1
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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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2
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Hector RE, Mertens JA, Nichols NN. Metabolic engineering of a stable haploid strain derived from lignocellulosic inhibitor tolerant Saccharomyces cerevisiae natural isolate YB-2625. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:190. [PMID: 38057826 DOI: 10.1186/s13068-023-02442-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Significant genetic diversity exists across Saccharomyces strains. Natural isolates and domesticated brewery and industrial strains are typically more robust than laboratory strains when challenged with inhibitory lignocellulosic hydrolysates. These strains also contain genes that are not present in lab strains and likely contribute to their superior inhibitor tolerance. However, many of these strains have poor sporulation efficiencies and low spore viability making subsequent gene analysis, further metabolic engineering, and genomic analyses of the strains challenging. This work aimed to develop an inhibitor tolerant haploid with stable mating type from S. cerevisiae YB-2625, which was originally isolated from bagasse. RESULTS Haploid spores isolated from four tetrads from strain YB-2625 were tested for tolerance to furfural and HMF. Due to natural mutations present in the HO-endonuclease, all haploid strains maintained a stable mating type. One of the haploids, YRH1946, did not flocculate and showed enhanced tolerance to furfural and HMF. The tolerant haploid strain was further engineered for xylose fermentation by integration of the genes for xylose metabolism at two separate genomic locations (ho∆ and pho13∆). In fermentations supplemented with inhibitors from acid hydrolyzed corn stover, the engineered haploid strain derived from YB-2625 was able to ferment all of the glucose and 19% of the xylose, whereas the engineered lab strains performed poorly in fermentations. CONCLUSIONS Understanding the molecular mechanisms of inhibitor tolerance will aid in developing strains with improved growth and fermentation performance using biomass-derived sugars. The inhibitor tolerant, xylose fermenting, haploid strain described in this work has potential to serve as a platform strain for identifying pathways required for inhibitor tolerance, and for metabolic engineering to produce fuels and chemicals from undiluted lignocellulosic hydrolysates.
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Affiliation(s)
- Ronald E Hector
- Agricultural Research Service, USDA, National Center for Agricultural Utilization Research, (Bioenergy Research), 1815 N University, Peoria, IL, 61604, USA.
| | - Jeffrey A Mertens
- Agricultural Research Service, USDA, National Center for Agricultural Utilization Research, (Bioenergy Research), 1815 N University, Peoria, IL, 61604, USA
| | - Nancy N Nichols
- Agricultural Research Service, USDA, National Center for Agricultural Utilization Research, (Bioenergy Research), 1815 N University, Peoria, IL, 61604, USA
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Identification of Mutations Responsible for Improved Xylose Utilization in an Adapted Xylose Isomerase Expressing Saccharomyces cerevisiae Strain. FERMENTATION 2022. [DOI: 10.3390/fermentation8120669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Economic conversion of biomass to biofuels and chemicals requires efficient and complete utilization of xylose. Saccharomyces cerevisiae strains engineered for xylose utilization are still considerably limited in their overall ability to metabolize xylose. In this study, we identified causative mutations resulting in improved xylose fermentation of an adapted S. cerevisiae strain expressing codon-optimized xylose isomerase and xylulokinase genes from the rumen bacterium Prevotella ruminicola. Genome sequencing identified single-nucleotide polymorphisms in seven open reading frames. Tetrad analysis showed that mutations in both PBS2 and PHO13 genes were required for increased xylose utilization. Single deletion of either PBS2 or PHO13 did not improve xylose utilization in strains expressing the xylose isomerase pathway. Saccharomyces can also be engineered for xylose metabolism using the xylose reductase/xylitol dehydrogenase genes from Scheffersomyces stipitis. In strains expressing the xylose reductase pathway, single deletion of PHO13 did show a significant increase xylose utilization, and further improvement in growth and fermentation was seen when PBS2 was also deleted. These findings will extend the understanding of metabolic limitations for xylose utilization in S. cerevisiae as well as understanding of how they differ among strains engineered with two different xylose utilization pathways.
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Cheng C, Wang WB, Sun ML, Tang RQ, Bai L, Alper HS, Zhao XQ. Deletion of NGG1 in a recombinant Saccharomyces cerevisiae improved xylose utilization and affected transcription of genes related to amino acid metabolism. Front Microbiol 2022; 13:960114. [PMID: 36160216 PMCID: PMC9493327 DOI: 10.3389/fmicb.2022.960114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Production of biofuels and biochemicals from xylose using yeast cell factory is of great interest for lignocellulosic biorefinery. Our previous studies revealed that a natural yeast isolate Saccharomyces cerevisiae YB-2625 has superior xylose-fermenting ability. Through integrative omics analysis, NGG1, which encodes a transcription regulator as well as a subunit of chromatin modifying histone acetyltransferase complexes was revealed to regulate xylose metabolism. Deletion of NGG1 in S. cerevisiae YRH396h, which is the haploid version of the recombinant yeast using S. cerevisiae YB-2625 as the host strain, improved xylose consumption by 28.6%. Comparative transcriptome analysis revealed that NGG1 deletion down-regulated genes related to mitochondrial function, TCA cycle, ATP biosynthesis, respiration, as well as NADH generation. In addition, the NGG1 deletion mutant also showed transcriptional changes in amino acid biosynthesis genes. Further analysis of intracellular amino acid content confirmed the effect of NGG1 on amino acid accumulation during xylose utilization. Our results indicated that NGG1 is one of the core nodes for coordinated regulation of carbon and nitrogen metabolism in the recombinant S. cerevisiae. This work reveals novel function of Ngg1p in yeast metabolism and provides basis for developing robust yeast strains to produce ethanol and biochemicals using lignocellulosic biomass.
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Affiliation(s)
- Cheng Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Meng-Lin Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui-Qi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Long Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Xin-Qing Zhao,
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Hector RE, Mertens JA, Nichols NN. Increased expression of the fluorescent reporter protein ymNeonGreen in Saccharomyces cerevisiae by reducing RNA secondary structure near the start codon. BIOTECHNOLOGY REPORTS 2022; 33:e00697. [PMID: 35036336 PMCID: PMC8749125 DOI: 10.1016/j.btre.2021.e00697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/06/2022]
Abstract
Stable secondary RNA structure 3′ of the start codon inhibits ymNeonGreen expression. Removing secondary RNA structure increased expression in S. cerevisiae and E. coli. Expression was increased 2-fold in S. cerevisiae. Expression was increased 3.8-fold in E. coli. Increased expression in S. cerevisiae was promoter independent.
Expression of a new fluorescent reporter protein called mNeonGreen, that is not based on the jellyfish green fluorescent protein (GFP) sequence, shows increased brightness and folding speed compared to enhanced GFP. However, in vivo brightness of mNeonGreen and its yeast-optimized variant ymNeonGreen in S. cerevisiae is lower than expected, limiting the use of this high quantum yield, fast-folding reporter in budding yeast. This study shows that secondary RNA structure near the start codon in the ymNeonGreen ORF inhibits expression in S. cerevisiae. Removing secondary structure, without altering the ymNeonGreen protein sequence, led to a 2 and 4-fold increase in fluorescence when expressed in S. cerevisiae and E. coli, respectively. In S. cerevisiae, increased fluorescence was seen with strong and weak promoters and led to higher transcript levels suggesting greater transcript stability and improved expression in the absence of stable secondary RNA structure near the start codon.
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Cortivo PRD, Aydos LF, Hickert LR, Rosa CA, Hector RE, Mertens JA, Ayub MAZ. Performance of xylose-fermenting yeasts in oat and soybean hulls hydrolysate and improvement of ethanol production using immobilized cell systems. Biotechnol Lett 2021; 43:2011-2026. [PMID: 34480641 DOI: 10.1007/s10529-021-03182-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 08/30/2021] [Indexed: 11/25/2022]
Abstract
We investigated the fermentation of a mixture of oat and soybean hulls (1:1) subjected to acid (AH) or enzymatic (EH) hydrolyses, with both showing high osmotic pressures (> 1200 Osm kg-1) for the production of ethanol. Yeasts of genera Spathaspora, Scheffersomyces, Sugiymaella, and Candida, most of them biodiverse Brazilian isolates and previously untested in bioprocesses, were cultivated in these hydrolysates. Spathaspora passalidarum UFMG-CM-469 showed the best ethanol production kinetics in suspended cells cultures in acid hydrolysate, under microaerobic and anaerobic conditions. This strain was immobilized in LentiKats® (polyvinyl alcohol) and cultured in AH and EH. Supplementation of hydrolysates with crude yeast extract and peptone was also performed. The highest ethanol production was obtained using hydrolysates supplemented with crude yeast extract (AH-CYE and EH-CYE) showing yields of 0.40 and 0.44 g g-1, and productivities of 0.39 and 0.29 g (L h)-1, respectively. The reuse of the immobilized cells was tested in sequential fermentations of AH-CYE, EH-CYE, and a mixture of acid and enzymatic hydrolysates (AEH-CYE) operated under batch fluidized bed, with ethanol yields ranging from 0.31 to 0.40 g g-1 and productivities from 0.14 to 0.23 g (L h)-1. These results warrant further research using Spathaspora yeasts for second-generation ethanol production.
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Affiliation(s)
- Paulo Roberto Dall Cortivo
- Biotechnology & Biochemical Engineering Laboratory (BiotecLab), Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, PO Box 15090, Porto Alegre, RS, 91501-970, Brazil
| | - Luiza Fichtner Aydos
- Biotechnology & Biochemical Engineering Laboratory (BiotecLab), Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, PO Box 15090, Porto Alegre, RS, 91501-970, Brazil
| | - Lilian Raquel Hickert
- State University of Rio Grande do Sul, Av. Bento Gonçalves, 8855, Porto Alegre, RS, 91540-000, Brazil
| | - Carlos Augusto Rosa
- Department of Microbiology, ICB, C.P. 486, State University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Ronald E Hector
- Bioenergy Research Unit, USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 North University Street, Peoria, IL, 61604, USA
| | - Jeffrey A Mertens
- Bioenergy Research Unit, USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 North University Street, Peoria, IL, 61604, USA
| | - Marco Antônio Záchia Ayub
- Biotechnology & Biochemical Engineering Laboratory (BiotecLab), Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, PO Box 15090, Porto Alegre, RS, 91501-970, Brazil.
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7
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Yang BX, Xie CY, Xia ZY, Wu YJ, Gou M, Tang YQ. Improving xylitol yield by deletion of endogenous xylitol-assimilating genes: a study of industrial Saccharomyces cerevisiae in fermentation of glucose and xylose. FEMS Yeast Res 2020; 20:5986616. [PMID: 33201998 DOI: 10.1093/femsyr/foaa061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/14/2020] [Indexed: 01/12/2023] Open
Abstract
Engineered Saccharomyces cerevisiae can reduce xylose to xylitol. However, in S.cerevisiae, there are several endogenous enzymes including xylitol dehydrogenase encoded by XYL2, sorbitol dehydrogenases encoded by SOR1/SOR2 and xylulokinase encoded by XKS1 may lead to the assimilation of xylitol. In this study, to increase xylitol accumulation, these genes were separately deleted through CRISPR/Cas9 system. Their effects on xylitol yield of an industrial S. cerevisiae CK17 overexpressing Candida tropicalis XYL1 (encoding xylose reductase) were investigated. Deletion of SOR1/SOR2 or XKS1 increased the xylitol yield in both batch and fed-batch fermentation with different concentrations of glucose and xylose. The analysis of the transcription level of key genes in the mutants during fed-batch fermentation suggests that SOR1/SOR2 are more crucially responsible for xylitol oxidation than XYL2 under the genetic background of S.cerevisiae CK17. The deletion of XKS1 gene could also weaken SOR1/SOR2 expression, thereby increasing the xylitol accumulation. The XKS1-deleted strain CK17ΔXKS1 produced 46.17 g/L of xylitol and reached a xylitol yield of 0.92 g/g during simultaneous saccharification and fermentation (SSF) of pretreated corn stover slurry. Therefore, the deletion of XKS1 gene provides a promising strategy to meet the industrial demands for xylitol production from lignocellulosic biomass.
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Affiliation(s)
- Bai-Xue Yang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Cai-Yun Xie
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Zi-Yuan Xia
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Ya-Jing Wu
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
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8
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Abatement of Inhibitors in Recycled Process Water from Biomass Fermentations Relieves Inhibition of a Saccharomyces cerevisiae Pentose Phosphate Pathway Mutant. FERMENTATION 2020. [DOI: 10.3390/fermentation6040107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Understanding the nature of fermentation inhibition in biomass hydrolysates and recycled fermentation process water is important for conversion of biomass to fuels and chemicals. This study used three mutants disrupted in genes important for tolerance to either oxidative stress, salinity, or osmolarity to ferment biomass hydrolysates in a xylose-fermenting Saccharomyces cerevisiae background. The S. cerevisiaeZWF1 mutant with heightened sensitivity to fermentation inhibitors was unable to ferment corn stover dilute-acid hydrolysate without conditioning of hydrolysate using a fungal strain, Coniochaeta ligniaria, to consume inhibitors. Growth of two other strains, a salt-sensitive HAL4 mutant and a GPD1 mutant sensitive to osmotic stress, was not negatively affected in hydrolysate compared to the parent xylose-metabolizing strain. In recycled fermentation process water, inhibition of the ZWF1 mutant could again be remediated by biological abatement, and no effect on growth was observed for any of the mutants compared to the parent strain.
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9
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Using high-throughput data and dynamic flux balance modeling techniques to identify points of constraint in xylose utilization in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s43393-020-00003-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Smekenov I, Bakhtambayeva M, Bissenbayev K, Saparbayev M, Taipakova S, Bissenbaev AK. Heterologous secretory expression of β-glucosidase from Thermoascus aurantiacus in industrial Saccharomyces cerevisiae strains. Braz J Microbiol 2019; 51:107-123. [PMID: 31776864 DOI: 10.1007/s42770-019-00192-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 11/14/2019] [Indexed: 10/25/2022] Open
Abstract
The use of plant biomass for biofuel production will require efficient utilization of the sugars in lignocellulose, primarily cellobiose, because it is the major soluble by-product of cellulose and acts as a strong inhibitor, especially for cellobiohydrolase, which plays a key role in cellulose hydrolysis. Commonly used ethanologenic yeast Saccharomyces cerevisiae is unable to utilize cellobiose; accordingly, genetic engineering efforts have been made to transfer β-glucosidase genes enabling cellobiose utilization. Nonetheless, laboratory yeast strains have been employed for most of this research, and such strains may be difficult to use in industrial processes because of their generally weaker resistance to stressors and worse fermenting abilities. The purpose of this study was to engineer industrial yeast strains to ferment cellobiose after stable integration of tabgl1 gene that encodes a β-glucosidase from Thermoascus aurantiacus (TaBgl1). The recombinant S. cerevisiae strains obtained in this study secrete TaBgl1, which can hydrolyze cellobiose and produce ethanol. This study clearly indicates that the extent of glycosylation of secreted TaBgl1 depends from the yeast strains used and is greatly influenced by carbon sources (cellobiose or glucose). The recombinant yeast strains showed high osmotolerance and resistance to various concentrations of ethanol and furfural and to high temperatures. Therefore, these yeast strains are suitable for ethanol production processes with saccharified lignocellulose.
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Affiliation(s)
- Izat Smekenov
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Marzhan Bakhtambayeva
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Kudaybergen Bissenbayev
- Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Nazarbayev Intellectual School, Almaty, Kazakhstan, 050044
| | - Murat Saparbayev
- Gustave Roussy Cancer Campus, CNRS UMR8200, Université Paris-Sud, F-94805, Villejuif Cedex, France
| | - Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Amangeldy K Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040. .,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.
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11
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Patiño MA, Ortiz JP, Velásquez M, Stambuk BU. d-Xylose consumption by nonrecombinant Saccharomyces cerevisiae: A review. Yeast 2019; 36:541-556. [PMID: 31254359 DOI: 10.1002/yea.3429] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/02/2019] [Accepted: 06/21/2019] [Indexed: 01/24/2023] Open
Abstract
Xylose is the second most abundant sugar in nature. Its efficient fermentation has been considered as a critical factor for a feasible conversion of renewable biomass resources into biofuels and other chemicals. The yeast Saccharomyces cerevisiae is of exceptional industrial importance due to its excellent capability to ferment sugars. However, although S. cerevisiae is able to ferment xylulose, it is considered unable to metabolize xylose, and thus, a lot of research has been directed to engineer this yeast with heterologous genes to allow xylose consumption and fermentation. The analysis of the natural genetic diversity of this yeast has also revealed some nonrecombinant S. cerevisiae strains that consume or even grow (modestly) on xylose. The genome of this yeast has all the genes required for xylose transport and metabolism through the xylose reductase, xylitol dehydrogenase, and xylulokinase pathway, but there seems to be problems in their kinetic properties and/or required expression. Self-cloning industrial S. cerevisiae strains overexpressing some of the endogenous genes have shown interesting results, and new strategies and approaches designed to improve these S. cerevisiae strains for ethanol production from xylose will also be presented in this review.
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Affiliation(s)
- Margareth Andrea Patiño
- Instituto de Biotecnología.,Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Pablo Ortiz
- Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - Mario Velásquez
- Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Boris U Stambuk
- Departamento de Bioquímica, Universidad Federal de Santa Catarina, Florianópolis, Brazil
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12
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Tsoi R, Dai Z, You L. Emerging strategies for engineering microbial communities. Biotechnol Adv 2019; 37:107372. [PMID: 30880142 DOI: 10.1016/j.biotechadv.2019.03.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 12/11/2022]
Abstract
From biosynthesis to bioremediation, microbes have been engineered to address a variety of biotechnological applications. A promising direction in these endeavors is harnessing the power of designer microbial consortia that consist of multiple populations with well-defined interactions. Consortia can accomplish tasks that are difficult or potentially impossible to achieve using monocultures. Despite their potential, the rules underlying microbial community maintenance and function (i.e. the task the consortium is engineered to carry out) are not well defined, though rapid progress is being made. This limited understanding is in part due to the greater challenges associated with increased complexity when dealing with multi-population interactions. Here, we review key features and design strategies that emerge from the analysis of both natural and engineered microbial communities. These strategies can provide new insights into natural consortia and expand the toolbox available to engineers working to develop novel synthetic consortia.
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Affiliation(s)
- Ryan Tsoi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Zhuojun Dai
- Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA.
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13
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Wu W, Rondon V, Weeks K, Pullammanappallil P, Ingram LO, Shanmugam KT. Phosphoric acid based pretreatment of switchgrass and fermentation of entire slurry to ethanol using a simplified process. BIORESOURCE TECHNOLOGY 2018; 251:171-180. [PMID: 29274857 DOI: 10.1016/j.biortech.2017.12.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 05/21/2023]
Abstract
Switchgrass (Alamo) was pretreated with phosphoric acid (0.75 and 1%, w/w) at three temperatures (160, 175 and 190 °C) and time (5, 7.5 and 10 min) using a steam gun. The slurry after pretreatment was liquefied by enzymes and the released sugars were fermented in a simultaneous saccharification and co-fermentation process to ethanol using ethanologenic Escherichia coli strain SL100. Among the three variables in pretreatment, temperature and time were critical in supporting ethanol titer and yield. Enzyme hydrolysis significantly increased the concentration of furans in slurries, apparently due to release of furans bound to the solids. The highest ethanol titer of 21.2 ± 0.3 g/L ethanol obtained at the pretreatment condition of 190-1-7.5 (temperature-acid concentration-time) and 10% solids loading accounted for 190 ± 2.9 g ethanol/kg of raw switch grass. This converts to 61.7 gallons of ethanol per ton of dry switchgrass, a value that is comparable to other published pretreatment conditions.
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Affiliation(s)
- Wei Wu
- Department of Microbiology and Cell Science, Gainesville, FL 32611, United States; Department of Agricultural and Biological Engineering, Gainesville, FL 32611, United States
| | - Vanessa Rondon
- Department of Microbiology and Cell Science, Gainesville, FL 32611, United States; Stan Mayfield Biorefinery, University of Florida, Gainesville, FL 32611, United States
| | - Kalvin Weeks
- Stan Mayfield Biorefinery, University of Florida, Gainesville, FL 32611, United States
| | | | - Lonnie O Ingram
- Department of Microbiology and Cell Science, Gainesville, FL 32611, United States; Stan Mayfield Biorefinery, University of Florida, Gainesville, FL 32611, United States
| | - K T Shanmugam
- Department of Microbiology and Cell Science, Gainesville, FL 32611, United States.
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14
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Cheng C, Tang RQ, Xiong L, Hector RE, Bai FW, Zhao XQ. Association of improved oxidative stress tolerance and alleviation of glucose repression with superior xylose-utilization capability by a natural isolate of Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:28. [PMID: 29441126 PMCID: PMC5798184 DOI: 10.1186/s13068-018-1018-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Saccharomyces cerevisiae wild strains generally have poor xylose-utilization capability, which is a major barrier for efficient bioconversion of lignocellulosic biomass. Laboratory adaption is commonly used to enhance xylose utilization of recombinant S. cerevisiae. Apparently, yeast cells could remodel the metabolic network for xylose metabolism. However, it still remains unclear why natural isolates of S. cerevisiae poorly utilize xylose. Here, we analyzed a unique S. cerevisiae natural isolate YB-2625 which has superior xylose metabolism capability in the presence of mixed-sugar. Comparative transcriptomic analysis was performed using S. cerevisiae YB-2625 grown in a mixture of glucose and xylose, and the model yeast strain S288C served as a control. Global gene transcription was compared at both the early mixed-sugar utilization stage and the latter xylose-utilization stage. RESULTS Genes involved in endogenous xylose-assimilation (XYL2 and XKS1), gluconeogenesis, and TCA cycle showed higher transcription levels in S. cerevisiae YB-2625 at the xylose-utilization stage, when compared to the reference strain. On the other hand, transcription factor encoding genes involved in regulation of glucose repression (MIG1, MIG2, and MIG3) as well as HXK2 displayed decreased transcriptional levels in YB-2625, suggesting the alleviation of glucose repression of S. cerevisiae YB-2625. Notably, genes encoding antioxidant enzymes (CTT1, CTA1, SOD2, and PRX1) showed higher transcription levels in S. cerevisiae YB-2625 in the xylose-utilization stage than that of the reference strain. Consistently, catalase activity of YB-2625 was 1.9-fold higher than that of S. cerevisiae S288C during the xylose-utilization stage. As a result, intracellular reactive oxygen species levels of S. cerevisiae YB-2625 were 43.3 and 58.6% lower than that of S288C at both sugar utilization stages. Overexpression of CTT1 and PRX1 in the recombinant strain S. cerevisiae YRH396 deriving from S. cerevisiae YB-2625 increased cell growth when xylose was used as the sole carbon source, leading to 13.5 and 18.1%, respectively, more xylose consumption. CONCLUSIONS Enhanced oxidative stress tolerance and relief of glucose repression are proposed to be two major mechanisms for superior xylose utilization by S. cerevisiae YB-2625. The present study provides insights into the innate regulatory mechanisms underlying xylose utilization in wild-type S. cerevisiae, which benefits the rapid development of robust yeast strains for lignocellulosic biorefineries.
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Affiliation(s)
- Cheng Cheng
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Rui-Qi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Liang Xiong
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Ronald E. Hector
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL USA
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
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15
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Influence of genetic background of engineered xylose-fermenting industrial Saccharomyces cerevisiae strains for ethanol production from lignocellulosic hydrolysates. J Ind Microbiol Biotechnol 2017; 44:1575-1588. [PMID: 28891041 DOI: 10.1007/s10295-017-1979-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
An industrial ethanol-producing Saccharomyces cerevisiae strain with genes of fungal oxido-reductive pathway needed for xylose fermentation integrated into its genome (YRH1415) was used to obtain haploids and diploid isogenic strains. The isogenic strains were more effective in metabolizing xylose than YRH1415 strain and able to co-ferment glucose and xylose in the presence of high concentrations of inhibitors resulting from the hydrolysis of lignocellulosic biomass (switchgrass). The rate of xylose consumption did not appear to be affected by the ploidy of strains or the presence of two copies of the xylose fermentation genes but by heterozygosity of alleles for xylose metabolism in YRH1415. Furthermore, inhibitor tolerance was influenced by the heterozygous genome of the industrial strain, which also showed a marked influenced on tolerance to increasing concentrations of toxic compounds, such as furfural. In this work, selection of haploid derivatives was found to be a useful strategy to develop efficient xylose-fermenting industrial yeast strains.
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16
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Ali SS, Wu J, Xie R, Zhou F, Sun J, Huang M. Screening and characterizing of xylanolytic and xylose-fermenting yeasts isolated from the wood-feeding termite, Reticulitermes chinensis. PLoS One 2017; 12:e0181141. [PMID: 28704553 PMCID: PMC5509302 DOI: 10.1371/journal.pone.0181141] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/21/2017] [Indexed: 11/20/2022] Open
Abstract
The effective fermentation of xylose remains an intractable challenge in bioethanol industry. The relevant xylanase enzyme is also in a high demand from industry for several biotechnological applications that inevitably in recent times led to many efforts for screening some novel microorganisms for better xylanase production and fermentation performance. Recently, it seems that wood-feeding termites can truly be considered as highly efficient natural bioreactors. The highly specialized gut systems of such insects are not yet fully realized, particularly, in xylose fermentation and xylanase production to advance industrial bioethanol technology as well as industrial applications of xylanases. A total of 92 strains from 18 yeast species were successfully isolated and identified from the gut of wood-feeding termite, Reticulitermes chinensis. Of these yeasts and strains, seven were identified for new species: Candida gotoi, Candida pseudorhagii, Hamamotoa lignophila, Meyerozyma guilliermondii, Sugiyamaella sp.1, Sugiyamaella sp. 2, and Sugiyamaella sp.3. Based on the phylogenetic and phenotypic characterization, the type strain of C. pseudorhagii sp. nov., which was originally designated strain SSA-1542T, was the most frequently occurred yeast from termite gut samples, showed the highly xylanolytic activity as well as D-xylose fermentation. The highest xylanase activity was recorded as 1.73 and 0.98 U/mL with xylan or D-xylose substrate, respectively, from SSA-1542T. Among xylanase-producing yeasts, four novel species were identified as D-xylose-fermenting yeasts, where the yeast, C. pseudorhagii SSA-1542T, showed the highest ethanol yield (0.31 g/g), ethanol productivity (0.31 g/L·h), and its fermentation efficiency (60.7%) in 48 h. Clearly, the symbiotic yeasts isolated from termite guts have demonstrated a competitive capability to produce xylanase and ferment xylose, suggesting that the wood-feeding termite gut is a promising reservoir for novel xylanases-producing and xylose-fermenting yeasts that are potentially valued for biorefinery industry.
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Affiliation(s)
- Sameh Samir Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Jian Wu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Rongrong Xie
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Feng Zhou
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- * E-mail:
| | - Miao Huang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
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17
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Lee WH, Jin YS. Improved ethanol production by engineered Saccharomyces cerevisiae expressing a mutated cellobiose transporter during simultaneous saccharification and fermentation. J Biotechnol 2017; 245:1-8. [DOI: 10.1016/j.jbiotec.2017.01.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/30/2016] [Accepted: 01/27/2017] [Indexed: 10/20/2022]
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18
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Metabolic engineering of a haploid strain derived from a triploid industrial yeast for producing cellulosic ethanol. Metab Eng 2017; 40:176-185. [DOI: 10.1016/j.ymben.2017.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/06/2017] [Accepted: 02/14/2017] [Indexed: 12/25/2022]
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19
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Saha BC, Kennedy GJ, Qureshi N, Cotta MA. Biological pretreatment of corn stover withPhlebia brevisporaNRRL-13108 for enhanced enzymatic hydrolysis and efficient ethanol production. Biotechnol Prog 2017; 33:365-374. [DOI: 10.1002/btpr.2420] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/17/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Badal C. Saha
- U.S. Department of Agriculture; Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service; Peoria IL 61604
| | - Gregory J. Kennedy
- U.S. Department of Agriculture; Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service; Peoria IL 61604
| | - Nasib Qureshi
- U.S. Department of Agriculture; Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service; Peoria IL 61604
| | - Michael A. Cotta
- U.S. Department of Agriculture; Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service; Peoria IL 61604
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20
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A Synthetic Hybrid Promoter for Xylose-Regulated Control of Gene Expression in Saccharomyces Yeasts. Mol Biotechnol 2016; 59:24-33. [DOI: 10.1007/s12033-016-9991-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast. Proc Natl Acad Sci U S A 2016; 113:E7428-E7437. [PMID: 27810962 DOI: 10.1073/pnas.1603577113] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The ability to rationally manipulate the transcriptional states of cells would be of great use in medicine and bioengineering. We have developed an algorithm, NetSurgeon, which uses genome-wide gene-regulatory networks to identify interventions that force a cell toward a desired expression state. We first validated NetSurgeon extensively on existing datasets. Next, we used NetSurgeon to select transcription factor deletions aimed at improving ethanol production in Saccharomyces cerevisiae cultures that are catabolizing xylose. We reasoned that interventions that move the transcriptional state of cells using xylose toward that of cells producing large amounts of ethanol from glucose might improve xylose fermentation. Some of the interventions selected by NetSurgeon successfully promoted a fermentative transcriptional state in the absence of glucose, resulting in strains with a 2.7-fold increase in xylose import rates, a 4-fold improvement in xylose integration into central carbon metabolism, or a 1.3-fold increase in ethanol production rate. We conclude by presenting an integrated model of transcriptional regulation and metabolic flux that will enable future efforts aimed at improving xylose fermentation to prioritize functional regulators of central carbon metabolism.
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22
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Batch Fermentation Options for High Titer Bioethanol Production from a SPORL Pretreated Douglas-Fir Forest Residue without Detoxification. FERMENTATION-BASEL 2016. [DOI: 10.3390/fermentation2030016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Fermentative High-Titer Ethanol Production from Douglas-Fir Forest Residue Without Detoxification Using SPORL: High SO2 Loading at Low Temperature. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1089/ind.2015.0028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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24
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Hu ML, Zha J, He LW, Lv YJ, Shen MH, Zhong C, Li BZ, Yuan YJ. Enhanced Bioconversion of Cellobiose by Industrial Saccharomyces cerevisiae Used for Cellulose Utilization. Front Microbiol 2016; 7:241. [PMID: 26973619 PMCID: PMC4776165 DOI: 10.3389/fmicb.2016.00241] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 02/15/2016] [Indexed: 01/26/2023] Open
Abstract
Cellobiose accumulation and the compromised temperature for yeast fermentation are the main limiting factors of enzymatic hydrolysis process during simultaneous saccharification and fermentation (SSF). In this study, genes encoding cellobiose transporter and β-glucosidase were introduced into an industrial Saccharomyces cerevisiae strain, and evolution engineering was carried out to improve the cellobiose utilization of the engineered yeast strain. The evolved strain exhibited significantly higher cellobiose consumption rate (2.8-fold) and ethanol productivity (4.9-fold) compared with its parent strain. Besides, the evolved strain showed a high cellobiose consumption rate of 3.67 g/L/h at 34°C and 3.04 g/L/h at 38°C. Moreover, little cellobiose was accumulated during SSF of Avicel using the evolved strain at 38°C, and the ethanol yield from Avicel increased by 23% from 0.34 to 0.42 g ethanol/g cellulose. Overexpression of the genes encoding cellobiose transporter and β-glucosidase accelerated cellobiose utilization, and the improvement depended on the strain background. The results proved that fast cellobiose utilization enhanced ethanol production by reducing cellobiose accumulation during SSF at high temperature.
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Affiliation(s)
- Meng-Long Hu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin UniversityTianjin, China
| | - Jian Zha
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin UniversityTianjin, China
| | - Lin-Wei He
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin UniversityTianjin, China
| | - Ya-Jin Lv
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin UniversityTianjin, China
| | - Ming-Hua Shen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin UniversityTianjin, China
| | - Cheng Zhong
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science and Technology Tianjin, China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin UniversityTianjin, China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin UniversityTianjin, China
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25
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dos Reis TF, de Lima PBA, Parachin NS, Mingossi FB, de Castro Oliveira JV, Ries LNA, Goldman GH. Identification and characterization of putative xylose and cellobiose transporters in Aspergillus nidulans. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:204. [PMID: 27708711 PMCID: PMC5037631 DOI: 10.1186/s13068-016-0611-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 09/06/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND The conversion of lignocellulosic biomass to biofuels (second-generation biofuel production) is an environmentally friendlier alternative to petroleum-based energy sources. Enzymatic deconstruction of lignocellulose, catalyzed by filamentous fungi such as Aspergillus nidulans, releases a mixture of mono- and polysaccharides, including hexose (glucose) and pentose (xylose) sugars, cellodextrins (cellobiose), and xylooligosaccharides (xylobiose). These sugars can subsequently be fermented by yeast cells to ethanol. One of the major drawbacks in this process lies in the inability of yeast, such as Saccharomyces cerevisiae, to successfully internalize sugars other than glucose. The aim of this study was, therefore, to screen the genome of A. nidulans, which encodes a multitude of sugar transporters, for transporters able to internalize non-glucose sugars and characterize them when introduced into S. cerevisiae. RESULTS This work identified two proteins in A. nidulans, CltA and CltB, with roles in cellobiose transport and cellulose signaling, respectively. CltA, when introduced into S. cerevisiae, conferred growth on low and high concentrations of cellobiose. Deletion of cltB resulted in reduced growth and extracellular cellulase activity in A. nidulans in the presence of cellobiose. CltB, when introduced into S. cerevisiae, was not able to confer growth on cellobiose, suggesting that this protein is a sensor rather than a transporter. However, we have shown that the introduction of additional functional copies of CltB increases the growth in the presence of low concentrations of cellobiose, strongly indicating CltB is able to transport cellobiose. Furthermore, a previously identified glucose transporter, HxtB, was also found to be a major xylose transporter in A. nidulans. In S. cerevisiae, HxtB conferred growth on xylose which was accompanied by ethanol production. CONCLUSIONS This work identified a cellobiose transporter, a xylose transporter, and a putative cellulose transceptor in A. nidulans. This is the first time that a sensor role for a protein in A. nidulans has been proposed. Both transporters are also able to transport glucose, highlighting the preference of A. nidulans for this carbon source. This work provides a basis for future studies which aim at characterizing and/or genetically engineering Aspergillus spp. transporters, which, in addition to glucose, can also internalize other carbon sources, to improve transport and fermentation of non-glucose sugars in S. cerevisiae.
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Affiliation(s)
- Thaila Fernanda dos Reis
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, Ribeirão Preto, SP CEP 14040-903 Brazil
| | | | - Nádia Skorupa Parachin
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, CEP 70910-900 Brazil
| | | | | | - Laure Nicolas Annick Ries
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, Ribeirão Preto, SP CEP 14040-903 Brazil
| | - Gustavo Henrique Goldman
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, Ribeirão Preto, SP CEP 14040-903 Brazil
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26
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Paixão SM, Ladeira SA, Silva TP, Arez BF, Roseiro JC, Martins MLL, Alves L. Sugarcane bagasse delignification with potassium hydroxide for enhanced enzymatic hydrolysis. RSC Adv 2016. [DOI: 10.1039/c5ra14908h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Alkali pretreatment of sugarcane bagasse biomass was shown to be effective for producing sugar-rich hydrolysates for biotechnological applications.
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Affiliation(s)
- S. M. Paixão
- LNEG – Laboratório Nacional de Energia e Geologia, IP
- Unidade de Bioenergia
- 1649-038 Lisboa
- Portugal
| | - S. A. Ladeira
- UENF – Universidade Estadual do Norte Fluminense Darcy Ribeiro
- LTA-CCTA
- RJ
- Brazil
| | - T. P. Silva
- LNEG – Laboratório Nacional de Energia e Geologia, IP
- Unidade de Bioenergia
- 1649-038 Lisboa
- Portugal
| | - B. F. Arez
- LNEG – Laboratório Nacional de Energia e Geologia, IP
- Unidade de Bioenergia
- 1649-038 Lisboa
- Portugal
| | - J. C. Roseiro
- LNEG – Laboratório Nacional de Energia e Geologia, IP
- Unidade de Bioenergia
- 1649-038 Lisboa
- Portugal
| | - M. L. L. Martins
- UENF – Universidade Estadual do Norte Fluminense Darcy Ribeiro
- LTA-CCTA
- RJ
- Brazil
| | - L. Alves
- LNEG – Laboratório Nacional de Energia e Geologia, IP
- Unidade de Bioenergia
- 1649-038 Lisboa
- Portugal
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27
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Xylose fermentation efficiency and inhibitor tolerance of the recombinant industrial Saccharomyces cerevisiae strain NAPX37. Appl Microbiol Biotechnol 2015; 100:1531-1542. [PMID: 26603762 DOI: 10.1007/s00253-015-7167-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/19/2015] [Accepted: 11/06/2015] [Indexed: 01/01/2023]
Abstract
Industrial yeast strains with good xylose fermentation ability and inhibitor tolerance are important for economical lignocellulosic bioethanol production. The flocculating industrial Saccharomyces cerevisiae strain NAPX37, harboring the xylose reductase-xylitol dehydrogenase (XR-XDH)-based xylose metabolic pathway, displayed efficient xylose fermentation during batch and continuous fermentation. During batch fermentation, the xylose consumption rates at the first 36 h were similar (1.37 g/L/h) when the initial xylose concentrations were 50 and 75 g/L, indicating that xylose fermentation was not inhibited even when the xylose concentration was as high as 75 g/L. The presence of glucose, at concentrations of up to 25 g/L, did not affect xylose consumption rate at the first 36 h. Strain NAPX37 showed stable xylose fermentation capacity during continuous ethanol fermentation using xylose as the sole sugar, for almost 1 year. Fermentation remained stable at a dilution rate of 0.05/h, even though the xylose concentration in the feed was as high as 100 g/L. Aeration rate, xylose concentration, and MgSO4 concentration were found to affect xylose consumption and ethanol yield. When the xylose concentration in the feed was 75 g/L, a high xylose consumption rate of 6.62 g/L/h and an ethanol yield of 0.394 were achieved under an aeration rate of 0.1 vvm, dilution rate of 0.1/h, and 5 mM MgSO4. In addition, strain NAPX37 exhibited good tolerance to inhibitors such as weak acids, furans, and phenolics during xylose fermentation. These findings indicate that strain NAPX37 is a promising candidate for application in the industrial production of lignocellulosic bioethanol.
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28
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Zhang J, Gu F, Zhu JY, Zalesny RS. Using a combined hydrolysis factor to optimize high titer ethanol production from sulfite-pretreated poplar without detoxification. BIORESOURCE TECHNOLOGY 2015; 186:223-231. [PMID: 25817033 DOI: 10.1016/j.biortech.2015.03.080] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/14/2015] [Accepted: 03/16/2015] [Indexed: 05/16/2023]
Abstract
Sulfite pretreatment to overcome the recalcitrance of lignocelluloses (SPORL) was applied to poplar NE222 chips in a range of chemical loadings, temperatures, and times. The combined hydrolysis factor (CHF) as a pretreatment severity accurately predicted xylan dissolution by SPORL. Good correlations between CHF and pretreated solids enzymatic digestibility, sugar yield, and the formations of furfural and acetic acid were obtained. Therefore, CHF was used to balance sugar yield with the formation of fermentation inhibitors for high titer ethanol production without detoxification. The results indicated that optimal sugar yield can be achieved at CHF=3.1, however, fermentation using un-detoxified whole slurries of NE222 pretreated at different severities by SPORL indicated CHF≈2 produced best results. An ethanol titer of 41 g/L was achieved at total solids of approximately 20 wt% without detoxification with a low cellulase loading of 15 FPU/g glucan (27 mL/kg untreated wood).
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Affiliation(s)
- Jingzhi Zhang
- School of Life Sci. Technol., Beijing Univ. Chem. Technol., Beijing, China; USDA Forest Service, Forest Products Laboratory, Madison, WI, USA
| | - Feng Gu
- USDA Forest Service, Forest Products Laboratory, Madison, WI, USA; Jiangsu Provincial Key Lab of Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing, China
| | - J Y Zhu
- USDA Forest Service, Forest Products Laboratory, Madison, WI, USA.
| | - Ronald S Zalesny
- USDA Forest Service, Northern Research Station, Rhinelander, WI, USA
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29
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Saunders LP, Bowman MJ, Mertens JA, Da Silva NA, Hector RE. Triacetic acid lactone production in industrial Saccharomyces yeast strains. ACTA ACUST UNITED AC 2015; 42:711-21. [DOI: 10.1007/s10295-015-1596-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/30/2015] [Indexed: 10/24/2022]
Abstract
Abstract
Triacetic acid lactone (TAL) is a potential platform chemical that can be produced in yeast. To evaluate the potential for industrial yeast strains to produce TAL, the g2ps1 gene encoding 2-pyrone synthase was transformed into 13 industrial yeast strains of varied genetic background. TAL production varied 63-fold between strains when compared in batch culture with glucose. Ethanol, acetate, and glycerol were also tested as potential carbon sources. Batch cultures with ethanol medium produced the highest titers. Therefore, fed-batch cultivation with ethanol feed was assayed for TAL production in bioreactors, producing our highest TAL titer, 5.2 g/L. Higher feed rates resulted in a loss of TAL and subsequent production of additional TAL side products. Finally, TAL efflux was measured and TAL is actively exported from S. cerevisiae cells. Percent yield for all strains was low, indicating that further metabolic engineering of the strains is required.
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Affiliation(s)
- Lauren P Saunders
- grid.417548.b 0000000404786311 Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service U.S. Department of Agriculture 1815 North University Street 61604 Peoria IL USA
| | - Michael J Bowman
- grid.417548.b 0000000404786311 Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service U.S. Department of Agriculture 1815 North University Street 61604 Peoria IL USA
| | - Jeffrey A Mertens
- grid.417548.b 0000000404786311 Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service U.S. Department of Agriculture 1815 North University Street 61604 Peoria IL USA
| | - Nancy A Da Silva
- grid.266093.8 0000000106687243 Department of Chemical Engineering and Materials Science University of California 92697 Irvine CA USA
| | - Ronald E Hector
- grid.417548.b 0000000404786311 Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service U.S. Department of Agriculture 1815 North University Street 61604 Peoria IL USA
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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: 21] [Impact Index Per Article: 2.1] [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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Zhu JY, Chandra MS, Gu F, Gleisner R, Reiner R, Sessions J, Marrs G, Gao J, Anderson D. Using sulfite chemistry for robust bioconversion of Douglas-fir forest residue to bioethanol at high titer and lignosulfonate: a pilot-scale evaluation. BIORESOURCE TECHNOLOGY 2015; 179:390-397. [PMID: 25553570 DOI: 10.1016/j.biortech.2014.12.052] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 05/19/2023]
Abstract
This study demonstrated at the pilot-scale (50 kg) use of Douglas-fir forest harvest residue, an underutilized forest biomass, for the production of high titer and high yield bioethanol using sulfite chemistry without solid-liquor separation and detoxification. Sulfite Pretreatment to Overcome the Recalcitrance of Lignocelluloses (SPORL) was directly applied to the ground forest harvest residue with no further mechanical size reduction, at a low temperature of 145°C and calcium bisulfite or total SO2 loadings of only 6.5 or 6.6 wt% on oven dry forest residue, respectively. The low temperature pretreatment facilitated high solids fermentation of the un-detoxified pretreated whole slurry. An ethanol yield of 282 L/tonne, equivalent to 70% theoretical, with a titer of 42 g/L was achieved. SPORL solubilized approximately 45% of the wood lignin as directly marketable lignosulfonate with properties equivalent to or better than a commercial lignosulfonate, important to improve the economics of biofuel production.
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Affiliation(s)
- J Y Zhu
- USDA Forest Service, Forest Products Lab, Madison, WI, USA.
| | - M Subhosh Chandra
- USDA Forest Service, Forest Products Lab, Madison, WI, USA; Dept. of Microbiology, Yogi Vemana University, Kadapa, India
| | - Feng Gu
- Jiangsu Provincial Key and Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing, China; USDA Forest Service, Forest Products Lab, Madison, WI, USA
| | | | - Rick Reiner
- USDA Forest Service, Forest Products Lab, Madison, WI, USA
| | - John Sessions
- College of Forestry, Oregon State University, Corvallis, OR, USA
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Cheng J, Leu SY, Zhu JY, Gleisner R. High titer and yield ethanol production from undetoxified whole slurry of Douglas-fir forest residue using pH profiling in SPORL. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:22. [PMID: 25709715 PMCID: PMC4337254 DOI: 10.1186/s13068-015-0205-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/15/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Forest residue is one of the most cost-effective feedstock for biofuel production. It has relatively high bulk density and can be harvested year round, advantageous for reducing transportation cost and eliminating onsite storage. However, forest residues, especially those from softwood species, are highly recalcitrant to biochemical conversion. A severe pretreatment for removing this recalcitrance can result in increased sugar degradation to inhibitors and hence cause difficulties in fermentation at high solid loadings. Here, we presented high titer ethanol production from Douglas-fir forest residue without detoxification. The strong recalcitrance of the Douglas-fir residue was removed by sulfite pretreatment to overcome the recalcitrance of lignocelluloses (SPORL). Sugar degradation to inhibitors was substantially reduced using a novel approach of "pH profiling" by delaying acid application in pretreatment, which facilitated the simultaneous enzymatic saccharification and fermentation of undetoxified whole slurry at a solid loading of 21%. RESULTS "pH profiling" reduced furan production by approximately 70% in using SPORL pretreating Douglas-fir forest residue (FS-10) comparing with the control run while without sacrificing enzymatic saccharification of the resultant substrate. pH profiling also reduced carbohydrate degradation. The improved carbohydrate yield in pretreated solids and reduced fermentation inhibitors with pH profiling resulted in a terminal ethanol titer of 48.9 ± 1.4 g/L and yield of 297 ± 9 L/tonne FS-10, which are substantially higher, i.e., by 27% in titer and by 38% in yield, than those of a control SPORL run without pH profiling. CONCLUSIONS Economical and large-volume production of commodity biofuels requires the utilization of feedstocks with low value (therefore low cost) and sustainably producible in large quantities, such as forest residues. However, most existing pretreatment technologies cannot remove the strong recalcitrance of forest residues to produce practically fermentable high titer sugars. Here, we demonstrated a commercially scalable and efficient technology capable of removing the strong recalcitrant nature of forest residues using "pH profiling" together with "low temperature SPORL". The resultant pretreated whole slurry of a Douglas-fir forest residue using this technology can be easily processed at high solids of 21% without detoxification to achieve a high ethanol yield of 297 L/tonne at 48.9 g/L. Graphical AbstractGraphic table of content.
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Affiliation(s)
- Jinlan Cheng
- />Jiangsu Provincial Key Lab of Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing, China
- />USDA Forest Service, Forest Products Laboratory, Madison, WI 53719 USA
| | - Shao-Yuan Leu
- />USDA Forest Service, Forest Products Laboratory, Madison, WI 53719 USA
- />Department of Civil and Environmental Engineering, Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - JY Zhu
- />USDA Forest Service, Forest Products Laboratory, Madison, WI 53719 USA
| | - Rolland Gleisner
- />USDA Forest Service, Forest Products Laboratory, Madison, WI 53719 USA
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Zhang X, Nghiem NP, Hicks KB, Johnston DB, Hector RE. Ethanol Production by High-Solids Simultaneous Saccharification and Fermentation of Cellulose-Enriched Barley Straw and Hull Residues Obtained by Alkaline Hydrogen Peroxide Pretreatment. Ind Biotechnol (New Rochelle N Y) 2014. [DOI: 10.1089/ind.2013.0031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xiu Zhang
- Department of Bioscience and Bioengineering, Beifang University of Nationalities, Yinchuan, Ningxia, People's Republic of China
| | - Nhuan P. Nghiem
- Sustainable Biofuels and Co-Products Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA
| | - Kevin B. Hicks
- Sustainable Biofuels and Co-Products Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA
| | - David B. Johnston
- Sustainable Biofuels and Co-Products Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA
| | - Ronald E. Hector
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Peoria, IL
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34
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Zhou H, Lan T, Dien BS, Hector RE, Zhu JY. Comparisons of fiveSaccharomyces cerevisiaestrains for ethanol production from SPORL-pretreated lodgepole pine. Biotechnol Prog 2014; 30:1076-83. [DOI: 10.1002/btpr.1937] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/08/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Haifeng Zhou
- School of Chemistry Chemical Eng.; South China University Technol.; Guangzhou China
- USDA Forest Service, Forest Products Laboratory; Madison WI
| | - Tianqing Lan
- School of Light Industry and Food Sciences; Kunming Polytechnic University; Kunming China
- USDA Forest Service, Forest Products Laboratory; Madison WI
| | - Bruce S. Dien
- USDA Agricultural Research Service; National Center for Agricultural Utilization Research; Peoria IL
| | - Ronald E. Hector
- USDA Agricultural Research Service; National Center for Agricultural Utilization Research; Peoria IL
| | - J. Y. Zhu
- USDA Forest Service, Forest Products Laboratory; Madison WI
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35
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Cheng J, Leu SY, Zhu JY, Jeffries TW. Ethanol production from non-detoxified whole slurry of sulfite-pretreated empty fruit bunches at a low cellulase loading. BIORESOURCE TECHNOLOGY 2014; 164:331-337. [PMID: 24874873 DOI: 10.1016/j.biortech.2014.04.102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 06/03/2023]
Abstract
Sulfite pretreatment to overcome the recalcitrance of lignocelluloses (SPORL) was applied to an empty fruit bunches (EFB) for ethanol production. SPORL facilitated delignification through lignin sulfonation and dissolution of xylan to result in a highly digestible substrate. The pretreated whole slurry was enzymatically saccharified at a solids loading of 18% using a relatively low cellulase loading of 15 FPU/g glucan and simultaneously fermented without detoxification using Saccharomyces cerevisiae of YRH400. An ethanol yield of 217 L/tonne EFB was achieved at titer of 32 g/L. Compared with literature studies, SPORL produced high ethanol yield and titer with much lower cellulase loading without detoxification.
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Affiliation(s)
- Jinlan Cheng
- Jiangsu Provincial Key Lab of Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing, China; USDA Forest Service, Forest Products Lab, Madison, WI 53719, USA
| | - Shao-Yuan Leu
- Dept. Civil Environ. Eng., Hong Kong Polytechnic University, Kowloon, Hong Kong; USDA Forest Service, Forest Products Lab, Madison, WI 53719, USA
| | - J Y Zhu
- USDA Forest Service, Forest Products Lab, Madison, WI 53719, USA; Dept. Biological Systems Eng., University of Wisconsin-Madison, Madison, WI 53705, USA.
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Kricka W, Fitzpatrick J, Bond U. Metabolic engineering of yeasts by heterologous enzyme production for degradation of cellulose and hemicellulose from biomass: a perspective. Front Microbiol 2014; 5:174. [PMID: 24795706 PMCID: PMC4001029 DOI: 10.3389/fmicb.2014.00174] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/31/2014] [Indexed: 11/13/2022] Open
Abstract
This review focuses on current approaches to metabolic engineering of ethanologenic yeast species for the production of bioethanol from complex lignocellulose biomass sources. The experimental strategies for the degradation of the cellulose and xylose-components of lignocellulose are reviewed. Limitations to the current approaches are discussed and novel solutions proposed.
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Affiliation(s)
- William Kricka
- School of Genetics and Microbiology, Department of Microbiology, Trinity College Dublin Dublin, Ireland
| | - James Fitzpatrick
- School of Genetics and Microbiology, Department of Microbiology, Trinity College Dublin Dublin, Ireland
| | - Ursula Bond
- School of Genetics and Microbiology, Department of Microbiology, Trinity College Dublin Dublin, Ireland
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37
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Zhou H, Leu SY, Wu X, Zhu JY, Gleisner R, Yang D, Qiu X, Horn E. Comparisons of high titer ethanol production and lignosulfonate properties by SPORL pretreatment of lodgepole pine at two temperatures. RSC Adv 2014. [DOI: 10.1039/c4ra03608e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mountain pine beetle killed lodgepole pine wood chips were pretreated by SPORL at 180 °C for 25 min and 165 °C for 75 min using the same chemical loadings, which represent the same pretreatment severity.
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Affiliation(s)
- Haifeng Zhou
- School of Chem. Chem. Eng
- South China Univ. Technol
- Guangzhou, China
- USDA Forest Service
- Forest Products Laboratory
| | - Shao-Yuan Leu
- USDA Forest Service
- Forest Products Laboratory
- Madison, USA
- Dept. Civil Environ. Eng
- Hong Kong Polytechnic University
| | - Xiaolei Wu
- School of Chem. Chem. Eng
- South China Univ. Technol
- Guangzhou, China
| | - J. Y. Zhu
- USDA Forest Service
- Forest Products Laboratory
- Madison, USA
| | | | - Dongjie Yang
- School of Chem. Chem. Eng
- South China Univ. Technol
- Guangzhou, China
| | - Xueqing Qiu
- School of Chem. Chem. Eng
- South China Univ. Technol
- Guangzhou, China
| | - Eric Horn
- BioPulping International, Inc
- Madison, USA
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38
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dos Reis TF, Menino JF, Bom VLP, Brown NA, Colabardini AC, Savoldi M, Goldman MHS, Rodrigues F, Goldman GH. Identification of glucose transporters in Aspergillus nidulans. PLoS One 2013; 8:e81412. [PMID: 24282591 PMCID: PMC3839997 DOI: 10.1371/journal.pone.0081412] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/12/2013] [Indexed: 11/18/2022] Open
Abstract
To characterize the mechanisms involved in glucose transport, in the filamentous fungus Aspergillus nidulans, we have identified four glucose transporter encoding genes hxtB-E. We evaluated the ability of hxtB-E to functionally complement the Saccharomyces cerevisiae EBY.VW4000 strain that is unable to grow on glucose, fructose, mannose or galactose as single carbon source. In S. cerevisiae HxtB-E were targeted to the plasma membrane. The expression of HxtB, HxtC and HxtE was able to restore growth on glucose, fructose, mannose or galactose, indicating that these transporters accept multiple sugars as a substrate through an energy dependent process. A tenfold excess of unlabeled maltose, galactose, fructose, and mannose were able to inhibit glucose uptake to different levels (50 to 80 %) in these s. cerevisiae complemented strains. Moreover, experiments with cyanide-m-chlorophenylhydrazone (CCCP), strongly suggest that hxtB, -C, and -E mediate glucose transport via active proton symport. The A. nidulans ΔhxtB, ΔhxtC or ΔhxtE null mutants showed ~2.5-fold reduction in the affinity for glucose, while ΔhxtB and -C also showed a 2-fold reduction in the capacity for glucose uptake. The ΔhxtD mutant had a 7.8-fold reduction in affinity, but a 3-fold increase in the capacity for glucose uptake. However, only the ΔhxtB mutant strain showed a detectable decreased rate of glucose consumption at low concentrations and an increased resistance to 2-deoxyglucose.
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Affiliation(s)
- Thaila Fernanda dos Reis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - João Filipe Menino
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
| | - Vinícius Leite Pedro Bom
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Neil Andrew Brown
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Ana Cristina Colabardini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Marcela Savoldi
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Helena S. Goldman
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
| | - Gustavo Henrique Goldman
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol – CTBE, Campinas, São Paulo, Brazil
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
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Harnessing genetic diversity in Saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass. Appl Environ Microbiol 2013; 80:540-54. [PMID: 24212571 DOI: 10.1128/aem.01885-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The fermentation of lignocellulose-derived sugars, particularly xylose, into ethanol by the yeast Saccharomyces cerevisiae is known to be inhibited by compounds produced during feedstock pretreatment. We devised a strategy that combined chemical profiling of pretreated feedstocks, high-throughput phenotyping of genetically diverse S. cerevisiae strains isolated from a range of ecological niches, and directed engineering and evolution against identified inhibitors to produce strains with improved fermentation properties. We identified and quantified for the first time the major inhibitory compounds in alkaline hydrogen peroxide (AHP)-pretreated lignocellulosic hydrolysates, including Na(+), acetate, and p-coumaric (pCA) and ferulic (FA) acids. By phenotyping these yeast strains for their abilities to grow in the presence of these AHP inhibitors, one heterozygous diploid strain tolerant to all four inhibitors was selected, engineered for xylose metabolism, and then allowed to evolve on xylose with increasing amounts of pCA and FA. After only 149 generations, one evolved isolate, GLBRCY87, exhibited faster xylose uptake rates in both laboratory media and AHP switchgrass hydrolysate than its ancestral GLBRCY73 strain and completely converted 115 g/liter of total sugars in undetoxified AHP hydrolysate into more than 40 g/liter ethanol. Strikingly, genome sequencing revealed that during the evolution from GLBRCY73, the GLBRCY87 strain acquired the conversion of heterozygous to homozygous alleles in chromosome VII and amplification of chromosome XIV. Our approach highlights that simultaneous selection on xylose and pCA or FA with a wild S. cerevisiae strain containing inherent tolerance to AHP pretreatment inhibitors has potential for rapid evolution of robust properties in lignocellulosic biofuel production.
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40
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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: 156] [Impact Index Per Article: 13.0] [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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41
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Zhou H, Zhu JY, Luo X, Leu SY, Wu X, Gleisner R, Dien BS, Hector RE, Yang D, Qiu X, Horn E, Negron J. Bioconversion of Beetle-Killed Lodgepole Pine Using SPORL: Process Scale-up Design, Lignin Coproduct, and High Solids Fermentation without Detoxification. Ind Eng Chem Res 2013. [DOI: 10.1021/ie402873y] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Haifeng Zhou
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
- USDA
Forest Service, Forest Products Laboratory, Madison, Wisconsin, United States
| | - J. Y. Zhu
- USDA
Forest Service, Forest Products Laboratory, Madison, Wisconsin, United States
| | - Xiaolin Luo
- USDA
Forest Service, Forest Products Laboratory, Madison, Wisconsin, United States
- College of Material Engineering, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shao-Yuan Leu
- USDA
Forest Service, Forest Products Laboratory, Madison, Wisconsin, United States
- Department
of Civil Environmental Engineering, Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Xiaolei Wu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
| | - Roland Gleisner
- USDA
Forest Service, Forest Products Laboratory, Madison, Wisconsin, United States
| | - Bruce S. Dien
- USDA
Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, Illlinois, United States
| | - Ronald E. Hector
- USDA
Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, Illlinois, United States
| | - Dongjie Yang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
| | - Xueqing Qiu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
| | - Eric Horn
- BioPulping International, Inc., Madison, Wisconsin, United States
| | - Jose Negron
- USDA
Forest Service, Rocky Mountain Research Station, Fort Collins, Colorado, United States
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42
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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: 44] [Impact Index Per Article: 3.7] [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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43
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Dien BS, O'Bryan PJ, Hector RE, Iten LB, Mitchell RB, Qureshi N, Sarath G, Vogel KP, Cotta MA. Conversion of switchgrass to ethanol using dilute ammonium hydroxide pretreatment: influence of ecotype and harvest maturity. ENVIRONMENTAL TECHNOLOGY 2013; 34:1837-1848. [PMID: 24350437 DOI: 10.1080/09593330.2013.833640] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Switchgrass (Panicum virgatum L.) is a perennial C4 grass that is being developed as a bioenergy crop because it has high production yields and suitable agronomic traits. Five switchgrass biomass samples from upland and lowland switchgrass ecotypes harvested at different stages or maturity were used in this study. Switchgrass samples contained 317.0-385.0 g glucans/kg switchgrass dry basis (db) and 579.3-660.2 g total structural carbohydrates/kg switchgrass, db. Carbohydrate contents were greater for the upland ecotype versus lowland ecotype and increased with harvest maturity. Pretreatment of switchgrass with dilute ammonium hydroxide (8% w/w ammonium loading) at 170 degrees C for 20 min was determined to be effective for preparing switchgrass for enzymatic conversion to monosaccharides; glucose recoveries were 66.9-90.5% and xylose recoveries 60.1-84.2% of maximum and decreased with increased maturity at harvest. Subsequently, pretreated switchgrass samples were converted to ethanol by simultaneous saccharification and fermentation using engineered xylose-fermenting Saccharomyces cerevisiae strain YRH400. Ethanol yields were 176.2-202.01/Mg of switchgrass (db) and followed a similar trend as observed for enzymatic sugar yields.
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Affiliation(s)
- Bruce S Dien
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 N. University Street, Peoria, IL 61604-3902, USA.
| | - Patricia J O'Bryan
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 N. University Street, Peoria, IL 61604-3902, USA
| | - Ronald E Hector
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 N. University Street, Peoria, IL 61604-3902, USA
| | - Loren B Iten
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 N. University Street, Peoria, IL 61604-3902, USA
| | - Robert B Mitchell
- Grain, Forage, and Bioenergy Research Unit, University of Nebraska, 137 Keim Hall, Box 830937, Lincoln, NE 68583-0937, USA
| | - Nasib Qureshi
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 N. University Street, Peoria, IL 61604-3902, USA
| | - Gautum Sarath
- Grain, Forage, and Bioenergy Research Unit, University of Nebraska, 137 Keim Hall, Box 830937, Lincoln, NE 68583-0937, USA
| | - Kenneth P Vogel
- Grain, Forage, and Bioenergy Research Unit, University of Nebraska, 137 Keim Hall, Box 830937, Lincoln, NE 68583-0937, USA
| | - Michael A Cotta
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 N. University Street, Peoria, IL 61604-3902, USA
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44
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Demeke MM, Dietz H, Li Y, Foulquié-Moreno MR, Mutturi S, Deprez S, Den Abt T, Bonini BM, Liden G, Dumortier F, Verplaetse A, Boles E, Thevelein JM. Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:89. [PMID: 23800147 PMCID: PMC3698012 DOI: 10.1186/1754-6834-6-89] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 06/12/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND The production of bioethanol from lignocellulose hydrolysates requires a robust, D-xylose-fermenting and inhibitor-tolerant microorganism as catalyst. The purpose of the present work was to develop such a strain from a prime industrial yeast strain, Ethanol Red, used for bioethanol production. RESULTS An expression cassette containing 13 genes including Clostridium phytofermentans XylA, encoding D-xylose isomerase (XI), and enzymes of the pentose phosphate pathway was inserted in two copies in the genome of Ethanol Red. Subsequent EMS mutagenesis, genome shuffling and selection in D-xylose-enriched lignocellulose hydrolysate, followed by multiple rounds of evolutionary engineering in complex medium with D-xylose, gradually established efficient D-xylose fermentation. The best-performing strain, GS1.11-26, showed a maximum specific D-xylose consumption rate of 1.1 g/g DW/h in synthetic medium, with complete attenuation of 35 g/L D-xylose in about 17 h. In separate hydrolysis and fermentation of lignocellulose hydrolysates of Arundo donax (giant reed), spruce and a wheat straw/hay mixture, the maximum specific D-xylose consumption rate was 0.36, 0.23 and 1.1 g/g DW inoculum/h, and the final ethanol titer was 4.2, 3.9 and 5.8% (v/v), respectively. In simultaneous saccharification and fermentation of Arundo hydrolysate, GS1.11-26 produced 32% more ethanol than the parent strain Ethanol Red, due to efficient D-xylose utilization. The high D-xylose fermentation capacity was stable after extended growth in glucose. Cell extracts of strain GS1.11-26 displayed 17-fold higher XI activity compared to the parent strain, but overexpression of XI alone was not enough to establish D-xylose fermentation. The high D-xylose consumption rate was due to synergistic interaction between the high XI activity and one or more mutations in the genome. The GS1.11-26 had a partial respiratory defect causing a reduced aerobic growth rate. CONCLUSIONS An industrial yeast strain for bioethanol production with lignocellulose hydrolysates has been developed in the genetic background of a strain widely used for commercial bioethanol production. The strain uses glucose and D-xylose with high consumption rates and partial cofermentation in various lignocellulose hydrolysates with very high ethanol yield. The GS1.11-26 strain shows highly promising potential for further development of an all-round robust yeast strain for efficient fermentation of various lignocellulose hydrolysates.
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Affiliation(s)
- Mekonnen M Demeke
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| | - Heiko Dietz
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Yingying Li
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| | - María R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| | - Sarma Mutturi
- Department of Chemical Engineering, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Sylvie Deprez
- Laboratory of Enzyme, Fermentation and Brewing Technology, KAHO Sint-Lieven University College, KU Leuven Association, Gebroeders De Smetstraat 1, 9000, Ghent, Flanders, Belgium
| | - Tom Den Abt
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| | - Beatriz M Bonini
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| | - Gunnar Liden
- Department of Chemical Engineering, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Françoise Dumortier
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| | - Alex Verplaetse
- Laboratory of Enzyme, Fermentation and Brewing Technology, KAHO Sint-Lieven University College, KU Leuven Association, Gebroeders De Smetstraat 1, 9000, Ghent, Flanders, Belgium
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
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Hector RE, Dien BS, Cotta MA, Mertens JA. Growth and fermentation of D-xylose by Saccharomyces cerevisiae expressing a novel D-xylose isomerase originating from the bacterium Prevotella ruminicola TC2-24. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:84. [PMID: 23721368 PMCID: PMC3673840 DOI: 10.1186/1754-6834-6-84] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 05/22/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND Saccharomyces cerevisiae strains expressing D-xylose isomerase (XI) produce some of the highest reported ethanol yields from D-xylose. Unfortunately, most bacterial XIs that have been expressed in S. cerevisiae are either not functional, require additional strain modification, or have low affinity for D-xylose. This study analyzed several XIs from rumen and intestinal microorganisms to identify enzymes with improved properties for engineering S. cerevisiae for D-xylose fermentation. RESULTS Four XIs originating from rumen and intestinal bacteria were isolated and expressed in a S. cerevisiae CEN.PK2-1C parental strain primed for D-xylose metabolism by over expression of its native D-xylulokinase. Three of the XIs were functional in S. cerevisiae, based on the strain's ability to grow in D-xylose medium. The most promising strain, expressing the XI mined from Prevotella ruminicola TC2-24, was further adapted for aerobic and fermentative growth by serial transfers of D-xylose cultures under aerobic, and followed by microaerobic conditions. The evolved strain had a specific growth rate of 0.23 h-1 on D-xylose medium, which is comparable to the best reported results for analogous S. cerevisiae strains including those expressing the Piromyces sp. E2 XI. When used to ferment D-xylose, the adapted strain produced 13.6 g/L ethanol in 91 h with a metabolic yield of 83% of theoretical. From analysis of the P. ruminicola XI, it was determined the enzyme possessed a Vmax of 0.81 μmole/min/mg protein and a Km of 34 mM. CONCLUSION This study identifies a new xylose isomerase from the rumen bacterium Prevotella ruminicola TC2-24 that has one of the highest affinities and specific activities compared to other bacterial and fungal D-xylose isomerases expressed in yeast. When expressed in S. cerevisiae and used to ferment D-xylose, very high ethanol yield was obtained. This new XI should be a promising resource for constructing other D-xylose fermenting strains, including industrial yeast genetic backgrounds.
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Affiliation(s)
- Ronald E Hector
- Bioenergy Research Unit, United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL 61604, USA
| | - Bruce S Dien
- Bioenergy Research Unit, United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL 61604, USA
| | - Michael A Cotta
- Bioenergy Research Unit, United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL 61604, USA
| | - Jeffrey A Mertens
- Bioenergy Research Unit, United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL 61604, USA
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Lan TQ, Gleisner R, Zhu JY, Dien BS, Hector RE. High titer ethanol production from SPORL-pretreated lodgepole pine by simultaneous enzymatic saccharification and combined fermentation. BIORESOURCE TECHNOLOGY 2013; 127:291-7. [PMID: 23138055 DOI: 10.1016/j.biortech.2012.09.111] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 08/10/2012] [Accepted: 09/28/2012] [Indexed: 05/17/2023]
Abstract
Lodgepole wood chips were pretreated by sulfite pretreatment to overcome recalcitrance of lignocelluloses (SPORL) at 25% solids loading and 180 °C for 20 min with sulfuric acid and sodium bisulfite charges of 2.2 and 8 wt/wt% on an oven-dry wood basis, respectively. The pretreated wood chips were disk-milled with pretreatment spent liquor and water, and the solid fraction was separated from the liquor stream. The liquor was neutralized and concentrated through vacuum evaporation. Quasi-simultaneous enzymatic saccharification of the cellulosic solids and combined fermentation with the concentrated liquor was conducted at up to 20% total solids loading. Fed-batching of the solids facilitated liquefaction and saccharification, as well as managing instantaneous inhibitor concentrations. At a commercial cellulase (CTec2) loading of only 9 FPU or 0.06 mL/g untreated wood, a maximum ethanol titer of 47.4 g/L was achieved, resulting in a calculated yield of 285 L/tonne of wood using Saccharomyces cerevisiae YRH400 at 35 °C and pH 5.5.
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Affiliation(s)
- T Q Lan
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
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Jin M, Sarks C, Gunawan C, Bice BD, Simonett SP, Avanasi Narasimhan R, Willis LB, Dale BE, Balan V, Sato TK. Phenotypic selection of a wild Saccharomyces cerevisiae strain for simultaneous saccharification and co-fermentation of AFEX™ pretreated corn stover. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:108. [PMID: 23890073 PMCID: PMC3729497 DOI: 10.1186/1754-6834-6-108] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 07/25/2013] [Indexed: 05/09/2023]
Abstract
BACKGROUND Simultaneous saccharification and co-fermentation (SSCF) process involves enzymatic hydrolysis of pretreated lignocellulosic biomass and fermentation of glucose and xylose in one bioreactor. The optimal temperatures for enzymatic hydrolysis are higher than the standard fermentation temperature of ethanologenic Saccharomyces cerevisiae. Moreover, degradation products resulting from biomass pretreatment impair fermentation of sugars, especially xylose, and can synergize with high temperature stress. One approach to resolve both concerns is to utilize a strain background with innate tolerance to both elevated temperatures and degradation products. RESULTS In this study, we screened a panel of 108 wild and domesticated Saccharomyces cerevisiae strains isolated from a wide range of environmental niches. One wild strain was selected based on its growth tolerance to simultaneous elevated temperature and AFEX™ (Ammonia Fiber Expansion) degradation products. After engineering the strain with two copies of the Scheffersomyces stipitis xylose reductase, xylitol dehydrogenase and xylulokinase genes, we compared the ability of this engineered strain to the benchmark 424A(LNH-ST) strain in ethanol production and xylose fermentation in standard lab medium and AFEX pretreated corn stover (ACS) hydrolysates, as well as in SSCF of ACS at different temperatures. In SSCF of 9% (w/w) glucan loading ACS at 35°C, the engineered strain showed higher cell viabilities and produced a similar amount of ethanol (51.3 g/L) compared to the benchmark 424A(LNH-ST) strain. CONCLUSION These results validate our approach in the selection of wild Saccharomyces cerevisiae strains with thermo-tolerance and degradation products tolerance properties for lignocellulosic biofuel production. The wild and domesticated yeast strains phenotyped in this work are publically available for others to use as genetic backgrounds for fermentation of their pretreated biomass at elevated temperatures.
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Affiliation(s)
- Mingjie Jin
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3900 Collins Road, Lansing, MI 48910, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
| | - Cory Sarks
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3900 Collins Road, Lansing, MI 48910, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
| | - Christa Gunawan
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3900 Collins Road, Lansing, MI 48910, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
| | - Benjamin D Bice
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI 53726, USA
| | - Shane P Simonett
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI 53706, USA
| | - Ragothaman Avanasi Narasimhan
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI 53726, USA
| | - Laura B Willis
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI 53726, USA
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI 53706, USA
- U.S. Department of Agriculture, Forest Products Laboratory, 1 Gifford Pinchot Dr, Madison, WI 53726, USA
| | - Bruce E Dale
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3900 Collins Road, Lansing, MI 48910, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
| | - Venkatesh Balan
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3900 Collins Road, Lansing, MI 48910, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI 53726, USA
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Zha J, Hu ML, Shen MH, Li BZ, Wang JY, Yuan YJ. Balance of XYL1 and XYL2 expression in different yeast chassis for improved xylose fermentation. Front Microbiol 2012; 3:355. [PMID: 23060871 PMCID: PMC3464680 DOI: 10.3389/fmicb.2012.00355] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 09/19/2012] [Indexed: 01/04/2023] Open
Abstract
Reducing xylitol formation is necessary in engineering xylose utilization in recombinant Saccharomyces cerevisiae for ethanol production through xylose reductase/xylitol dehydrogenase pathway. To balance the expression of XYL1 and mutant XYL2 encoding xylose reductase (XR) and NADP+-dependent xylitol dehydrogenase (XDH), respectively, we utilized a strategy combining chassis selection and direct fine-tuning of XYL1 and XYL2 expression in this study. A XYL1 gene under the control of various promoters of ADH1, truncated ADH1 and PGK1, and a mutated XYL2 with different copy numbers were constructed into different xylose-utilizing modules, which were then expressed in two yeast chassises W303a and L2612. The strategy enabled an improved L2612-derived recombinant strain with XYL1 controlled by promoter PGK1 and with two copies of XYL2. The strain exhibited a 21.3% lower xylitol yield and a 40.0% higher ethanol yield. The results demonstrate the feasibility of the combinatorial strategy for construction of an efficient xylose-fermenting S. cerevisiae.
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Affiliation(s)
- Jian Zha
- Key Laboratory of Systems Bioengineering (Tianjin University), Ministry of Education, Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, P. R. China
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Xia T, Eiteman MA, Altman E. Simultaneous utilization of glucose, xylose and arabinose in the presence of acetate by a consortium of Escherichia coli strains. Microb Cell Fact 2012; 11:77. [PMID: 22691294 PMCID: PMC3514249 DOI: 10.1186/1475-2859-11-77] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 06/07/2012] [Indexed: 11/21/2022] Open
Abstract
Background The efficient microbial utilization of lignocellulosic hydrolysates has remained challenging because this material is composed of multiple sugars and also contains growth inhibitors such as acetic acid (acetate). Using an engineered consortium of strains derived from Escherichia coli C and a synthetic medium containing acetate, glucose, xylose and arabinose, we report on both the microbial removal of acetate and the subsequent simultaneous utilization of the sugars. Results In a first stage, a strain unable to utilize glucose, xylose and arabinose (ALS1392, strain E. coli C ptsG manZ glk crr xylA araA) removed 3 g/L acetate within 30 hours. In a subsequent second stage, three E. coli strains (ALS1370, ALS1371, ALS1391), which are each engineered to utilize only one sugar, together simultaneously utilized glucose, xylose and arabinose. The effect of non-metabolizable sugars on the metabolism of the target sugar was minimal. Additionally the deletions necessary to prevent the consumption of one sugar only minimally affected the consumption of a desired sugar. For example, the crr deletion necessary to prevent glucose consumption reduced xylose and arabinose utilization by less than 15% compared to the wild-type. Similarly, the araA deletion used to exclude arabinose consumption did not affect xylose- and glucose-consumption. Conclusions Despite the modest reduction in the overall rate of sugar consumption due to the various deletions that were required to generate the consortium of strains, the approach constitutes a significant improvement in any single-organism approach to utilize sugars found in lignocellulosic hydrolysate in the presence of acetate.
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Affiliation(s)
- Tian Xia
- Center for Molecular BioEngineering, Department of Biological and Agricultural Engineering, University of Georgia, Athens, GA 30602, USA
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50
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Bowman MJ, Dien BS, Hector RE, Sarath G, Cotta MA. Liquid chromatography-mass spectrometry investigation of enzyme-resistant xylooligosaccharide structures of switchgrass associated with ammonia pretreatment, enzymatic saccharification, and fermentation. BIORESOURCE TECHNOLOGY 2012; 110:437-47. [PMID: 22330596 DOI: 10.1016/j.biortech.2012.01.062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 01/03/2012] [Accepted: 01/13/2012] [Indexed: 05/11/2023]
Abstract
Switchgrass is a potential source of renewable biomass for conversion to liquid biofuels. Efficient conversion requires effective strategies for pretreatment and enzymatic saccharification to produce fermentable sugars. Standard analysis of fermentation liquids includes detection of monosaccharides and ethanol to determine efficiency of conversion. Larger components, specifically oligosaccharides, are typically not measured due to the structural complexity of the products; however, as oligosaccharides they represent carbon available in biomass that is not converted to liquid fuels. In this study, ammonia-pretreated switchgrass was enzymatically depolymerized either independently or under simultaneous saccharification and fermentation conditions. Residual oligosaccharides were reducing end-labeled followed by hydrophilic interaction liquid chromatography mass spectrometry/mass spectrometry analysis. These data reveal 20 oligosaccharide peaks with distinct retention times and tandem mass spectrometry fragmentation patterns representing 13 different oligosaccharide compositions. All measured compositions were smaller than a chain length of six and were neither linear xylooligosaccharides nor modified with phenolic esters. This work represents a robust method to monitor and identify unhydrolyzed oligosaccharides from fermentations, thereby permitting the screening of targeted enzymatic activities to promote the complete hydrolysis of xylan.
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Affiliation(s)
- Michael J Bowman
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, 1815 N. University Street, Peoria, IL 61604, USA.
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