51
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Tamayo Rojas SA, Schmidl S, Boles E, Oreb M. Glucose-induced internalization of the S. cerevisiae galactose permease Gal2 is dependent on phosphorylation and ubiquitination of its aminoterminal cytoplasmic tail. FEMS Yeast Res 2021; 21:6206829. [PMID: 33791789 DOI: 10.1093/femsyr/foab019] [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: 02/03/2021] [Accepted: 03/29/2021] [Indexed: 12/22/2022] Open
Abstract
The hexose permease Gal2 of Saccharomyces cerevisiae is expressed only in the presence of its physiological substrate galactose. Glucose tightly represses the GAL2 gene and also induces the clearance of the transporter from the plasma membrane by ubiquitination and subsequent degradation in the vacuole. Although many factors involved in this process, especially those responsible for the upstream signaling, have been elucidated, the mechanisms by which Gal2 is specifically targeted by the ubiquitination machinery have remained elusive. Here, we show that ubiquitination occurs within the N-terminal cytoplasmic tail and that the arrestin-like proteins Bul1 and Rod1 are likely acting as adaptors for docking of the ubiquitin E3-ligase Rsp5. We further demonstrate that phosphorylation on multiple residues within the tail is indispensable for the internalization and possibly represents a primary signal that might trigger the recruitment of arrestins to the transporter. In addition to these new fundamental insights, we describe Gal2 mutants with improved stability in the presence of glucose, which should prove valuable for engineering yeast strains utilizing complex carbohydrate mixtures present in hydrolysates of lignocellulosic or pectin-rich biomass.
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Affiliation(s)
- Sebastian A Tamayo Rojas
- Faculty of Biological Sciences, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, Frankfurt am Main 60438, Germany
| | - Sina Schmidl
- Faculty of Biological Sciences, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, Frankfurt am Main 60438, Germany
| | - Eckhard Boles
- Faculty of Biological Sciences, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, Frankfurt am Main 60438, Germany
| | - Mislav Oreb
- Faculty of Biological Sciences, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, Frankfurt am Main 60438, Germany
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52
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Qiao Y, Zhou J, Lu X, Zong H, Zhuge B. Improving the productivity of Candida glycerinogenes in the fermentation of ethanol from non-detoxified sugarcane bagasse hydrolysate by a hexose transporter mutant. J Appl Microbiol 2021; 131:1787-1799. [PMID: 33694233 DOI: 10.1111/jam.15059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/09/2021] [Accepted: 03/02/2021] [Indexed: 11/27/2022]
Abstract
AIMS In this study, we attempted to increase the productivity of Candida glycerinogenes yeast for ethanol production from non-detoxified sugarcane bagasse hydrolysates (NDSBH) by identifying the hexose transporter in this yeast that makes a high contribution to glucose consumption, and by adding additional copies of this transporter and enhancing its membrane localisation stability (MLS). METHODS AND RESULTS Based on the knockout and overexpression of key hexose transporter genes and the characterisation of their promoter properties, we found that Cghxt4 and Cghxt6 play major roles in the early and late stages of fermentation, respectively, with Cghxt4 contributing most to glucose consumption. Next, subcellular localisation analysis revealed that a common mutation of two ubiquitination sites (K9 and K538) in Cghxt4 improved its MLS. Finally, we overexpressed this Cghxt4 mutant (Cghxt4.2A) using a strong promoter, PCgGAP , which resulted in a significant increase in the ethanol productivity of C. glycerinogenes in the NDSBH medium. Specifically, the recombinant strain showed 18 and 25% higher ethanol productivity than the control in two kinds of YP-NDSBH medium (YP-NDSBH1G160 and YP-NDSBH2G160 ), respectively. CONCLUSIONS The hexose transporter mutant Cghxt4.2A (Cghxt4K9A,K538A ) with multiple copies and high MLS was able to significantly increase the ethanol productivity of C. glycerinogenes in NDSBH. SIGNIFICANCE AND IMPACT OF THE STUDY Our results provide a promising strategy for constructing efficient strains for ethanol production.
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Affiliation(s)
- Y Qiao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - J Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - X Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - H Zong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - B Zhuge
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
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53
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Shanmugam KT, Ingram LO. Principles and practice of designing microbial biocatalysts for fuel and chemical production. J Ind Microbiol Biotechnol 2021; 49:6158391. [PMID: 33686428 PMCID: PMC9118985 DOI: 10.1093/jimb/kuab016] [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: 11/20/2020] [Accepted: 03/03/2021] [Indexed: 11/14/2022]
Abstract
The finite nature of fossil fuels and the environmental impact of its use have raised interest in alternate renewable energy sources. Specifically, non-food carbohydrates, such as lignocellulosic biomass, can be used to produce next generation biofuels, including cellulosic ethanol and other non-ethanol fuels like butanol. However, currently there is no native microorganism that can ferment all lignocellulosic sugars to fuel molecules. Thus, research is focused on engineering improved microbial biocatalysts for production of liquid fuels at high productivity, titer and yield. A clear understanding and application of the basic principles of microbial physiology and biochemistry are crucial to achieve this goal. In this review, we present and discuss the construction of microbial biocatalysts that integrate these principles with ethanol-producing Escherichia coli as an example of metabolic engineering. These principles also apply to fermentation of lignocellulosic sugars to other chemicals that are currently produced from petroleum.
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Affiliation(s)
- K T Shanmugam
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lonnie O Ingram
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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54
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Sarkar P, Goswami G, Mukherjee M, Das D. Heterologous expression of xylose specific transporter improves xylose utilization by recombinant Zymomonas mobilis strain in presence of glucose. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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55
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Bañares AB, Nisola GM, Valdehuesa KNG, Lee WK, Chung WJ. Engineering of xylose metabolism in Escherichia coli for the production of valuable compounds. Crit Rev Biotechnol 2021; 41:649-668. [PMID: 33563072 DOI: 10.1080/07388551.2021.1873243] [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: 12/16/2022]
Abstract
The lignocellulosic sugar d-xylose has recently gained prominence as an inexpensive alternative substrate for the production of value-added compounds using genetically modified organisms. Among the prokaryotes, Escherichia coli has become the de facto host for the development of engineered microbial cell factories. The favored status of E. coli resulted from a century of scientific explorations leading to a deep understanding of its systems. However, there are limited literature reviews that discuss engineered E. coli as a platform for the conversion of d-xylose to any target compounds. Additionally, available critical review articles tend to focus on products rather than the host itself. This review aims to provide relevant and current information about significant advances in the metabolic engineering of d-xylose metabolism in E. coli. This focusses on unconventional and synthetic d-xylose metabolic pathways as several review articles have already discussed the engineering of native d-xylose metabolism. This paper, in particular, is essential to those who are working on engineering of d-xylose metabolism using E. coli as the host.
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Affiliation(s)
- Angelo B Bañares
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Grace M Nisola
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Kris N G Valdehuesa
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Gyeonggi, South Korea
| | - Wook-Jin Chung
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
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56
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Agrimi G, Steiger MG. Metabolite transport and its impact on metabolic engineering approaches. FEMS Microbiol Lett 2021; 368:6120592. [PMID: 33501487 DOI: 10.1093/femsle/fnaa211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022] Open
Affiliation(s)
- Gennaro Agrimi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Campus Universitario, Via Orabona 4, 70125, Bari, Italy
| | - Matthias G Steiger
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
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57
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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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58
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Kwon DH, Kim SB, Park, JB, Ha SJ. Overexpression of Mutant Galactose Permease ( ScGal2_N376F) Effective for Utilization of Glucose/Xylose or Glucose/ Galactose Mixture by Engineered Kluyveromyces marxianus. J Microbiol Biotechnol 2020; 30:1944-1949. [PMID: 33046681 PMCID: PMC9728301 DOI: 10.4014/jmb.2008.08035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022]
Abstract
Mutant sugar transporter ScGAL2-N376F was overexpressed in Kluyveromyces marxianus for efficient utilization of xylose, which is one of the main components of cellulosic biomass. K. marxianus ScGal2_N376F, the ScGAL2-N376F-overexpressing strain, exhibited 47.04 g/l of xylose consumption and 26.55 g/l of xylitol production, as compared to the parental strain (24.68 g/l and 7.03 g/l, respectively) when xylose was used as the sole carbon source. When a mixture of glucose and xylose was used as the carbon source, xylose consumption and xylitol production rates were improved by 195% and 360%, respectively, by K. marxianus ScGal2_N376F. Moreover, the glucose consumption rate was improved by 27% as compared to that in the parental strain. Overexpression of both wild-type ScGAL2 and mutant ScGAL2-N376F showed 48% and 52% enhanced sugar consumption and ethanol production rates, respectively, when a mixture of glucose and galactose was used as the carbon source, which is the main component of marine biomass. As shown in this study, ScGAL2-N376F overexpression can be applied for the efficient production of biofuels or biochemicals from cellulosic or marine biomass.
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Affiliation(s)
- Deok-Ho Kwon
- Department of Bioengineering and Technology, Kangwon National University, Chuncheon 2434, Republic of Korea,Interdisciplinary Program in Biohealth-Machinery Convergence Engineering, Kangwon National University, Chuncheon 2441, Republic of Korea
| | - Saet-Byeol Kim
- Department of Bioengineering and Technology, Kangwon National University, Chuncheon 2434, Republic of Korea
| | - Jae-Bum Park,
- Department of Bioengineering and Technology, Kangwon National University, Chuncheon 2434, Republic of Korea
| | - Suk-Jin Ha
- Department of Bioengineering and Technology, Kangwon National University, Chuncheon 2434, Republic of Korea,Institute of Fermentation and Brewing, Kangwon National University, Chuncheon 4341, Republic of Korea,Interdisciplinary Program in Biohealth-Machinery Convergence Engineering, Kangwon National University, Chuncheon 2441, Republic of Korea,Corresponding author Phone: +82-33-250-6278 Fax: +82-33-243-6350 E-mail:
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59
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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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60
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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61
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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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62
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Sun L, Jin YS. Xylose Assimilation for the Efficient Production of Biofuels and Chemicals by Engineered Saccharomyces cerevisiae. Biotechnol J 2020; 16:e2000142. [PMID: 33135317 DOI: 10.1002/biot.202000142] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 10/15/2020] [Indexed: 11/09/2022]
Abstract
Microbial conversion of plant biomass into fuels and chemicals offers a practical solution to global concerns over limited natural resources, environmental pollution, and climate change. Pursuant to these goals, researchers have put tremendous efforts and resources toward engineering the yeast Saccharomyces cerevisiae to efficiently convert xylose, the second most abundant sugar in lignocellulosic biomass, into various fuels and chemicals. Here, recent advances in metabolic engineering of yeast is summarized to address bottlenecks on xylose assimilation and to enable simultaneous co-utilization of xylose and other substrates in lignocellulosic hydrolysates. Distinct characteristics of xylose metabolism that can be harnessed to produce advanced biofuels and chemicals are also highlighted. Although many challenges remain, recent research investments have facilitated the efficient fermentation of xylose and simultaneous co-consumption of xylose and glucose. In particular, understanding xylose-induced metabolic rewiring in engineered yeast has encouraged the use of xylose as a carbon source for producing various non-ethanol bioproducts. To boost the lignocellulosic biomass-based bioeconomy, much attention is expected to promote xylose-utilizing efficiency via reprogramming cellular regulatory networks, to attain robust co-fermentation of xylose and other cellulosic carbon sources under industrial conditions, and to exploit the advantageous traits of yeast xylose metabolism for producing diverse fuels and chemicals.
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Affiliation(s)
- Liang Sun
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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63
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Characterization of two sugar transporters responsible for efficient xylose uptake in an oleaginous yeast Candida tropicalis SY005. Arch Biochem Biophys 2020; 695:108645. [PMID: 33122161 DOI: 10.1016/j.abb.2020.108645] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/02/2020] [Accepted: 10/17/2020] [Indexed: 01/01/2023]
Abstract
Microbial conversion of lignocellulosic feedstock to the target bioproduct requires efficient assimilation of its constituent sugars, a large part of which comprises of glucose and xylose. This study aims to identify and characterize sugar transporters capable of xylose uptake in an oleaginous strain of the industrially relevant yeast Candida tropicalis. In silico database mining resulted in two sugar transporter proteins- CtStp1 and CtStp2, containing conserved amino acid residues and motifs that have been previously reported to be involved in xylose transport in other organisms. Several softwares predicted the likelihood of 10-12 transmembrane (TM) helices to be present in both the Stps, while molecular modelling showed 12 TM helices that were organized into a typical structure found in the major facilitator superfamily of transporters. Docking with different sugars also predicted favorable interactions. Heterologous expression in a Saccharomyces cerevisiae strain harboring functional xylose metabolic genes validated the broad substrate specificity of the two Stps. Each transporter supported prominent growth of recombinant S. cerevisiae strains on six sugars including xylose at various concentrations. Expression of CtSTP1 and CtSTP2 along with the xylose metabolic genes in yeast transformants grown in presence of xylose was confirmed by transcript detection. Growth curve and sugar consumption profiles revealed uptake of both glucose and xylose simultaneously by the recombinant yeast strains, though CtStp1 showed relatively less effect of glucose repression in mixed sugars and was a better transporter of xylose than CtStp2. Such glucose-xylose utilizing efficient transporters can be effective tools for developing co-fermenting yeasts through genetic engineering in future, with noteworthy applications in renewable biomass utilization.
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64
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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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65
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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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66
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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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67
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Nijland JG, Li X, Shin HY, de Waal PP, Driessen AJM. Efficient, D-glucose insensitive, growth on D-xylose by an evolutionary engineered Saccharomyces cerevisiae strain. FEMS Yeast Res 2020; 19:5647354. [PMID: 31782779 DOI: 10.1093/femsyr/foz083] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 11/28/2019] [Indexed: 12/17/2022] Open
Abstract
Optimizing D-xylose consumption in Saccharomyces cerevisiae is essential for cost-efficient cellulosic bioethanol production. An evolutionary engineering approach was used to elevate D-xylose consumption in a xylose-fermenting S. cerevisiae strain carrying the D-xylose-specific N367I mutation in the endogenous chimeric Hxt36 hexose transporter. This strain carries a quadruple hexokinase deletion that prevents glucose utilization, and allows for selection of improved growth rates on D-xylose in the presence of high D-glucose concentrations. Evolutionary engineering resulted in D-glucose-insensitive growth and consumption of D-xylose, which could be attributed to glucose insensitive D-xylose uptake via a novel chimeric Hxt37 N367I transporter that emerged from a fusion of the HXT36 and HXT7 genes, and a down regulation of a set of Hxt transporters that mediate glucose sensitive xylose transport. RNA sequencing revealed the downregulation of HXT1 and HXT2 which, together with the deletion of HXT7, resulted in a 21% reduction of the expression of all plasma membrane transporters genes. Morphological analysis showed an increased cell size and corresponding increased cell surface area of the evolved strain, which could be attributed to genome duplication. Mixed strain fermentation of the D-xylose-consuming strain DS71054-evo6 with the D-glucose consuming CEN.PK113-7D strain resulted in decreased residual sugar concentrations and improved ethanol production yields compared to a strain which sequentially consumes D-glucose and D-xylose.
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Affiliation(s)
- Jeroen G Nijland
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology (GBB), University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Xiang Li
- Department of Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology (GBB), University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Hyun Yong Shin
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology (GBB), University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Paul P de Waal
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology (GBB), University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Nijenborgh 7, 9747AG, Groningen, The Netherlands
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68
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Zhou L, Wen Z, Wang Z, Zhang Y, Ledesma-Amaro R, Jin M. Evolutionary Engineering Improved d-Glucose/Xylose Cofermentation of Yarrowia lipolytica. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c00896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Linlin Zhou
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Zedi Wang
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Yuwei Zhang
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | | | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
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69
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Zhu Y, Zhou C, Wang Y, Li C. Transporter Engineering for Microbial Manufacturing. Biotechnol J 2020; 15:e1900494. [PMID: 32298528 DOI: 10.1002/biot.201900494] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/30/2020] [Indexed: 01/08/2023]
Abstract
Microbes play an important role in biotransformation and biosynthesis of biofuels, natural products, and polymers. Therefore, microbial manufacturing has been widely used in medicine, industry, and agriculture. However, common strategies including enzyme engineering, pathway optimization, and host engineering are generally inadequate to obtain an efficient microbial production system. Transporter engineering provides an alternative strategy to promote the transmembrane transfer of substrates, intermediates, and final products in microbial cells and thus enhances production by alleviating feedback inhibition and cytotoxicity caused by final products. According to the current studies in transport engineering, native transporters usually have low expression and poor transportation ability, resulting in inefficient transport processes and microbial production. In this review, current approaches for transporter mining, characterization, and verification are comprehensively summarized. Practical approaches to enhance the transport system in engineered cells, such as balancing transporter overexpression and cell growth, and evolution of native transporters are discussed. Furthermore, the applications of transporter engineering in microbial manufacturing, including enhancement of substrate utilization, concentration of metabolic flux to the target pathway, and acceleration of efflux and recovery of products, demonstrate its outstanding advantages and promising prospects.
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Affiliation(s)
- Ying Zhu
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Chen Zhou
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Ying Wang
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Chun Li
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
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70
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Su B, Song D, Zhu H. Metabolic Engineering of Saccharomyces cerevisiae for Enhanced Carotenoid Production From Xylose-Glucose Mixtures. Front Bioeng Biotechnol 2020; 8:435. [PMID: 32478054 PMCID: PMC7240070 DOI: 10.3389/fbioe.2020.00435] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/15/2020] [Indexed: 01/31/2023] Open
Abstract
Co-utilization of xylose and glucose from lignocellulosic biomass is an economically feasible bioprocess for chemical production. Many strategies have been implemented for efficiently assimilating xylose which is one of the predominant sugars of lignocellulosic biomass. However, there were few reports about engineering Saccharomyces cerevisiae for carotenoid production from xylose-glucose mixtures. Herein, we developed a platform for facilitating carotenoid production in S. cerevisiae by fermentation of xylose-glucose mixtures. Firstly, a xylose assimilation pathway with mutant xylose reductase (XYL1m), xylitol dehydrogenase (XYL2), and xylulokinase (XK) was constructed for utilizing xylose. Then, introduction of phosphoketolase (PK) pathway, deletion of Pho13 and engineering yeast hexose transporter Gal2 were conducted to improve carotenoid yields. The final strain SC105 produced a 1.6-fold higher production from mixed sugars than that from glucose in flask culture. In fed-batch fermentation with continuous feeding of mixed sugars, carotenoid production represented a 2.6-fold higher. To the best of our knowledge, this is the first report that S. cerevisiae was engineered to utilize xylose-glucose mixtures for carotenoid production with a considerable high yield. The present study exhibits a promising advantage of xylose-glucose mixtures assimilating strain as an industrial carotenoid producer from lignocellulosic biomass.
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Affiliation(s)
- Buli Su
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Dandan Song
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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71
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Vasylyshyn R, Kurylenko O, Ruchala J, Shevchuk N, Kuliesiene N, Khroustalyova G, Rapoport A, Daugelavicius R, Dmytruk K, Sibirny A. Engineering of sugar transporters for improvement of xylose utilization during high-temperature alcoholic fermentation in Ogataea polymorpha yeast. Microb Cell Fact 2020; 19:96. [PMID: 32334587 PMCID: PMC7183630 DOI: 10.1186/s12934-020-01354-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/18/2020] [Indexed: 01/28/2023] Open
Abstract
Background Xylose transport is one of the bottlenecks in the conversion of lignocellulosic biomass to ethanol. Xylose consumption by the wild-type strains of xylose-utilizing yeasts occurs once glucose is depleted resulting in a long fermentation process and overall slow and incomplete conversion of sugars liberated from lignocellulosic hydrolysates. Therefore, the engineering of endogenous transporters for the facilitation of glucose-xylose co-consumption is an important prerequisite for efficient ethanol production from lignocellulosic hydrolysates. Results In this study, several engineering approaches formerly used for the low-affinity glucose transporters in Saccharomyces cerevisiae, were successfully applied for earlier identified transporter Hxt1 in Ogataea polymorpha to improve xylose consumption (engineering involved asparagine substitution to alanine at position 358 and replacement of N-terminal lysine residues predicted to be the target of ubiquitination for arginine residues). Moreover, the modified versions of S. cerevisiae Hxt7 and Gal2 transporters also led to improved xylose fermentation when expressed in O. polymorpha. Conclusions The O. polymorpha strains with modified Hxt1 were characterized by simultaneous utilization of both glucose and xylose, in contrast to the wild-type and parental strain with elevated ethanol production from xylose. When the engineered Hxt1 transporter was introduced into constructed earlier advanced ethanol producer form xylose, the resulting strain showed further increase in ethanol accumulation during xylose fermentation. The overexpression of heterologous S. cerevisiae Gal2 had a less profound positive effects on sugars uptake rate, while overexpression of Hxt7 revealed the least impact on sugars consumption.
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Affiliation(s)
- Roksolana Vasylyshyn
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Olena Kurylenko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Justyna Ruchala
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine.,Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, Rzeszow, 35-601, Poland
| | - Nadiya Shevchuk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Neringa Kuliesiene
- Department of Biochemistry, Faculty of Natural Sciences, Vytautas Magnus University, Vileikos 8, 44404, Kaunas, Lithuania
| | - Galina Khroustalyova
- Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Str., 1-537, Riga, 1004, Latvia.,Latvian - Ukrainian Joint International Laboratory of Microbial Cell Biology, Jelgavas Str., 1, Riga LV-1004, Latvia, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Alexander Rapoport
- Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Str., 1-537, Riga, 1004, Latvia.,Latvian - Ukrainian Joint International Laboratory of Microbial Cell Biology, Jelgavas Str., 1, Riga LV-1004, Latvia, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Rimantas Daugelavicius
- Department of Biochemistry, Faculty of Natural Sciences, Vytautas Magnus University, Vileikos 8, 44404, Kaunas, Lithuania
| | - Kostyantyn Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Andriy Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine. .,Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, Rzeszow, 35-601, Poland. .,Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Str., 1-537, Riga, 1004, Latvia. .,Latvian - Ukrainian Joint International Laboratory of Microbial Cell Biology, Jelgavas Str., 1, Riga LV-1004, Latvia, Drahomanov Street, 14/16, Lviv, 79005, Ukraine.
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72
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Jiang Y, Shen Y, Gu L, Wang Z, Su N, Niu K, Guo W, Hou S, Bao X, Tian C, Fang X. Identification and Characterization of an Efficient d-Xylose Transporter in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2702-2710. [PMID: 32054270 DOI: 10.1021/acs.jafc.9b07113] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
d-Xylose is the most abundant hemicellulosic monomer on earth, but wild-type Saccharomyces cerevisiae has very limited d-xylose uptake capacity. We conducted bioprospecting for new sugar transporters from the d-xylose-consuming filamentous fungus Trichoderma reesei and identified three candidates belonging to the major facilitator superfamily. When they were expressed in yeast and assayed for d-xylose uptake, one of them, Xltr1p, had d-xylose transport activity that was more efficient than that of Gal2p, an endogenous yeast transporter. Site-directed mutagenesis was used to examine the functional contributions of 13 amino acid residues for the uptake of d-xylose, and these experiments identified particular amino acids that function distinctly in d-xylose vs glucose transport (e.g., F300). Excitingly, the yeast strain expressing the N326FXltr1p variant was able to carry a "high efficiency" transport for d-xylose but was nearly unable to utilize glucose; in contrast, the strain with the F300AXltr1p variant grew on glucose but lost d-xylose transport activity.
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Affiliation(s)
- Yi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- College of Bioengineering, Qilu University of Technology, Jinan 250100, China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhenzhen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Ning Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Wei Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Shaoli Hou
- Yantai Huakangrongzan Biotechnology Co., Ltd, Yantai 264006, China
| | - Xiaoming Bao
- College of Bioengineering, Qilu University of Technology, Jinan 250100, China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
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73
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Oreb M. Construction of artificial membrane transport metabolons – an emerging strategy in metabolic engineering. FEMS Microbiol Lett 2020; 367:5735437. [DOI: 10.1093/femsle/fnaa027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/11/2020] [Indexed: 12/18/2022] Open
Abstract
ABSTRACT
The term ‘membrane transport metabolon’ refers to the physical association of membrane transporters with enzymes that metabolize the transported substrates. In naturally evolved systems, physiological relevance of coupling transport with sequential enzymatic reactions resides, for instance, in faster turnover rates, protection of substrates from competing pathways or shielding the cellular environment from toxic compounds. Such underlying principles offer attractive possibilities for metabolic engineering approaches and concepts for constructing artificial transporter-enzyme complexes are recently being developed. In this minireview, the modes of substrate channeling across biological membranes and design principles for artificial transport metabolons are discussed.
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Affiliation(s)
- Mislav Oreb
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
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74
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Onyeabor M, Martinez R, Kurgan G, Wang X. Engineering transport systems for microbial production. ADVANCES IN APPLIED MICROBIOLOGY 2020; 111:33-87. [PMID: 32446412 DOI: 10.1016/bs.aambs.2020.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The rapid development in the field of metabolic engineering has enabled complex modifications of metabolic pathways to generate a diverse product portfolio. Manipulating substrate uptake and product export is an important research area in metabolic engineering. Optimization of transport systems has the potential to enhance microbial production of renewable fuels and chemicals. This chapter comprehensively reviews the transport systems critical for microbial production as well as current genetic engineering strategies to improve transport functions and thus production metrics. In addition, this chapter highlights recent advancements in engineering microbial efflux systems to enhance cellular tolerance to industrially relevant chemical stress. Lastly, future directions to address current technological gaps are discussed.
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Affiliation(s)
- Moses Onyeabor
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Rodrigo Martinez
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Gavin Kurgan
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Xuan Wang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.
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Razali SA, Shamsir MS. Characterisation of a catalytic triad and reaction selectivity in the dual mechanism of the catalyse hydride transfer in xylitol phosphate dehydrogenase. J Mol Graph Model 2020; 97:107548. [PMID: 32023508 DOI: 10.1016/j.jmgm.2020.107548] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/04/2020] [Accepted: 01/22/2020] [Indexed: 10/25/2022]
Abstract
Xylitol is a high-value low-calorie sweetener used as sugar substitute in food and pharmaceutical industry. Xylitol phosphate dehydrogenase (XPDH) catalyses the conversion of d-xylulose 5-phosphate (XU5P) and d-ribulose 5-phosphate (RU5P) to xylitol and ribitol respectively in the presence of nicotinamide adenine dinucleotide hydride (NADH). Although these enzymes have been shown to produce xylitol and ribitol, there is an incomplete understanding of the mechanism of the catalytic events of these reactions and the detailed mechanism has yet to be elucidated. The main goal of this work is to analyse the conformational changes of XPDH-bound ligands such as zinc, NADH, XU5P, and RU5P to elucidate the key amino acids involved in the substrate binding. In silico modelling, comparative molecular dynamics simulations, interaction analysis and conformational study were carried out on three XPDH enzymes of the Medium-chain dehydrogenase (MDR) family in order to elucidate the atomistic details of conformational transition, especially on the open and closed state of XPDH. The analysis also revealed the possible mechanism of substrate specificity that are responsible in the catalyse hydride transfer are the residues His58 and Ser39 which would act as the proton donor for reduction of XU5P and RU5P respectively. The structural comparison and MD simulations displayed a significant difference in the conformational dynamics of the catalytic and coenzyme loops between Apo and XPDH-complexes and highlight the contribution of newly found triad residues. This study would assist future mutagenesis study and enzyme modification work to increase the catalysis efficiency of xylitol production in the industry.
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Affiliation(s)
- Siti Aisyah Razali
- Bioinformatics, Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Bioinformatics Research Group (BIRG), Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group (BIRG), Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia; Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, 84600 Muar, Johor, Malaysia
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76
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Zhao Z, Xian M, Liu M, Zhao G. Biochemical routes for uptake and conversion of xylose by microorganisms. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:21. [PMID: 32021652 PMCID: PMC6995148 DOI: 10.1186/s13068-020-1662-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/21/2020] [Indexed: 05/23/2023]
Abstract
Xylose is a major component of lignocellulose and the second most abundant sugar present in nature. Efficient utilization of xylose is required for the development of economically viable processes to produce biofuels and chemicals from biomass. However, there are still some bottlenecks in the bioconversion of xylose, including the fact that some microorganisms cannot assimilate xylose naturally and that the uptake and metabolism of xylose are inhibited by glucose, which is usually present with xylose in lignocellulose hydrolysate. To overcome these issues, numerous efforts have been made to discover, characterize, and engineer the transporters and enzymes involved in xylose utilization to relieve glucose inhibition and to develop recombinant microorganisms to produce fuels and chemicals from xylose. Here we describe a recent advancement focusing on xylose-utilizing pathways, biosynthesis of chemicals from xylose, and engineering strategies used to improve the conversion efficiency of xylose.
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Affiliation(s)
- Zhe Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Min Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
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77
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78
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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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79
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Alballa M, Aplop F, Butler G. TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information. PLoS One 2020; 15:e0227683. [PMID: 31935244 PMCID: PMC6959595 DOI: 10.1371/journal.pone.0227683] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 12/26/2019] [Indexed: 11/24/2022] Open
Abstract
Transporters mediate the movement of compounds across the membranes that separate the cell from its environment and across the inner membranes surrounding cellular compartments. It is estimated that one third of a proteome consists of membrane proteins, and many of these are transport proteins. Given the increase in the number of genomes being sequenced, there is a need for computational tools that predict the substrates that are transported by the transmembrane transport proteins. In this paper, we present TranCEP, a predictor of the type of substrate transported by a transmembrane transport protein. TranCEP combines the traditional use of the amino acid composition of the protein, with evolutionary information captured in a multiple sequence alignment (MSA), and restriction to important positions of the alignment that play a role in determining the specificity of the protein. Our experimental results show that TranCEP significantly outperforms the state-of-the-art predictors. The results quantify the contribution made by each type of information used.
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Affiliation(s)
- Munira Alballa
- Department of Computer Science and Software Engineering, Concordia University, Montréal, Québec, Canada
- College of Computer and Information Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Faizah Aplop
- School of Informatics and Applied Mathematics, Universiti Malaysia Terengganu, Malaysia
| | - Gregory Butler
- Department of Computer Science and Software Engineering, Concordia University, Montréal, Québec, Canada
- Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec, Canada
- * E-mail:
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80
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Hoang Nguyen Tran P, Ko JK, Gong G, Um Y, Lee SM. Improved simultaneous co-fermentation of glucose and xylose by Saccharomyces cerevisiae for efficient lignocellulosic biorefinery. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:12. [PMID: 31993090 PMCID: PMC6975041 DOI: 10.1186/s13068-019-1641-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/19/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Lignocellulosic biorefinery offers economical and sustainable production of fuels and chemicals. Saccharomyces cerevisiae, a promising industrial host for biorefinery, has been intensively developed to expand its product profile. However, the sequential and slow conversion of xylose into target products remains one of the main challenges for realizing efficient industrial lignocellulosic biorefinery. RESULTS In this study, we developed a powerful mixed-sugar co-fermenting strain of S. cerevisiae, XUSEA, with improved xylose conversion capacity during simultaneous glucose/xylose co-fermentation. To reinforce xylose catabolism, the overexpression target in the pentose phosphate pathway was selected using a DNA assembler method and overexpressed increasing xylose consumption and ethanol production by twofold. The performance of the newly engineered strain with improved xylose catabolism was further boosted by elevating fermentation temperature and thus significantly reduced the co-fermentation time by half. Through combined efforts of reinforcing the pathway of xylose catabolism and elevating the fermentation temperature, XUSEA achieved simultaneous co-fermentation of lignocellulosic hydrolysates, composed of 39.6 g L-1 glucose and 23.1 g L-1 xylose, within 24 h producing 30.1 g L-1 ethanol with a yield of 0.48 g g-1. CONCLUSIONS Owing to its superior co-fermentation performance and ability for further engineering, XUSEA has potential as a platform in a lignocellulosic biorefinery toward realizing a more economical and sustainable process for large-scale bioethanol production.
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Affiliation(s)
- Phuong Hoang Nguyen Tran
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
- Green School, Korea University, Seoul, 02841 Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
- Green School, Korea University, Seoul, 02841 Republic of Korea
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81
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Francois JM, Alkim C, Morin N. Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:118. [PMID: 32670405 PMCID: PMC7341569 DOI: 10.1186/s13068-020-01744-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/01/2020] [Indexed: 05/08/2023]
Abstract
Lignocellulose is the most abundant biomass on earth with an annual production of about 2 × 1011 tons. It is an inedible renewable carbonaceous resource that is very rich in pentose and hexose sugars. The ability of microorganisms to use lignocellulosic sugars can be exploited for the production of biofuels and chemicals, and their concurrent biotechnological processes could advantageously replace petrochemicals' processes in a medium to long term, sustaining the emerging of a new economy based on bio-based products from renewable carbon sources. One of the major issues to reach this objective is to rewire the microbial metabolism to optimally configure conversion of these lignocellulosic-derived sugars into bio-based products in a sustainable and competitive manner. Systems' metabolic engineering encompassing synthetic biology and evolutionary engineering appears to be the most promising scientific and technological approaches to meet this challenge. In this review, we examine the most recent advances and strategies to redesign natural and to implement non-natural pathways in microbial metabolic framework for the assimilation and conversion of pentose and hexose sugars derived from lignocellulosic material into industrial relevant chemical compounds leading to maximal yield, titer and productivity. These include glycolic, glutaric, mesaconic and 3,4-dihydroxybutyric acid as organic acids, monoethylene glycol, 1,4-butanediol and 1,2,4-butanetriol, as alcohols. We also discuss the big challenges that still remain to enable microbial processes to become industrially attractive and economically profitable.
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Affiliation(s)
- Jean Marie Francois
- Toulouse Biotechnology Institute, CNRS, INRA, LISBP INSA, 135 Avenue de Rangueil, Toulouse Cedex 04, 31077 France
- Toulouse White Biotechnology (TWB, UMS INRA/INSA/CNRS), NAPA CENTER Bât B, 3 Rue Ariane 31520, Ramonville Saint-Agnes, France
| | - Ceren Alkim
- Toulouse Biotechnology Institute, CNRS, INRA, LISBP INSA, 135 Avenue de Rangueil, Toulouse Cedex 04, 31077 France
- Toulouse White Biotechnology (TWB, UMS INRA/INSA/CNRS), NAPA CENTER Bât B, 3 Rue Ariane 31520, Ramonville Saint-Agnes, France
| | - Nicolas Morin
- Toulouse Biotechnology Institute, CNRS, INRA, LISBP INSA, 135 Avenue de Rangueil, Toulouse Cedex 04, 31077 France
- Toulouse White Biotechnology (TWB, UMS INRA/INSA/CNRS), NAPA CENTER Bât B, 3 Rue Ariane 31520, Ramonville Saint-Agnes, France
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82
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De novo biosynthesis of 8-hydroxyoctanoic acid via a medium-chain length specific fatty acid synthase and cytochrome P450 in Saccharomyces cerevisiae. Metab Eng Commun 2019; 10:e00111. [PMID: 31867212 PMCID: PMC6906673 DOI: 10.1016/j.mec.2019.e00111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 11/29/2022] Open
Abstract
Terminally hydroxylated fatty acids or dicarboxylic acids are industrially relevant compounds with broad applications. Here, we present the proof of principle for the de novo biosynthesis of 8-hydroxyoctanoic acid from glucose and ethanol in the yeast Saccharomyces cerevisiae. Toxicity tests with medium-chain length ω-hydroxy fatty acids and dicarboxylic acids revealed little or no growth impairments on yeast cultures even at higher concentrations. The ability of various heterologous cytochrome P450 enzymes in combination with their cognate reductases for ω-hydroxylation of externally fed octanoic acid were compared. Finally, the most efficient P450 enzyme system was expressed in a yeast strain, whose fatty acid synthase was engineered for octanoic acid production, resulting in de novo biosynthesis of 8-hydroxyoctanoic acid up to 3 mg/l. Accumulation of octanoic acid revealed that cytochromes P450 activities were limiting 8-hydroxyoctanoic acid synthesis. The hydroxylation of both externally added and intracellularly produced octanoic acid was strongly dependent on the carbon source used, with ethanol being preferred. We further identified the availability of heme, a cofactor needed for P450 activity, as a limiting factor of 8-hydroxyoctanoic acid biosynthesis. Low toxic effects of medium-chain ω-hydroxy fatty acids on yeast cells . Systematic comparison of cytochrome P450 enzyme activities on octanoic acid . De novo biosynthesis of 8-hydroxyoctanoic acid . Improvement of cytochrome P450 activity with ethanol or by addition of hemin .
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83
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Zhang C, Xue Q, Hou J, Mohsin A, Zhang M, Guo M, Zhu Y, Bao J, Wang J, Xiao W, Cao L. In-Depth Two-Stage Transcriptional Reprogramming and Evolutionary Engineering of Saccharomyces cerevisiae for Efficient Bioethanol Production from Xylose with Acetate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12002-12012. [PMID: 31595746 DOI: 10.1021/acs.jafc.9b05095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In order to achieve rapid xylose utilization in the presence of acetate, improved yeast strains were engineered for higher bioethanol production. First, a six-gene cluster, including XYL1/XYL2/XKS1/TAL1/PYK1/MGT05196, was generated by using an in-depth two-stage (glucose and xylose) transcription reprogramming strategy in an evolutionary adapted strain of CE7, resulting in two improved engineered strains WXY46 and WXY53. Through a combined screening of xylose and glucose stage-specific promoters between tricarboxylic acid (TCA)/HSP and constitutive types, respectively, WXY46 with the constitutive promoters showed a much higher ethanol yield than that of WXY53 with the TCA/HSP promoters. Second, an optimized strain WXY74 was obtained by using more copies of a six-gene cluster, which resulted in a higher ethanol yield of 0.500 g/g total sugars with acetate conditions. At last, simultaneous saccharification and co-fermentation were performed by using the evolved WXY74 strain, which produced 58.4 g/L of ethanol from wheat straw waste and outperformed previous haploid XR-XDH strains.
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Affiliation(s)
- Cheng Zhang
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| | - Qian Xue
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| | - Junyan Hou
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Mei Zhang
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Yixuan Zhu
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Jingyu Wang
- Department of Chemical Engineering and Materials Science , University of Minnesota , Twin Cities, Minneapolis , Minnesota 55455 , United States
| | - Wei Xiao
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| | - Limin Cao
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
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Ruchala J, Kurylenko OO, Dmytruk KV, Sibirny AA. Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts (Scheffersomyces stipitis, Ogataea polymorpha). J Ind Microbiol Biotechnol 2019; 47:109-132. [PMID: 31637550 PMCID: PMC6970964 DOI: 10.1007/s10295-019-02242-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022]
Abstract
This review summarizes progress in the construction of efficient yeast ethanol producers from glucose/sucrose and lignocellulose. Saccharomyces cerevisiae is the major industrial producer of first-generation ethanol. The different approaches to increase ethanol yield and productivity from glucose in S. cerevisiae are described. Construction of the producers of second-generation ethanol is described for S. cerevisiae, one of the best natural xylose fermenters, Scheffersomyces stipitis and the most thermotolerant yeast known Ogataea polymorpha. Each of these organisms has some advantages and drawbacks. S. cerevisiae is the primary industrial ethanol producer and is the most ethanol tolerant natural yeast known and, however, cannot metabolize xylose. S. stipitis can effectively ferment both glucose and xylose and, however, has low ethanol tolerance and requires oxygen for growth. O. polymorpha grows and ferments at high temperatures and, however, produces very low amounts of ethanol from xylose. Review describes how the mentioned drawbacks could be overcome.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Olena O Kurylenko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Kostyantyn V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland.
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85
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Mixed carbon substrates: a necessary nuisance or a missed opportunity? Curr Opin Biotechnol 2019; 62:15-21. [PMID: 31513988 DOI: 10.1016/j.copbio.2019.07.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 06/24/2019] [Accepted: 07/03/2019] [Indexed: 11/20/2022]
Abstract
Although fermentation with single carbon sources is the preferred mode of operation in current industrial biotechnology, the use of multiple substrates has been continuously investigated throughout the years. Generally, microbial metabolism varies significantly when cells are presented with mixed carbon substrates compared to a single carbon-energy source, as different nutrients interact in complex ways within the metabolic network. By exploiting these distinct modes of interaction, researchers have identified unique opportunities to optimize metabolism using mixed carbon sources. Here we review situations where process yield and productivity are markedly improved through the judicious introduction of substrate mixtures. Our goal is to illustrate that with proper design of the choice of substrates and the way they are introduced to cultures, metabolic optimization with mixed substrates can be a unique strategy that complements genetic engineering techniques to enhance cell performance beyond what is accomplished in single substrate fermentations.
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86
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Patiño MA, Ortiz JP, Velásquez M, Stambuk BU. d-Xylose consumption by nonrecombinant Saccharomyces cerevisiae: A review. Yeast 2019; 36:541-556. [PMID: 31254359 DOI: 10.1002/yea.3429] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/02/2019] [Accepted: 06/21/2019] [Indexed: 01/24/2023] Open
Abstract
Xylose is the second most abundant sugar in nature. Its efficient fermentation has been considered as a critical factor for a feasible conversion of renewable biomass resources into biofuels and other chemicals. The yeast Saccharomyces cerevisiae is of exceptional industrial importance due to its excellent capability to ferment sugars. However, although S. cerevisiae is able to ferment xylulose, it is considered unable to metabolize xylose, and thus, a lot of research has been directed to engineer this yeast with heterologous genes to allow xylose consumption and fermentation. The analysis of the natural genetic diversity of this yeast has also revealed some nonrecombinant S. cerevisiae strains that consume or even grow (modestly) on xylose. The genome of this yeast has all the genes required for xylose transport and metabolism through the xylose reductase, xylitol dehydrogenase, and xylulokinase pathway, but there seems to be problems in their kinetic properties and/or required expression. Self-cloning industrial S. cerevisiae strains overexpressing some of the endogenous genes have shown interesting results, and new strategies and approaches designed to improve these S. cerevisiae strains for ethanol production from xylose will also be presented in this review.
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Affiliation(s)
- Margareth Andrea Patiño
- Instituto de Biotecnología.,Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Pablo Ortiz
- Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - Mario Velásquez
- Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Boris U Stambuk
- Departamento de Bioquímica, Universidad Federal de Santa Catarina, Florianópolis, Brazil
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Guirimand GGY, Bamba T, Matsuda M, Inokuma K, Morita K, Kitada Y, Kobayashi Y, Yukawa T, Sasaki K, Ogino C, Hasunuma T, Kondo A. Combined Cell Surface Display of β‐
d
‐Glucosidase (BGL), Maltose Transporter (MAL11), and Overexpression of Cytosolic Xylose Reductase (XR) in
Saccharomyces cerevisiae
Enhance Cellobiose/Xylose Coutilization for Xylitol Bioproduction from Lignocellulosic Biomass. Biotechnol J 2019; 14:e1800704. [DOI: 10.1002/biot.201800704] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 06/10/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Gregory G. Y. Guirimand
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Engineering Biology Research CenterKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Takahiro Bamba
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Mami Matsuda
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Kentaro Inokuma
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Engineering Biology Research CenterKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Kenta Morita
- Department of Chemical Science and Engineering, Graduate School of EngineeringKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Research Facility Center for Science and TechnologyKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Yuki Kitada
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Yuma Kobayashi
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Takahiro Yukawa
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Kengo Sasaki
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Engineering Biology Research CenterKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Chiaki Ogino
- Engineering Biology Research CenterKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Department of Chemical Science and Engineering, Graduate School of EngineeringKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Engineering Biology Research CenterKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and InnovationKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Engineering Biology Research CenterKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Department of Chemical Science and Engineering, Graduate School of EngineeringKobe University 1‐1 Rokkodai 657‐8501 Nada Kobe Japan
- Biomass Engineering ProgramRIKEN 1‐7‐22 Suehiro‐cho 230‐0045 Tsurumi‐ku, Yokohama Kanagawa Japan
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Felipe Hernández-Pérez A, de Arruda PV, Sene L, da Silva SS, Kumar Chandel A, de Almeida Felipe MDG. Xylitol bioproduction: state-of-the-art, industrial paradigm shift, and opportunities for integrated biorefineries. Crit Rev Biotechnol 2019; 39:924-943. [DOI: 10.1080/07388551.2019.1640658] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - Priscila Vaz de Arruda
- Department of Bioprocess Engineering and Biotechnology-COEBB/TD, Universidade Tecnológica Federal do Paraná, Toledo, Brazil
| | - Luciane Sene
- Center for Exact and Technological Sciences, Universidade Estadual do Oeste de Paraná (UNIOESTE), Cascavel, Brazil
| | - Silvio Silvério da Silva
- Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo, Lorena, Brazil
| | - Anuj Kumar Chandel
- Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo, Lorena, Brazil
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89
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Seike T, Kobayashi Y, Sahara T, Ohgiya S, Kamagata Y, Fujimori KE. Molecular evolutionary engineering of xylose isomerase to improve its catalytic activity and performance of micro-aerobic glucose/xylose co-fermentation in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:139. [PMID: 31178927 PMCID: PMC6551904 DOI: 10.1186/s13068-019-1474-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/23/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Expression of d-xylose isomerase having high catalytic activity in Saccharomyces cerevisiae (S. cerevisiae) is a prerequisite for efficient and economical production of bioethanol from cellulosic biomass. Although previous studies demonstrated functional expression of several xylose isomerases (XI) in S. cerevisiae, identification of XIs having higher catalytic activity is needed. Here, we report a new strategy to improve xylose fermentation in the S. cerevisiae strain IR-2 that involves an evolutionary engineering to select top-performing XIs from eight previously reported XIs derived from various species. RESULTS Eight XI genes shown to have good expression in S. cerevisiae were introduced into the strain IR-2 having a deletion of GRE3 and XKS1 overexpression that allows use of d-xylose as a carbon source. Each transformant was evaluated under aerobic and micro-aerobic culture conditions. The strain expressing XI from Lachnoclostridium phytofermentans ISDg (LpXI) had the highest d-xylose consumption rate after 72 h of micro-aerobic fermentation on d-glucose and d-xylose mixed medium. To enhance LpXI catalytic activity, we performed random mutagenesis using error-prone polymerase chain reaction (PCR), which yielded two LpXI candidates, SS82 and SS92, that showed markedly improved fermentation performance. The LpXI genes in these clones carried either T63I or V162A/N303T point mutations. The SS120 strain expressing LpXI with the double mutation of T63I/V162A assimilated nearly 85 g/L d-glucose and 35 g/L d-xylose to produce 53.3 g/L ethanol in 72 h with an ethanol yield of approximately 0.44 (g/g-input sugars). An in vitro enzyme assay showed that, compared to wild-type, the LpXI double mutant in SS120 had a considerably higher V max (0.107 µmol/mg protein/min) and lower K m (37.1 mM). CONCLUSIONS This study demonstrated that LpXI has the highest d-xylose consumption rate among the XIs expressed in IR-2 under micro-aerobic co-fermentation conditions. A combination of novel mutations (T63I and V162A) significantly improved the enzymatic activity of LpXI, indicating that LpXI-T63I/V162A would be a potential construct for highly efficient production of cellulosic ethanol.
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Affiliation(s)
- Taisuke Seike
- Bioproduction Research Institute (BPRI), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
- Present Address: Center for Biosystems Dynamics Research (BDR), RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874 Japan
| | - Yosuke Kobayashi
- Bioproduction Research Institute (BPRI), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
- Present Address: Biomaterial in Tokyo Company Limited, 4-7 Kashiwa-Inter-Minami, Kashiwa, Chiba 277-0872 Japan
| | - Takehiko Sahara
- Bioproduction Research Institute (BPRI), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
| | - Satoru Ohgiya
- Bioproduction Research Institute (BPRI), National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido 062-8517 Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute (BPRI), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
| | - Kazuhiro E. Fujimori
- Bioproduction Research Institute (BPRI), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
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90
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da Silva RR, Prista C, Loureiro Dias MC, Boscolo M, da Silva R, Gomes E. Improved Utility of Pentoses from Lignocellulolytic Hydrolysate: Challenges and Perspectives for Enabling Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5919-5921. [PMID: 31099567 DOI: 10.1021/acs.jafc.9b02809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Ronivaldo Rodrigues da Silva
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE) , Universidade Estadual Paulista (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
| | - Catarina Prista
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia , Universidade de Lisboa , Tapada da Ajuda, 1349-017 Lisboa , Portugal
| | - Maria Conceição Loureiro Dias
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia , Universidade de Lisboa , Tapada da Ajuda, 1349-017 Lisboa , Portugal
| | - Mauricio Boscolo
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE) , Universidade Estadual Paulista (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
| | - Roberto da Silva
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE) , Universidade Estadual Paulista (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
| | - Eleni Gomes
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE) , Universidade Estadual Paulista (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
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91
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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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92
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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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93
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Hitschler J, Boles E. De novo production of aromatic m-cresol in Saccharomyces cerevisiae mediated by heterologous polyketide synthases combined with a 6-methylsalicylic acid decarboxylase. Metab Eng Commun 2019; 9:e00093. [PMID: 31193192 PMCID: PMC6520567 DOI: 10.1016/j.mec.2019.e00093] [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: 03/12/2019] [Revised: 04/17/2019] [Accepted: 04/29/2019] [Indexed: 11/16/2022] Open
Abstract
As a flavor and platform chemical, m-cresol (3-methylphenol) is a valuable industrial compound that currently is mainly synthesized by chemical methods from fossil resources. In this study, we present the first biotechnological de novo production of m-cresol from sugar in complex yeast extract-peptone medium with the yeast Saccharomyces cerevisiae. A heterologous pathway based on the decarboxylation of the polyketide 6-methylsalicylic acid (6-MSA) was introduced into a CEN.PK yeast strain. For synthesis of 6-MSA, expression of different variants of 6-MSA synthases (MSASs) were compared. Overexpression of codon-optimized MSAS from Penicillium patulum together with activating phosphopantetheinyl transferase npgA from Aspergillus nidulans resulted in up to 367 mg/L 6-MSA production. Additional genomic integration of the genes had a strongly promoting effect and 6-MSA titers reached more than 2 g/L. Simultaneous expression of 6-MSA decarboxylase patG from A. clavatus led to the complete conversion of 6-MSA and production of up to 589 mg/L m-cresol. As addition of 450–750 mg/L m-cresol to yeast cultures nearly completely inhibited growth our data suggest that the toxicity of m-cresol might be the limiting factor for higher production titers. Expression of 6-methylsalicylic acid synthase (MSAS) and decarboxylase enables m-cresol production from sugars in complex medium in S. cerevisiae 6-methylsalicylic acid synthase is limiting 6-MSA and m-cresol production rates Genomic integration of heterologous genes improves product titers Toxicity of m-cresol to yeast cells limits increased production titers
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Key Words
- 6-Methylsalicylic acid decarboxylase
- 6-Methylsalicylic acid synthase
- 6-methylsalicylic acid decarboxylase, PatG
- 6-methylsalicylic acid synthase, MSAS
- 6-methylsalicylic acid, 6-MSA
- Acyl carrier protein, ACP
- Acyltransferase, AT
- Codon-optimization
- Polyketide synthase
- Saccharomyces cerevisiae
- ketoreductase, KR
- ketosynthase, KS
- m-Cresol
- optical density, OD
- phosphopantetheinyl transferase, PPT
- polyketide synthase, PKS
- thioester hydrolase, TH
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Affiliation(s)
- Julia Hitschler
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438, Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438, Frankfurt am Main, Germany
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94
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Liu CG, Xiao Y, Xia XX, Zhao XQ, Peng L, Srinophakun P, Bai FW. Cellulosic ethanol production: Progress, challenges and strategies for solutions. Biotechnol Adv 2019; 37:491-504. [DOI: 10.1016/j.biotechadv.2019.03.002] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 02/18/2019] [Accepted: 03/03/2019] [Indexed: 11/16/2022]
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95
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Seppälä S, Yoo JI, Yur D, O'Malley MA. Heterologous transporters from anaerobic fungi bolster fluoride tolerance in Saccharomyces cerevisiae. Metab Eng Commun 2019; 9:e00091. [PMID: 31016136 PMCID: PMC6475669 DOI: 10.1016/j.mec.2019.e00091] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 03/22/2019] [Accepted: 04/09/2019] [Indexed: 12/21/2022] Open
Abstract
Membrane-embedded transporters are crucial for the stability and performance of microbial production strains. Apart from engineering known transporters derived from model systems, it is equally important to identify transporters from nonconventional organisms that confer advantageous traits for biotechnological applications. Here, we transferred genes encoding fluoride exporter (FEX) proteins from three strains of early-branching anaerobic fungi (Neocallimastigomycota) to Saccharomyces cerevisiae. The heterologous transporters are localized to the plasma membrane and complement a fluoride-sensitive yeast strain that is lacking endogenous fluoride transporters up to 10.24 mM fluoride. Furthermore, we show that fusing an amino-terminal leader sequence to FEX proteins in yeast elevates protein yields, yet inadvertently causes a loss of transporter function. Adaptive laboratory evolution of FEX proteins restores fluoride tolerance of these strains, in one case exceeding the solute tolerance observed in wild type S. cerevisiae; however, the underlying molecular mechanisms and cause for the increased tolerance in the evolved strains remain elusive. Our results suggest that microbial cultures can achieve solvent tolerance through different adaptive trajectories, and the study is a promising step towards the identification, production, and biotechnological application of membrane proteins from nonconventional fungi. First report describing the heterologous production of functional ion transport proteins sourced from anaerobic gut fungi. Codon-optimization enables production of functional, gut fungal membrane proteins in S. cerevisiae but not in E. coli. Addition of an N-terminal leader peptide elevates membrane protein yields yet diminishes cellular activity. Adaptive laboratory evolution restores cellular fluoride export activity in yeast to levels exceeding native tolerance.
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Affiliation(s)
- Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Justin I. Yoo
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Daniel Yur
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
- Corresponding author.
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96
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Online monitoring of the redox potential in microaerobic and anaerobic Scheffersomyces stipitis fermentations. Biotechnol Lett 2019; 41:753-761. [DOI: 10.1007/s10529-019-02674-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/02/2019] [Indexed: 12/30/2022]
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97
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Podolsky IA, Seppälä S, Lankiewicz TS, Brown JL, Swift CL, O'Malley MA. Harnessing Nature's Anaerobes for Biotechnology and Bioprocessing. Annu Rev Chem Biomol Eng 2019; 10:105-128. [PMID: 30883214 DOI: 10.1146/annurev-chembioeng-060718-030340] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Industrial biotechnology has the potential to decrease our reliance on petroleum for fuel and bio-based chemical production and also enable valorization of waste streams. Anaerobic microorganisms thrive in resource-limited environments and offer an array of novel bioactivities in this regard that could revolutionize biomanufacturing. However, they have not been adopted for widespread industrial use owing to their strict growth requirements, limited number of available strains, difficulty in scale-up, and genetic intractability. This review provides an overview of current and future uses for anaerobes in biotechnology and bioprocessing in the postgenomic era. We focus on the recently characterized anaerobic fungi (Neocallimastigomycota) native to the digestive tract of large herbivores, which possess a trove of enzymes, pathways, transporters, and other biomolecules that can be harnessed for numerous biotechnological applications. Resolving current genetic intractability, scale-up, and cultivation challenges will unlock the potential of these lignocellulolytic fungi and other nonmodel micro-organisms to accelerate bio-based production.
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Affiliation(s)
- Igor A Podolsky
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Thomas S Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Jennifer L Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Candice L Swift
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
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98
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Li X, Chen Y, Nielsen J. Harnessing xylose pathways for biofuels production. Curr Opin Biotechnol 2019; 57:56-65. [PMID: 30785001 DOI: 10.1016/j.copbio.2019.01.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/04/2019] [Accepted: 01/15/2019] [Indexed: 01/02/2023]
Abstract
Energy security, environmental pollution, and economic development drive the development of alternatives to fossil fuels as an urgent global priority. Lignocellulosic biomass has the potential to contribute to meeting the demand for biofuel production via hydrolysis and fermentation of released sugars, such as glucose, xylose, and arabinose. Construction of robust cell factories requires introducing and rewiring of their metabolism to efficiently use all these sugars. Here, we review recent advances in re-constructing pathways for metabolism of pentoses, with special focus on xylose metabolism in the most widely used cell factories Saccharomyces cerevisiae and Escherichia coli. We also highlight engineering advanced biofuels-synthesis pathways and describes progress toward overcoming the challenges facing adoption of large-scale biofuel production.
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Affiliation(s)
- Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark; Wallenberg Center for Protein Research, Chalmers University of Technology, Gothenburg, Sweden.
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99
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McCarty NS, Ledesma-Amaro R. Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology. Trends Biotechnol 2019; 37:181-197. [PMID: 30497870 PMCID: PMC6340809 DOI: 10.1016/j.tibtech.2018.11.002] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022]
Abstract
Microbial consortia have been used in biotechnology processes, including fermentation, waste treatment, and agriculture, for millennia. Today, synthetic biologists are increasingly engineering microbial consortia for diverse applications, including the bioproduction of medicines, biofuels, and biomaterials from inexpensive carbon sources. An improved understanding of natural microbial ecosystems, and the development of new tools to construct synthetic consortia and program their behaviors, will vastly expand the functions that can be performed by communities of interacting microorganisms. Here, we review recent advancements in synthetic biology tools and approaches to engineer synthetic microbial consortia, discuss ongoing and emerging efforts to apply consortia for various biotechnological applications, and suggest future applications.
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Affiliation(s)
- Nicholas S. McCarty
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
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100
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Hua Y, Wang J, Zhu Y, Zhang B, Kong X, Li W, Wang D, Hong J. Release of glucose repression on xylose utilization in Kluyveromyces marxianus to enhance glucose-xylose co-utilization and xylitol production from corncob hydrolysate. Microb Cell Fact 2019; 18:24. [PMID: 30709398 PMCID: PMC6359873 DOI: 10.1186/s12934-019-1068-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/20/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Lignocellulosic biomass is one of the most abundant materials for biochemicals production. However, efficient co-utilization of glucose and xylose from the lignocellulosic biomass is a challenge due to the glucose repression in microorganisms. Kluyveromyces marxianus is a thermotolerant and efficient xylose-utilizing yeast. To realize the glucose-xylose co-utilization, analyzing the glucose repression of xylose utilization in K. marxianus is necessary. In addition, a glucose-xylose co-utilization platform strain will facilitate the construction of lignocellulosic biomass-utilizing strains. RESULTS Through gene disruption, hexokinase 1 (KmHXK1) and sucrose non-fermenting 1 (KmSNF1) were proved to be involved in the glucose repression of xylose utilization while disruption of the downstream genes of cyclic AMP-protein kinase A (cAMP-PKA) signaling pathway or sucrose non-fermenting 3 (SNF3) glucose-sensing pathway did not alleviate the repression. Furthermore, disruption of the gene of multicopy inhibitor of GAL gene expression (KmMIG1) alleviated the glucose repression on some nonglucose sugars (galactose, sucrose, and raffinose) but still kept glucose repression of xylose utilization. Real-time PCR analysis of the xylose utilization related genes transcription confirmed these results, and besides, revealed that xylitol dehydrogenase gene (KmXYL2) was the critical gene for xylose utilization and stringently regulated by glucose repression. Many other genes of candidate targets interacting with SNF1 were also evaluated by disruption, but none proved to be the key regulator in the pathway of the glucose repression on xylose utilization. Therefore, there may exist other signaling pathway(s) for glucose repression on xylose consumption. Based on these results, a thermotolerant xylose-glucose co-consumption platform strain of K. marxianus was constructed. Then, exogenous xylose reductase and xylose-specific transporter genes were overexpressed in the platform strain to obtain YHY013. The YHY013 could efficiently co-utilized the glucose and xylose from corncob hydrolysate or xylose mother liquor for xylitol production (> 100 g/L) even with inexpensive organic nitrogen sources. CONCLUSIONS The analysis of the glucose repression in K. marxianus laid the foundation for construction of the glucose-xylose co-utilizing platform strain. The efficient xylitol production strain further verified the potential of the platform strain in exploitation of lignocellulosic biomass.
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Affiliation(s)
- Yan Hua
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, 230026, Anhui, People's Republic of China
| | - Jichao Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yelin Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Biao Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Xin Kong
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, 230026, Anhui, People's Republic of China
| | - Wenjie Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Dongmei Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, 230026, Anhui, People's Republic of China
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, 230026, Anhui, People's Republic of China.
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