaterials. The readily available hexoses are easily utilized by microbes due to the presence of transporters and native metabolic pathways. But, utilization of pentose sugar viz., xylose and arabinose are still challenging due to several reasons including (i) the absence of the particular native pathways and transporters, (ii) the presence of inhibitors, and (iii) lower uptake of pentose sugars. These challenges can be overcome by manipulating metabolic pathways/glycosidic enzymes cascade by using genetic engineering tools involving inverse-metabolic engineering, ex-vivo isomerization, Adaptive Laboratory Evolution, Directed Metabolic Engineering, etc. Metabolic engineering of bacteria and fungi for the utilization of pentose sugars for bioethanol production is the focus area of research in the current decade. This review outlines current approaches to biofuel development and strategies involved in the metabolic engineering of different microbes that can uptake pentose for bioethanol production.
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Affiliation(s)
- Ayush Saxena
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Akhtar Hussain
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Fouziya Parveen
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Mohammad Ashfaque
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
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8
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Donzella L, Sousa MJ, Morrissey JP. Evolution and functional diversification of yeast sugar transporters. Essays Biochem 2023; 67:811-827. [PMID: 36928992 PMCID: PMC10500205 DOI: 10.1042/ebc20220233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
While simple sugars such as monosaccharides and disaccharide are the typical carbon source for most yeasts, whether a species can grow on a particular sugar is generally a consequence of presence or absence of a suitable transporter to enable its uptake. The most common transporters that mediate sugar import in yeasts belong to the major facilitator superfamily (MFS). Some of these, for example the Saccharomyces cerevisiae Hxt proteins have been extensively studied, but detailed information on many others is sparce. In part, this is because there are many lineages of MFS transporters that are either absent from, or poorly represented in, the model S. cerevisiae, which actually has quite a restricted substrate range. It is important to address this knowledge gap to gain better understanding of the evolution of yeasts and to take advantage of sugar transporters to exploit or engineer yeasts for biotechnological applications. This article examines the full repertoire of MFS proteins in representative budding yeasts (Saccharomycotina). A comprehensive analysis of 139 putative sugar transporters retrieved from 10 complete genomes sheds new light on the diversity and evolution of this family. Using the phylogenetic lens, it is apparent that proteins have often been misassigned putative functions and this can now be corrected. It is also often seen that patterns of expansion of particular genes reflects the differential importance of transport of specific sugars (and related molecules) in different yeasts, and this knowledge also provides an improved resource for the selection or design of tailored transporters.
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Affiliation(s)
- Lorena Donzella
- School of Microbiology, Environmental Research Institute, APC Microbiome Ireland, SUSFERM Research Centre, University College Cork, T12 K8AF, Cork, Ireland
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Maria João Sousa
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - John P Morrissey
- School of Microbiology, Environmental Research Institute, APC Microbiome Ireland, SUSFERM Research Centre, University College Cork, T12 K8AF, Cork, Ireland
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9
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Liu J, Yang J, Yuan L, Wu C, Jiang Y, Zhuang W, Ying H, Yang S. Modulated Arabinose Uptake and cAMP Signaling Synergistically Improve Glucose and Arabinose Consumption in Recombinant Yeast. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12797-12806. [PMID: 37592391 DOI: 10.1021/acs.jafc.3c04386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
During the production of ethanol from lignocellulose-derived sugars, recombinant yeasts tend to utilize xylose and arabinose after glucose exhaustion. So far, many glucose-insensitive pentose transporters have been reported to counteract this phenomenon, but few studies have described intracellular factors. In this study, the combination of adaptive evolution, comparative genomics, and genetic complementation revealed that the hexokinase-deficient (Hxk0) arabinose-fermenting Saccharomyces cerevisiae requires the arabinose transporter variant Gal2-N376T and the mutations of guanine nucleotide exchange factor Cdc25 to overcome glucose restriction during arabinose assimilation. The results showed that the Hxk0 recombinant yeasts could lower the metabolic/physiological threshold of cell proliferation by downregulating the intracellular cAMP levels, resulting in smaller cells and increased arabinose assimilation under glucose restriction. In the medium containing 80 g/L glucose and 20 g/L arabinose, the evolved strain restoring the hexokinase activity completed fermentation at 22 h, compared to 24 h for the parental strain. Overall, the experimental results provide new insights into glucose repression of biorefinery yeasts.
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Affiliation(s)
- Jinle Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Junjie Yang
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lihua Yuan
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chunhua Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Sheng Yang
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
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10
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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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11
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Borgström C, Persson VC, Rogova O, Osiro KO, Lundberg E, Spégel P, Gorwa-Grauslund M. Using phosphoglucose isomerase-deficient (pgi1Δ) Saccharomyces cerevisiae to map the impact of sugar phosphate levels on D-glucose and D-xylose sensing. Microb Cell Fact 2022; 21:253. [PMID: 36456947 PMCID: PMC9713995 DOI: 10.1186/s12934-022-01978-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Despite decades of engineering efforts, recombinant Saccharomyces cerevisiae are still less efficient at converting D-xylose sugar to ethanol compared to the preferred sugar D-glucose. Using GFP-based biosensors reporting for the three main sugar sensing routes, we recently demonstrated that the sensing response to high concentrations of D-xylose is similar to the response seen on low concentrations of D-glucose. The formation of glycolytic intermediates was hypothesized to be a potential cause of this sensing response. In order to investigate this, glycolysis was disrupted via the deletion of the phosphoglucose isomerase gene (PGI1) while intracellular sugar phosphate levels were monitored using a targeted metabolomic approach. Furthermore, the sugar sensing of the PGI1 deletants was compared to the PGI1-wildtype strains in the presence of various types and combinations of sugars. RESULTS Metabolomic analysis revealed systemic changes in intracellular sugar phosphate levels after deletion of PGI1, with the expected accumulation of intermediates upstream of the Pgi1p reaction on D-glucose and downstream intermediates on D-xylose. Moreover, the analysis revealed a preferential formation of D-fructose-6-phosphate from D-xylose, as opposed to the accumulation of D-fructose-1,6-bisphosphate that is normally observed when PGI1 deletants are incubated on D-fructose. This may indicate a role of PFK27 in D-xylose sensing and utilization. Overall, the sensing response was different for the PGI1 deletants, and responses to sugars that enter the glycolysis upstream of Pgi1p (D-glucose and D-galactose) were more affected than the response to those entering downstream of the reaction (D-fructose and D-xylose). Furthermore, the simultaneous exposure to sugars that entered upstream and downstream of Pgi1p (D-glucose with D-fructose, or D-glucose with D-xylose) resulted in apparent synergetic activation and deactivation of the Snf3p/Rgt2p and cAMP/PKA pathways, respectively. CONCLUSIONS Overall, the sensing assays indicated that the previously observed D-xylose response stems from the formation of downstream metabolic intermediates. Furthermore, our results indicate that the metabolic node around Pgi1p and the level of D-fructose-6-phosphate could represent attractive engineering targets for improved D-xylose utilization.
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Affiliation(s)
- Celina Borgström
- grid.4514.40000 0001 0930 2361Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden ,grid.17063.330000 0001 2157 2938Present Address: BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Viktor C. Persson
- grid.4514.40000 0001 0930 2361Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Oksana Rogova
- grid.4514.40000 0001 0930 2361Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Lund, Sweden
| | - Karen O. Osiro
- grid.4514.40000 0001 0930 2361Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden ,Present Address: Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasília, DF 70770-901 Brazil
| | - Ester Lundberg
- grid.4514.40000 0001 0930 2361Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Peter Spégel
- grid.4514.40000 0001 0930 2361Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Lund, Sweden
| | - Marie Gorwa-Grauslund
- grid.4514.40000 0001 0930 2361Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
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Fiamenghi MB, Bueno JGR, Camargo AP, Borelli G, Carazzolle MF, Pereira GAG, dos Santos LV, José J. Machine learning and comparative genomics approaches for the discovery of xylose transporters in yeast. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:57. [PMID: 35596177 PMCID: PMC9123741 DOI: 10.1186/s13068-022-02153-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/05/2022] [Indexed: 11/15/2022]
Abstract
Background The need to mitigate and substitute the use of fossil fuels as the main energy matrix has led to the study and development of biofuels as an alternative. Second-generation (2G) ethanol arises as one biofuel with great potential, due to not only maintaining food security, but also as a product from economically interesting crops such as energy-cane. One of the main challenges of 2G ethanol is the inefficient uptake of pentose sugars by industrial yeast Saccharomyces cerevisiae, the main organism used for ethanol production. Understanding the main drivers for xylose assimilation and identify novel and efficient transporters is a key step to make the 2G process economically viable. Results By implementing a strategy of searching for present motifs that may be responsible for xylose transport and past adaptations of sugar transporters in xylose fermenting species, we obtained a classifying model which was successfully used to select four different candidate transporters for evaluation in the S. cerevisiae hxt-null strain, EBY.VW4000, harbouring the xylose consumption pathway. Yeast cells expressing the transporters SpX, SpH and SpG showed a superior uptake performance in xylose compared to traditional literature control Gxf1. Conclusions Modelling xylose transport with the small data available for yeast and bacteria proved a challenge that was overcome through different statistical strategies. Through this strategy, we present four novel xylose transporters which expands the repertoire of candidates targeting yeast genetic engineering for industrial fermentation. The repeated use of the model for characterizing new transporters will be useful both into finding the best candidates for industrial utilization and to increase the model’s predictive capabilities. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02153-7.
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Rojas SAT, Boles E, Oreb M. A yeast-based in vivo assay system for analyzing efflux of sugars mediated by glucose and xylose transporters. FEMS Yeast Res 2022; 21:6653521. [PMID: 35918180 DOI: 10.1093/femsyr/foac038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/14/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Sugar transporter research focuses on the sugar uptake into cells. Under certain physiological conditions, however, the intracellular accumulation and secretion of carbohydrates (efflux) are relevant processes in many cell types. Currently, no cell-based system is available for specifically investigating glucose efflux. Therefore, we designed a system based on a hexose transporter-deficient Saccharomyces cerevisiae strain, in which the disaccharide maltose is provided as a donor of intracellular glucose. By deleting the hexokinase genes, we prevented the metabolization of glucose and thereby achieved the accumulation of growth-inhibitory glucose levels inside the cells. When a permease mediating glucose efflux is expressed in this system, the inhibitory effect is relieved proportionally to the capacity of the introduced transporter. The assay is thereby suitable for screening of transporters and quantitative analyses of their glucose efflux capacities. Moreover, by simultaneous provision of intracellular glucose and extracellular xylose, we investigated how each sugar influences the transport of the other one from the opposite side of the membrane. Thereby, we could show that the xylose transporter variant Gal2N376F is insensitive not only to extracellular but also to intracellular glucose. Considering the importance of sugar transporters in biotechnology, the assay could facilitate new developments in a variety of applications.
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Affiliation(s)
- Sebastian A Tamayo Rojas
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mislav Oreb
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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Sugarcane Bagasse-Based Ethanol Production and Utilization of Its Vinasse for Xylitol Production as an Approach in Integrated Biorefinery. FERMENTATION 2022. [DOI: 10.3390/fermentation8070340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Biorefinery of sugarcane bagasse into ethanol and xylitol was investigated in this study. Ethanol fermentation of sugarcane bagasse hydrolysate was carried out by Saccharomyces cerevisiae. After ethanol distillation, the vinasse containing xylose was used to produce xylitol through fermentation by Candida guilliermondii TISTR 5068. During the ethanol fermentation, it was not necessary to supplement a nitrogen source to the hydrolysate. Approximately 50 g/L of bioethanol was produced after 36 h of fermentation. The vinasse was successfully used to produce xylitol. Supplementing the vinasse with 1 g/L of yeast extract improved xylitol production 1.4-fold. Cultivating the yeast with 10% controlled dissolved oxygen resulted in the best xylitol production and yields of 10.2 ± 1.12 g/L and 0.74 ± 0.04 g/g after 60 h fermentation. Supplementing the vinasse with low fraction of molasses to improve xylitol production did not yield a positive result. The supplementation caused decreases of up to 34% in xylitol production rate, 24% in concentration, and 24% in yield.
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Fermentation performance of a Mexican native Clavispora lusitaniae strain for xylitol and ethanol production from xylose, glucose and cellobiose. Enzyme Microb Technol 2022; 160:110094. [PMID: 35810624 DOI: 10.1016/j.enzmictec.2022.110094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 11/21/2022]
Abstract
Lignocellulose hydrolysates are rich in fermentable sugars such as xylose, cellobiose and glucose, with high potential in the biotechnology industry to obtain bioproducts of higher economic value. Thus, it is important to search for and study new yeast strains that co-consume these sugars to achieve better yields and productivity in the processes. The yeast Clavispora lusitaniae CDBB-L-2031, a native strain isolated from mezcal must, was studied under various culture conditions to potentially produce ethanol and xylitol due to its ability to assimilate xylose, cellobiose and glucose. This yeast produced ethanol under microaerobic conditions with yields of 0.451 gethanol/gglucose and 0.344 gethanol/gcellobiose, when grown on 1% glucose or cellobiose, respectively. In mixtures (0.5% each) of glucose:xylose and glucose:xylose:cellobiose the yields were 0.367 gethanol/gGX and 0. 380 gethanol/gGXC, respectively. Likewise, in identical conditions, C. lusitaniae produced xylitol from xylose with a yield of 0.421 gxylitol/gxylose. In 5% glucose or xylose, this yeast had better ethanol and xylitol titers and yields, respectively. However, glucose negatively affected xylitol production in the mixture of both sugars (3% each), producing only ethanol. Xylose reductase (XR) and xylitol dehydrogenase (XDH) activities were evaluated in cultures growing on xylose or glucose, obtaining the highest values in cultures on xylose at 8 h (25.9 and 6.22 mU/mg, respectively). While in glucose cultures, XR and XDH activities were detected once this substrate was consumed (4.06 and 3.32 mU/mg, respectively). Finally, the XYL1 and XYL2 genes encoding xylose reductase and xylitol dehydrogenase, respectively, were up-regulated by xylose, whereas glucose down-regulated their expression.
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16
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de Mello FDSB, Maneira C, Suarez FUL, Nagamatsu S, Vargas B, Vieira C, Secches T, Coradini ALV, Silvello MADC, Goldbeck R, Pereira GAG, Teixeira GS. Rational engineering of industrial S. cerevisiae: towards xylitol production from sugarcane straw. J Genet Eng Biotechnol 2022; 20:80. [PMID: 35612634 PMCID: PMC9133290 DOI: 10.1186/s43141-022-00359-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/02/2022] [Indexed: 12/15/2022]
Abstract
Background Sugarcane hemicellulosic material is a compelling source of usually neglected xylose that could figure as feedstock to produce chemical building blocks of high economic value, such as xylitol. In this context, Saccharomyces cerevisiae strains typically used in the Brazilian bioethanol industry are a robust chassis for genetic engineering, given their robustness towards harsh operational conditions and outstanding fermentation performance. Nevertheless, there are no reports on the use of these strains for xylitol production using sugarcane hydrolysate. Results Potential single-guided RNA off-targets were analyzed in two preeminent industrial strains (PE-2 and SA-1), providing a database of 5′-NGG 20 nucleotide sequences and guidelines for the fast and cost-effective CRISPR editing of such strains. After genomic integration of a NADPH-preferring xylose reductase (XR), FMYX (SA-1 hoΔ::xyl1) and CENPKX (CEN.PK-122 hoΔ::xyl1) were tested in varying cultivation conditions for xylitol productivity to infer influence of the genetic background. Near-theoretical yields were achieved for all strains; however, the industrial consistently outperformed the laboratory strain. Batch fermentation of raw sugarcane straw hydrolysate with remaining solid particles represented a challenge for xylose metabolization, and 3.65 ± 0.16 g/L xylitol titer was achieved by FMYX. Finally, quantification of NADPH — cofactor implied in XR activity — revealed that FMYX has 33% more available cofactors than CENPKX. Conclusions Although widely used in several S. cerevisiae strains, this is the first report of CRISPR-Cas9 editing major yeast of the Brazilian bioethanol industry. Fermentative assays of xylose consumption revealed that NADPH availability is closely related to mutant strains’ performance. We also pioneer the use of sugarcane straw as a substrate for xylitol production. Finally, we demonstrate how industrial background SA-1 is a compelling chassis for the second-generation industry, given its inhibitor tolerance and better redox environment that may favor production of reduced sugars. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00359-8.
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Affiliation(s)
| | - Carla Maneira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Frank Uriel Lizarazo Suarez
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil.,School of Basic Sciences, University of Pamplona, Pamplona, Colombia
| | - Sheila Nagamatsu
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Beatriz Vargas
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Carla Vieira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Thais Secches
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Alessando L V Coradini
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Rosana Goldbeck
- School of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil.
| | - Gleidson Silva Teixeira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil.,School of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
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Choi HJ, Jin YS, Lee WH. Effects of Engineered Saccharomyces cerevisiae Fermenting Cellobiose through Low-Energy-Consuming Phosphorolytic Pathway in Simultaneous Saccharification and Fermentation. J Microbiol Biotechnol 2022; 32:117-125. [PMID: 34949751 PMCID: PMC9628822 DOI: 10.4014/jmb.2111.11047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/07/2021] [Indexed: 12/15/2022]
Abstract
Until recently, four types of cellobiose-fermenting Saccharomyces cerevisiae strains have been developed by introduction of a cellobiose metabolic pathway based on either intracellular β-glucosidase (GH1-1) or cellobiose phosphorylase (CBP), along with either an energy-consuming active cellodextrin transporter (CDT-1) or a non-energy-consuming passive cellodextrin facilitator (CDT-2). In this study, the ethanol production performance of two cellobiose-fermenting S. cerevisiae strains expressing mutant CDT-2 (N306I) with GH1-1 or CBP were compared with two cellobiose-fermenting S. cerevisiae strains expressing mutant CDT-1 (F213L) with GH1-1 or CBP in the simultaneous saccharification and fermentation (SSF) of cellulose under various conditions. It was found that, regardless of the SSF conditions, the phosphorolytic cellobiose-fermenting S. cerevisiae expressing mutant CDT-2 with CBP showed the best ethanol production among the four strains. In addition, during SSF contaminated by lactic acid bacteria, the phosphorolytic cellobiose-fermenting S. cerevisiae expressing mutant CDT-2 with CBP showed the highest ethanol production and the lowest lactate formation compared with those of other strains, such as the hydrolytic cellobiose-fermenting S. cerevisiae expressing mutant CDT-1 with GH1-1, and the glucose-fermenting S. cerevisiae with extracellular β-glucosidase. These results suggest that the cellobiose-fermenting yeast strain exhibiting low energy consumption can enhance the efficiency of the SSF of cellulosic biomass.
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Affiliation(s)
- Hyo-Jin Choi
- Department of Bioenergy Science and Technology, and Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Corresponding authors Y.S. Jin Phone: +217-333-7981 Fax: +217-333-0508 E-mail:
| | - Won-Heong Lee
- Department of Bioenergy Science and Technology, and Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea,Department of Food Science and Human Nutrition, and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,
W.H. Lee Phone: +82-62-530-2046 Fax: +82-62-530-2047 E-mail:
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18
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Insights into cell robustness against lignocellulosic inhibitors and insoluble solids in bioethanol production processes. Sci Rep 2022; 12:557. [PMID: 35017613 PMCID: PMC8752620 DOI: 10.1038/s41598-021-04554-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/24/2021] [Indexed: 11/28/2022] Open
Abstract
Increasing yeast robustness against lignocellulosic-derived inhibitors and insoluble solids in bioethanol production is essential for the transition to a bio-based economy. This work evaluates the effect exerted by insoluble solids on yeast tolerance to inhibitory compounds, which is crucial in high gravity processes. Adaptive laboratory evolution (ALE) was applied on a xylose-fermenting Saccharomyces cerevisiae strain to simultaneously increase the tolerance to lignocellulosic inhibitors and insoluble solids. The evolved strain gave rise to a fivefold increase in bioethanol yield in fermentation experiments with high concentration of inhibitors and 10% (w/v) of water insoluble solids. This strain also produced 5% (P > 0.01) more ethanol than the parental in simultaneous saccharification and fermentation of steam-exploded wheat straw, mainly due to an increased xylose consumption. In response to the stress conditions (solids and inhibitors) imposed in ALE, cells induced the expression of genes related to cell wall integrity (SRL1, CWP2, WSC2 and WSC4) and general stress response (e.g., CDC5, DUN1, CTT1, GRE1), simultaneously repressing genes related to protein synthesis and iron transport and homeostasis (e.g., FTR1, ARN1, FRE1), ultimately leading to the improved phenotype. These results contribute towards understanding molecular mechanisms that cells might use to convert lignocellulosic substrates effectively.
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Identification of a glucose-insensitive variant of Gal2 from Saccharomyces cerevisiae exhibiting a high pentose transport capacity. Sci Rep 2021; 11:24404. [PMID: 34937866 PMCID: PMC8695581 DOI: 10.1038/s41598-021-03822-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/06/2021] [Indexed: 12/04/2022] Open
Abstract
As abundant carbohydrates in renewable feedstocks, such as pectin-rich and lignocellulosic hydrolysates, the pentoses arabinose and xylose are regarded as important substrates for production of biofuels and chemicals by engineered microbial hosts. Their efficient transport across the cellular membrane is a prerequisite for economically viable fermentation processes. Thus, there is a need for transporter variants exhibiting a high transport rate of pentoses, especially in the presence of glucose, another major constituent of biomass-based feedstocks. Here, we describe a variant of the galactose permease Gal2 from Saccharomyces cerevisiae (Gal2N376Y/M435I), which is fully insensitive to competitive inhibition by glucose, but, at the same time, exhibits an improved transport capacity for xylose compared to the wildtype protein. Due to this unique property, it significantly reduces the fermentation time of a diploid industrial yeast strain engineered for efficient xylose consumption in mixed glucose/xylose media. When the N376Y/M435I mutations are introduced into a Gal2 variant resistant to glucose-induced degradation, the time necessary for the complete consumption of xylose is reduced by approximately 40%. Moreover, Gal2N376Y/M435I confers improved growth of engineered yeast on arabinose. Therefore, it is a valuable addition to the toolbox necessary for valorization of complex carbohydrate mixtures.
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20
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Novel Propagation Strategy of Saccharomyces cerevisiae for Enhanced Xylose Metabolism during Fermentation on Softwood Hydrolysate. FERMENTATION 2021. [DOI: 10.3390/fermentation7040288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An economically viable production of second-generation bioethanol by recombinant xylose-fermenting Saccharomyces cerevisiae requires higher xylose fermentation rates and improved glucose–xylose co-consumption. Moreover, xylose-fermenting S. cerevisiae recognises xylose as a non-fermentable rather than a fermentable carbon source, which might partly explain why xylose is not fermented into ethanol as efficiently as glucose. This study proposes propagating S. cerevisiae on non-fermentable carbon sources to enhance xylose metabolism during fermentation. When compared to yeast grown on sucrose, cells propagated on a mix of ethanol and glycerol in shake flasks showed up to 50% higher xylose utilisation rate (in a defined xylose medium) and a double maximum fermentation rate, together with an improved C5/C6 co-consumption (on an industrial softwood hydrolysate). Based on these results, an automated propagation protocol was developed, using a fed-batch approach and the respiratory quotient to guide the ethanol and glycerol-containing feed. This successfully produced 71.29 ± 0.91 g/L yeast with an average productivity of 1.03 ± 0.05 g/L/h. These empirical findings provide the basis for the design of a simple, yet effective yeast production strategy to be used in the second-generation bioethanol industry for increased fermentation efficiency.
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21
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Li J, Chen B, Gu S, Zhao Z, Liu Q, Sun T, Zhang Y, Wu T, Liu D, Sun W, Tian C. Coordination of consolidated bioprocessing technology and carbon dioxide fixation to produce malic acid directly from plant biomass in Myceliophthora thermophila. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:186. [PMID: 34556173 PMCID: PMC8461902 DOI: 10.1186/s13068-021-02042-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Consolidated bioprocessing (CBP) technique is a promising strategy for biorefinery construction, producing bulk chemicals directly from plant biomass without extra hydrolysis steps. Fixing and channeling CO2 into carbon metabolism for increased carbon efficiency in producing value-added compounds is another strategy for cost-effective bio-manufacturing. It has not been reported whether these two strategies can be combined in one microbial platform. RESULTS In this study, using the cellulolytic thermophilic fungus Myceliophthora thermophila, we designed and constructed a novel biorefinery system DMCC (Direct microbial conversion of biomass with CO2 fixation) through incorporating two CO2 fixation modules, PYC module and Calvin-Benson-Bassham (CBB) pathway. Harboring the both modules, the average rate of fixing and channeling 13CO2 into malic acid in strain CP51 achieved 44.4, 90.7, and 80.7 mg/L/h, on xylose, glucose, and cellulose, respectively. The corresponding titers of malic acid were up to 42.1, 70.4, and 70.1 g/L, respectively, representing the increases of 40%, 10%, and 7%, respectively, compared to the parental strain possessing only PYC module. The DMCC system was further improved by enhancing the pentose uptake ability. Using raw plant biomass as the feedstock, yield of malic acid produced by the DMCC system was up to 0.53 g/g, with 13C content of 0.44 mol/mol malic acid, suggesting DMCC system can produce 1 t of malic acid from 1.89 t of biomass and fix 0.14 t CO2 accordingly. CONCLUSIONS This study designed and constructed a novel biorefinery system named DMCC, which can convert raw plant biomass and CO2 into organic acid efficiently, presenting a promising strategy for cost-effective production of value-added compounds in biorefinery. The DMCC system is one of great options for realization of carbon neutral economy.
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Affiliation(s)
- Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Bingchen Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shuying Gu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhen Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Tao Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Yongli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Taju Wu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Defei Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
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22
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Kuanyshev N, Deewan A, Jagtap SS, Liu J, Selvam B, Chen LQ, Shukla D, Rao CV, Jin YS. Identification and analysis of sugar transporters capable of co-transporting glucose and xylose simultaneously. Biotechnol J 2021; 16:e2100238. [PMID: 34418308 DOI: 10.1002/biot.202100238] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/04/2021] [Accepted: 08/18/2021] [Indexed: 11/09/2022]
Abstract
Simultaneous co-fermentation of glucose and xylose is a key desired trait of engineered Saccharomyces cerevisiae for efficient and rapid production of biofuels and chemicals. However, glucose strongly inhibits xylose transport by endogenous hexose transporters of S. cerevisiae. We identified structurally distant sugar transporters (Lipomyces starkeyi LST1_205437 and Arabidopsis thaliana AtSWEET7) capable of co-transporting glucose and xylose from previously unexplored oleaginous yeasts and plants. Kinetic analysis showed that LST1_205437 had lenient glucose inhibition on xylose transport and AtSWEET7 transported glucose and xylose simultaneously with no inhibition. Modelling studies of LST1_205437 revealed that Ala335 residue at sugar binding site can accommodates both glucose and xylose. Docking studies with AtSWEET7 revealed that Trp59, Trp183, Asn145, and Asn179 residues stabilized the interactions with sugars, allowing both xylose and glucose to be co-transported. In addition, we altered sugar preference of LST1_205437 by single amino acid mutation at Asn365. Our findings provide a new mechanistic insight on glucose and xylose transport mechanism of sugar transporters and the identified sugar transporters can be employed to develop engineered yeast strains for producing cellulosic biofuels and chemicals.
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Affiliation(s)
- Nurzhan Kuanyshev
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Anshu Deewan
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sujit Sadashiv Jagtap
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jingjing Liu
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Balaji Selvam
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Li-Qing Chen
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher V Rao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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23
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Lee WH, Jin YS. Observation of Cellodextrin Accumulation Resulted from Non-Conventional Secretion of Intracellular β-Glucosidase by Engineered Saccharomyces cerevisiae Fermenting Cellobiose. J Microbiol Biotechnol 2021; 31:1035-1043. [PMID: 34226403 PMCID: PMC9705985 DOI: 10.4014/jmb.2105.05018] [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: 05/14/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022]
Abstract
Although engineered Saccharomyces cerevisiae fermenting cellobiose is useful for the production of biofuels from cellulosic biomass, cellodextrin accumulation is one of the main problems reducing ethanol yield and productivity in cellobiose fermentation with S. cerevisiae expressing cellodextrin transporter (CDT) and intracellular β-glucosidase (GH1-1). In this study, we investigated the reason for the cellodextrin accumulation and how to alleviate its formation during cellobiose fermentation using engineered S. cerevisiae fermenting cellobiose. From the series of cellobiose fermentation using S. cerevisiae expressing only GH1-1 under several culture conditions, it was discovered that small amounts of GH1-1 were secreted and cellodextrin was generated through trans-glycosylation activity of the secreted GH1-1. As GH1-1 does not have a secretion signal peptide, non-conventional protein secretion might facilitate the secretion of GH1-1. In cellobiose fermentations with S. cerevisiae expressing only GH1-1, knockout of TLG2 gene involved in non-conventional protein secretion pathway significantly delayed cellodextrin formation by reducing the secretion of GH1-1 by more than 50%. However, in cellobiose fermentations with S. cerevisiae expressing both GH1-1 and CDT-1, TLG2 knockout did not show a significant effect on cellodextrin formation, although secretion of GH1-1 was reduced by more than 40%. These results suggest that the development of new intracellular β-glucosidase, not influenced by non-conventional protein secretion, is required for better cellobiose fermentation performances of engineered S. cerevisiae fermenting cellobiose.
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Affiliation(s)
- Won-Heong Lee
- Department of Food Science and Human Nutrition, and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Department of Bioenergy Science and Technology, and Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea,Corresponding author Phone: +82-62-530-2046 Fax: +82-62-530-2047 E-mail:
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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24
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Wang H, Sun T, Zhao Z, Gu S, Liu Q, Wu T, Wang D, Tian C, Li J. Transcriptional Profiling of Myceliophthora thermophila on Galactose and Metabolic Engineering for Improved Galactose Utilization. Front Microbiol 2021; 12:664011. [PMID: 33995328 PMCID: PMC8113861 DOI: 10.3389/fmicb.2021.664011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Abstract
Efficient biological conversion of all sugars from lignocellulosic biomass is necessary for the cost-effective production of biofuels and commodity chemicals. Galactose is one of the most abundant sugar in many hemicelluloses, and it will be important to capture this carbon for an efficient bioconversion process of plant biomass. Thermophilic fungus Myceliophthora thermophila has been used as a cell factory to produce biochemicals directly from renewable polysaccharides. In this study, we draw out the two native galactose utilization pathways, including the Leloir pathway and oxido-reductive pathway, and identify the significance and contribution of them, through transcriptional profiling analysis of M. thermophila and its mutants on galactose. We find that galactokinase was necessary for galactose transporter expression, and disruption of galK resulted in decreased galactose utilization. Through metabolic engineering, both galactokinase deletion and galactose transporter overexpression can activate internal the oxido-reductive pathway and improve the consumption rate of galactose. Finally, the heterologous galactose-degradation pathway, De Ley–Doudoroff (DLD) pathway, was successfully integrated into M. thermophila, and the consumption rate of galactose in the engineered strain was increased by 57%. Our study focuses on metabolic engineering for accelerating galactose utilization in a thermophilic fungus that will be beneficial for the rational design of fungal strains to produce biofuels and biochemicals from a variety of feedstocks with abundant galactose.
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Affiliation(s)
- Hanyu Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tao Sun
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhen Zhao
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Shuying Gu
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qian Liu
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Taju Wu
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Depei Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Chaoguang Tian
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jingen Li
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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25
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Baptista SL, Costa CE, Cunha JT, Soares PO, Domingues L. Metabolic engineering of Saccharomyces cerevisiae for the production of top value chemicals from biorefinery carbohydrates. Biotechnol Adv 2021; 47:107697. [PMID: 33508428 DOI: 10.1016/j.biotechadv.2021.107697] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/16/2022]
Abstract
The implementation of biorefineries for a cost-effective and sustainable production of energy and chemicals from renewable carbon sources plays a fundamental role in the transition to a circular economy. The US Department of Energy identified a group of key target compounds that can be produced from biorefinery carbohydrates. In 2010, this list was revised and included organic acids (lactic, succinic, levulinic and 3-hydroxypropionic acids), sugar alcohols (xylitol and sorbitol), furans and derivatives (hydroxymethylfurfural, furfural and furandicarboxylic acid), biohydrocarbons (isoprene), and glycerol and its derivatives. The use of substrates like lignocellulosic biomass that impose harsh culture conditions drives the quest for the selection of suitable robust microorganisms. The yeast Saccharomyces cerevisiae, widely utilized in industrial processes, has been extensively engineered to produce high-value chemicals. For its robustness, ease of handling, genetic toolbox and fitness in an industrial context, S. cerevisiae is an ideal platform for the founding of sustainable bioprocesses. Taking these into account, this review focuses on metabolic engineering strategies that have been applied to S. cerevisiae for converting renewable resources into the previously identified chemical targets. The heterogeneity of each chemical and its manufacturing process leads to inevitable differences between the development stages of each process. Currently, 8 of 11 of these top value chemicals have been already reported to be produced by recombinant S. cerevisiae. While some of them are still in an early proof-of-concept stage, others, like xylitol or lactic acid, are already being produced from lignocellulosic biomass. Furthermore, the constant advances in genome-editing tools, e.g. CRISPR/Cas9, coupled with the application of innovative process concepts such as consolidated bioprocessing, will contribute for the establishment of S. cerevisiae-based biorefineries.
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Affiliation(s)
- Sara L Baptista
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Carlos E Costa
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Pedro O Soares
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal.
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26
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Datamining and functional environmental genomics reassess the phylogenetics and functional diversity of fungal monosaccharide transporters. Appl Microbiol Biotechnol 2021; 105:647-660. [PMID: 33394157 DOI: 10.1007/s00253-020-11076-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/14/2020] [Accepted: 12/23/2020] [Indexed: 10/22/2022]
Abstract
Sugar transporters are essential components of carbon metabolism and have been extensively studied to control sugar uptake by yeasts and filamentous fungi used in fermentation processes. Based on published information on characterized fungal sugar porters, we show that this protein family encompasses phylogenetically distinct clades. While several clades encompass transporters that seemingly specialized on specific "sugar-related" molecules (e.g., myo-inositol, charged sugar analogs), others include mostly either mono- or di/oligosaccharide low-specificity transporters. To address the issue of substrate specificity of sugar transporters, that protein primary sequences do not fully reveal, we screened "multi-species" soil eukaryotic cDNA libraries for mannose transporters, a sugar that had never been used to select transporters. We obtained 19 environmental transporters, mostly from Basidiomycota and Ascomycota. Among them, one belonged to the unusual "Fucose H+ Symporter" family, which is only known in Fungi for a rhamnose transporter in Aspergillus niger. Functional analysis of the 19 transporters by expression in yeast and for two of them in Xenopus laevis oocytes for electrophysiological measurements indicated that most of them showed a preference for D-mannose over other tested D-C6 (glucose, fructose, galactose) or D-C5 (xylose) sugars. For the several glucose and fructose-negative transporters, growth of the corresponding recombinant yeast strains was prevented on mannose in the presence of one of these sugars that may act by competition for the binding site. Our results highlight the potential of environmental genomics to figure out the functional diversity of key fungal protein families and that can be explored in a context of biotechnology. KEY POINTS: • Most fungal sugar transporters accept several sugars as substrates. • Transporters, belonging to 2 protein families, were isolated from soil cDNA libraries. • Environmental transporters featured novel substrate specificities.
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27
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Schmidl S, Iancu CV, Reifenrath M, Choe JY, Oreb M. A label-free real-time method for measuring glucose uptake kinetics in yeast. FEMS Yeast Res 2020; 21:6041724. [PMID: 33338229 DOI: 10.1093/femsyr/foaa069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/16/2020] [Indexed: 01/19/2023] Open
Abstract
Glucose uptake assays commonly rely on the isotope-labeled sugar, which is associated with radioactive waste and exposure of the experimenter to radiation. Here, we show that the rapid decrease of the cytosolic pH after a glucose pulse to starved Saccharomyces cerevisiae cells is dependent on the rate of sugar uptake and can be used to determine the kinetic parameters of sugar transporters. The pH-sensitive green fluorescent protein variant pHluorin is employed as a genetically encoded biosensor to measure the rate of acidification as a proxy of transport velocity in real time. The measurements are performed in the hexose transporter-deficient (hxt0) strain EBY.VW4000 that has been previously used to characterize a plethora of sugar transporters from various organisms. Therefore, this method provides an isotope-free, fluorometric approach for kinetic characterization of hexose transporters in a well-established yeast expression system.
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Affiliation(s)
- Sina Schmidl
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Cristina V Iancu
- Department of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC27834, USA
| | - Mara Reifenrath
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Jun-Yong Choe
- Department of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC27834, USA
| | - Mislav Oreb
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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28
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van der Hoek SA, Borodina I. Transporter engineering in microbial cell factories: the ins, the outs, and the in-betweens. Curr Opin Biotechnol 2020; 66:186-194. [PMID: 32927362 PMCID: PMC7758712 DOI: 10.1016/j.copbio.2020.08.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022]
Abstract
Engineering the transport of small molecules is an effective approach to improve the performance of microbial cell factories. Transporter engineering can improve the utilization of low-cost alternative substrates, reduce the loss of pathway intermediates, and increase the titer and production rate of the target product. However, transporters are not commonly engineered in strain development programs because the functions of most of the transport proteins are not known. In the recent years, a variety of methods have been developed for identification of transporters for specific substrates and for characterizing transport mechanisms. This review presents recent examples of successful transport engineering for cell factories and discusses the methods for transporter identification and characterization.
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Affiliation(s)
- Steven A van der Hoek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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29
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Nijland JG, Shin HY, Dore E, Rudinatha D, de Waal PP, Driessen AJM. D-glucose overflow metabolism in an evolutionary engineered high-performance D-xylose consuming Saccharomyces cerevisiae strain. FEMS Yeast Res 2020; 21:6000216. [PMID: 33232441 PMCID: PMC7811511 DOI: 10.1093/femsyr/foaa062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/20/2020] [Indexed: 11/26/2022] Open
Abstract
Co-consumption of D-xylose and D-glucose by Saccharomyces cerevisiae is essential for cost-efficient cellulosic bioethanol production. There is a need for improved sugar conversion rates to minimize fermentation times. Previously, we have employed evolutionary engineering to enhance D-xylose transport and metabolism in the presence of D-glucose in a xylose-fermenting S. cerevisiae strain devoid of hexokinases. Re-introduction of Hxk2 in the high performance xylose-consuming strains restored D-glucose utilization during D-xylose/D-glucose co-metabolism, but at rates lower than the non-evolved strain. In the absence of D-xylose, D-glucose consumption was similar to the parental strain. The evolved strains accumulated trehalose-6-phosphate during sugar co-metabolism, and showed an increased expression of trehalose pathway genes. Upon the deletion of TSL1, trehalose-6-phosphate levels were decreased and D-glucose consumption and growth on mixed sugars was improved. The data suggest that D-glucose/D-xylose co-consumption in high-performance D-xylose consuming strains causes the glycolytic flux to saturate. Excess D-glucose is phosphorylated enters the trehalose pathway resulting in glucose recycling and energy dissipation, accumulation of trehalose-6-phosphate which inhibits the hexokinase activity, and release of trehalose into the medium.
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Affiliation(s)
- Jeroen G Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
| | - Hyun Yong Shin
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
| | - Eleonora Dore
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
| | - Donny Rudinatha
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
| | - Paul P de Waal
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
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30
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Díaz-Fernández D, Muñoz-Fernández G, Martín VI, Revuelta JL, Jiménez A. Sugar transport for enhanced xylose utilization in Ashbya gossypii. J Ind Microbiol Biotechnol 2020; 47:1173-1179. [PMID: 33037458 PMCID: PMC7728639 DOI: 10.1007/s10295-020-02320-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/03/2020] [Indexed: 10/26/2022]
Abstract
The co-utilization of mixed (pentose/hexose) sugars constitutes a challenge for microbial fermentations. The fungus Ashbya gossypii, which is currently exploited for the industrial production of riboflavin, has been presented as an efficient biocatalyst for the production of biolipids using xylose-rich substrates. However, the utilization of xylose in A. gossypii is hindered by hexose sugars. Three A. gossypii homologs (AFL204C, AFL205C and AFL207C) of the yeast HXT genes that code for hexose transporters have been identified and characterized by gene-targeting approaches. Significant differences in the expression profile of the HXT homologs were found in response to different concentrations of sugars. More importantly, an amino acid replacement (N355V) in AFL205Cp, introduced by CRISPR/Cas9-mediated genomic edition, notably enhanced the utilization of xylose in the presence of glucose. Hence, the introduction of the afl205c-N355V allele in engineered strains of A. gossypii will further benefit the utilization of mixed sugars in this fungus.
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Affiliation(s)
- David Díaz-Fernández
- Metabolic Engineering Group, Departamento de Microbiología Y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Gloria Muñoz-Fernández
- Metabolic Engineering Group, Departamento de Microbiología Y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Victoria Isabel Martín
- Metabolic Engineering Group, Departamento de Microbiología Y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Departamento de Microbiología Y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | - Alberto Jiménez
- Metabolic Engineering Group, Departamento de Microbiología Y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
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31
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Yukawa T, Bamba T, Guirimand G, Matsuda M, Hasunuma T, Kondo A. Optimization of 1,2,4-butanetriol production from xylose in Saccharomyces cerevisiae by metabolic engineering of NADH/NADPH balance. Biotechnol Bioeng 2020; 118:175-185. [PMID: 32902873 DOI: 10.1002/bit.27560] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/09/2020] [Accepted: 08/27/2020] [Indexed: 01/02/2023]
Abstract
1,2,4-Butanetriol (BT) is used as a precursor for the synthesis of various pharmaceuticals and the energetic plasticizer 1,2,4-butanetriol trinitrate. In Saccharomyces cerevisiae, BT is biosynthesized from xylose via heterologous four enzymatic reactions catalyzed by xylose dehydrogenase, xylonate dehydratase, 2-ketoacid decarboxylase, and alcohol dehydrogenase. We here aimed to improve the BT yield in S. cerevisiae by genetic engineering. First, the amount of the key intermediate 2-keto-3-deoxy-xylonate as described previously was successfully reduced in 41% by multiple integrations of Lactococcus lactis 2-ketoacid decarboxylase gene kdcA into the yeast genome. Since the heterologous BT synthetic pathway is independent of yeast native metabolism, this manipulation has led to NADH/NADPH imbalance and deficiency during BT production. Overexpression of the NADH kinase POS5Δ17 lacking the mitochondrial targeting sequence to relieve NADH/NADPH imbalance resulted in the BT titer of 2.2 g/L (31% molar yield). Feeding low concentrations of glucose and xylose to support the supply of NADH resulted in BT titer of 6.6 g/L with (57% molar yield). Collectively, improving the NADH/NADPH ratio and supply from glucose are essential for the construction of a xylose pathway, such as the BT synthetic pathway, independent of native yeast metabolism.
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Affiliation(s)
- Takahiro Yukawa
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Takahiro Bamba
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Gregory Guirimand
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Biomolécules et Biotechnologies Végétales, EA 2106, Département of Agronomie, productions animale et végétale et agro-alimentaire, Université de Tours, Tours, France.,LE STUDIUM, Loire Valley Institute for Advanced Studies, Orléans, France
| | - Mami Matsuda
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Engineering Biology Research Center, Kobe University, Kobe, Japan.,Biomass Engineering Program, RIKEN, Yokohama, Kanagawa, Japan
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32
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Naseri G, Mueller-Roeber B. A Step-by-Step Protocol for COMPASS, a Synthetic Biology Tool for Combinatorial Gene Assembly. Methods Mol Biol 2020; 2205:277-303. [PMID: 32809205 DOI: 10.1007/978-1-0716-0908-8_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
For industry-scale production of high-value chemicals in microbial cell factories, the elimination of metabolic flux imbalances is a critical aspect. However, a priori knowledge about the genetic design of optimal production pathways is typically not available. COMPASS, COMbinatorial Pathway ASSembly, is a rapid cloning method for the balanced expression of multiple genes in biochemical pathways. The method generates thousands of individual DNA constructs in modular, parallel, and high-throughput manner. COMPASS employs inducible artificial transcription factors derived from plant (Arabidopsis thaliana) regulators to control the expression of pathway genes in yeast (Saccharomyces cerevisiae). It utilizes homologous recombination for parts assembly and employs a positive selection scheme to identify correctly assembled pathway variants after both in vivo and in vitro recombination. Finally, COMPASS is equipped with a CRISPR/Cas9 genome modification system allowing for the one-step multilocus integration of genes. Although COMPASS was initially developed for pathway engineering, it can equally be employed for balancing gene expression in other synthetic biology projects.
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Affiliation(s)
- Gita Naseri
- Department of Molecular Biology, University of Potsdam, Potsdam, Germany
| | - Bernd Mueller-Roeber
- Department of Molecular Biology, University of Potsdam, Potsdam, Germany. .,Plant Signalling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany. .,Department of Plant Development, Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria.
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Bueno JGR, Borelli G, Corrêa TLR, Fiamenghi MB, José J, de Carvalho M, de Oliveira LC, Pereira GAG, dos Santos LV. Novel xylose transporter Cs4130 expands the sugar uptake repertoire in recombinant Saccharomyces cerevisiae strains at high xylose concentrations. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:145. [PMID: 32818042 PMCID: PMC7427733 DOI: 10.1186/s13068-020-01782-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/04/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND The need to restructure the world's energy matrix based on fossil fuels and mitigate greenhouse gas emissions stimulated the development of new biobased technologies for renewable energy. One promising and cleaner alternative is the use of second-generation (2G) fuels, produced from lignocellulosic biomass sugars. A major challenge on 2G technologies establishment is the inefficient assimilation of the five-carbon sugar xylose by engineered Saccharomyces cerevisiae strains, increasing fermentation time. The uptake of xylose across the plasma membrane is a critical limiting step and the budding yeast S. cerevisiae is not designed with a broad transport system and regulatory mechanisms to assimilate xylose in a wide range of concentrations present in 2G processes. RESULTS Assessing diverse microbiomes such as the digestive tract of plague insects and several decayed lignocellulosic biomasses, we isolated several yeast species capable of using xylose. Comparative fermentations selected the yeast Candida sojae as a potential source of high-affinity transporters. Comparative genomic analysis elects four potential xylose transporters whose properties were evaluated in the transporter null EBY.VW4000 strain carrying the xylose-utilizing pathway integrated into the genome. While the traditional xylose transporter Gxf1 allows an improved growth at lower concentrations (10 g/L), strains containing Cs3894 and Cs4130 show opposite responses with superior xylose uptake at higher concentrations (up to 50 g/L). Docking and normal mode analysis of Cs4130 and Gxf1 variants pointed out important residues related to xylose transport, identifying key differences regarding substrate translocation comparing both transporters. CONCLUSIONS Considering that xylose concentrations in second-generation hydrolysates can reach high values in several designed processes, Cs4130 is a promising novel candidate for xylose uptake. Here, we demonstrate a novel eukaryotic molecular transporter protein that improves growth at high xylose concentrations and can be used as a promising target towards engineering efficient pentose utilization in yeast.
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Affiliation(s)
- João Gabriel Ribeiro Bueno
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo 13083-100 Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Guilherme Borelli
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo 13083-100 Brazil
| | - Mateus Bernabe Fiamenghi
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Juliana José
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Murilo de Carvalho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Leandro Cristante de Oliveira
- Department of Physics-Institute of Biosciences, Humanities and Exact Sciences, UNESP, São Paulo State University, São José do Rio Preto, São Paulo 15054-000 Brazil
| | - Gonçalo A. G. Pereira
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Leandro Vieira dos Santos
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo 13083-100 Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
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Nijland JG, Driessen AJM. Engineering of Pentose Transport in Saccharomyces cerevisiae for Biotechnological Applications. Front Bioeng Biotechnol 2020; 7:464. [PMID: 32064252 PMCID: PMC7000353 DOI: 10.3389/fbioe.2019.00464] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/19/2019] [Indexed: 01/05/2023] Open
Abstract
Lignocellulosic biomass yields after hydrolysis, besides the hexose D-glucose, D-xylose, and L-arabinose as main pentose sugars. In second generation bioethanol production utilizing the yeast Saccharomyces cerevisiae, it is critical that all three sugars are co-consumed to obtain an economically feasible and robust process. Since S. cerevisiae is unable to metabolize pentose sugars, metabolic pathway engineering has been employed to introduce the respective pathways for D-xylose and L-arabinose metabolism. However, S. cerevisiae lacks specific pentose transporters, and these sugars enter the cell with low affinity via glucose transporters of the Hxt family. Therefore, in the presence of D-glucose, utilization of D-xylose and L-arabinose is poor as the Hxt transporters prefer D-glucose. To solve this problem, heterologous expression of pentose transporters has been attempted but often with limited success due to poor expression and stability, and/or low turnover. A more successful approach is the engineering of the endogenous Hxt transporter family and evolutionary selection for D-glucose insensitive growth on pentose sugars. This has led to the identification of a critical and conserved asparagine residue in Hxt transporters that, when mutated, reduces the D-glucose affinity while leaving the D-xylose affinity mostly unaltered. Likewise, mutant Gal2 transporter have been selected supporting specific uptake of L-arabinose. In fermentation experiments, the transporter mutants support efficient uptake and consumption of pentose sugars, and even co-consumption of D-xylose and D-glucose when used at industrial concentrations. Further improvements are obtained by interfering with the post-translational inactivation of Hxt transporters at high or low D-glucose concentrations. Transporter engineering solved major limitations in pentose transport in yeast, now allowing for co-consumption of sugars that is limited only by the rates of primary metabolism. This paves the way for a more economical second-generation biofuels production process.
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Affiliation(s)
- Jeroen G Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, Netherlands
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35
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López MG, Irla M, Brito LF, Wendisch VF. Characterization of D-Arabitol as Newly Discovered Carbon Source of Bacillus methanolicus. Front Microbiol 2019; 10:1725. [PMID: 31417519 PMCID: PMC6685057 DOI: 10.3389/fmicb.2019.01725] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/12/2019] [Indexed: 11/13/2022] Open
Abstract
Bacillus methanolicus is a Gram-positive, thermophilic, methanol-utilizing bacterium. As a facultative methylotroph, B. methanolicus is also known to utilize D-mannitol, D-glucose and, as recently discovered, sugar alcohol D-arabitol. While metabolic pathways for utilization of methanol, mannitol and glucose are known, catabolism of arabitol has not yet been characterized in B. methanolicus. In this work we present the elucidation of this hitherto uncharted pathway. In order to confirm our predictions regarding genes coding for arabitol utilization, we performed differential gene expression analysis of B. methanolicus MGA3 cells grown on arabitol as compared to mannitol via transcriptome sequencing (RNA-seq). We identified a gene cluster comprising eight genes that was up-regulated during growth with arabitol as a sole carbon source. The RNA-seq results were subsequently confirmed via qRT-PCR experiments. The transcriptional organization of the gene cluster identified via RNA-seq was analyzed and it was shown that the arabitol utilization genes are co-transcribed in an operon that spans from BMMGA3_RS07325 to BMMGA3_RS07365. Since gene deletion studies are currently not possible in B. methanolicus, two complementation experiments were performed in an arabitol negative Corynebacterium glutamicum strain using the four genes discovered via RNA-seq analysis as coding for a putative PTS for arabitol uptake (BMMGA3_RS07330, BMMGA3_RS07335, and BMMGA3_RS07340 renamed to atlABC) and a putative arabitol phosphate dehydrogenase (BMMGA3_RS07345 renamed to atlD). C. glutamicum is a natural D-arabitol utilizer that requires arabitol dehydrogenase MtlD for arabitol catabolism. The C. glutamicum mtlD deletion mutant was chosen for complementation experiments. Heterologous expression of atlABCD as well as the arabitol phosphate dehydrogenase gene atlD from B. methanolicus alone restored growth of the C. glutamicum ΔmtlD mutant with arabitol. Furthermore, D-arabitol phosphate dehydrogenase activities could be detected in crude extracts of B. methanolicus and these were higher in arabitol-grown cells than in methanol- or mannitol-grown cells. Thus, B. methanolicus possesses an arabitol inducible operon encoding, amongst others, a putative PTS system and an arabitol phosphate dehydrogenase for uptake and activation of arabitol as growth substrate.
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Affiliation(s)
- Marina Gil López
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Marta Irla
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany.,Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Luciana F Brito
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany.,Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
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Osiro KO, Borgström C, Brink DP, Fjölnisdóttir BL, Gorwa-Grauslund MF. Exploring the xylose paradox in Saccharomyces cerevisiae through in vivo sugar signalomics of targeted deletants. Microb Cell Fact 2019; 18:88. [PMID: 31122246 PMCID: PMC6532234 DOI: 10.1186/s12934-019-1141-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 05/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There have been many successful strategies to implement xylose metabolism in Saccharomyces cerevisiae, but no effort has so far enabled xylose utilization at rates comparable to that of glucose (the preferred sugar of this yeast). Many studies have pointed towards the engineered yeast not sensing that xylose is a fermentable carbon source despite growing and fermenting on it, which is paradoxical. We have previously used fluorescent biosensor strains to in vivo monitor the sugar signalome in yeast engineered with xylose reductase and xylitol dehydrogenase (XR/XDH) and have established that S. cerevisiae senses high concentrations of xylose with the same signal as low concentration of glucose, which may explain the poor utilization. RESULTS In the present study, we evaluated the effects of three deletions (ira2∆, isu1∆ and hog1∆) that have recently been shown to display epistatic effects on a xylose isomerase (XI) strain. Through aerobic and anaerobic characterization, we showed that the proposed effects in XI strains were for the most part also applicable in the XR/XDH background. The ira2∆isu1∆ double deletion led to strains with the highest specific xylose consumption- and ethanol production rates but also the lowest biomass titre. The signalling response revealed that ira2∆isu1∆ changed the low glucose-signal in the background strain to a simultaneous signalling of high and low glucose, suggesting that engineering of the signalome can improve xylose utilization. CONCLUSIONS The study was able to correlate the previously proposed beneficial effects of ira2∆, isu1∆ and hog1∆ on S. cerevisiae xylose uptake, with a change in the sugar signalome. This is in line with our previous hypothesis that the key to resolve the xylose paradox lies in the sugar sensing and signalling networks. These results indicate that the future engineering targets for improved xylose utilization should probably be sought not in the metabolic networks, but in the signalling ones.
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Affiliation(s)
- Karen O Osiro
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Celina Borgström
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
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Wu Y, Xu S, Gao X, Li M, Li D, Lu W. Enhanced protopanaxadiol production from xylose by engineered Yarrowia lipolytica. Microb Cell Fact 2019; 18:83. [PMID: 31103047 PMCID: PMC6525355 DOI: 10.1186/s12934-019-1136-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/08/2019] [Indexed: 12/21/2022] Open
Abstract
Background As renewable biomass, lignocellulose remains one of the major choices for most countries in tackling global energy shortage and environment pollution. Efficient utilization of xylose, an important monosaccharide in lignocellulose, is essential for the production of high-value compounds, such as ethanol, lipids, and isoprenoids. Protopanaxadiol (PPD), a kind of isoprenoids, has important medical values and great market potential. Results The engineered protopanaxadiol-producing Yarrowia lipolytica strain, which can use xylose as the sole carbon source, was constructed by introducing xylose reductase (XR) and xylitol dehydrogenase (XDH) from Scheffersomyces stipitis, overexpressing endogenous xylulose kinase (ylXKS) and heterologous PPD synthetic modules, and then 18.18 mg/L of PPD was obtained. Metabolic engineering strategies such as regulating cofactor balance, enhancing precursor flux, and improving xylose metabolism rate via XR (K270R/N272D) mutation, the overexpression of tHMG1/ERG9/ERG20 and transaldolase (TAL)/transketolase (TKL)/xylose transporter (TX), were implemented to enhance PPD production. The final Y14 strain exhibited the greatest PPD titer from xylose by fed-batch fermentation in a 5-L fermenter, reaching 300.63 mg/L [yield, 2.505 mg/g (sugar); productivity, 2.505 mg/L/h], which was significantly higher than the titer of glucose fermentation [titer, 167.17 mg/L; yield, 1.194 mg/g (sugar); productivity, 1.548 mg/L/h]. Conclusion The results showed that xylose was more suitable for PPD synthesis than glucose due to the enhanced carbon flux towards acetyl-CoA, the precursor for PPD biosynthetic pathway. This is the first report to produce PPD in Y. lipolytica with xylose as the sole carbon source, which developed a promising strategy for the efficient production of high-value triterpenoid compounds. Electronic supplementary material The online version of this article (10.1186/s12934-019-1136-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yufen Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China.,Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
| | - Shuo Xu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China.,Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
| | - Xiao Gao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China.,Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
| | - Man Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China.,Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
| | - Dashuai Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China.,Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
| | - Wenyu Lu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China. .,Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, People's Republic of China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China.
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38
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Verhoeven MD, Bracher JM, Nijland JG, Bouwknegt J, Daran JMG, Driessen AJM, van Maris AJA, Pronk JT. Laboratory evolution of a glucose-phosphorylation-deficient, arabinose-fermenting S. cerevisiae strain reveals mutations in GAL2 that enable glucose-insensitive l-arabinose uptake. FEMS Yeast Res 2019; 18:5026172. [PMID: 29860442 PMCID: PMC6044391 DOI: 10.1093/femsyr/foy062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/30/2018] [Indexed: 12/28/2022] Open
Abstract
Cas9-assisted genome editing was used to construct an engineered glucose-phosphorylation-negative S. cerevisiae strain, expressing the Lactobacillus plantaruml-arabinose pathway and the Penicillium chrysogenum transporter PcAraT. This strain, which showed a growth rate of 0.26 h−1 on l-arabinose in aerobic batch cultures, was subsequently evolved for anaerobic growth on l-arabinose in the presence of d-glucose and d-xylose. In four strains isolated from two independent evolution experiments the galactose-transporter gene GAL2 had been duplicated, with all alleles encoding Gal2N376T or Gal2N376I substitutions. In one strain, a single GAL2 allele additionally encoded a Gal2T89I substitution, which was subsequently also detected in the independently evolved strain IMS0010. In 14C-sugar-transport assays, Gal2N376S, Gal2N376T and Gal2N376I substitutions showed a much lower glucose sensitivity of l-arabinose transport and a much higher Km for d-glucose transport than wild-type Gal2. Introduction of the Gal2N376I substitution in a non-evolved strain enabled growth on l-arabinose in the presence of d-glucose. Gal2N376T, T89I and Gal2T89I variants showed a lower Km for l-arabinose and a higher Km for d-glucose than wild-type Gal2, while reverting Gal2N376T, T89I to Gal2N376 in an evolved strain negatively affected anaerobic growth on l-arabinose. This study indicates that optimal conversion of mixed-sugar feedstocks may require complex ‘transporter landscapes’, consisting of sugar transporters with complementary kinetic and regulatory properties.
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Affiliation(s)
- Maarten D Verhoeven
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jasmine M Bracher
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jeroen G Nijland
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jonna Bouwknegt
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Moreno AD, Carbone A, Pavone R, Olsson L, Geijer C. Evolutionary engineered Candida intermedia exhibits improved xylose utilization and robustness to lignocellulose-derived inhibitors and ethanol. Appl Microbiol Biotechnol 2018; 103:1405-1416. [PMID: 30498977 PMCID: PMC6394480 DOI: 10.1007/s00253-018-9528-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 10/25/2018] [Accepted: 11/17/2018] [Indexed: 01/27/2023]
Abstract
The development of robust microorganisms that can efficiently ferment both glucose and xylose represents one of the major challenges in achieving a cost-effective lignocellulosic bioethanol production. Candida intermedia is a non-conventional, xylose-utilizing yeast species with a high-capacity xylose transport system. The natural ability of C. intermedia to produce ethanol from xylose makes it attractive as a non-GMO alternative for lignocellulosic biomass conversion in biorefineries. We have evaluated the fermentation capacity and the tolerance to lignocellulose-derived inhibitors and the end product, ethanol, of the C. intermedia strain CBS 141442 isolated from steam-exploded wheat straw hydrolysate. In a mixed sugar fermentation medium, C. intermedia CBS 141442 co-fermented glucose and xylose, although with a preference for glucose over xylose. The strain was clearly more sensitive to inhibitors and ethanol when consuming xylose than glucose. C. intermedia CBS 141442 was also subjected to evolutionary engineering with the aim of increasing its tolerance to inhibitors and ethanol, and thus improving its fermentation capacity under harsh conditions. The resulting evolved population was able to ferment a 50% (v/v) steam-exploded wheat straw hydrolysate (which was completely inhibitory to the parental strain), improving the sugar consumption and the final ethanol concentration. The evolved population also exhibited a better tolerance to ethanol when growing in a xylose medium supplemented with 35.5 g/L ethanol. These results highlight the potential of C. intermedia CBS 141442 to become a robust yeast for the conversion of lignocellulose to ethanol.
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Affiliation(s)
- Antonio D Moreno
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, 41296, Gothenburg, Sweden.,Department of Energy, Biofuels Unit, CIEMAT, Madrid, Spain
| | - Antonella Carbone
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Rosita Pavone
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Lisbeth Olsson
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, 41296, Gothenburg, Sweden.
| | - Cecilia Geijer
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, 41296, Gothenburg, Sweden
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Cunha JT, Romaní A, Costa CE, Sá-Correia I, Domingues L. Molecular and physiological basis of Saccharomyces cerevisiae tolerance to adverse lignocellulose-based process conditions. Appl Microbiol Biotechnol 2018; 103:159-175. [PMID: 30397768 DOI: 10.1007/s00253-018-9478-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/27/2022]
Abstract
Lignocellulose-based biorefineries have been gaining increasing attention to substitute current petroleum-based refineries. Biomass processing requires a pretreatment step to break lignocellulosic biomass recalcitrant structure, which results in the release of a broad range of microbial inhibitors, mainly weak acids, furans, and phenolic compounds. Saccharomyces cerevisiae is the most commonly used organism for ethanol production; however, it can be severely distressed by these lignocellulose-derived inhibitors, in addition to other challenging conditions, such as pentose sugar utilization and the high temperatures required for an efficient simultaneous saccharification and fermentation step. Therefore, a better understanding of the yeast response and adaptation towards the presence of these multiple stresses is of crucial importance to design strategies to improve yeast robustness and bioconversion capacity from lignocellulosic biomass. This review includes an overview of the main inhibitors derived from diverse raw material resultants from different biomass pretreatments, and describes the main mechanisms of yeast response to their presence, as well as to the presence of stresses imposed by xylose utilization and high-temperature conditions, with a special emphasis on the synergistic effect of multiple inhibitors/stressors. Furthermore, successful cases of tolerance improvement of S. cerevisiae are highlighted, in particular those associated with other process-related physiologically relevant conditions. Decoding the overall yeast response mechanisms will pave the way for the integrated development of sustainable yeast cell-based biorefineries.
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Affiliation(s)
- Joana T Cunha
- Centre of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal
| | - Aloia Romaní
- Centre of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal
| | - Carlos E Costa
- Centre of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Lucília Domingues
- Centre of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal.
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Baptista SL, Cunha JT, Romaní A, Domingues L. Xylitol production from lignocellulosic whole slurry corn cob by engineered industrial Saccharomyces cerevisiae PE-2. BIORESOURCE TECHNOLOGY 2018; 267:481-491. [PMID: 30041142 DOI: 10.1016/j.biortech.2018.07.068] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
In this work, the industrial Saccharomyces cerevisiae PE-2 strain, presenting innate capacity for xylitol accumulation, was engineered for xylitol production by overexpression of the endogenous GRE3 gene and expression of different xylose reductases from Pichia stipitis. The best-performing GRE3-overexpressing strain was capable to produce 148.5 g/L of xylitol from high xylose-containing media, with a 0.95 g/g yield, and maintained close to maximum theoretical yields (0.89 g/g) when tested in non-detoxified corn cob hydrolysates. Furthermore, a successful integrated strategy was developed for the production of xylitol from whole slurry corn cob in a presaccharification and simultaneous saccharification and fermentation process (15% solid loading and 36 FPU) reaching xylitol yield of 0.93 g/g and a productivity of 0.54 g/L·h. This novel approach results in an intensified valorization of lignocellulosic biomass for xylitol production in a fully integrated process and represents an advance towards a circular economy.
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Affiliation(s)
- Sara L Baptista
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Aloia Romaní
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
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Papapetridis I, Verhoeven MD, Wiersma SJ, Goudriaan M, van Maris AJA, Pronk JT. Laboratory evolution for forced glucose-xylose co-consumption enables identification of mutations that improve mixed-sugar fermentation by xylose-fermenting Saccharomyces cerevisiae. FEMS Yeast Res 2018; 18:4996351. [PMID: 29771304 PMCID: PMC6001886 DOI: 10.1093/femsyr/foy056] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/14/2018] [Indexed: 01/18/2023] Open
Abstract
Simultaneous fermentation of glucose and xylose can contribute to improved productivity and robustness of yeast-based processes for bioethanol production from lignocellulosic hydrolysates. This study explores a novel laboratory evolution strategy for identifying mutations that contribute to simultaneous utilisation of these sugars in batch cultures of Saccharomyces cerevisiae. To force simultaneous utilisation of xylose and glucose, the genes encoding glucose-6-phosphate isomerase (PGI1) and ribulose-5-phosphate epimerase (RPE1) were deleted in a xylose-isomerase-based xylose-fermenting strain with a modified oxidative pentose-phosphate pathway. Laboratory evolution of this strain in serial batch cultures on glucose-xylose mixtures yielded mutants that rapidly co-consumed the two sugars. Whole-genome sequencing of evolved strains identified mutations in HXK2, RSP5 and GAL83, whose introduction into a non-evolved xylose-fermenting S. cerevisiae strain improved co-consumption of xylose and glucose under aerobic and anaerobic conditions. Combined deletion of HXK2 and introduction of a GAL83G673T allele yielded a strain with a 2.5-fold higher xylose and glucose co-consumption ratio than its xylose-fermenting parental strain. These two modifications decreased the time required for full sugar conversion in anaerobic bioreactor batch cultures, grown on 20 g L-1 glucose and 10 g L-1 xylose, by over 24 h. This study demonstrates that laboratory evolution and genome resequencing of microbial strains engineered for forced co-consumption is a powerful approach for studying and improving simultaneous conversion of mixed substrates.
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Affiliation(s)
| | | | - Sanne J Wiersma
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Maaike Goudriaan
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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43
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Oehling V, Klaassen P, Frick O, Dusny C, Schmid A. l-Arabinose triggers its own uptake via induction of the arabinose-specific Gal2p transporter in an industrial Saccharomyces cerevisiae strain. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:231. [PMID: 30159031 PMCID: PMC6106821 DOI: 10.1186/s13068-018-1231-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/17/2018] [Indexed: 06/08/2023]
Abstract
Bioethanol production processes with Saccharomyces cerevisiae using lignocellulosic biomass as feedstock are challenged by the simultaneous utilization of pentose and hexose sugars from biomass hydrolysates. The pentose uptake into the cell represents a crucial role for the efficiency of the process. The focus of the here presented study was to understand the uptake and conversion of the pentose l-arabinose in S. cerevisiae and reveal its regulation by d-glucose and d-galactose. Gal2p-the most prominent transporter enabling l-arabinose uptake in S. cerevisiae wild-type strains-has an affinity for the transport of l-arabinose, d-glucose, and d-galactose. d-Galactose was reported for being mandatory for inducing GAL2 expression. GAL2 expression is also known to be regulated by d-glucose-mediated carbon catabolite repression, as well as catabolite inactivation. The results of the present study demonstrate that l-arabinose can be used as sole carbon and energy source by the recombinant industrial strain S. cerevisiae DS61180. RT-qPCR and RNA-Seq experiments confirmed that l-arabinose can trigger its own uptake via the induction of GAL2 expression. Expression levels of GAL2 during growth on l-arabinose reached up to 21% of those obtained with d-galactose as sole carbon and energy source. l-Arabinose-induced GAL2 expression was also subject to catabolite repression by d-glucose. Kinetic investigations of substrate uptake, biomass, and product formation during growth on a mixture of d-glucose/l-arabinose revealed impairment of growth and ethanol production from l-arabinose upon d-glucose depletion. The presence of d-glucose is thus preventing the fermentation of l-arabinose in S. cerevisiae DS61180. Comparative transcriptome studies including the wild-type and a precursor strain delivered hints for an increased demand in ATP production and cofactor regeneration during growth of S. cerevisiae DS61180 on l-arabinose. Our results thus emphasize that cofactor and energy metabolism demand attention if the combined conversion of hexose and pentose sugars is intended, for example in biorefineries using lignocellulosics.
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Affiliation(s)
- Verena Oehling
- Laboratory of Chemical Biotechnology, Department of Biochemical & Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | | | - Oliver Frick
- Laboratory of Chemical Biotechnology, Department of Biochemical & Chemical Engineering, TU Dortmund University, Dortmund, Germany
- Present Address: Department of Solar Materials, Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany
| | - Christian Dusny
- Laboratory of Chemical Biotechnology, Department of Biochemical & Chemical Engineering, TU Dortmund University, Dortmund, Germany
- Present Address: Department of Solar Materials, Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany
| | - Andreas Schmid
- Laboratory of Chemical Biotechnology, Department of Biochemical & Chemical Engineering, TU Dortmund University, Dortmund, Germany
- Present Address: Department of Solar Materials, Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany
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Verhoeven MD, de Valk SC, Daran JMG, van Maris AJA, Pronk JT. Fermentation of glucose-xylose-arabinose mixtures by a synthetic consortium of single-sugar-fermenting Saccharomyces cerevisiae strains. FEMS Yeast Res 2018; 18:5054444. [DOI: 10.1093/femsyr/foy075] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/13/2018] [Indexed: 11/15/2022] Open
Affiliation(s)
- Maarten D Verhoeven
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sophie C de Valk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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45
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Abstract
As the simplest eukaryotic model system, the unicellular yeast Saccharomyces cerevisiae is ideally suited for quick and simple functional studies as well as for high-throughput screening. We generated a strain deficient for all endogenous hexose transporters, which has been successfully used to clone, characterize, and engineer carbohydrate transporters from different source organisms. Here we present basic protocols for handling this strain and characterizing sugar transporters heterologously expressed in it.
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46
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Lane S, Dong J, Jin YS. Value-added biotransformation of cellulosic sugars by engineered Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2018; 260:380-394. [PMID: 29655899 DOI: 10.1016/j.biortech.2018.04.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 05/26/2023]
Abstract
The substantial research efforts into lignocellulosic biofuels have generated an abundance of valuable knowledge and technologies for metabolic engineering. In particular, these investments have led to a vast growth in proficiency of engineering the yeast Saccharomyces cerevisiae for consuming lignocellulosic sugars, enabling the simultaneous assimilation of multiple carbon sources, and producing a large variety of value-added products by introduction of heterologous metabolic pathways. While microbial conversion of cellulosic sugars into large-volume low-value biofuels is not currently economically feasible, there may still be opportunities to produce other value-added chemicals as regulation of cellulosic sugar metabolism is quite different from glucose metabolism. This review summarizes these recent advances with an emphasis on employing engineered yeast for the bioconversion of lignocellulosic sugars into a variety of non-ethanol value-added products.
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Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jia Dong
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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47
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Spagnuolo M, Shabbir Hussain M, Gambill L, Blenner M. Alternative Substrate Metabolism in Yarrowia lipolytica. Front Microbiol 2018; 9:1077. [PMID: 29887845 PMCID: PMC5980982 DOI: 10.3389/fmicb.2018.01077] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/07/2018] [Indexed: 11/13/2022] Open
Abstract
Recent advances in genetic engineering capabilities have enabled the development of oleochemical producing strains of Yarrowia lipolytica. Much of the metabolic engineering effort has focused on pathway engineering of the product using glucose as the feedstock; however, alternative substrates, including various other hexose and pentose sugars, glycerol, lipids, acetate, and less-refined carbon feedstocks, have not received the same attention. In this review, we discuss recent work leading to better utilization of alternative substrates. This review aims to provide a comprehensive understanding of the current state of knowledge for alternative substrate utilization, suggest potential pathways identified through homology in the absence of prior characterization, discuss recent work that either identifies, endogenous or cryptic metabolism, and describe metabolic engineering to improve alternative substrate utilization. Finally, we describe the critical questions and challenges that remain for engineering Y. lipolytica for better alternative substrate utilization.
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Affiliation(s)
- Michael Spagnuolo
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
| | - Murtaza Shabbir Hussain
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
| | - Lauren Gambill
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
- Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, United States
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
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48
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Díaz T, Fillet S, Campoy S, Vázquez R, Viña J, Murillo J, Adrio JL. Combining evolutionary and metabolic engineering in Rhodosporidium toruloides for lipid production with non-detoxified wheat straw hydrolysates. Appl Microbiol Biotechnol 2018; 102:3287-3300. [DOI: 10.1007/s00253-018-8810-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/17/2018] [Accepted: 01/22/2018] [Indexed: 12/28/2022]
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49
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Lane S, Xu H, Oh EJ, Kim H, Lesmana A, Jeong D, Zhang G, Tsai CS, Jin YS, Kim SR. Glucose repression can be alleviated by reducing glucose phosphorylation rate in Saccharomyces cerevisiae. Sci Rep 2018; 8:2613. [PMID: 29422502 PMCID: PMC5805702 DOI: 10.1038/s41598-018-20804-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/19/2018] [Indexed: 01/06/2023] Open
Abstract
Microorganisms commonly exhibit preferential glucose consumption and diauxic growth when cultured in mixtures of glucose and other sugars. Although various genetic perturbations have alleviated the effects of glucose repression on consumption of specific sugars, a broadly applicable mechanism remains unknown. Here, we report that a reduction in the rate of glucose phosphorylation alleviates the effects of glucose repression in Saccharomyces cerevisiae. Through adaptive evolution under a mixture of xylose and the glucose analog 2-deoxyglucose, we isolated a mutant strain capable of simultaneously consuming glucose and xylose. Genome sequencing of the evolved mutant followed by CRISPR/Cas9-based reverse engineering revealed that mutations in the glucose phosphorylating enzymes (Hxk1, Hxk2, Glk1) were sufficient to confer simultaneous glucose and xylose utilization. We then found that varying hexokinase expression with an inducible promoter led to the simultaneous utilization of glucose and xylose. Interestingly, no mutations in sugar transporters occurred during the evolution, and no specific transporter played an indispensable role in simultaneous sugar utilization. Additionally, we demonstrated that slowing glucose consumption also enabled simultaneous utilization of glucose and galactose. These results suggest that the rate of intracellular glucose phosphorylation is a decisive factor for metabolic regulations of mixed sugars.
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Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Haiqing Xu
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Eun Joong Oh
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Heejin Kim
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Anastashia Lesmana
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Guochang Zhang
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ching-Sung Tsai
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. .,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea. .,Institute of Agricultural Science & Technology, Kyungpook National University, Daegu, Republic of Korea.
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50
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Bracher JM, Verhoeven MD, Wisselink HW, Crimi B, Nijland JG, Driessen AJM, Klaassen P, van Maris AJA, Daran JMG, Pronk JT. The Penicillium chrysogenum transporter PcAraT enables high-affinity, glucose-insensitive l-arabinose transport in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:63. [PMID: 29563966 PMCID: PMC5848512 DOI: 10.1186/s13068-018-1047-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 02/08/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND l-Arabinose occurs at economically relevant levels in lignocellulosic hydrolysates. Its low-affinity uptake via the Saccharomyces cerevisiae Gal2 galactose transporter is inhibited by d-glucose. Especially at low concentrations of l-arabinose, uptake is an important rate-controlling step in the complete conversion of these feedstocks by engineered pentose-metabolizing S. cerevisiae strains. RESULTS Chemostat-based transcriptome analysis yielded 16 putative sugar transporter genes in the filamentous fungus Penicillium chrysogenum whose transcript levels were at least threefold higher in l-arabinose-limited cultures than in d-glucose-limited and ethanol-limited cultures. Of five genes, that encoded putative transport proteins and showed an over 30-fold higher transcript level in l-arabinose-grown cultures compared to d-glucose-grown cultures, only one (Pc20g01790) restored growth on l-arabinose upon expression in an engineered l-arabinose-fermenting S. cerevisiae strain in which the endogenous l-arabinose transporter, GAL2, had been deleted. Sugar transport assays indicated that this fungal transporter, designated as PcAraT, is a high-affinity (Km = 0.13 mM), high-specificity l-arabinose-proton symporter that does not transport d-xylose or d-glucose. An l-arabinose-metabolizing S. cerevisiae strain in which GAL2 was replaced by PcaraT showed 450-fold lower residual substrate concentrations in l-arabinose-limited chemostat cultures than a congenic strain in which l-arabinose import depended on Gal2 (4.2 × 10-3 and 1.8 g L-1, respectively). Inhibition of l-arabinose transport by the most abundant sugars in hydrolysates, d-glucose and d-xylose was far less pronounced than observed with Gal2. Expression of PcAraT in a hexose-phosphorylation-deficient, l-arabinose-metabolizing S. cerevisiae strain enabled growth in media supplemented with both 20 g L-1 l-arabinose and 20 g L-1 d-glucose, which completely inhibited growth of a congenic strain in the same condition that depended on l-arabinose transport via Gal2. CONCLUSION Its high affinity and specificity for l-arabinose, combined with limited sensitivity to inhibition by d-glucose and d-xylose, make PcAraT a valuable transporter for application in metabolic engineering strategies aimed at engineering S. cerevisiae strains for efficient conversion of lignocellulosic hydrolysates.
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Affiliation(s)
- Jasmine M. Bracher
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Maarten D. Verhoeven
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - H. Wouter Wisselink
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
- Present Address: Isobionics, Urmonderbaan 22-B 45, 6167 RD Geleen, The Netherlands
| | - Barbara Crimi
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
- Present Address: Institut de Génétique Humaine, UMR9002-CNRS-UM, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Jeroen G. Nijland
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paul Klaassen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Antonius J. A. van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
- Present Address: Division of Industrial Biotechnology, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Centre, 20691 Stockholm, Sweden
| | - Jean-Marc G. Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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