101
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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: 2.2] [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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102
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Braconi D, Bernardini G, Santucci A. Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. J Proteomics 2015; 137:19-34. [PMID: 26365628 DOI: 10.1016/j.jprot.2015.09.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/29/2015] [Accepted: 09/02/2015] [Indexed: 12/13/2022]
Abstract
The budding yeast Saccharomyces cerevisiae represents a well-consolidated and widely used eukaryotic model, with a number of features that make it an ideal organism to carry out functional toxicological studies. Several advantages are permitted by the use of yeast cells, as the possibility to identify molecular biomarkers, unknown mechanisms of action and novel potential targets. Thanks to the evolutionary conservation, yeast can provide also useful clues allowing the prioritization of more complex analyses and toxicity predictions in higher eukaryotes. The last two decades were incredibly fruitful for yeast "omics", but referring to the analysis of the effects of pesticides on yeast much still remains to be done. Furthermore, a deeper knowledge of the effects of environmental pollutants on biotechnological processes associated with the use of yeasts is to be hoped.
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Affiliation(s)
- Daniela Braconi
- Dipartimento di Biotecnologie, Chimica e Farmacia, via A. Moro 2, Università degli Studi di Siena, 53100 Siena, Italy
| | - Giulia Bernardini
- Dipartimento di Biotecnologie, Chimica e Farmacia, via A. Moro 2, Università degli Studi di Siena, 53100 Siena, Italy
| | - Annalisa Santucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, via A. Moro 2, Università degli Studi di Siena, 53100 Siena, Italy.
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103
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White biotechnology: State of the art strategies for the development of biocatalysts for biorefining. Biotechnol Adv 2015; 33:1653-70. [PMID: 26303096 DOI: 10.1016/j.biotechadv.2015.08.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/31/2015] [Accepted: 08/17/2015] [Indexed: 12/31/2022]
Abstract
White biotechnology is a term that is now often used to describe the implementation of biotechnology in the industrial sphere. Biocatalysts (enzymes and microorganisms) are the key tools of white biotechnology, which is considered to be one of the key technological drivers for the growing bioeconomy. Biocatalysts are already present in sectors such as the chemical and agro-food industries, and are used to manufacture products as diverse as antibiotics, paper pulp, bread or advanced polymers. This review proposes an original and global overview of highly complementary fields of biotechnology at both enzyme and microorganism level. A certain number of state of the art approaches that are now being used to improve the industrial fitness of biocatalysts particularly focused on the biorefinery sector are presented. The first part deals with the technologies that underpin the development of industrial biocatalysts, notably the discovery of new enzymes and enzyme improvement using directed evolution techniques. The second part describes the toolbox available by the cell engineer to shape the metabolism of microorganisms. And finally the last part focuses on the 'omic' technologies that are vital for understanding and guide microbial engineering toward more efficient microbial biocatalysts. Altogether, these techniques and strategies will undoubtedly help to achieve the challenging task of developing consolidated bioprocessing (i.e. CBP) readily available for industrial purpose.
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104
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Oshoma CE, Greetham D, Louis EJ, Smart KA, Phister TG, Powell C, Du C. Screening of Non- Saccharomyces cerevisiae Strains for Tolerance to Formic Acid in Bioethanol Fermentation. PLoS One 2015; 10:e0135626. [PMID: 26284784 PMCID: PMC4540574 DOI: 10.1371/journal.pone.0135626] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/24/2015] [Indexed: 11/18/2022] Open
Abstract
Formic acid is one of the major inhibitory compounds present in hydrolysates derived from lignocellulosic materials, the presence of which can significantly hamper the efficiency of converting available sugars into bioethanol. This study investigated the potential for screening formic acid tolerance in non-Saccharomyces cerevisiae yeast strains, which could be used for the development of advanced generation bioethanol processes. Spot plate and phenotypic microarray methods were used to screen the formic acid tolerance of 7 non-Saccharomyces cerevisiae yeasts. S. kudriavzeii IFO1802 and S. arboricolus 2.3319 displayed a higher formic acid tolerance when compared to other strains in the study. Strain S. arboricolus 2.3319 was selected for further investigation due to its genetic variability among the Saccharomyces species as related to Saccharomyces cerevisiae and availability of two sibling strains: S. arboricolus 2.3317 and 2.3318 in the lab. The tolerance of S. arboricolus strains (2.3317, 2.3318 and 2.3319) to formic acid was further investigated by lab-scale fermentation analysis, and compared with S. cerevisiae NCYC2592. S. arboricolus 2.3319 demonstrated improved formic acid tolerance and a similar bioethanol synthesis capacity to S. cerevisiae NCYC2592, while S. arboricolus 2.3317 and 2.3318 exhibited an overall inferior performance. Metabolite analysis indicated that S. arboricolus strain 2.3319 accumulated comparatively high concentrations of glycerol and glycogen, which may have contributed to its ability to tolerate high levels of formic acid.
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Affiliation(s)
- Cyprian E. Oshoma
- Bioenergy and Brewing Science Building, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, United Kingdom
| | - Darren Greetham
- Bioenergy and Brewing Science Building, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, United Kingdom
| | - Edward J. Louis
- Centre for Genetic Architecture of Complex Traits, University of Leicester, Leicester, United Kingdom
| | | | - Trevor G. Phister
- PepsiCo Int. Beaumont Park, Leycroft Road, Leicester, United Kingdom
| | - Chris Powell
- Bioenergy and Brewing Science Building, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, United Kingdom
| | - Chenyu Du
- Bioenergy and Brewing Science Building, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, United Kingdom
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, United Kingdom
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105
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Petrovič U. Next-generation biofuels: a new challenge for yeast. Yeast 2015; 32:583-93. [DOI: 10.1002/yea.3082] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/16/2015] [Accepted: 06/16/2015] [Indexed: 11/11/2022] Open
Affiliation(s)
- Uroš Petrovič
- Jožef Stefan Institute; Department of Molecular and Biomedical Sciences; Ljubljana Slovenia
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106
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Soma Y, Hanai T. Self-induced metabolic state switching by a tunable cell density sensor for microbial isopropanol production. Metab Eng 2015; 30:7-15. [DOI: 10.1016/j.ymben.2015.04.005] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/08/2015] [Accepted: 04/10/2015] [Indexed: 11/30/2022]
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107
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Teramura H, Sasaki K, Oshima T, Aikawa S, Matsuda F, Okamoto M, Shirai T, Kawaguchi H, Ogino C, Yamasaki M, Kikuchi J, Kondo A. Changes in Lignin and Polysaccharide Components in 13 Cultivars of Rice Straw following Dilute Acid Pretreatment as Studied by Solution-State 2D 1H-13C NMR. PLoS One 2015; 10:e0128417. [PMID: 26083431 PMCID: PMC4470627 DOI: 10.1371/journal.pone.0128417] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/27/2015] [Indexed: 11/18/2022] Open
Abstract
A renewable raw material, rice straw is pretreated for biorefinery usage. Solution-state two-dimensional (2D) 1H-13 C hetero-nuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy, was used to analyze 13 cultivars of rice straw before and after dilute acid pretreatment, to characterize general changes in the lignin and polysaccharide components. Intensities of most (15 of 16) peaks related to lignin aromatic regions, such as p-coumarate, guaiacyl, syringyl, p-hydroxyphenyl, and cinnamyl alcohol, and methoxyl, increased or remained unchanged after pretreatment. In contrast, intensities of most (11 of 13) peaks related to lignin aliphatic linkages or ferulate decreased. Decreased heterogeneity in the intensities of three peaks related to cellulose components in acid-insoluble residues resulted in similar glucose yield (0.45-0.59 g/g-dry biomass). Starch-derived components showed positive correlations (r = 0.71 to 0.96) with glucose, 5-hydroxymethylfurfural (5-HMF), and formate concentrations in the liquid hydrolysates, and negative correlations (r = -0.95 to -0.97) with xylose concentration and acid-insoluble residue yield. These results showed the fate of lignin and polysaccharide components by pretreatment, suggesting that lignin aromatic regions and cellulose components were retained in the acid insoluble residues and starch-derived components were transformed into glucose, 5-HMF, and formate in the liquid hydrolysate.
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Affiliation(s)
- Hiroshi Teramura
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
| | - Kengo Sasaki
- Organization of Advanced Science and Technology, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
| | - Tomoko Oshima
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
| | - Shimpei Aikawa
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, Japan
- RIKEN Biomass Engineering Program, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Mami Okamoto
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Uzurano, Kasai, Hyogo, Japan
| | - Tomokazu Shirai
- RIKEN Biomass Engineering Program, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Hideo Kawaguchi
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Uzurano, Kasai, Hyogo, Japan
| | - Jun Kikuchi
- RIKEN Biomass Engineering Program, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Graduate School of Medical Life Science, Yokohama City University, Suehirocho, Tsurumi-ku, Yokohama, Japan
- Graduate School of Bioagricultural Sciences and School of Agricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
- RIKEN Biomass Engineering Program, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- * E-mail:
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108
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Improving conversion yield of fermentable sugars into fuel ethanol in 1st generation yeast-based production processes. Curr Opin Biotechnol 2015; 33:81-6. [DOI: 10.1016/j.copbio.2014.12.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/08/2014] [Accepted: 12/14/2014] [Indexed: 11/22/2022]
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109
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Kurosawa K, Laser J, Sinskey AJ. Tolerance and adaptive evolution of triacylglycerol-producing Rhodococcus opacus to lignocellulose-derived inhibitors. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:76. [PMID: 26052344 PMCID: PMC4456722 DOI: 10.1186/s13068-015-0258-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/29/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Lignocellulosic biomass has been investigated as a renewable non-food source for production of biofuels. A significant technical challenge to using lignocellulose is the presence of microbial growth inhibitors generated during pretreatment processes. Triacylglycerols (TAGs) are potential precursors for lipid-based biofuel production. Rhodococcus opacus MITXM-61 is an oleaginous bacterium capable of producing large amounts of TAGs on high concentrations of glucose and xylose present in lignocellulosic hydrolysates. However, this strain is sensitive to ligonocellulose-derived inhibitors. To understand the toxic effects of the inhibitors in lignocellulosic hydrolysates, strain MITXM-61 was examined for tolerance toward the potential inhibitors and was subjected to adaptive evolution for the resistance to the inhibitors. RESULTS We investigated growth-inhibitory effects by potential lignocellulose-derived inhibitors of phenols (lignin, vanillin, 4-hydroxybenzaldehyde (4-HB), syringaldehyde), furans (furfural and 5-hydroxymethyl-2-furaldehyde), and organic acids (levulinic acid, formic acid, and acetic acid) on the growth and TAG production of strain MITXM-61. Phenols and furans exhibited potent inhibitory effects at a concentration of 1 g L(-1), while organic acids had insignificant impacts at concentrations of up to 2 g L(-1). In an attempt to improve the inhibitor tolerance of strain MITXM-61, we evaluated the adaptation of this strain to the potential inhibitors. Adapted mutants were generated on defined agar media containing lignin, 4-HB, and syringaldehyde. Strain MITXM-61(SHL33) with improved multiple resistance of lignin, 4-HB, and syringaldehyde was constructed through adaptive evolution-based strategies. The evolved strain exhibited a two- to threefold increase in resistance to lignin, 4-HB, and syringaldehyde at 50% growth-inhibitory concentrations, compared to the parental strain. When grown in genuine lignocellulosic hydrolysates of corn stover, wheat straw, and hardwood containing growth inhibitors, strain MITXM-61(SHL33) exhibited a markedly shortened lag phase in comparison with that of strain MITXM-61. CONCLUSION This study provides important clues to overcome the negative effects of inhibitors in lignocellulosic hydrolysates on TAG production of R. opacus cells. The findings can contribute to significant progress in detoxified pretreatment of hydrolysates and development of more efficient strains for industrial TAG fermentations of R. opacus using lignocellulosic biomass.
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Affiliation(s)
- Kazuhiko Kurosawa
- />Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Josephine Laser
- />Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- />Present address: Institute of Biotechnology, Department Applied and Molecular Microbiology Berlin University of Technology, Gustav-Meyer-Allee 25, Berlin, D-13355 Germany
| | - Anthony J Sinskey
- />Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- />Engineering Systems Division, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
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110
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Ida K, Ishii J, Matsuda F, Kondo T, Kondo A. Eliminating the isoleucine biosynthetic pathway to reduce competitive carbon outflow during isobutanol production by Saccharomyces cerevisiae. Microb Cell Fact 2015; 14:62. [PMID: 25925006 PMCID: PMC4417518 DOI: 10.1186/s12934-015-0240-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 04/02/2015] [Indexed: 11/10/2022] Open
Abstract
Background Isobutanol is an important biorefinery target alcohol that can be used as a fuel, fuel additive, or commodity chemical. Baker’s yeast, Saccharomyces cerevisiae, is a promising organism for the industrial manufacture of isobutanol because of its tolerance for low pH and resistance to autolysis. It has been reported that gene deletion of the pyruvate dehydrogenase complex, which is directly involved in pyruvate metabolism, improved isobutanol production by S. cerevisiae. However, the engineering strategies available for S. cerevisiae are immature compared to those available for bacterial hosts such as Escherichia coli, and several pathways in addition to pyruvate metabolism compete with isobutanol production. Results The isobutyrate, pantothenate or isoleucine biosynthetic pathways were deleted to reduce the outflow of carbon competing with isobutanol biosynthesis in S. cerevisiae. The judicious elimination of these competing pathways increased isobutanol production. ILV1 encodes threonine ammonia-lyase, the enzyme that converts threonine to 2-ketobutanoate, a precursor for isoleucine biosynthesis. S. cerevisiae mutants in which ILV1 had been deleted displayed 3.5-fold increased isobutanol productivity. The ΔILV1 strategy was further combined with two previously established engineering strategies (activation of two steps of the Ehrlich pathway and the transhydrogenase-like shunt), providing 11-fold higher isobutanol productivity as compared to the parent strain. The titer and yield of this engineered strain was 224 ± 5 mg/L and 12.04 ± 0.23 mg/g glucose, respectively. Conclusions The deletion of competitive pathways to reduce the outflow of carbon, including ILV1 deletion, is an important strategy for increasing isobutanol production by S. cerevisiae.
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Affiliation(s)
- Kengo Ida
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Jun Ishii
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Fumio Matsuda
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 565-0871, Japan. .,RIKEN Biomass Engineering Program, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
| | - Takashi Kondo
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,Present address: Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan.
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,RIKEN Biomass Engineering Program, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
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111
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Engineering Saccharomyces pastorianus for the co-utilisation of xylose and cellulose from biomass. Microb Cell Fact 2015; 14:61. [PMID: 25928878 PMCID: PMC4417197 DOI: 10.1186/s12934-015-0242-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/08/2015] [Indexed: 01/24/2023] Open
Abstract
Background Lignocellulosic biomass is a viable source of renewable energy for bioethanol production. For the efficient conversion of biomass into bioethanol, it is essential that sugars from both the cellulose and hemicellulose fractions of lignocellulose be utilised. Results We describe the development of a recombinant yeast system for the fermentation of cellulose and xylose, the most abundant pentose sugar in the hemicellulose fraction of biomass. The brewer’s yeast Saccharomyces pastorianus was chosen as a host as significantly higher recombinant enzyme activities are achieved, when compared to the more commonly used S. cerevisiae. When expressed in S. pastorianus, the Trichoderma reesei xylose oxidoreductase pathway was more efficient at alcohol production from xylose than the xylose isomerase pathway. The alcohol yield was influenced by the concentration of xylose in the medium and was significantly improved by the additional expression of a gene encoding for xylulose kinase. The xylose reductase, xylitol dehydrogenase and xylulose kinase genes were co-expressed with genes encoding for the three classes of T. reesei cellulases, namely endoglucanase (EG2), cellobiohydrolysase (CBH2) and β-glucosidase (BGL1). The initial metabolism of xylose by the engineered strains facilitated production of cellulases at fermentation temperatures. The sequential metabolism of xylose and cellulose generated an alcohol yield of 82% from the available sugars. Several different types of biomass, such as the energy crop Miscanthus sinensis and the industrial waste, brewer’s spent grains, were examined as biomass sources for fermentation using the developed yeast strains. Xylose metabolism and cell growth were inhibited in fermentations carried out with acid-treated spent grain liquor, resulting in a 30% reduction in alcohol yield compared to fermentations carried out with mixed sugar substrates. Conclusions Reconstitution of complete enzymatic pathways for cellulose hydrolysis and xylose utilisation in S. pastorianus facilitates the co-fermentation of cellulose and xylose without the need for added exogenous cellulases and provides a basis for the development of a consolidated process for co-utilisation of hemicellulose and cellulose sugars. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0242-4) contains supplementary material, which is available to authorized users.
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112
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Compounds inhibiting the bioconversion of hydrothermally pretreated lignocellulose. Appl Microbiol Biotechnol 2015; 99:4201-12. [DOI: 10.1007/s00253-015-6595-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 04/06/2015] [Accepted: 04/09/2015] [Indexed: 01/02/2023]
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113
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Zhang Y, Liu ZL, Song M. ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion. Nucleic Acids Res 2015; 43:4393-407. [PMID: 25897127 PMCID: PMC4482087 DOI: 10.1093/nar/gkv358] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 04/06/2015] [Indexed: 12/14/2022] Open
Abstract
Analysis of rewired upstream subnetworks impacting downstream differential gene expression aids the delineation of evolving molecular mechanisms. Cumulative statistics based on conventional differential correlation are limited for subnetwork rewiring analysis since rewiring is not necessarily equivalent to change in correlation coefficients. Here we present a computational method ChiNet to quantify subnetwork rewiring by statistical heterogeneity that enables detection of potential genotype changes causing altered transcription regulation in evolving organisms. Given a differentially expressed downstream gene set, ChiNet backtracks a rewired upstream subnetwork from a super-network including gene interactions known to occur under various molecular contexts. We benchmarked ChiNet for its high accuracy in distinguishing rewired artificial subnetworks, in silico yeast transcription-metabolic subnetworks, and rewired transcription subnetworks for Candida albicans versus Saccharomyces cerevisiae, against two differential-correlation based subnetwork rewiring approaches. Then, using transcriptome data from tolerant S. cerevisiae strain NRRL Y-50049 and a wild-type intolerant strain, ChiNet identified 44 metabolic pathways affected by rewired transcription subnetworks anchored to major adaptively activated transcription factor genes YAP1, RPN4, SFP1 and ROX1, in response to toxic chemical challenges involved in lignocellulose-to-biofuels conversion. These findings support the use of ChiNet in rewiring analysis of subnetworks where differential interaction patterns resulting from divergent nonlinear dynamics abound.
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Affiliation(s)
- Yang Zhang
- Department of Computer Science, New Mexico State University, Las Cruces, NM 88003, USA
| | - Z Lewis Liu
- National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - Mingzhou Song
- Department of Computer Science, New Mexico State University, Las Cruces, NM 88003, USA
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114
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Kawaguchi H, Teramura H, Uematsu K, Hara KY, Hasunuma T, Hirano K, Sazuka T, Kitano H, Tsuge Y, Kahar P, Niimi-Nakamura S, Oinuma KI, Takaya N, Kasuga S, Ogino C, Kondo A. Phenyllactic acid production by simultaneous saccharification and fermentation of pretreated sorghum bagasse. BIORESOURCE TECHNOLOGY 2015; 182:169-178. [PMID: 25689311 DOI: 10.1016/j.biortech.2015.01.097] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 06/04/2023]
Abstract
Dilute acid-pretreated sorghum bagasse, which was predominantly composed of glucan (59%) and xylose (7.2%), was used as a lignocellulosic feedstock for d-phenyllactic acid (PhLA) production by a recombinant Escherichia coli strain expressing phenylpyruvate reductase from Wickerhamia fluorescens. During fermentation with enzymatic hydrolysate of sorghum bagasse as a carbon source, the PhLA yield was reduced by 35% compared to filter paper hydrolysate, and metabolomics analysis revealed that NAD(P)H regeneration and intracellular levels of erythrose-4-phosphate and phosphoenolpyruvate for PhLA biosynthesis markedly reduced. Compared to separate hydrolysis and fermentation (SHF) with sorghum bagasse hydrolysate, simultaneous saccharification and fermentation (SSF) of sorghum bagasse under glucose limitation conditions yielded 4.8-fold more PhLA with less accumulation of eluted components, including p-coumaric acid and aldehydes, which inhibited PhLA fermentation. These results suggest that gradual enzymatic hydrolysis during SSF enhances PhLA production under glucose limitation and reduces the accumulation of fermentation inhibitors, collectively leading to increased PhLA yield.
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Affiliation(s)
- Hideo Kawaguchi
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Hiroshi Teramura
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Kouji Uematsu
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Kiyotaka Y Hara
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Ko Hirano
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
| | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
| | - Hidemi Kitano
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
| | - Yota Tsuge
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Prihardi Kahar
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Satoko Niimi-Nakamura
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Ken-Ichi Oinuma
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Shigemitsu Kasuga
- Education and Research Center of Alpine Field Science, Faculty of Agriculture, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Turumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Challenges for the production of bioethanol from biomass using recombinant yeasts. ADVANCES IN APPLIED MICROBIOLOGY 2015; 92:89-125. [PMID: 26003934 DOI: 10.1016/bs.aambs.2015.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Lignocellulose biomass, one of the most abundant renewable resources on the planet, is an alternative sustainable energy source for the production of second-generation biofuels. Energy in the form of simple or complex carbohydrates can be extracted from lignocellulose biomass and fermented by microorganisms to produce bioethanol. Despite 40 years of active and cutting-edge research invested into the development of technologies to produce bioethanol from lignocellulosic biomass, the process remains commercially unviable. This review describes the achievements that have been made in generating microorganisms capable of utilizing both simple and complex sugars from lignocellulose biomass and the fermentation of these sugars into ethanol. We also provide a discussion on the current "roadblocks" standing in the way of making second-generation bioethanol a commercially viable alternative to fossil fuels.
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Nugroho RH, Yoshikawa K, Shimizu H. Metabolomic analysis of acid stress response in Saccharomyces cerevisiae. J Biosci Bioeng 2015; 120:396-404. [PMID: 25795572 DOI: 10.1016/j.jbiosc.2015.02.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 12/24/2022]
Abstract
Acid stress has been reported to inhibit cell growth and decrease productivity during bio-production processes. In this study, a metabolomics approach was conducted to understand the effect of lactic acid induced stress on metabolite pools in Saccharomyces cerevisiae. Cells were cultured with lactic acid as the acidulant, with or without initial pH control, i.e., at pH 6 or pH 2.5, respectively. Under conditions of low pH, lactic acid led to a decrease in the intracellular pH and specific growth rate; however, these parameters remained unaltered in the cultures with pH control. Capillary electrophoresis-mass spectrometry followed by a statistical principal component analysis was used to identify the metabolites and measure the increased concentrations of ATP, glutathione and proline during severe acid stress. Addition of proline to the acidified cultures improved the specific growth rates. We hypothesized that addition of proline protected the cells from acid stress by combating acid-induced oxidative stress. Lactic acid diffusion into the cell resulted in intracellular acidification, which elicited an oxidative stress response and resulted in increased glutathione levels.
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Affiliation(s)
- Riyanto Heru Nugroho
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Katsunori Yoshikawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Kim SK, Jin YS, Choi IG, Park YC, Seo JH. Enhanced tolerance of Saccharomyces cerevisiae to multiple lignocellulose-derived inhibitors through modulation of spermidine contents. Metab Eng 2015; 29:46-55. [PMID: 25724339 DOI: 10.1016/j.ymben.2015.02.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 01/06/2015] [Accepted: 02/17/2015] [Indexed: 01/13/2023]
Abstract
Fermentation inhibitors present in lignocellulose hydrolysates are inevitable obstacles for achieving economic production of biofuels and biochemicals by industrial microorganisms. Here we show that spermidine (SPD) functions as a chemical elicitor for enhanced tolerance of Saccharomyces cerevisiae against major fermentation inhibitors. In addition, the feasibility of constructing an engineered S. cerevisiae strain capable of tolerating toxic levels of the major inhibitors without exogenous addition of SPD was explored. Specifically, we altered expression levels of the genes in the SPD biosynthetic pathway. Also, OAZ1 coding for ornithine decarboxylase (ODC) antizyme and TPO1 coding for the polyamine transport protein were disrupted to increase intracellular SPD levels through alleviation of feedback inhibition on ODC and prevention of SPD excretion, respectively. Especially, the strain with combination of OAZ1 and TPO1 double disruption and overexpression of SPE3 not only contained spermidine content of 1.1mg SPD/g cell, which was 171% higher than that of the control strain, but also exhibited 60% and 33% shorter lag-phase period than that of the control strain under the medium containing furan derivatives and acetic acid, respectively. While we observed a positive correlation between intracellular SPD contents and tolerance phenotypes among the engineered strains accumulating different amounts of intracellular SPD, too much SPD accumulation is likely to cause metabolic burden. Therefore, genetic perturbations for intracellular SPD levels should be optimized in terms of metabolic burden and SPD contents to construct inhibitor tolerant yeast strains. We also found that the genes involved in purine biosynthesis and cell wall and chromatin stability were related to the enhanced tolerance phenotypes to furfural. The robust strains constructed in this study can be applied for producing chemicals and advanced biofuels from cellulosic hydrolysates.
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Affiliation(s)
- Sun-Ki Kim
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul 151-921, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - In-Geol Choi
- College of Life sciences and Biotechnology, Korea University, Seoul 136-713, Republic of Korea
| | - Yong-Cheol Park
- Department of Bio and Fermentation Convergence, Kookmin University, Seoul 136-702, Republic of Korea
| | - Jin-Ho Seo
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul 151-921, Republic of Korea.
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Tanaka K, Iwasaki K, Morimoto T, Matsuse T, Hasunuma T, Takenaka S, Chumsakul O, Ishikawa S, Ogasawara N, Yoshida KI. Hyperphosphorylation of DegU cancels CcpA-dependent catabolite repression of rocG in Bacillus subtilis. BMC Microbiol 2015; 15:43. [PMID: 25880922 PMCID: PMC4348106 DOI: 10.1186/s12866-015-0373-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 02/04/2015] [Indexed: 11/18/2022] Open
Abstract
Background The two-component regulatory system, involving the histidine sensor kinase DegS and response regulator DegU, plays an important role to control various cell processes in the transition phase of Bacillus subtilis. The degU32 allele in strain 1A95 is characterized by the accumulation of phosphorylated form of DegU (DegU-P). Results Growing 1A95 cells elevated the pH of soytone-based medium more than the parental strain 168 after the onset of the transition phase. The rocG gene encodes a catabolic glutamate dehydrogenase that catalyzes one of the main ammonia-releasing reactions. Inactivation of rocG abolished 1A95-mediated increases in the pH of growth media. Thus, transcription of the rocG locus was examined, and a novel 3.7-kb transcript covering sivA, rocG, and rocA was found in 1A95 but not 168 cells. Increased intracellular fructose 1,6-bisphosphate (FBP) levels are known to activate the HPr kinase HPrK, and to induce formation of the P-Ser-HPr/CcpA complex, which binds to catabolite responsive elements (cre) and exerts CcpA-dependent catabolite repression. A putative cre found within the intergenic region between sivA and rocG, and inactivation of ccpA led to creation of the 3.7-kb transcript in 168 cells. Analyses of intermediates in central carbon metabolism revealed that intracellular FBP levels were lowered earlier in 1A95 than in 168 cells. A genome wide transcriptome analysis comparing 1A95 and 168 cells suggested similar events occurring in other catabolite repressive loci involving induction of lctE encoding lactate dehydrogenase. Conclusions Under physiological conditions the 3.7-kb rocG transcript may be tightly controlled by a roadblock mechanism involving P-Ser-HPr/CcpA in 168 cells, while in 1A95 cells abolished repression of the 3.7-kb transcript. Accumulation of DegU-P in 1A95 affects central carbon metabolism involving lctE enhanced by unknown mechanisms, downregulates FBP levels earlier, and inactivates HPrK to allow the 3.7-kb transcription, and thus similar events may occur in other catabolite repressive loci. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0373-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kosei Tanaka
- Organization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan.
| | - Kana Iwasaki
- Department of Agrobioscience, Kobe University, Kobe, Hyogo, Japan.
| | - Takuya Morimoto
- Biological Science Laboratories, Kao Corporation, Haga, Tochigi, Japan. .,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
| | | | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan.
| | - Shinji Takenaka
- Organization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan. .,Department of Agrobioscience, Kobe University, Kobe, Hyogo, Japan.
| | - Onuma Chumsakul
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
| | - Shu Ishikawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
| | - Naotake Ogasawara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
| | - Ken-ichi Yoshida
- Organization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan. .,Department of Agrobioscience, Kobe University, Kobe, Hyogo, Japan.
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Wan C, Zhang M, Fang Q, Xiong L, Zhao X, Hasunuma T, Bai F, Kondo A. The impact of zinc sulfate addition on the dynamic metabolic profiling of Saccharomyces cerevisiae subjected to long term acetic acid stress treatment and identification of key metabolites involved in the antioxidant effect of zinc. Metallomics 2015; 7:322-32. [DOI: 10.1039/c4mt00275j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zinc modulates cellular amino acid metabolism and redox balance to exert its antioxidant effect.
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Affiliation(s)
- Chun Wan
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
| | - Mingming Zhang
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
| | - Qing Fang
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
| | - Liang Xiong
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
| | - Xinqing Zhao
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
- School of Life Science and Biotechnology
- Shanghai Jiaotong University
| | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology
- Kobe University
- Kobe 657-8501, Japan
| | - Fengwu Bai
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
- School of Life Science and Biotechnology
- Shanghai Jiaotong University
| | - Akihiko Kondo
- Department of Chemical Science and Engineering
- Graduate School of Engineering
- Kobe University
- Kobe 657-8501, Japan
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120
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Wang X, Bai X, Chen DF, Chen FZ, Li BZ, Yuan YJ. Increasing proline and myo-inositol improves tolerance of Saccharomyces cerevisiae to the mixture of multiple lignocellulose-derived inhibitors. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:142. [PMID: 26379774 PMCID: PMC4570682 DOI: 10.1186/s13068-015-0329-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 08/28/2015] [Indexed: 05/14/2023]
Abstract
BACKGROUND The development of robust microbes with tolerance to the combined lignocellulose-derived inhibitors is critical for the efficient cellulosic ethanol production. However, the lack of understanding on the inhibition mechanism limited the rational engineering of tolerant strain. Here, through the metabolomic analysis of an adaptation process of Saccharomyces cerevisiae to representative inhibitors, i.e., furfural, acetic acid and phenol (FAP), we figured out the new candidates for improving inhibitor tolerance. RESULTS After metabolomic analysis, proline and myo-inositol were identified as the potential metabolites responsible for strain tolerance to inhibitors. The deletion of genes involved in proline or myo-inositol synthesis weakened strain tolerance against FAP stress. On the contrary, the addition of proline or myo-inositol in medium exerted a protective effect on cell growth under FAP stress. Furthermore, the enhancement of proline or myo-inositol synthesis by overexpressing key gene PRO1 or INO1 conferred yeast strain significantly increased FAP tolerance. All the recombinant strains finished the fermentation within 60 h under FAP stress, while the control strain was still in the lag phase. Meanwhile, it was found that the intracellular level of reactive oxygen species (ROS) under FAP condition was decreased with the increase of proline content, suggesting the function of proline as a ROS scavenger to protect strains from inhibitor damage. CONCLUSION Increasing proline and myo-inositol were uncovered as the new determinants for improving strain tolerance to FAP under the guidance of metabolomics. Meanwhile, this study displayed the powerful application of metabolomics to develop rational strategies to increase stress tolerance and provided valuable insights into the design of recombinant microbes for the complex traits.
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Affiliation(s)
- Xin Wang
- />Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- />SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Xue Bai
- />Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- />SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Dong-Fang Chen
- />School of Management and Economics, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Fu-Zan Chen
- />School of Management and Economics, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Bing-Zhi Li
- />Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- />SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Ying-Jin Yuan
- />Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- />SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
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121
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van der Pol EC, Bakker RR, Baets P, Eggink G. By-products resulting from lignocellulose pretreatment and their inhibitory effect on fermentations for (bio)chemicals and fuels. Appl Microbiol Biotechnol 2014; 98:9579-93. [PMID: 25370992 DOI: 10.1007/s00253-014-6158-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/09/2014] [Accepted: 10/12/2014] [Indexed: 11/30/2022]
Abstract
Lignocellulose might become an important feedstock for the future development of the biobased economy. Although up to 75 % of the lignocellulose dry weight consists of sugar, it is present in a polymerized state and cannot be used directly in most fermentation processes for the production of chemicals and fuels. Several methods have been developed to depolymerize the sugars present in lignocellulose, making the sugars available for fermentation. In this review, we describe five different pretreatment methods and their effect on the sugar and non-sugar fraction of lignocellulose. For several pretreatment methods and different types of lignocellulosic biomass, an overview is given of by-products formed. Most unwanted by-products present after pretreatment are dehydrated sugar monomers (furans), degraded lignin polymers (phenols) and small organic acids. Qualitative and quantitative effects of these by-products on fermentation processes have been studied. We conclude this review by giving an overview of techniques and methods to decrease inhibitory effects of unwanted by-products.
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Affiliation(s)
- Edwin C van der Pol
- Food and Biobased Research, Wageningen University and Research Center, PO Box 17, 6700 AA, Wageningen, Netherlands,
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Khattab SMR, Kodaki T. Efficient bioethanol production by overexpression of endogenous Saccharomyces cerevisiae xylulokinase and NADPH-dependent aldose reductase with mutated strictly NADP+-dependent Pichia stipitis xylitol dehydrogenase. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.07.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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123
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Sasaki D, Sasaki K, Tsuge Y, Morita M, Kondo A. Comparison of metabolomic profiles of microbial communities between stable and deteriorated methanogenic processes. BIORESOURCE TECHNOLOGY 2014; 172:83-90. [PMID: 25237777 DOI: 10.1016/j.biortech.2014.08.054] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/09/2014] [Accepted: 08/11/2014] [Indexed: 05/27/2023]
Abstract
Central metabolite profiles from glucose in microbial communities during methanogenic process were compared between a stable methanogenic reactor (MR) and a deteriorated reactor (DR). The concentrations of intracellular metabolites related to the Embden-Meyerhof and pentose phosphate pathways, with the exception of pyruvate, remained high in the MR, showing increased carbon flux in the glycolysis pathway during stable methanogenesis. Extracellular acetate temporarily accumulated in the MR, consistent with higher ATP level in the MR. Intracellular concentrations of the intermediates in the reductive branch of tricarboxylic acid cycle, malate, fumarate, and succinate were higher in the DR. Low NADH/NAD(+) ratio both in the MR and DR would suggest NADH consumption during acetate and lactate/succinate production in the MR and DR, respectively. Intracellular glutamate levels were higher in the MR, correlating with lower NADPH/NADP(+) ratio concentrations in the MR. These findings contribute to a better understanding of the metabolic state during stable methanogenesis.
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Affiliation(s)
- Daisuke Sasaki
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Kengo Sasaki
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Yota Tsuge
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Masahiko Morita
- Bioengineering Sector, Environmental Science Research Laboratory, Central Research Institute of Electric Power Industry, 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
| | - Akihiko Kondo
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan; Biomass Engineering Program, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Wang Y, Shi M, Niu X, Zhang X, Gao L, Chen L, Wang J, Zhang W. Metabolomic basis of laboratory evolution of butanol tolerance in photosynthetic Synechocystis sp. PCC 6803. Microb Cell Fact 2014; 13:151. [PMID: 25366096 PMCID: PMC4234862 DOI: 10.1186/s12934-014-0151-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/18/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent efforts demonstrated the potential application of cyanobacteria as a "microbial cell factory" to produce butanol directly from CO2. However, cyanobacteria have very low tolerance to the toxic butanol, which limits the economic viability of this renewable system. RESULTS Through a long-term experimental evolution process, we achieved a 150% increase of the butanol tolerance in a model cyanobacterium Synechocystis sp. PCC 6803 after a continuous 94 passages for 395 days in BG11 media amended with gradually increased butanol concentration from 0.2% to 0.5% (v/v). To decipher the molecular mechanism responsible for the tolerance increase, we employed an integrated GC-MS and LC-MS approach to determine metabolomic profiles of the butanol-tolerant Synechocystis strains isolated from several stages of the evolution, and then applied PCA and WGCNA network analyses to identify the key metabolites and metabolic modules related to the increased tolerance. The results showed that unstable metabolites of 3-phosphoglyceric acid (3PG), D-fructose 6-phosphate (F6P), D-glucose 6-phosphate (G6P), NADPH, phosphoenolpyruvic acid (PEP), D-ribose 5-phosphate (R5P), and stable metabolites of glycerol, L-serine and stearic acid were differentially regulated during the evolution process, which could be related to tolerance increase to butanol in Synechocystis. CONCLUSIONS The study provided the first time-series description of the metabolomic changes related to the gradual increase of butanol tolerance, and revealed a metabolomic basis important for rational tolerance engineering in Synechocystis.
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Affiliation(s)
- Yaxing Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, P.R. China. .,Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, P.R. China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China.
| | - Mengliang Shi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, P.R. China. .,Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, P.R. China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China.
| | - Xiangfeng Niu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, P.R. China. .,Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, P.R. China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China.
| | - Xiaoqing Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, P.R. China. .,Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, P.R. China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China.
| | - Lianju Gao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, P.R. China. .,Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, P.R. China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China.
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, P.R. China. .,Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, P.R. China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China.
| | - Jiangxin Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, P.R. China. .,Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, P.R. China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China.
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, P.R. China. .,Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, P.R. China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China.
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125
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Sévin DC, Kuehne A, Zamboni N, Sauer U. Biological insights through nontargeted metabolomics. Curr Opin Biotechnol 2014; 34:1-8. [PMID: 25461505 DOI: 10.1016/j.copbio.2014.10.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 10/03/2014] [Accepted: 10/03/2014] [Indexed: 01/10/2023]
Abstract
Metabolomics is increasingly employed to investigate metabolism and its reciprocal crosstalk with cellular signaling and regulation. In recent years, several nontargeted metabolomics methods providing substantial metabolome coverage have been developed. Here, we review and compare the contributions of traditional targeted and nontargeted metabolomics in advancing different research areas ranging from biotechnology to human health. Although some studies demonstrated the power of nontargeted profiling in generating unexpected and yet highly important insights, we found that most mechanistic links were still revealed by hypothesis-driven targeted methods. Novel computational approaches for formal interpretation of complex metabolic patterns and integration of complementary molecular layers are required to tap the full potential of nontargeted metabolomics for data-driven, discovery-oriented research and rapidly nucleating novel biological insights.
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Affiliation(s)
- Daniel C Sévin
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland; PhD Program on Systems Biology, Life Science Zurich, Switzerland
| | - Andreas Kuehne
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland; PhD Program on Systems Biology, Life Science Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
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Hasunuma T, Hori Y, Sakamoto T, Ochiai M, Hatanaka H, Kondo A. Development of a GIN11/FRT-based multiple-gene integration technique affording inhibitor-tolerant, hemicellulolytic, xylose-utilizing abilities to industrial Saccharomyces cerevisiae strains for ethanol production from undetoxified lignocellulosic hemicelluloses. Microb Cell Fact 2014; 13:145. [PMID: 25306430 PMCID: PMC4198627 DOI: 10.1186/s12934-014-0145-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/03/2014] [Indexed: 11/30/2022] Open
Abstract
Background Bioethanol produced by the yeast Saccharomyces cerevisiae is currently one of the most promising alternatives to conventional transport fuels. Lignocellulosic hemicelluloses obtained after hydrothermal pretreatment are important feedstock for bioethanol production. However, hemicellulosic materials cannot be directly fermented by yeast: xylan backbone of hemicelluloses must first be hydrolyzed by heterologous hemicellulases to release xylose, and the yeast must then ferment xylose in the presence of fermentation inhibitors generated during the pretreatment. Results A GIN11/FRT-based multiple-gene integration system was developed for introducing multiple functions into the recombinant S. cerevisiae strains engineered with the xylose metabolic pathway. Antibiotic markers were efficiently recycled by a novel counter selection strategy using galactose-induced expression of both FLP recombinase gene and GIN11 flanked by FLP recombinase recognition target (FRT) sequences. Nine genes were functionally expressed in an industrial diploid strain of S. cerevisiae: endoxylanase gene from Trichoderma reesei, xylosidase gene from Aspergillus oryzae, β-glucosidase gene from Aspergillus aculeatus, xylose reductase and xylitol dehydrogenase genes from Scheffersomyces stipitis, and XKS1, TAL1, FDH1 and ADH1 variant from S. cerevisiae. The genes were introduced using the homozygous integration system and afforded hemicellulolytic, xylose-assimilating and inhibitor-tolerant abilities to the strain. The engineered yeast strain demonstrated 2.7-fold higher ethanol titer from hemicellulosic material than a xylose-assimilating yeast strain. Furthermore, hemicellulolytic enzymes displayed on the yeast cell surface hydrolyzed hemicelluloses that were not hydrolyzed by a commercial enzyme, leading to increased sugar utilization for improved ethanol production. Conclusions The multifunctional yeast strain, developed using a GIN11/FRT-based marker recycling system, achieved direct conversion of hemicellulosic biomass to ethanol without the addition of exogenous hemicellulolytic enzymes. No detoxification processes were required. The multiple-gene integration technique is a powerful approach for introducing and improving the biomass fermentation ability of industrial diploid S. cerevisiae strains. Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0145-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Yoshimi Hori
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Takatoshi Sakamoto
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Misa Ochiai
- Suntory Research Center, 1-1-1 Wakayamadai, Shimamoto-cho, Osaka, Mishima-gun, 618-8503, Japan.
| | - Haruyo Hatanaka
- Suntory Research Center, 1-1-1 Wakayamadai, Shimamoto-cho, Osaka, Mishima-gun, 618-8503, Japan.
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,Biomass Engineering Program, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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127
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Sakihama Y, Hasunuma T, Kondo A. Improved ethanol production from xylose in the presence of acetic acid by the overexpression of the HAA1 gene in Saccharomyces cerevisiae. J Biosci Bioeng 2014; 119:297-302. [PMID: 25282639 DOI: 10.1016/j.jbiosc.2014.09.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/22/2014] [Accepted: 09/02/2014] [Indexed: 10/24/2022]
Abstract
The hydrolysis of lignocellulosic biomass liberates sugars, primarily glucose and xylose, which are subsequently converted to ethanol by microbial fermentation. The rapid and efficient fermentation of xylose by recombinant Saccharomyces cerevisiae strains is limited by weak acids generated during biomass pretreatment processes. In particular, acetic acid negatively affects cell growth, xylose fermentation rate, and ethanol production. The ability of S. cerevisiae to efficiently utilize xylose in the presence of acetic acid is an essential requirement for the cost-effective production of ethanol from lignocellulosic hydrolysates. Here, an acetic acid-responsive transcriptional activator, HAA1, was overexpressed in a recombinant xylose-fermenting S. cerevisiae strain to yield BY4741X/HAA1. This strain exhibited improved cell growth and ethanol production from xylose under aerobic and oxygen limited conditions, respectively, in the presence of acetic acid. The HAA1p regulon enhanced transcript levels in BY4741X/HAA1. The disruption of PHO13, a p-nitrophenylphosphatase gene, in BY4741X/HAA1 led to further improvement in both yeast growth and the ability to ferment xylose, indicating that HAA1 overexpression and PHO13 deletion act by different mechanisms to enhance ethanol production.
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Affiliation(s)
- Yuri Sakihama
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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128
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Zinc, magnesium, and calcium ion supplementation confers tolerance to acetic acid stress in industrialSaccharomyces cerevisiaeutilizing xylose. Biotechnol J 2014; 9:1519-25. [DOI: 10.1002/biot.201300553] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 04/30/2014] [Accepted: 06/11/2014] [Indexed: 11/07/2022]
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129
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Almeida CM, Gomes D, Faro C, Simões I. Engineering a cardosin B-derived rennet for sheep and goat cheese manufacture. Appl Microbiol Biotechnol 2014; 99:269-81. [DOI: 10.1007/s00253-014-5902-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/11/2014] [Accepted: 06/16/2014] [Indexed: 01/26/2023]
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130
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Li YC, Gou ZX, Liu ZS, Tang YQ, Akamatsu T, Kida K. Synergistic effects of TAL1 over-expression and PHO13 deletion on the weak acid inhibition of xylose fermentation by industrial Saccharomyces cerevisiae strain. Biotechnol Lett 2014; 36:2011-21. [DOI: 10.1007/s10529-014-1581-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 06/04/2014] [Indexed: 01/06/2023]
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131
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Metabolomic and Transcriptomic Analysis for Rate-Limiting Metabolic Steps in Xylose Utilization by RecombinantCandida utilis. Biosci Biotechnol Biochem 2014; 77:1441-8. [DOI: 10.1271/bbb.130093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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132
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Comparative Profiling Analysis of Central Metabolites inEuglena gracilisunder Various Cultivation Conditions. Biosci Biotechnol Biochem 2014; 75:2253-6. [DOI: 10.1271/bbb.110482] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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133
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Tokuyama K, Ohno S, Yoshikawa K, Hirasawa T, Tanaka S, Furusawa C, Shimizu H. Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli. Microb Cell Fact 2014; 13:64. [PMID: 24885133 PMCID: PMC4019354 DOI: 10.1186/1475-2859-13-64] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 04/21/2014] [Indexed: 11/11/2022] Open
Abstract
Background 3-hydroxypropionic acid (3HP) is an important chemical precursor for the production of bioplastics. Microbial production of 3HP from glycerol has previously been developed through the optimization of culture conditions and the 3HP biosynthesis pathway. In this study, a novel strategy for improving 3HP production in Escherichia coli was investigated by the modification of central metabolism based on a genome-scale metabolic model and experimental validation. Results Metabolic simulation identified the double knockout of tpiA and zwf as a candidate for improving 3HP production. A 3HP-producing strain was constructed by the expression of glycerol dehydratase and aldehyde dehydrogenase. The double knockout of tpiA and zwf increased the percentage carbon-molar yield (C-mol%) of 3HP on consumed glycerol 4.4-fold (20.1 ± 9.2 C-mol%), compared to the parental strain. Increased extracellular methylglyoxal concentrations in the ΔtpiA Δzwf strain indicated that glycerol catabolism was occurring through the methylglyoxal pathway, which converts dihydroxyacetone phosphate to pyruvate, as predicted by the metabolic model. Since the ΔtpiA Δzwf strain produced abundant 1,3-propanediol as a major byproduct (37.7 ± 13.2 C-mol%), yqhD, which encodes an enzyme involved in the production of 1,3-propanediol, was disrupted in the ΔtpiA Δzwf strain. The 3HP yield of the ΔtpiA Δzwf ΔyqhD strain (33.9 ± 1.2 C-mol%) was increased 1.7-fold further compared to the ΔtpiA Δzwf strain and by 7.4-fold compared to the parental strain. Conclusion This study successfully increased 3HP production by 7.4-fold in the ΔtpiA Δzwf ΔyqhD E. coli strain by the modification of the central metabolism, based on metabolic simulation and experimental validation of engineered strains.
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Affiliation(s)
| | | | | | | | | | | | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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134
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Soma Y, Tsuruno K, Wada M, Yokota A, Hanai T. Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch. Metab Eng 2014; 23:175-84. [DOI: 10.1016/j.ymben.2014.02.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/15/2014] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
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135
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Mir BA, Mewalal R, Mizrachi E, Myburg AA, Cowan DA. Recombinant hyperthermophilic enzyme expression in plants: a novel approach for lignocellulose digestion. Trends Biotechnol 2014; 32:281-9. [PMID: 24732021 DOI: 10.1016/j.tibtech.2014.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 02/14/2014] [Accepted: 03/05/2014] [Indexed: 10/25/2022]
Abstract
Plant biomass, as an abundant renewable carbon source, is a promising alternative to fossil fuels. However, the enzymes most commonly used for depolymerization of lignocellulosic biomass are expensive, and the development of cost-effective alternative conversion technologies would be desirable. One possible option is the heterologous expression of genes encoding lignocellulose-digesting enzymes in plant tissues. To overcome simultaneously issues of toxicity and incompatibility with high-temperature steam explosion processes, the use of heterologous genes encoding hyperthermophilic enzymes may be an attractive alternative. This approach could reduce the need for exogenous enzyme additions prior to fermentation, reducing the cost of the complete processing operation. This review highlights recent advances and future prospects for using hyperthermophilic enzymes in the biofuels industry.
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Affiliation(s)
- Bilal Ahmad Mir
- Center for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Private bag X20, Pretoria 0028, South Africa; Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
| | - Ritesh Mewalal
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
| | - Don A Cowan
- Center for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Private bag X20, Pretoria 0028, South Africa.
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136
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Greetham D, Wimalasena T, Kerruish DWM, Brindley S, Ibbett RN, Linforth RL, Tucker G, Phister TG, Smart KA. Development of a phenotypic assay for characterisation of ethanologenic yeast strain sensitivity to inhibitors released from lignocellulosic feedstocks. J Ind Microbiol Biotechnol 2014; 41:931-45. [PMID: 24664516 DOI: 10.1007/s10295-014-1431-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/26/2014] [Indexed: 12/16/2022]
Abstract
Inhibitors released by the breakdown of plant cell walls prevent efficient conversion of sugar into ethanol. The aim of this study was to develop a fast and reliable inhibitor sensitivity assay for ethanologenic yeast strains. The assay comprised bespoke 96-well plates containing inhibitors in isolation or combination in a format that was compatible with the Phenotypic Microarray Omnilog reader (Biolog, hayward, CA, USA). A redox reporter within the assay permits analysis of inhibitor sensitivity in aerobic and/or anaerobic conditions. Results from the assay were verified using growth on spot plates and tolerance assays in which maintenance of viability was assessed. The assay allows for individual and synergistic effects of inhibitors to be determined. It was observed that the presence of both acetic and formic acid significantly inhibited the yeast strains assessed, although this impact could be partially mitigated by buffering to neutral pH. Scheffersomyces stipitis, Candida spp., and Pichia guilliermondii demonstrated increased sensitivity to short chain weak acids at concentrations typically present in lignocellulosic hydrolysates. S. cerevisiae exhibited robustness to short chain weak acids at these concentrations. However, S. stipitis, Candida spp., and P. guilliermondii displayed increased tolerance to HMF when compared to that observed for S. cerevisiae. The results demonstrate that the phenotypic microarray assay developed in the current study is a valuable tool that can be used to identify yeast strains with desirable resistance to inhibitory compounds found in lignocellulosic hydrolysates.
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Affiliation(s)
- D Greetham
- Bioenergy and Brewing Science, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, Leicestershire, LE12 6RD, UK,
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137
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Hasunuma T, Ismail KSK, Nambu Y, Kondo A. Co-expression of TAL1 and ADH1 in recombinant xylose-fermenting Saccharomyces cerevisiae improves ethanol production from lignocellulosic hydrolysates in the presence of furfural. J Biosci Bioeng 2014; 117:165-169. [DOI: 10.1016/j.jbiosc.2013.07.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 07/03/2013] [Accepted: 07/15/2013] [Indexed: 10/26/2022]
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138
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Koppram R, Tomás-Pejó E, Xiros C, Olsson L. Lignocellulosic ethanol production at high-gravity: challenges and perspectives. Trends Biotechnol 2014; 32:46-53. [DOI: 10.1016/j.tibtech.2013.10.003] [Citation(s) in RCA: 253] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/07/2013] [Accepted: 10/10/2013] [Indexed: 11/30/2022]
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139
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Teramura H, Oshima T, Matsuda F, Sasaki K, Ogino C, Yamasaki M, Kondo A. Glucose content in the liquid hydrolysate after dilute acid pretreatment is affected by the starch content in rice straw. BIORESOURCE TECHNOLOGY 2013; 149:520-524. [PMID: 24140898 DOI: 10.1016/j.biortech.2013.09.109] [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: 07/23/2013] [Revised: 09/20/2013] [Accepted: 09/24/2013] [Indexed: 06/02/2023]
Abstract
Lignocellulosic biomass, such as rice straw, is often utilized as a bioresource after being hydrolyzed using dilute acid and separated into liquid hydrolysate and acid-insoluble residue. However, the biomass component that determines the distribution between liquid hydrolysate and acid-insoluble residue has not yet been clarified. In this study, the glucose content in the liquid hydrolysate and weight of acid-insoluble residue of 13 rice cultivars were analyzed. Starch content was positively correlated with glucose content in the liquid hydrolysate, and negatively correlated with acid-insoluble residue weight. These results indicate that the glucose in the liquid hydrolysate is mainly liberated from starch rather than cellulose in the rice straw. These observations suggest that starch content is a good indicator of the glucose distribution between the liquid hydrolysate and insoluble residue.
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Affiliation(s)
- Hiroshi Teramura
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
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140
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Isolation and characterization of a mutant recombinant Saccharomyces cerevisiae strain with high efficiency xylose utilization. J Biosci Bioeng 2013; 116:706-15. [DOI: 10.1016/j.jbiosc.2013.05.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 05/13/2013] [Accepted: 05/18/2013] [Indexed: 11/22/2022]
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141
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Ferrer-Miralles N, Villaverde A. Bacterial cell factories for recombinant protein production; expanding the catalogue. Microb Cell Fact 2013; 12:113. [PMID: 24245806 PMCID: PMC3842683 DOI: 10.1186/1475-2859-12-113] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 01/08/2023] Open
Affiliation(s)
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193 Barcelona, Spain.
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142
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Imamoglu E, Dalay MC, Sukan FV. Regional Differences in Rice Hulls Supply for Bioethanol Production. Appl Biochem Biotechnol 2013; 171:2065-74. [DOI: 10.1007/s12010-013-0504-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 08/30/2013] [Indexed: 11/27/2022]
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143
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Wang X, Jin M, Balan V, Jones AD, Li X, Li BZ, Dale BE, Yuan YJ. Comparative metabolic profiling revealed limitations in xylose-fermenting yeast during co-fermentation of glucose and xylose in the presence of inhibitors. Biotechnol Bioeng 2013; 111:152-64. [DOI: 10.1002/bit.24992] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xin Wang
- Key Laboratory of Systems Bioengineering; Ministry of Education; Department of Pharmaceutical Engineering; School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 P.R. China
| | - Mingjie Jin
- Biomass Conversion Research Laboratory (BCRL); Department of Chemical Engineering and Materials Science; Michigan State University; 3900 Collins Road MBI International Building Lansing Michigan 48910
| | - Venkatesh Balan
- Biomass Conversion Research Laboratory (BCRL); Department of Chemical Engineering and Materials Science; Michigan State University; 3900 Collins Road MBI International Building Lansing Michigan 48910
| | - A. Daniel Jones
- Department of Biochemistry and Molecular Biology; Michigan State University; East Lansing Michigan
- Department of Chemistry; Michigan State University; East Lansing Michigan
| | - Xia Li
- Key Laboratory of Systems Bioengineering; Ministry of Education; Department of Pharmaceutical Engineering; School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 P.R. China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering; Ministry of Education; Department of Pharmaceutical Engineering; School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 P.R. China
| | - Bruce E. Dale
- Biomass Conversion Research Laboratory (BCRL); Department of Chemical Engineering and Materials Science; Michigan State University; 3900 Collins Road MBI International Building Lansing Michigan 48910
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering; Ministry of Education; Department of Pharmaceutical Engineering; School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 P.R. China
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144
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Hyland PB, Mun SLS, Mahadevan R. Prediction of Weak Acid Toxicity inSaccharomyces cerevisiaeUsing Genome-Scale Metabolic Models. Ind Biotechnol (New Rochelle N Y) 2013. [DOI: 10.1089/ind.2013.0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Patrick B Hyland
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Serene Lock-Sow Mun
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
- CO2 Management Mission Oriented Research, Universiti Teknologi PETRONAS, Tronoh, Malaysia
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
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145
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Matsushika A, Nagashima A, Goshima T, Hoshino T. Fermentation of xylose causes inefficient metabolic state due to carbon/energy starvation and reduced glycolytic flux in recombinant industrial Saccharomyces cerevisiae. PLoS One 2013; 8:e69005. [PMID: 23874849 PMCID: PMC3706439 DOI: 10.1371/journal.pone.0069005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/04/2013] [Indexed: 11/18/2022] Open
Abstract
In the present study, comprehensive, quantitative metabolome analysis was carried out on the recombinant glucose/xylose-cofermenting S. cerevisiae strain MA-R4 during fermentation with different carbon sources, including glucose, xylose, or glucose/xylose mixtures. Capillary electrophoresis time-of-flight mass spectrometry was used to determine the intracellular pools of metabolites from the central carbon pathways, energy metabolism pathways, and the levels of twenty amino acids. When xylose instead of glucose was metabolized by MA-R4, glycolytic metabolites including 3- phosphoglycerate, 2- phosphoglycerate, phosphoenolpyruvate, and pyruvate were dramatically reduced, while conversely, most pentose phosphate pathway metabolites such as sedoheptulose 7- phosphate and ribulose 5-phosphate were greatly increased. These results suggest that the low metabolic activity of glycolysis and the pool of pentose phosphate pathway intermediates are potential limiting factors in xylose utilization. It was further demonstrated that during xylose fermentation, about half of the twenty amino acids declined, and the adenylate/guanylate energy charge was impacted due to markedly decreased adenosine triphosphate/adenosine monophosphate and guanosine triphosphate/guanosine monophosphate ratios, implying that the fermentation of xylose leads to an inefficient metabolic state where the biosynthetic capabilities and energy balance are severely impaired. In addition, fermentation with xylose alone drastically increased the level of citrate in the tricarboxylic acid cycle and increased the aromatic amino acids tryptophan and tyrosine, strongly supporting the view that carbon starvation was induced. Interestingly, fermentation with xylose alone also increased the synthesis of the polyamine spermidine and its precursor S-adenosylmethionine. Thus, differences in carbon substrates, including glucose and xylose in the fermentation medium, strongly influenced the dynamic metabolism of MA-R4. These results provide a metabolic explanation for the low ethanol productivity on xylose compared to glucose.
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Affiliation(s)
- Akinori Matsushika
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology, Hiroshima, Japan.
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146
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Sample preparation for the metabolomics investigation of poly-gamma-glutamate-producing Bacillus licheniformis by GC–MS. J Microbiol Methods 2013; 94:61-7. [DOI: 10.1016/j.mimet.2013.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 04/16/2013] [Accepted: 04/21/2013] [Indexed: 11/19/2022]
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147
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Hasunuma T, Kikuyama F, Matsuda M, Aikawa S, Izumi Y, Kondo A. Dynamic metabolic profiling of cyanobacterial glycogen biosynthesis under conditions of nitrate depletion. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2943-54. [PMID: 23658429 PMCID: PMC3697948 DOI: 10.1093/jxb/ert134] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Cyanobacteria represent a globally important biomass because they are responsible for a substantial proportion of primary production in the hydrosphere. Arthrospira platensis is a fast-growing halophilic cyanobacterium capable of accumulating glycogen and has the potential to serve as a feedstock in the fermentative production of third-generation biofuels. Accordingly, enhancing cyanobacterial glycogen production is a promising biofuel production strategy. However, the regulatory mechanism of glycogen metabolism in cyanobacteria is poorly understood. The aim of the present study was to determine the metabolic flux of glycogen biosynthesis using a dynamic metabolomic approach. Time-course profiling of widely targeted cyanobacterial metabolic intermediates demonstrated a global metabolic reprogramming that involves transient increases in the levels of some amino acids during the glycogen production phase induced by nitrate depletion. Also, in vivo labelling with NaH(13)CO3 enabled direct measurement of metabolic intermediate turnover in A. platensis, revealing that under conditions of nitrate depletion glycogen is biosynthesized with carbon derived from amino acids released from proteins via gluconeogenesis. This dynamic metabolic profiling approach provided conclusive evidence of temporal alterations in the metabolic profile in cyanobacterial cells.
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Affiliation(s)
- Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
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148
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Ismail KSK, Sakamoto T, Hasunuma T, Kondo A. Time-based comparative transcriptomics in engineered xylose-utilizing Saccharomyces cerevisiae identifies temperature-responsive genes during ethanol production. J Ind Microbiol Biotechnol 2013; 40:1039-50. [PMID: 23748446 DOI: 10.1007/s10295-013-1293-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/14/2013] [Indexed: 01/07/2023]
Abstract
Agricultural residues comprising lignocellulosic materials are excellent sources of pentose sugar, which can be converted to ethanol as fuel. Ethanol production via consolidated bioprocessing requires a suitable microorganism to withstand the harsh fermentation environment of high temperature, high ethanol concentration, and exposure to inhibitors. We genetically enhanced an industrial Saccharomyces cerevisiae strain, sun049, enabling it to uptake xylose as the sole carbon source at high fermentation temperature. This strain was able to produce 13.9 g/l ethanol from 50 g/l xylose at 38 °C. To better understand the xylose consumption ability during long-term, high-temperature conditions, we compared by transcriptomics two fermentation conditions: high temperature (38 °C) and control temperature (30 °C) during the first 12 h of fermentation. This is the first long-term, time-based transcriptomics approach, and it allowed us to discover the role of heat-responsive genes when xylose is the sole carbon source. The results suggest that genes related to amino acid, cell wall, and ribosomal protein synthesis are down-regulated under heat stress. To allow cell stability and continuous xylose uptake in order to produce ethanol, hexose transporter HXT5, heat shock proteins, ubiquitin proteins, and proteolysis were all induced at high temperature. We also speculate that the strong relationship between high temperature and increased xylitol accumulation represents the cell's mechanism to protect itself from heat degradation.
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Affiliation(s)
- Ku Syahidah Ku Ismail
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada, Kobe, 657-8501, Japan
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Yamashita Y, Yamaoka M, Hasunuma T, Ashida H, Yoshida KI. Detection of orally administered inositol stereoisomers in mouse blood plasma and their effects on translocation of glucose transporter 4 in skeletal muscle cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:4850-4854. [PMID: 23641877 DOI: 10.1021/jf305322t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Simple pharmacological studies on inositol stereoisomers are presented in this study. Male ICR mice were orally administered 1 g/kg BW of three inositol stereoisomers, myo-inositol (MI), d-chiro-inositol (DCI), and scyllo-inositol (SI), and blood plasma samples and skeletal muscle fractions were prepared after an hour. The plasma samples were subjected to gas chromatography-coupled time-of-flight mass spectrometry (GC-TOF-MS) analysis. None of the three stereoisomers was seen in untreated samples, but substantial amounts ranging from 2.5 to 6.5 mM were detected only after administration, indicating that orally administered inositol stereoisomers were readily absorbed and their levels elevated in the bloodstream. In addition, plasma of SI-administered animals contained substantial MI, suggesting a possible metabolic conversion of SI to MI. In the skeletal muscle fractions, glucose transporter type 4 (GLUT4) content in the plasma membrane increased, indicating that inositol stereoisomers stimulated GLUT4 translocation.
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Affiliation(s)
- Yoko Yamashita
- Department of Agrobioscience and ‡Organization of Advanced Science and Technology, Kobe University , 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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Bonnet C, Rigaud C, Chanteclaire E, Blandais C, Tassy-Freches E, Arico C, Javaud C. PCR on yeast colonies: an improved method for glyco-engineered Saccharomyces cerevisiae. BMC Res Notes 2013; 6:201. [PMID: 23688076 PMCID: PMC3664073 DOI: 10.1186/1756-0500-6-201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 05/08/2013] [Indexed: 01/13/2023] Open
Abstract
Background Saccharomyces cerevisiae is extensively used in bio-industries. However, its genetic engineering to introduce new metabolism pathways can cause unexpected phenotypic alterations. For example, humanisation of the glycosylation pathways is a high priority pharmaceutical industry goal for production of therapeutic glycoproteins in yeast. Genomic modifications can lead to several described physiological changes: biomass yields decrease, temperature sensitivity or cell wall structure modifications. We have observed that deletion of several N-mannosyltransferases in Saccharomyces cerevisiae, results in strains that can no longer be analyzed by classical PCR on yeast colonies. Findings In order to validate our glyco-engineered Saccharomyces cerevisiae strains, we developed a new protocol to carry out PCR directly on genetically modified yeast colonies. A liquid culture phase, combined with the use of a Hot Start DNA polymerase, allows a 3-fold improvement of PCR efficiency. The results obtained are repeatable and independent of the targeted sequence; as such the protocol is well adapted for intensive screening applications. Conclusions The developed protocol enables by-passing of many of the difficulties associated with PCR caused by phenotypic modifications brought about by humanisation of the glycosylation in yeast and allows rapid validation of glyco-engineered Saccharomyces cerevisiae cells. It has the potential to be extended to other yeast strains presenting cell wall structure modifications.
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