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Ma XY, Coleman B, Prabhu P, Wen F. Segmentation and evaluation of pathway module efficiency: Quantitative approach to monitor and overcome evolving bottlenecks in xylose to ethanol pathway. BIORESOURCE TECHNOLOGY 2024; 395:130377. [PMID: 38278451 DOI: 10.1016/j.biortech.2024.130377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Engineering microbes that can efficiently ferment xylose to ethanol is critical to the development of renewable fuels from lignocellulosic biomass. To accelerate the strain optimization process, a method termed Segmentation and Evaluation of Pathway Module Efficiency (SEPME) was developed to enable rapid and iterative identification and removal of metabolic bottlenecks. Using SEPME, the overall pathway was segmented into two modules: the upstream xylose assimilation pathway and the downstream pentose phosphate pathway, glycolysis, and fermentation. The efficiencies of both modules were then quantified to identify the rate controlling module, followed by analyses of control coefficients, reaction rates, and byproduct concentrations to narrow down targets within the module. SEPME analysis revealed that as the strain was engineered with increasing xylose-to-ethanol yields, the bottlenecks shifted within a module and across the two modules. Guided by SEPME, these bottlenecks were removed one by one, and a strain approaching the theoretical ethanol yield was obtained.
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Affiliation(s)
- Xiao Yin Ma
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States; Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Bryan Coleman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States; Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Ponnandy Prabhu
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States; Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, MI 48109, United States.
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Li F, Bai W, Zhang Y, Zhang Z, Zhang D, Shen N, Yuan J, Zhao G, Wang X. Construction of an economical xylose-utilizing Saccharomyces cerevisiae and its ethanol fermentation. FEMS Yeast Res 2024; 24:foae001. [PMID: 38268490 PMCID: PMC10855017 DOI: 10.1093/femsyr/foae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 01/03/2024] [Accepted: 01/23/2024] [Indexed: 01/26/2024] Open
Abstract
Traditional industrial Saccharomyces cerevisiae could not metabolize xylose due to the lack of a specific enzyme system for the reaction from xylose to xylulose. This study aims to metabolically remould industrial S. cerevisiae for the purpose of utilizing both glucose and xylose with high efficiency. Heterologous gene xylA from Piromyces and homologous genes related to xylose utilization were selected to construct expression cassettes and integrated into genome. The engineered strain was domesticated with industrial material under optimizing conditions subsequently to further improve xylose utilization rates. The resulting S. cerevisiae strain ABX0928-0630 exhibits a rapid growth rate and possesses near 100% xylose utilization efficiency to produce ethanol with industrial material. Pilot-scale fermentation indicated the predominant feature of ABX0928-0630 for industrial application, with ethanol yield of 0.48 g/g sugars after 48 hours and volumetric xylose consumption rate of 0.87 g/l/h during the first 24 hours. Transcriptome analysis during the modification and domestication process revealed a significant increase in the expression level of pathways associated with sugar metabolism and sugar sensing. Meanwhile, genes related to glycerol lipid metabolism exhibited a pattern of initial increase followed by a subsequent decrease, providing a valuable reference for the construction of efficient xylose-fermenting strains.
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Affiliation(s)
- Fan Li
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Biochemical and Bioenergy (Zhaodong) Co., Ltd., No. 24, Zhaolan Road, Zhaodong City, Suihua, Heilongjiang 151100, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Wenxin Bai
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
| | - Yuan Zhang
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Zijian Zhang
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
| | - Deguo Zhang
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
- COFCO Biotechnology Co., Ltd., No. 1, Zhongliang Avenue, Yuhui District, Bengbu, Anhui 233010, China
| | - Naidong Shen
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Jingwei Yuan
- COFCO Biochemical and Bioenergy (Zhaodong) Co., Ltd., No. 24, Zhaolan Road, Zhaodong City, Suihua, Heilongjiang 151100, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Guomiao Zhao
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Xiaoyan Wang
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
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Wang LR, Zhang ZX, Nong FT, Li J, Huang PW, Ma W, Zhao QY, Sun XM. Engineering the xylose metabolism in Schizochytrium sp. to improve the utilization of lignocellulose. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:114. [PMID: 36289497 PMCID: PMC9609267 DOI: 10.1186/s13068-022-02215-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/15/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Schizochytrium sp. is a heterotrophic, oil-producing microorganism that can efficiently produce lipids. However, the industrial production of bulk chemicals using Schizochytrium sp. is still not economically viable due to high-cost culture medium. Replacing glucose with cheap and renewable lignocellulose is a highly promising approach to reduce production costs, but Schizochytrium sp. cannot efficiently metabolize xylose, a major pentose in lignocellulosic biomass. RESULTS In order to improve the utilization of lignocellulose by Schizochytrium sp., we cloned and functionally characterized the genes encoding enzymes involved in the xylose metabolism. The results showed that the endogenous xylose reductase and xylulose kinase genes possess corresponding functional activities. Additionally, attempts were made to construct a strain of Schizochytrium sp. that can effectively use xylose by using genetic engineering techniques to introduce exogenous xylitol dehydrogenase/xylose isomerase; however, the introduction of heterologous xylitol dehydrogenase did not produce a xylose-utilizing engineered strain, whereas the introduction of xylose isomerase did. The results showed that the engineered strain 308-XI with an exogenous xylose isomerase could consume 8.2 g/L xylose over 60 h of cultivation. Xylose consumption was further elevated to 11.1 g/L when heterologous xylose isomerase and xylulose kinase were overexpressed simultaneously. Furthermore, cultivation of 308-XI-XK(S) using lignocellulosic hydrolysates, which contained glucose and xylose, yielded a 22.4 g/L of dry cell weight and 5.3 g/L of total lipid titer, respectively, representing 42.7 and 30.4% increases compared to the wild type. CONCLUSION This study shows that engineering of Schizochytrium sp. to efficiently utilize xylose is conducive to improve its utilization of lignocellulose, which can reduce the costs of industrial lipid production.
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Affiliation(s)
- Ling-Ru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu, China
| | - Zi-Xu Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu, China
| | - Fang-Tong Nong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu, China
| | - Jin Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu, China
| | - Peng-Wei Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu, China
| | - Wang Ma
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu, China
| | - Quan-Yu Zhao
- School of Pharmaceutical Science, Nanjing Tech University, No. 30 Puzhu South Road, Pukou District, Nanjing, Jiangsu, China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu, China.
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Cellulosic Ethanol Production Using a Dual Functional Novel Yeast. Int J Microbiol 2022; 2022:7853935. [PMID: 35295685 PMCID: PMC8920679 DOI: 10.1155/2022/7853935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
Reducing the cost of cellulosic ethanol production, especially for cellulose hydrolytic enzymes, is vital to growing a sustainable and efficient cellulosic ethanol industry and bio-based economy. Using an ethanologenic yeast able to produce hydrolytic enzymes, such as Clavispora NRRL Y-50464, is one solution. NRRL Y-50464 is fast-growing and robust, and tolerates inhibitory compounds 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF) associated with lignocellulose-to-fuel conversion. It produces three forms of β-glucosidase isozymes, BGL1, BGL2, and BGL3, and ferment cellobiose as the sole carbon source. These β-glucosidases exhibited desirable enzyme kinetic parameters and high levels of enzyme-specific activity toward cellobiose and many oligosaccharide substrates. They tolerate the product inhibition of glucose and ethanol, and are stable to temperature and pH conditions. These characteristics are desirable for more efficient cellulosic ethanol production by simultaneous saccharification and fermentation. NRRL Y-50464 provided the highest cellulosic ethanol titers and conversion rates at lower cellulase loadings, using either pure cellulose or agricultural residues, as so far reported in the literature. This review summarizes NRRL Y-50464 performance on cellulosic ethanol production from refined cellulose, rice straw, and corn stover processed in various ways, in the presence or absence of furfural and HMF. This dual functional yeast has potential to serve as a prototype for the development of next-generation biocatalysts. Perspectives on continued strain development and process engineering improvements for more efficient cellulosic ethanol production from lignocellulosic materials are also discussed.
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Miyamoto RY, de Melo RR, de Mesquita Sampaio IL, de Sousa AS, Morais ER, Sargo CR, Zanphorlin LM. Paradigm shift in xylose isomerase usage: a novel scenario with distinct applications. Crit Rev Biotechnol 2021; 42:693-712. [PMID: 34641740 DOI: 10.1080/07388551.2021.1962241] [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] [Indexed: 10/20/2022]
Abstract
Isomerases are enzymes that induce physical changes in a molecule without affecting the original molecular formula. Among this class of enzymes, xylose isomerases (XIs) are the most studied to date, partly due to their extensive application in industrial processes to produce high-fructose corn sirups. In recent years, the need for sustainable initiatives has triggered efforts to improve the biobased economy through the use of renewable raw materials. In this context, D-xylose usage is crucial as it is the second-most abundant sugar in nature. The application of XIs in biotransforming xylose, enabling downstream metabolism in several microorganisms, is a smart strategy for ensuring a low-carbon footprint and producing several value-added biochemicals with broad industrial applications such as in the food, cosmetics, pharmaceutical, and polymer industries. Considering recent advancements that have expanded the range of applications of XIs, this review provides a comprehensive and concise overview of XIs, from their primary sources to the biochemical and structural features that influence their mechanisms of action. This comprehensive review may help address the challenges involved in XI applications in different industries and facilitate the exploitation of xylose bioprocesses.
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Affiliation(s)
- Renan Yuji Miyamoto
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Faculty of Pharmaceutical Sciences (FCF), State University of Campinas (UNICAMP), Campinas, Brazil
| | - Ricardo Rodrigues de Melo
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Isabelle Lobo de Mesquita Sampaio
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Faculty of Food Engineering (FEA), State University of Campinas (UNICAMP), Campinas, Brazil
| | - Amanda Silva de Sousa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Edvaldo Rodrigo Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Faculty of Food Engineering (FEA), State University of Campinas (UNICAMP), Campinas, Brazil
| | - Cintia Regina Sargo
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Leticia Maria Zanphorlin
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
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Zan X, Sun J, Chu L, Cui F, Huo S, Song Y, Koffas MAG. Improved glucose and xylose co-utilization by overexpression of xylose isomerase and/or xylulokinase genes in oleaginous fungus Mucor circinelloides. Appl Microbiol Biotechnol 2021; 105:5565-5575. [PMID: 34215904 DOI: 10.1007/s00253-021-11392-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/28/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022]
Abstract
Most of the oleaginous microorganisms cannot assimilate xylose in the presence of glucose, which is the major bottleneck in the bioconversion of lignocellulose to biodiesel. Our present study revealed that overexpression of xylose isomerase (XI) gene xylA or xylulokinase (XK) gene xks1 increased the xylose consumption by 25 to 37% and enhanced the lipid content by 8 to 28% during co-fermentation of glucose and xylose. In xylA overexpressing strain Mc-XI, the activity of XI was 1.8-fold higher and the mRNA level of xylA at 24 h and 48 h was 11- and 13-fold higher than that of the control, respectively. In xks1 overexpressing strain Mc-XK, the mRNA level of xks1 was 4- to 11-fold of that of the control strain and the highest XK activity of 950 nmol min-1 mg-1 at 72 h which was 2-fold higher than that of the control. Additionally, expression of a translational fusion of xylA and xks1 further enhanced the xylose utilization rate by 45%. Our results indicated that overexpression of xylA and/or xks1 is a promising strategy to improve the xylose and glucose co-utilization, alleviate the glucose repression, and produce lipid from lignocellulosic biomass in the oleaginous fungus M. circinelloides. KEY POINTS: • Overexpressing xylA or xks1 increased the xylose consumption and the lipid content. • The xylose isomerase activity and the xylA mRNA level were enhanced in strain Mc-XI. • Co-expression of xylA and xks1 further enhanced the xylose utilization rate by 45%.
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Affiliation(s)
- Xinyi Zan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Jianing Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Linfang Chu
- School of Food Science and Technology, Jiang University, Wuxi, 214000, People's Republic of China
| | - Fengjie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Shuhao Huo
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255049, People's Republic of China.
| | - Mattheos A G Koffas
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
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Sharma S, Arora A. Tracking strategic developments for conferring xylose utilization/fermentation by Saccharomyces cerevisiae. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01590-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Abstract
Purpose
Efficient ethanol production through lignocellulosic biomass hydrolysates could solve energy crisis as it is economically sustainable and ecofriendly. Saccharomyces cerevisiae is the work horse for lignocellulosic bioethanol production at industrial level. But its inability to ferment and utilize xylose limits the overall efficacy of the process.
Method
Data for the review was selected using different sources, such as Biofuels digest, Statista, International energy agency (IEA). Google scholar was used as a search engine to search literature for yeast metabolic engineering approaches. Keywords used were metabolic engineering of yeast for bioethanol production from lignocellulosic biomass.
Result
Through these approaches, interconnected pathways can be targeted randomly. Moreover, the improved strains genetic makeup can help us understand the mechanisms involved for this purpose.
Conclusion
This review discusses all possible approaches for metabolic engineering of yeast. These approaches may reveal unknown hidden mechanisms and construct ways for the researchers to produce novel and modified strains.
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Improving Xylose Fermentation in Saccharomyces cerevisiae by Expressing Nuclear-Localized Hexokinase 2. Microorganisms 2020; 8:microorganisms8060856. [PMID: 32517148 PMCID: PMC7356972 DOI: 10.3390/microorganisms8060856] [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: 05/19/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
Understanding the relationship between xylose and the metabolic regulatory systems is a prerequisite to enhance xylose utilization in recombinant S. cerevisiae strains. Hexokinase 2 (Hxk2p) is an intracellular glucose sensor that localizes to the cytoplasm or the nucleus depending on the carbon source. Hxk2p interacts with Mig1p to regulate gene transcription in the nucleus. Here, we investigated the effect of nucleus-localized Hxk2p and Mig1p on xylose fermentation. The results show that the expression of HXK2S14A, which encodes a constitutively nucleus-localized Hxk2p, increased the xylose consumption rate, the ethanol production rate, and the ethanol yield of the engineered yeast strain by 23.5%, 78.6% and 42.6%, respectively. The deletion of MIG1 decreased xylose utilization and eliminated the positive effect of Hxk2p. We then performed RNA-seq and found that the targets of Hxk2pS14A on xylose were mainly genes that encode RNA-binding proteins. This is very different from the known targets of Mig1p and supports the notion that the Hxk2p-Mig1p interaction is abolished in the presence of xylose. These results will improve our understanding of the interrelation between the Snf1p-Mig1p-Hxk2p glucose signaling pathway and xylose utilization in S. cerevisiae and suggests that the expression of HXK2S14A could be a viable strategy to improve xylose utilization.
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Simulating Extracellular Glucose Signals Enhances Xylose Metabolism in Recombinant Saccharomyces cerevisiae. Microorganisms 2020; 8:microorganisms8010100. [PMID: 31936831 PMCID: PMC7022881 DOI: 10.3390/microorganisms8010100] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/30/2019] [Accepted: 01/08/2020] [Indexed: 12/24/2022] Open
Abstract
Efficient utilization of both glucose and xylose from lignocellulosic biomass would be economically beneficial for biofuel production. Recombinant Saccharomyces cerevisiae strains with essential genes and metabolic networks for xylose metabolism can ferment xylose; however, the efficiency of xylose fermentation is much lower than that of glucose, the preferred carbon source of yeast. Implications from our previous work suggest that activation of the glucose sensing system may benefit xylose metabolism. Here, we show that deleting cAMP phosphodiesterase genes PDE1 and PDE2 increased PKA activity of strains, and consequently, increased xylose utilization. Compared to the wild type strain, the specific xylose consumption rate (rxylose) of the pde1Δ pde2Δ mutant strains increased by 50%; the specific ethanol-producing rate (rethanol) of the strain increased by 70%. We also show that HXT1 and HXT2 transcription levels slightly increased when xylose was present. We also show that HXT1 and HXT2 transcription levels slightly increased when xylose was present. Deletion of either RGT2 or SNF3 reduced expression of HXT1 in strains cultured in 1 g L−1 xylose, which suggests that xylose can bind both Snf3 and Rgt2 and slightly alter their conformations. Deletion of SNF3 significantly weakened the expression of HXT2 in the yeast cultured in 40 g L−1 xylose, while deletion of RGT2 did not weaken expression of HXT2, suggesting that S. cerevisiae mainly depends on Snf3 to sense a high concentration of xylose (40 g L−1). Finally, we show that deletion of Rgt1, increased rxylose by 24% from that of the control. Our findings indicate how S. cerevisiae may respond to xylose and this study provides novel targets for further engineering of xylose-fermenting strains.
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Geijer C, Faria-Oliveira F, Moreno AD, Stenberg S, Mazurkewich S, Olsson L. Genomic and transcriptomic analysis of Candida intermedia reveals the genetic determinants for its xylose-converting capacity. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:48. [PMID: 32190113 PMCID: PMC7068945 DOI: 10.1186/s13068-020-1663-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/21/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND An economically viable production of biofuels and biochemicals from lignocellulose requires microorganisms that can readily convert both the cellulosic and hemicellulosic fractions into product. The yeast Candida intermedia displays a high capacity for uptake and conversion of several lignocellulosic sugars including the abundant pentose d-xylose, an underutilized carbon source since most industrially relevant microorganisms cannot naturally ferment it. Thus, C. intermedia constitutes an important source of knowledge and genetic information that could be transferred to industrial microorganisms such as Saccharomyces cerevisiae to improve their capacity to ferment lignocellulose-derived xylose. RESULTS To understand the genetic determinants that underlie the metabolic properties of C. intermedia, we sequenced the genomes of both the in-house-isolated strain CBS 141442 and the reference strain PYCC 4715. De novo genome assembly and subsequent analysis revealed C. intermedia to be a haploid species belonging to the CTG clade of ascomycetous yeasts. The two strains have highly similar genome sizes and number of protein-encoding genes, but they differ on the chromosomal level due to numerous translocations of large and small genomic segments. The transcriptional profiles for CBS 141442 grown in medium with either high or low concentrations of glucose and xylose were determined through RNA-sequencing analysis, revealing distinct clusters of co-regulated genes in response to different specific growth rates, carbon sources and osmotic stress. Analysis of the genomic and transcriptomic data also identified multiple xylose reductases, one of which displayed dual NADH/NADPH co-factor specificity that likely plays an important role for co-factor recycling during xylose fermentation. CONCLUSIONS In the present study, we performed the first genomic and transcriptomic analysis of C. intermedia and identified several novel genes for conversion of xylose. Together the results provide insights into the mechanisms underlying saccharide utilization in C. intermedia and reveal potential target genes to aid in xylose fermentation in S. cerevisiae.
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Affiliation(s)
- Cecilia Geijer
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fábio Faria-Oliveira
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Antonio D. Moreno
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Present Address: Biofuels Unit, Department of Energy, CIEMAT, Madrid, Spain
| | - Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Scott Mazurkewich
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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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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12
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Ye S, Jeong D, Shon JC, Liu KH, Kim KH, Shin M, Kim SR. Deletion of PHO13 improves aerobic L-arabinose fermentation in engineered Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2019; 46:1725-1731. [PMID: 31501960 DOI: 10.1007/s10295-019-02233-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/31/2019] [Indexed: 10/26/2022]
Abstract
Pentose sugars are increasingly being used in industrial applications of Saccharomyces cerevisiae. Although L-arabinose is a highlighted pentose that has been identified as next-generation biomass, arabinose fermentation has not yet undergone extensive development for industrial utilization. In this study, we integrated a heterologous fungal arabinose pathway with a deletion of PHO13 phosphatase gene. PHO13 deletion increased arabinose consumption rate and specific ethanol productivity under aerobic conditions and consequently depleted sedoheptulose by activation of the TAL1 gene. Global metabolite profiling indicated upregulation of the pentose phosphate pathway and downstream effects such as trehalose accumulation and downregulation of the TCA cycle. Our results suggest that engineering of PHO13 has ample potential for arabinose conversion to ethanol as an industrial source for biofuels.
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Affiliation(s)
- Suji Ye
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Jong Cheol Shon
- Department of Environmental Toxicology Research Center, Korea Institute of Toxicology, Jinju, Republic of Korea.,College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Kwang-Hyeon Liu
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Minhye Shin
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea.
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea.
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13
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Li YC, Xie CY, Yang BX, Tang YQ, Wu B, Sun ZY, Gou M, Xia ZY. Comparative Transcriptome Analysis of Recombinant Industrial Saccharomyces cerevisiae Strains with Different Xylose Utilization Pathways. Appl Biochem Biotechnol 2019; 189:1007-1019. [DOI: 10.1007/s12010-019-03060-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/22/2019] [Indexed: 01/03/2023]
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14
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Wagner ER, Myers KS, Riley NM, Coon JJ, Gasch AP. PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production. PLoS One 2019; 14:e0212389. [PMID: 31112537 PMCID: PMC6528989 DOI: 10.1371/journal.pone.0212389] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/29/2019] [Indexed: 12/25/2022] Open
Abstract
Lignocellulosic biomass offers a sustainable source for biofuel production that does not compete with food-based cropping systems. Importantly, two critical bottlenecks prevent economic adoption: many industrially relevant microorganisms cannot ferment pentose sugars prevalent in lignocellulosic medium, leaving a significant amount of carbon unutilized. Furthermore, chemical biomass pretreatment required to release fermentable sugars generates a variety of toxins, which inhibit microbial growth and metabolism, specifically limiting pentose utilization in engineered strains. Here we dissected genetic determinants of anaerobic xylose fermentation and stress tolerance in chemically pretreated corn stover biomass, called hydrolysate. We previously revealed that loss-of-function mutations in the stress-responsive MAP kinase HOG1 and negative regulator of the RAS/Protein Kinase A (PKA) pathway, IRA2, enhances anaerobic xylose fermentation. However, these mutations likely reduce cells' ability to tolerate the toxins present in lignocellulosic hydrolysate, making the strain especially vulnerable to it. We tested the contributions of Hog1 and PKA signaling via IRA2 or PKA negative regulatory subunit BCY1 to metabolism, growth, and stress tolerance in corn stover hydrolysate and laboratory medium with mixed sugars. We found mutations causing upregulated PKA activity increase growth rate and glucose consumption in various media but do not have a specific impact on xylose fermentation. In contrast, mutation of HOG1 specifically increased xylose usage. We hypothesized improving stress tolerance would enhance the rate of xylose consumption in hydrolysate. Surprisingly, increasing stress tolerance did not augment xylose fermentation in lignocellulosic medium in this strain background, suggesting other mechanisms besides cellular stress limit this strain's ability for anaerobic xylose fermentation in hydrolysate.
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Affiliation(s)
- Ellen R. Wagner
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI United States of America
| | - Kevin S. Myers
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI United States of America
| | - Nicholas M. Riley
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI United States of America
- Genome Center of Wisconsin, University of Wisconsin–Madison, Madison, WI United States of America
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison WI United States of America
- Morgridge Institute for Research, Madison, WI United States of America
| | - Audrey P. Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI United States of America
- Genome Center of Wisconsin, University of Wisconsin–Madison, Madison, WI United States of America
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI United States of America
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15
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Shin M, Kim JW, Ye S, Kim S, Jeong D, Lee DY, Kim JN, Jin YS, Kim KH, Kim SR. Comparative global metabolite profiling of xylose-fermenting Saccharomyces cerevisiae SR8 and Scheffersomyces stipitis. Appl Microbiol Biotechnol 2019; 103:5435-5446. [PMID: 31001747 DOI: 10.1007/s00253-019-09829-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/18/2019] [Accepted: 04/04/2019] [Indexed: 01/22/2023]
Abstract
Bioconversion of lignocellulosic biomass into ethanol requires efficient xylose fermentation. Previously, we developed an engineered Saccharomyces cerevisiae strain, named SR8, through rational and inverse metabolic engineering strategies, thereby improving its xylose fermentation and ethanol production. However, its fermentation characteristics have not yet been fully evaluated. In this study, we investigated the xylose fermentation and metabolic profiles for ethanol production in the SR8 strain compared with native Scheffersomyces stipitis. The SR8 strain showed a higher maximum ethanol titer and xylose consumption rate when cultured with a high concentration of xylose, mixed sugars, and under anaerobic conditions than Sch. stipitis. However, its ethanol productivity was less on 40 g/L xylose as the sole carbon source, mainly due to the formation of xylitol and glycerol. Global metabolite profiling indicated different intracellular production rates of xylulose and glycerol-3-phosphate in the two strains. In addition, compared with Sch. stipitis, SR8 had increased abundances of metabolites from sugar metabolism and decreased abundances of metabolites from energy metabolism and free fatty acids. These results provide insights into how to control and balance redox cofactors for the production of fuels and chemicals from xylose by the engineered S. cerevisiae.
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Affiliation(s)
- Minhye Shin
- Department of Biotechnology, Graduate School, Korea University, Seoul, Korea
| | - Jeong-Won Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Korea
| | - Suji Ye
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Korea
| | - Sooah Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Korea
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Korea
| | - Do Yup Lee
- Department of Bio and Fermentation Convergence Technology, BK21 PLUS Program, Kookmin University, Seoul, Korea
| | - Jong Nam Kim
- Department of Food Science and Nutrition, Dongseo University, Busan, Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, the University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Korea
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Korea.
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16
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Gao M, Ploessl D, Shao Z. Enhancing the Co-utilization of Biomass-Derived Mixed Sugars by Yeasts. Front Microbiol 2019; 9:3264. [PMID: 30723464 PMCID: PMC6349770 DOI: 10.3389/fmicb.2018.03264] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/14/2018] [Indexed: 12/11/2022] Open
Abstract
Plant biomass is a promising carbon source for producing value-added chemicals, including transportation biofuels, polymer precursors, and various additives. Most engineered microbial hosts and a select group of wild-type species can metabolize mixed sugars including oligosaccharides, hexoses, and pentoses that are hydrolyzed from plant biomass. However, most of these microorganisms consume glucose preferentially to non-glucose sugars through mechanisms generally defined as carbon catabolite repression. The current lack of simultaneous mixed-sugar utilization limits achievable titers, yields, and productivities. Therefore, the development of microbial platforms capable of fermenting mixed sugars simultaneously from biomass hydrolysates is essential for economical industry-scale production, particularly for compounds with marginal profits. This review aims to summarize recent discoveries and breakthroughs in the engineering of yeast cell factories for improved mixed-sugar co-utilization based on various metabolic engineering approaches. Emphasis is placed on enhanced non-glucose utilization, discovery of novel sugar transporters free from glucose repression, native xylose-utilizing microbes, consolidated bioprocessing (CBP), improved cellulase secretion, and creation of microbial consortia for improving mixed-sugar utilization. Perspectives on the future development of biorenewables industry are provided in the end.
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Affiliation(s)
- Meirong Gao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States
| | - Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States.,The Ames Laboratory, Iowa State University, Ames, IA, United States.,The Interdisciplinary Microbiology Program, Biorenewables Research Laboratory, Iowa State University, Ames, IA, United States
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17
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Lane S, Dong J, Jin YS. Value-added biotransformation of cellulosic sugars by engineered Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2018; 260:380-394. [PMID: 29655899 DOI: 10.1016/j.biortech.2018.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 05/26/2023]
Abstract
The substantial research efforts into lignocellulosic biofuels have generated an abundance of valuable knowledge and technologies for metabolic engineering. In particular, these investments have led to a vast growth in proficiency of engineering the yeast Saccharomyces cerevisiae for consuming lignocellulosic sugars, enabling the simultaneous assimilation of multiple carbon sources, and producing a large variety of value-added products by introduction of heterologous metabolic pathways. While microbial conversion of cellulosic sugars into large-volume low-value biofuels is not currently economically feasible, there may still be opportunities to produce other value-added chemicals as regulation of cellulosic sugar metabolism is quite different from glucose metabolism. This review summarizes these recent advances with an emphasis on employing engineered yeast for the bioconversion of lignocellulosic sugars into a variety of non-ethanol value-added products.
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Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jia Dong
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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18
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Spagnuolo M, Shabbir Hussain M, Gambill L, Blenner M. Alternative Substrate Metabolism in Yarrowia lipolytica. Front Microbiol 2018; 9:1077. [PMID: 29887845 PMCID: PMC5980982 DOI: 10.3389/fmicb.2018.01077] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/07/2018] [Indexed: 11/13/2022] Open
Abstract
Recent advances in genetic engineering capabilities have enabled the development of oleochemical producing strains of Yarrowia lipolytica. Much of the metabolic engineering effort has focused on pathway engineering of the product using glucose as the feedstock; however, alternative substrates, including various other hexose and pentose sugars, glycerol, lipids, acetate, and less-refined carbon feedstocks, have not received the same attention. In this review, we discuss recent work leading to better utilization of alternative substrates. This review aims to provide a comprehensive understanding of the current state of knowledge for alternative substrate utilization, suggest potential pathways identified through homology in the absence of prior characterization, discuss recent work that either identifies, endogenous or cryptic metabolism, and describe metabolic engineering to improve alternative substrate utilization. Finally, we describe the critical questions and challenges that remain for engineering Y. lipolytica for better alternative substrate utilization.
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Affiliation(s)
- Michael Spagnuolo
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
| | - Murtaza Shabbir Hussain
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
| | - Lauren Gambill
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
- Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, United States
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
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19
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Wei S, Liu Y, Wu M, Ma T, Bai X, Hou J, Shen Y, Bao X. Disruption of the transcription factors Thi2p and Nrm1p alleviates the post-glucose effect on xylose utilization in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:112. [PMID: 29686730 PMCID: PMC5901872 DOI: 10.1186/s13068-018-1112-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/06/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND The recombinant Saccharomyces cerevisiae strains that acquired the ability to utilize xylose through metabolic and evolutionary engineering exhibit good performance when xylose is the sole carbon source in the medium (designated the X stage in the present work). However, the xylose consumption rate of strains is generally low after glucose depletion during glucose-xylose co-fermentation, despite the presence of xylose in the medium (designated the GX stage in the present work). Glucose fermentation appears to reduce the capacity of these strains to "recognize" xylose during the GX stage, a phenomenon termed the post-glucose effect on xylose metabolism. RESULTS Two independent xylose-fermenting S. cerevisiae strains derived from a haploid laboratory strain and a diploid industrial strain were used in the present study. Their common characteristics were investigated to reveal the mechanism underlying the post-glucose effect and to develop methods to alleviate this effect. Both strains showed lower growth and specific xylose consumption rates during the GX stage than during the X stage. Glycolysis, the pentose phosphate pathway, and translation-related gene expression were reduced; meanwhile, genes in the tricarboxylic acid cycle and glyoxylic acid cycle demonstrated higher expression during the GX stage than during the X stage. The effects of 11 transcription factors (TFs) whose expression levels significantly differed between the GX and X stages in both strains were investigated. Knockout of THI2 promoted ribosome synthesis, and the growth rate, specific xylose utilization rate, and specific ethanol production rate of the strain increased by 17.4, 26.8, and 32.4%, respectively, in the GX stage. Overexpression of the ribosome-related genes RPL9A, RPL7B, and RPL7A also enhanced xylose utilization in a corresponding manner. Furthermore, the overexpression of NRM1, which is related to the cell cycle, increased the growth rate by 8.7%, the xylose utilization rate by 30.0%, and the ethanol production rate by 76.6%. CONCLUSIONS The TFs Thi2p and Nrm1p exerted unexpected effects on the post-glucose effect, enhancing ribosome synthesis and altering the cell cycle, respectively. The results of this study will aid in maintaining highly efficient xylose metabolism during glucose-xylose co-fermentation, which is utilized for lignocellulosic bioethanol production.
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Affiliation(s)
- Shan Wei
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
- School of Life Science, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
| | - Yanan Liu
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
- School of Life Science, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
| | - Meiling Wu
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
- School of Life Science, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
| | - Tiantai Ma
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
- School of Life Science, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
| | - Xiangzheng Bai
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
- School of Life Science, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
- School of Life Science, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
- School of Life Science, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
- School of Life Science, Shandong University, Shan Da Nan Road 27, Jinan, 250100 China
- Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Daxue Rd 3501, Jinan, 250353 China
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20
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Feng Q, Liu ZL, Weber SA, Li S. Signature pathway expression of xylose utilization in the genetically engineered industrial yeast Saccharomyces cerevisiae. PLoS One 2018; 13:e0195633. [PMID: 29621349 PMCID: PMC5886582 DOI: 10.1371/journal.pone.0195633] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/25/2018] [Indexed: 01/18/2023] Open
Abstract
Haploid laboratory strains of Saccharomyces cerevisiae are commonly used for genetic engineering to enable their xylose utilization but little is known about the industrial yeast which is often recognized as diploid and as well as haploid and tetraploid. Here we report three unique signature pathway expression patterns and gene interactions in the centre metabolic pathways that signify xylose utilization of genetically engineered industrial yeast S. cerevisiae NRRL Y-50463, a diploid yeast. Quantitative expression analysis revealed outstanding high levels of constitutive expression of YXI, a synthesized yeast codon-optimized xylose isomerase gene integrated into chromosome XV of strain Y-50463. Comparative expression analysis indicated that the YXI was necessary to initiate the xylose metabolic pathway along with a set of heterologous xylose transporter and utilization facilitating genes including XUT4, XUT6, XKS1 and XYL2. The highly activated transketolase and transaldolase genes TKL1, TKL2, TAL1 and NQM1 as well as their complex interactions in the non-oxidative pentose phosphate pathway branch were critical for the serial of sugar transformation to drive the metabolic flow into glycolysis for increased ethanol production. The significantly increased expression of the entire PRS gene family facilitates functions of the life cycle and biosynthesis superpathway for the yeast. The outstanding higher levels of constitutive expression of YXI and the first insight into the signature pathway expression and the gene interactions in the closely related centre metabolic pathways from the industrial yeast aid continued efforts for development of the next-generation biocatalyst. Our results further suggest the industrial yeast is a desirable delivery vehicle for new strain development for efficient lignocellulose-to-advanced biofuels production.
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Affiliation(s)
- Quanzhou Feng
- Bioenergy Research Unit, US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL, United States of America
- Institute of New Energy Technology, Tsinghua University, Haidian Qu, Beijing, China
| | - Z. Lewis Liu
- Bioenergy Research Unit, US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL, United States of America
- USDA-MOST Joint Research Center for Biofuels, Peoria, IL, United States of America
- * E-mail: (ZLL); (SL)
| | - Scott A. Weber
- Bioenergy Research Unit, US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL, United States of America
| | - Shizhong Li
- Institute of New Energy Technology, Tsinghua University, Haidian Qu, Beijing, China
- USDA-MOST Joint Research Center for Biofuels, Peoria, IL, United States of America
- * E-mail: (ZLL); (SL)
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21
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Bioethanol a Microbial Biofuel Metabolite; New Insights of Yeasts Metabolic Engineering. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation4010016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Xylose transport in yeast for lignocellulosic ethanol production: Current status. J Biosci Bioeng 2017; 125:259-267. [PMID: 29196106 DOI: 10.1016/j.jbiosc.2017.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/07/2017] [Accepted: 10/10/2017] [Indexed: 01/07/2023]
Abstract
Lignocellulosic ethanol has been considered as an alternative transportation fuel. Utilization of hemicellulosic fraction in lignocelluloses is crucial in economical production of lignocellulosic ethanol. However, this fraction has not efficiently been utilized by traditional yeast Saccharomyces cerevisiae. Genetically modified S. cerevisiae, which can utilize xylose, has several limitations including low ethanol yield, redox imbalance, and undesired metabolite formation similar to native xylose utilizing yeasts. Besides, xylose uptake is a major issue, where sugar transport system plays an important role. These genetically modified and wild-type yeast strains have further been engineered for improved xylose uptake. Various techniques have been employed to facilitate the xylose transportation in these strains. The present review is focused on the sugar transport machineries, mechanisms of xylose transport, limitations and how to deal with xylose transport for xylose assimilation in yeast cells. The recent advances in different techniques to facilitate the xylose transportation have also been discussed.
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23
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Miskovic L, Alff-Tuomala S, Soh KC, Barth D, Salusjärvi L, Pitkänen JP, Ruohonen L, Penttilä M, Hatzimanikatis V. A design-build-test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:166. [PMID: 28674555 PMCID: PMC5485749 DOI: 10.1186/s13068-017-0838-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/06/2017] [Indexed: 05/28/2023]
Abstract
BACKGROUND Recent advancements in omics measurement technologies have led to an ever-increasing amount of available experimental data that necessitate systems-oriented methodologies for efficient and systematic integration of data into consistent large-scale kinetic models. These models can help us to uncover new insights into cellular physiology and also to assist in the rational design of bioreactor or fermentation processes. Optimization and Risk Analysis of Complex Living Entities (ORACLE) framework for the construction of large-scale kinetic models can be used as guidance for formulating alternative metabolic engineering strategies. RESULTS We used ORACLE in a metabolic engineering problem: improvement of the xylose uptake rate during mixed glucose-xylose consumption in a recombinant Saccharomyces cerevisiae strain. Using the data from bioreactor fermentations, we characterized network flux and concentration profiles representing possible physiological states of the analyzed strain. We then identified enzymes that could lead to improved flux through xylose transporters (XTR). For some of the identified enzymes, including hexokinase (HXK), we could not deduce if their control over XTR was positive or negative. We thus performed a follow-up experiment, and we found out that HXK2 deletion improves xylose uptake rate. The data from the performed experiments were then used to prune the kinetic models, and the predictions of the pruned population of kinetic models were in agreement with the experimental data collected on the HXK2-deficient S. cerevisiae strain. CONCLUSIONS We present a design-build-test cycle composed of modeling efforts and experiments with a glucose-xylose co-utilizing recombinant S. cerevisiae and its HXK2-deficient mutant that allowed us to uncover interdependencies between upper glycolysis and xylose uptake pathway. Through this cycle, we also obtained kinetic models with improved prediction capabilities. The present study demonstrates the potential of integrated "modeling and experiments" systems biology approaches that can be applied for diverse applications ranging from biotechnology to drug discovery.
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Affiliation(s)
- Ljubisa Miskovic
- Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | | | - Keng Cher Soh
- Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Dorothee Barth
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | | | | | - Laura Ruohonen
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
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24
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Kwak S, Jin YS. Production of fuels and chemicals from xylose by engineered Saccharomyces cerevisiae: a review and perspective. Microb Cell Fact 2017; 16:82. [PMID: 28494761 PMCID: PMC5425999 DOI: 10.1186/s12934-017-0694-9] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 05/02/2017] [Indexed: 02/06/2023] Open
Abstract
Efficient xylose utilization is one of the most important pre-requisites for developing an economic microbial conversion process of terrestrial lignocellulosic biomass into biofuels and biochemicals. A robust ethanol producing yeast Saccharomyces cerevisiae has been engineered with heterologous xylose assimilation pathways. A two-step oxidoreductase pathway consisting of NAD(P)H-linked xylose reductase and NAD+-linked xylitol dehydrogenase, and one-step isomerase pathway using xylose isomerase have been employed to enable xylose assimilation in engineered S. cerevisiae. However, the resulting engineered yeast exhibited inefficient and slow xylose fermentation. In order to improve the yield and productivity of xylose fermentation, expression levels of xylose assimilation pathway enzymes and their kinetic properties have been optimized, and additional optimizations of endogenous or heterologous metabolisms have been achieved. These efforts have led to the development of engineered yeast strains ready for the commercialization of cellulosic bioethanol. Interestingly, xylose metabolism by engineered yeast was preferably respiratory rather than fermentative as in glucose metabolism, suggesting that xylose can serve as a desirable carbon source capable of bypassing metabolic barriers exerted by glucose repression. Accordingly, engineered yeasts showed superior production of valuable metabolites derived from cytosolic acetyl-CoA and pyruvate, such as 1-hexadecanol and lactic acid, when the xylose assimilation pathway and target synthetic pathways were optimized in an adequate manner. While xylose has been regarded as a sugar to be utilized because it is present in cellulosic hydrolysates, potential benefits of using xylose instead of glucose for yeast-based biotechnological processes need to be realized.
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Affiliation(s)
- Suryang Kwak
- Department of Food Science and Human Nutrition and Carl R. Woose Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition and Carl R. Woose Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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25
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Li YJ, Wang MM, Chen YW, Wang M, Fan LH, Tan TW. Engineered yeast with a CO 2-fixation pathway to improve the bio-ethanol production from xylose-mixed sugars. Sci Rep 2017; 7:43875. [PMID: 28262754 PMCID: PMC5338314 DOI: 10.1038/srep43875] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/01/2017] [Indexed: 11/25/2022] Open
Abstract
Bio-ethanol production from lignocellulosic raw materials could serve as a sustainable potential for improving the supply of liquid fuels in face of the food-to-fuel competition and the growing energy demand. Xylose is the second abundant sugar of lignocelluloses hydrolysates, but its commercial-scale conversion to ethanol by fermentation is challenged by incomplete and inefficient utilization of xylose. Here, we use a coupled strategy of simultaneous maltose utilization and in-situ carbon dioxide (CO2) fixation to achieve efficient xylose fermentation by the engineered Saccharomyces cerevisiae. Our results showed that the introduction of CO2 as electron acceptor for nicotinamide adenine dinucleotide (NADH) oxidation increased the total ethanol productivity and yield at the expense of simultaneous maltose and xylose utilization. Our achievements present an innovative strategy using CO2 to drive and redistribute the central pathways of xylose to desirable products and demonstrate a possible breakthrough in product yield of sugars.
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Affiliation(s)
- Yun-Jie Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- National Energy R&D Center for Biorefinery, Beijing, People’s Republic of China
- Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
| | - Miao-Miao Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- National Energy R&D Center for Biorefinery, Beijing, People’s Republic of China
- Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
| | - Ya-Wei Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- National Energy R&D Center for Biorefinery, Beijing, People’s Republic of China
- Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
| | - Meng Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- National Energy R&D Center for Biorefinery, Beijing, People’s Republic of China
- Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
| | - Li-Hai Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- National Energy R&D Center for Biorefinery, Beijing, People’s Republic of China
- Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
| | - Tian-Wei Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- National Energy R&D Center for Biorefinery, Beijing, People’s Republic of China
- Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
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26
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Zhang GC, Turner TL, Jin YS. Enhanced xylose fermentation by engineered yeast expressing NADH oxidase through high cell density inoculums. ACTA ACUST UNITED AC 2017; 44:387-395. [DOI: 10.1007/s10295-016-1899-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/25/2016] [Indexed: 12/22/2022]
Abstract
Abstract
Accumulation of reduced byproducts such as glycerol and xylitol during xylose fermentation by engineered Saccharomyces cerevisiae hampers the economic production of biofuels and chemicals from cellulosic hydrolysates. In particular, engineered S. cerevisiae expressing NADPH-linked xylose reductase (XR) and NAD+-linked xylitol dehydrogenase (XDH) produces substantial amounts of the reduced byproducts under anaerobic conditions due to the cofactor difference of XR and XDH. While the additional expression of a water-forming NADH oxidase (NoxE) from Lactococcus lactis in engineered S. cerevisiae with the XR/XDH pathway led to reduced glycerol and xylitol production and increased ethanol yields from xylose, volumetric ethanol productivities by the engineered yeast decreased because of growth defects from the overexpression of noxE. In this study, we introduced noxE into an engineered yeast strain (SR8) exhibiting near-optimal xylose fermentation capacity. To overcome the growth defect caused by the overexpression of noxE, we used a high cell density inoculum for xylose fermentation by the SR8 expressing noxE. The resulting strain, SR8N, not only showed a higher ethanol yield and lower byproduct yields, but also exhibited a high ethanol productivity during xylose fermentation. As noxE overexpression elicits a negligible growth defect on glucose conditions, the beneficial effects of noxE overexpression were substantial when a mixture of glucose and xylose was used. Consumption of glucose led to rapid cell growth and therefore enhanced the subsequent xylose fermentation. As a result, the SR8N strain produced more ethanol and fewer byproducts from a mixture of glucose and xylose than the parental SR8 strain without noxE overexpression. Our results suggest that the growth defects from noxE overexpression can be overcome in the case of fermenting lignocellulose-derived sugars such as glucose and xylose.
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Affiliation(s)
- Guo-Chang Zhang
- grid.35403.31 0000000419369991 Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign 1206 W. Gregory Drive 61801 Urbana IL USA
- grid.35403.31 0000000419369991 Department of Food Science and Human Nutrition University of Illinois at Urbana-Champaign 61801 Urbana IL USA
| | - Timothy L Turner
- grid.35403.31 0000000419369991 Department of Food Science and Human Nutrition University of Illinois at Urbana-Champaign 61801 Urbana IL USA
| | - Yong-Su Jin
- grid.35403.31 0000000419369991 Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign 1206 W. Gregory Drive 61801 Urbana IL USA
- grid.35403.31 0000000419369991 Department of Food Science and Human Nutrition University of Illinois at Urbana-Champaign 61801 Urbana IL USA
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27
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Costa CE, Romaní A, Cunha JT, Johansson B, Domingues L. Integrated approach for selecting efficient Saccharomyces cerevisiae for industrial lignocellulosic fermentations: Importance of yeast chassis linked to process conditions. BIORESOURCE TECHNOLOGY 2017; 227:24-34. [PMID: 28013133 DOI: 10.1016/j.biortech.2016.12.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/02/2016] [Accepted: 12/04/2016] [Indexed: 05/22/2023]
Abstract
In this work, four robust yeast chassis isolated from industrial environments were engineered with the same xylose metabolic pathway. The recombinant strains were physiologically characterized in synthetic xylose and xylose-glucose medium, on non-detoxified hemicellulosic hydrolysates of fast-growing hardwoods (Eucalyptus and Paulownia) and agricultural residues (corn cob and wheat straw) and on Eucalyptus hydrolysate at different temperatures. Results show that the co-consumption of xylose-glucose was dependent on the yeast background. Moreover, heterogeneous results were obtained among different hydrolysates and temperatures for each individual strain pointing to the importance of designing from the very beginning a tailor-made yeast considering the specific raw material and process.
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Affiliation(s)
- Carlos E Costa
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Aloia Romaní
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Björn Johansson
- CBMA - Center of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.
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28
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Internalization of Heterologous Sugar Transporters by Endogenous α-Arrestins in the Yeast Saccharomyces cerevisiae. Appl Environ Microbiol 2016; 82:7074-7085. [PMID: 27694235 PMCID: PMC5118918 DOI: 10.1128/aem.02148-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/23/2016] [Indexed: 01/03/2023] Open
Abstract
When expressed in Saccharomyces cerevisiae using either of two constitutive yeast promoters (PGK1prom and CCW12prom), the transporters CDT-1 and CDT-2 from the filamentous fungus Neurospora crassa are able to catalyze, respectively, active transport and facilitated diffusion of cellobiose (and, for CDT-2, also xylan and its derivatives). In S. cerevisiae, endogenous permeases are removed from the plasma membrane by clathrin-mediated endocytosis and are marked for internalization through ubiquitinylation catalyzed by Rsp5, a HECT class ubiquitin:protein ligase (E3). Recruitment of Rsp5 to specific targets is mediated by a 14-member family of endocytic adaptor proteins, termed α-arrestins. Here we demonstrate that CDT-1 and CDT-2 are subject to α-arrestin-mediated endocytosis, that four α-arrestins (Rod1, Rog3, Aly1, and Aly2) are primarily responsible for this internalization, that the presence of the transport substrate promotes transporter endocytosis, and that, at least for CDT-2, residues located in its C-terminal cytosolic domain are necessary for its efficient endocytosis. Both α-arrestin-deficient cells expressing CDT-2 and otherwise wild-type cells expressing CDT-2 mutants unresponsive to α-arrestin-driven internalization exhibit an increased level of plasma membrane-localized transporter compared to that of wild-type cells, and they grow, utilize the transport substrate, and generate ethanol anaerobically better than control cells. IMPORTANCE Ethanolic fermentation of the breakdown products of plant biomass by budding yeast Saccharomyces cerevisiae remains an attractive biofuel source. To achieve this end, genes for heterologous sugar transporters and the requisite enzyme(s) for subsequent metabolism have been successfully expressed in this yeast. For one of the heterologous transporters examined in this study, we found that the amount of this protein residing in the plasma membrane was the rate-limiting factor for utilization of the cognate carbon source (cellobiose) and its conversion to ethanol.
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29
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High-titer-ethanol production from cellulosic hydrolysate by an engineered strain of Saccharomyces cerevisiae during an in situ removal process reducing the inhibition of ethanol on xylose metabolism. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.04.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Nielsen F, Zacchi G, Galbe M, Wallberg O. Prefermentation improves ethanol yield in separate hydrolysis and cofermentation of steam-pretreated wheat straw. ACTA ACUST UNITED AC 2016. [DOI: 10.1186/s40508-016-0054-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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31
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Jo SE, Seong YJ, Lee HS, Lee SM, Kim SJ, Park K, Park YC. Microaerobic conversion of xylose to ethanol in recombinant Saccharomyces cerevisiae SX6 MUT expressing cofactor-balanced xylose metabolic enzymes and deficient in ALD6. J Biotechnol 2016; 227:72-78. [DOI: 10.1016/j.jbiotec.2016.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/27/2016] [Accepted: 04/04/2016] [Indexed: 11/30/2022]
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32
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Zhang L, Ma Y, Zhao C, He B, Zhu X, Yang W. Entrapment of Xylanase within a Polyethylene Glycol Net-Cloth Grafted on Polypropylene Nonwoven Fabrics with Exceptional Operational Stability and Its Application for Hydrolysis of Corncob Hemicelluloses. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.6b00254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lihua Zhang
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuhong Ma
- Key Laboratory of Carbon Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029, China
| | - Changwen Zhao
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Bin He
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xing Zhu
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wantai Yang
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
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33
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Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae. Sci Rep 2016; 6:19512. [PMID: 26781725 PMCID: PMC4726032 DOI: 10.1038/srep19512] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/09/2015] [Indexed: 12/24/2022] Open
Abstract
Enhancing xylose utilization has been a major focus in Saccharomyces cerevisiae strain-engineering efforts. The incentive for these studies arises from the need to use all sugars in the typical carbon mixtures that comprise standard renewable plant-biomass-based carbon sources. While major advances have been made in developing utilization pathways, the efficient import of five carbon sugars into the cell remains an important bottleneck in this endeavor. Here we use an engineered S. cerevisiae BY4742 strain, containing an established heterologous xylose utilization pathway, and imposed a laboratory evolution regime with xylose as the sole carbon source. We obtained several evolved strains with improved growth phenotypes and evaluated the best candidate using genome resequencing. We observed remarkably few single nucleotide polymorphisms in the evolved strain, among which we confirmed a single amino acid change in the hexose transporter HXT7 coding sequence to be responsible for the evolved phenotype. The mutant HXT7(F79S) shows improved xylose uptake rates (Vmax = 186.4 ± 20.1 nmol•min−1•mg−1) that allows the S. cerevisiae strain to show significant growth with xylose as the sole carbon source, as well as partial co-utilization of glucose and xylose in a mixed sugar cultivation.
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34
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Shalley Sharma, Sonia Sharma, Surender Singh, Lata, Anju Arora. Improving Yeast Strains for Pentose Hexose Co-fermentation: Successes and Hurdles. SPRINGER PROCEEDINGS IN ENERGY 2016. [DOI: 10.1007/978-81-322-2773-1_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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35
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Qi X, Zha J, Liu GG, Zhang W, Li BZ, Yuan YJ. Heterologous xylose isomerase pathway and evolutionary engineering improve xylose utilization in Saccharomyces cerevisiae. Front Microbiol 2015; 6:1165. [PMID: 26539187 PMCID: PMC4612707 DOI: 10.3389/fmicb.2015.01165] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 10/08/2015] [Indexed: 12/24/2022] Open
Abstract
Xylose utilization is one key issue for the bioconversion of lignocelluloses. It is a promising approach to engineering heterologous pathway for xylose utilization in Saccharomyces cerevisiae. Here, we constructed a xylose-fermenting yeast SyBE001 through combinatorial fine-tuning the expression of XylA and endogenous XKS1. Additional overexpression of genes RKI1, RPE1, TKL1, and TAL1 in the non-oxidative pentose phosphate pathway (PPP) in SyBE001 increased the xylose consumption rate by 1.19-fold. By repetitive adaptation, the xylose utilization rate was further increased by ∼10-fold in the resultant strain SyBE003. Gene expression analysis identified a variety of genes with significantly changed expression in the PPP, glycolysis and the tricarboxylic acid cycle in SyBE003.
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Affiliation(s)
- Xin Qi
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Jian Zha
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Gao-Gang Liu
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Weiwen Zhang
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
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36
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Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures. Appl Microbiol Biotechnol 2015; 100:969-85. [DOI: 10.1007/s00253-015-7038-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 09/14/2015] [Accepted: 09/22/2015] [Indexed: 12/27/2022]
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37
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Lee TC, Xiong W, Paddock T, Carrieri D, Chang IF, Chiu HF, Ungerer J, Hank Juo SH, Maness PC, Yu J. Engineered xylose utilization enhances bio-products productivity in the cyanobacterium Synechocystis sp. PCC 6803. Metab Eng 2015; 30:179-189. [DOI: 10.1016/j.ymben.2015.06.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/06/2015] [Accepted: 06/03/2015] [Indexed: 01/14/2023]
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38
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Park JB, Kim JS, Jang SW, Hong E, Ha SJ. The Application of Thermotolerant Yeast Kluyveromyces marxianus as a Potential Industrial Workhorse for Biofuel Production. ACTA ACUST UNITED AC 2015. [DOI: 10.7841/ksbbj.2015.30.3.125] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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39
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Kim SM, Guo J, Kwak S, Jin YS, Lee DK, Singh V. Effects of genetic variation and growing condition of prairie cordgrass on feedstock composition and ethanol yield. BIORESOURCE TECHNOLOGY 2015; 183:70-77. [PMID: 25723129 DOI: 10.1016/j.biortech.2015.02.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 02/06/2015] [Accepted: 02/07/2015] [Indexed: 06/04/2023]
Abstract
Prairie cordgrass (Spartina pectinata L.) has the potential to be a feedstock for bioethanol. It is native to North America, and has extensive genetic diversity. Eleven natural populations of prairie cordgrass harvested in 2011 and 2012 were studied. Compositions of the samples showed significant differences within the same year, and between the two years. Two highest, one medium and two lowest glucan concentration samples from each year were selected to evaluate ethanol yield after dilute acid pretreatment and simultaneous saccharification and co-fermentation using Saccharomycescerevisiae SR8 that can ferment both glucose and xylose. Up to 88% of theoretical ethanol yields were achieved. Our research demonstrates the potential of prairie cordgrass as a dedicated energy crop with ethanol yields of 205.0-275.6 g/kg biomass and 1748-4368 L/ha, depending on feedstock composition and biomass yield. These ethanol yields are comparable with those of switchgrass, corn stover and bagasse.
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Affiliation(s)
- Sun Min Kim
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, 1304 West Pennsylvania Avenue, Urbana, IL 61801, United States
| | - Jia Guo
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1102 South Goodwin Avenue, Urbana, IL 61801, United States
| | - Suryang Kwak
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 905 South Goodwin Avenue, Urbana, IL 61801, United States
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 905 South Goodwin Avenue, Urbana, IL 61801, United States; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States
| | - D K Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1102 South Goodwin Avenue, Urbana, IL 61801, United States
| | - Vijay Singh
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, 1304 West Pennsylvania Avenue, Urbana, IL 61801, United States.
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40
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Challenges for the production of bioethanol from biomass using recombinant yeasts. ADVANCES IN APPLIED MICROBIOLOGY 2015; 92:89-125. [PMID: 26003934 DOI: 10.1016/bs.aambs.2015.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Lignocellulose biomass, one of the most abundant renewable resources on the planet, is an alternative sustainable energy source for the production of second-generation biofuels. Energy in the form of simple or complex carbohydrates can be extracted from lignocellulose biomass and fermented by microorganisms to produce bioethanol. Despite 40 years of active and cutting-edge research invested into the development of technologies to produce bioethanol from lignocellulosic biomass, the process remains commercially unviable. This review describes the achievements that have been made in generating microorganisms capable of utilizing both simple and complex sugars from lignocellulose biomass and the fermentation of these sugars into ethanol. We also provide a discussion on the current "roadblocks" standing in the way of making second-generation bioethanol a commercially viable alternative to fossil fuels.
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41
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Wasylenko TM, Stephanopoulos G. Metabolomic and (13)C-metabolic flux analysis of a xylose-consuming Saccharomyces cerevisiae strain expressing xylose isomerase. Biotechnol Bioeng 2014; 112:470-83. [PMID: 25311863 DOI: 10.1002/bit.25447] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/11/2014] [Accepted: 08/27/2014] [Indexed: 11/09/2022]
Abstract
Over the past two decades, significant progress has been made in the engineering of xylose-consuming Saccharomyces cerevisiae strains for production of lignocellulosic biofuels. However, the ethanol productivities achieved on xylose are still significantly lower than those observed on glucose for reasons that are not well understood. We have undertaken an analysis of central carbon metabolite pool sizes and metabolic fluxes on glucose and on xylose under aerobic and anaerobic conditions in a strain capable of rapid xylose assimilation via xylose isomerase in order to investigate factors that may limit the rate of xylose fermentation. We find that during xylose utilization the flux through the non-oxidative Pentose Phosphate Pathway (PPP) is high but the flux through the oxidative PPP is low, highlighting an advantage of the strain employed in this study. Furthermore, xylose fails to elicit the full carbon catabolite repression response that is characteristic of glucose fermentation in S. cerevisiae. We present indirect evidence that the incomplete activation of the fermentation program on xylose results in a bottleneck in lower glycolysis, leading to inefficient re-oxidation of NADH produced in glycolysis.
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Affiliation(s)
- Thomas M Wasylenko
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, 02139, Massachussetts
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42
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Lisha KP, Sarkar D. In silico analysis of bioethanol production from glucose/xylose mixtures during fed-batch fermentation of co-culture and mono-culture systems. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-014-0320-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Ethanol Production from Xylo-oligosaccharides by Xylose-FermentingSaccharomyces cerevisiaeExpressing β-Xylosidase. Biosci Biotechnol Biochem 2014; 75:1140-6. [DOI: 10.1271/bbb.110043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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44
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Petrova P, Ivanova V. Perspectives for the Production of Bioethanol from Lignocellulosic Materials. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2010.10817894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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45
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Kim SR, Park YC, Jin YS, Seo JH. Strain engineering of Saccharomyces cerevisiae for enhanced xylose metabolism. Biotechnol Adv 2013; 31:851-61. [DOI: 10.1016/j.biotechadv.2013.03.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 02/23/2013] [Accepted: 03/04/2013] [Indexed: 12/27/2022]
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46
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Expression of Arabidopsis thaliana xylose isomerase gene and its effect on ethanol production in Flammulina velutipes. Fungal Biol 2013; 117:776-82. [PMID: 24295916 DOI: 10.1016/j.funbio.2013.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 09/04/2013] [Accepted: 09/30/2013] [Indexed: 11/21/2022]
Abstract
To improve the pentose fermentation rate in Flammulina velutipes, the putative xylose isomerase (XI) gene from Arabidopsis thaliana was cloned and introduced into F. velutipes and the gene expression was evaluated in transformants. mRNA expression of the putative XI gene and XI activity were observed in two transformants, indicating that the putative gene from A. thaliana was successfully expressed in F. velutipes as a xylose isomerase. In addition, ethanol production from xylose was increased in the recombinant strains. This is the first report demonstrating the possibility of using plant genes as candidates for improving the characteristics of F. velutipes.
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Zha J, Shen M, Hu M, Song H, Yuan Y. Enhanced expression of genes involved in initial xylose metabolism and the oxidative pentose phosphate pathway in the improved xylose-utilizing Saccharomyces cerevisiae through evolutionary engineering. J Ind Microbiol Biotechnol 2013; 41:27-39. [PMID: 24113893 DOI: 10.1007/s10295-013-1350-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 09/17/2013] [Indexed: 01/03/2023]
Abstract
Fermentation of xylose in lignocellulosic hydrolysates by Saccharomyces cerevisiae has been achieved through heterologous expression of the xylose reductase (XR)-xylitol dehydrogenase (XDH) pathway. However, the fermentation efficiency is far from the requirement for industrial application due to high yield of the byproduct xylitol, low ethanol yield, and low xylose consumption rate. Through evolutionary engineering, an improved xylose-utilizing strain SyBE005 was obtained with 78.3 % lower xylitol production and a 2.6-fold higher specific ethanol production rate than those of the parent strain SyBE004, which expressed an engineered NADP(+)-preferring XDH. The transcriptional differences between SyBE005 and SyBE004 were investigated by quantitative RT-PCR. Genes including XYL1, XYL2, and XKS1 in the initial xylose metabolic pathway showed the highest up-regulation in SyBE005. The increased expression of XYL1 and XYL2 correlated with enhanced enzymatic activities of XR and XDH. In addition, the expression level of ZWF1 in the oxidative pentose phosphate pathway increased significantly in SyBE005, indicating an elevated demand for NADPH from XR. Genes involved in the TCA cycle (LAT1, CIT1, CIT2, KGD1, KGD, SDH2) and gluconeogenesis (ICL1, PYC1) were also up-regulated in SyBE005. Genomic analysis revealed that point mutations in transcriptional regulators CYC8 and PHD1 might be responsible for the altered expression. In addition, a mutation (Y89S) in ZWF1 was identified which might improve NADPH production in SyBE005. Our results suggest that increasing the expression of XYL1, XYL2, XKS1, and enhancing NADPH supply are promising strategies to improve xylose fermentation in recombinant S. cerevisiae.
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Affiliation(s)
- Jian Zha
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin, 300072, People's Republic of China
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Salusjärvi L, Kaunisto S, Holmström S, Vehkomäki ML, Koivuranta K, Pitkänen JP, Ruohonen L. Overexpression of NADH-dependent fumarate reductase improves D-xylose fermentation in recombinant Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2013; 40:1383-92. [PMID: 24113892 DOI: 10.1007/s10295-013-1344-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/09/2013] [Indexed: 01/31/2023]
Abstract
Deviation from optimal levels and ratios of redox cofactors NAD(H) and NADP(H) is common when microbes are metabolically engineered. The resulting redox imbalance often reduces the rate of substrate utilization as well as biomass and product formation. An example is the metabolism of D-xylose by recombinant Saccharomyces cerevisiae strains expressing xylose reductase and xylitol dehydrogenase encoding genes from Scheffersomyces stipitis. This pathway requires both NADPH and NAD(+). The effect of overexpressing the glycosomal NADH-dependent fumarate reductase (FRD) of Trypanosoma brucei in D-xylose-utilizing S. cerevisiae alone and together with an endogenous, cytosol directed NADH-kinase (POS5Δ17) was studied as one possible solution to overcome this imbalance. Expression of FRD and FRD + POS5Δ17 resulted in 60 and 23 % increase in ethanol yield, respectively, on D-xylose under anaerobic conditions. At the same time, xylitol yield decreased in the FRD strain suggesting an improvement in redox balance. We show that fumarate reductase of T. brucei can provide an important source of NAD(+) in yeast under anaerobic conditions, and can be useful for metabolic engineering strategies where the redox cofactors need to be balanced. The effects of FRD and NADH-kinase on aerobic and anaerobic D-xylose and D-glucose metabolism are discussed.
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Affiliation(s)
- Laura Salusjärvi
- VTT, Technical Research Centre of Finland, PO Box 1000, 02044, VTT, Finland,
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Koivistoinen OM, Kuivanen J, Barth D, Turkia H, Pitkänen JP, Penttilä M, Richard P. Glycolic acid production in the engineered yeasts Saccharomyces cerevisiae and Kluyveromyces lactis. Microb Cell Fact 2013; 12:82. [PMID: 24053654 PMCID: PMC3850452 DOI: 10.1186/1475-2859-12-82] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/15/2013] [Indexed: 11/24/2022] Open
Abstract
Background Glycolic acid is a C2 hydroxy acid that is a widely used chemical compound. It can be polymerised to produce biodegradable polymers with excellent gas barrier properties. Currently, glycolic acid is produced in a chemical process using fossil resources and toxic chemicals. Biotechnological production of glycolic acid using renewable resources is a desirable alternative. Results The yeasts Saccharomyces cerevisiae and Kluyveromyces lactis are suitable organisms for glycolic acid production since they are acid tolerant and can grow in the presence of up to 50 g l-1 glycolic acid. We engineered S. cerevisiae and K. lactis for glycolic acid production using the reactions of the glyoxylate cycle to produce glyoxylic acid and then reducing it to glycolic acid. The expression of a high affinity glyoxylate reductase alone already led to glycolic acid production. The production was further improved by deleting genes encoding malate synthase and the cytosolic form of isocitrate dehydrogenase. The engineered S. cerevisiae strain produced up to about 1 g l-1 of glycolic acid in a medium containing d-xylose and ethanol. Similar modifications in K. lactis resulted in a much higher glycolic acid titer. In a bioreactor cultivation with d-xylose and ethanol up to 15 g l-1 of glycolic acid was obtained. Conclusions This is the first demonstration of engineering yeast to produce glycolic acid. Prior to this work glycolic acid production through the glyoxylate cycle has only been reported in bacteria. The benefit of a yeast host is the possibility for glycolic acid production also at low pH, which was demonstrated in flask cultivations. Production of glycolic acid was first shown in S. cerevisiae. To test whether a Crabtree negative yeast would be better suited for glycolic acid production we engineered K. lactis in the same way and demonstrated it to be a better host for glycolic acid production.
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Affiliation(s)
- Outi M Koivistoinen
- VTT Technical Research Centre of Finland, Tietotie 2, Espoo FI-02044, P,O, Box 1000, VTT, Finland.
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Ismail KSK, Sakamoto T, Hasunuma T, Kondo A. Time-based comparative transcriptomics in engineered xylose-utilizing Saccharomyces cerevisiae identifies temperature-responsive genes during ethanol production. J Ind Microbiol Biotechnol 2013; 40:1039-50. [PMID: 23748446 DOI: 10.1007/s10295-013-1293-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/14/2013] [Indexed: 01/07/2023]
Abstract
Agricultural residues comprising lignocellulosic materials are excellent sources of pentose sugar, which can be converted to ethanol as fuel. Ethanol production via consolidated bioprocessing requires a suitable microorganism to withstand the harsh fermentation environment of high temperature, high ethanol concentration, and exposure to inhibitors. We genetically enhanced an industrial Saccharomyces cerevisiae strain, sun049, enabling it to uptake xylose as the sole carbon source at high fermentation temperature. This strain was able to produce 13.9 g/l ethanol from 50 g/l xylose at 38 °C. To better understand the xylose consumption ability during long-term, high-temperature conditions, we compared by transcriptomics two fermentation conditions: high temperature (38 °C) and control temperature (30 °C) during the first 12 h of fermentation. This is the first long-term, time-based transcriptomics approach, and it allowed us to discover the role of heat-responsive genes when xylose is the sole carbon source. The results suggest that genes related to amino acid, cell wall, and ribosomal protein synthesis are down-regulated under heat stress. To allow cell stability and continuous xylose uptake in order to produce ethanol, hexose transporter HXT5, heat shock proteins, ubiquitin proteins, and proteolysis were all induced at high temperature. We also speculate that the strong relationship between high temperature and increased xylitol accumulation represents the cell's mechanism to protect itself from heat degradation.
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Affiliation(s)
- Ku Syahidah Ku Ismail
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada, Kobe, 657-8501, Japan
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