1
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Zhang X, Zheng Y, Zhou C, Cao J, Pan D, Cai Z, Wu Z, Xia Q. Comparative physiological and transcriptomic analysis of sono-biochemical control over post-acidification of Lactobacillus delbrueckii subsp. bulgaricus. Food Microbiol 2024; 122:104563. [PMID: 38839237 DOI: 10.1016/j.fm.2024.104563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/27/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
Thermosonication (UT) prestress treatments combining with varied fermentation patterns has been revealed as an effective method to regulate post-acidification as exerted by Lactobacillus delbrueckii subsp. bulgaricus (L. delbrueckii), but sono-biochemical controlling mechanisms remain elusive. This study employed physiological and transcriptomic analysis to explore the response mechanism of L. delbrueckii to UT-induced microstress (600 W, 33 kHz, 10 min). UT stress-induced inhibition of acidification of L. delbrueckii during (post)-fermentation was first confirmed, relying on the UT process parameters such as stress exposure duration and UT power. The significantly enhanced membrane permeability in cells treated by 600 W for 10 min than the microbes stressed by 420 W for 20 min suggested the higher dependence of UT-derived stresses on the treatment durations, relative to the ultrasonic powers. In addition, ultrasonication treatment-induced changes in cell membrane integrity enhanced and/or disrupted permeability of L. delbrueckii, resulting in an imbalance in intracellular conditions associated with corresponding alterations in metabolic behaviors and fermentation efficiencies. UT-prestressed inoculum exhibited a 21.46% decrease in the membrane potential during the lag phase compared to untreated samples, with an intracellular pH of 5.68 ± 0.12, attributed to the lower activities of H+-ATPase and lactate dehydrogenase due to UT stress pretreatments. Comparative transcriptomic analysis revealed that UT prestress influenced the genes related to glycolysis, pyruvate metabolism, fatty acid synthesis, and ABC transport. The genes encoding 3-oxoacyl-[acyl-carrier-protein] reductases I, II, and III, CoA carboxylase, lactate dehydrogenase, pyruvate oxidase, glucose-6-phosphate isomerase, and glycerol-3-phosphate dehydrogenase were downregulated, thus identifying the relevance of the UT microstresses-downregulated absorption and utilization of carbohydrates with the attenuated fatty acid production and energy metabolisms. These findings could contribute to provide a better understanding of the inactivated effects on the post-acidification of L. delbrueckii by ultrasonic pretreatments, thus providing theoretical basis for the targeted optimization of acidification inhibition efficiencies for yogurt products during chilled preservation processes.
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Affiliation(s)
- Xiaohui Zhang
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China
| | - Yuanrong Zheng
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, 200436, China
| | - Changyu Zhou
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China
| | - Jinxuan Cao
- School of Food and Health, China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, 11 Fucheng Road, Beijing, 100048, China
| | - Daodong Pan
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China
| | - Zhendong Cai
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China
| | - Zhen Wu
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China.
| | - Qiang Xia
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China.
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2
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Choi B, Tafur Rangel A, Kerkhoven EJ, Nygård Y. Engineering of Saccharomyces cerevisiae for enhanced metabolic robustness and L-lactic acid production from lignocellulosic biomass. Metab Eng 2024; 84:23-33. [PMID: 38788894 DOI: 10.1016/j.ymben.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/19/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024]
Abstract
Metabolic engineering for high productivity and increased robustness is needed to enable sustainable biomanufacturing of lactic acid from lignocellulosic biomass. Lactic acid is an important commodity chemical used for instance as a monomer for production of polylactic acid, a biodegradable polymer. Here, rational and model-based optimization was used to engineer a diploid, xylose fermenting Saccharomyces cerevisiae strain to produce L-lactic acid. The metabolic flux was steered towards lactic acid through the introduction of multiple lactate dehydrogenase encoding genes while deleting ERF2, GPD1, and CYB2. A production of 93 g/L of lactic acid with a yield of 0.84 g/g was achieved using xylose as the carbon source. To increase xylose utilization and reduce acetic acid synthesis, PHO13 and ALD6 were also deleted from the strain. Finally, CDC19 encoding a pyruvate kinase was overexpressed, resulting in a yield of 0.75 g lactic acid/g sugars consumed, when the substrate used was a synthetic lignocellulosic hydrolysate medium, containing hexoses, pentoses and inhibitors such as acetate and furfural. Notably, modeling also provided leads for understanding the influence of oxygen in lactic acid production. High lactic acid production from xylose, at oxygen-limitation could be explained by a reduced flux through the oxidative phosphorylation pathway. On the contrast, higher oxygen levels were beneficial for lactic acid production with the synthetic hydrolysate medium, likely as higher ATP concentrations are needed for tolerating the inhibitors therein. The work highlights the potential of S. cerevisiae for industrial production of lactic acid from lignocellulosic biomass.
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Affiliation(s)
- Bohyun Choi
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Albert Tafur Rangel
- Department of Life Sciences, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Eduard J Kerkhoven
- Department of Life Sciences, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark; SciLifeLab, Chalmers University of Technology, Gothenburg, Sweden
| | - Yvonne Nygård
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden; VTT Technical Research Centre of Finland Ltd, Espoo, Finland.
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3
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Eigenfeld M, Wittmann L, Kerpes R, Schwaminger SP, Becker T. Studying the impact of cell age on the yeast growth behaviour of Saccharomyces pastorianus var. carlsbergensis by magnetic separation. Biotechnol J 2023; 18:e2200610. [PMID: 37014328 DOI: 10.1002/biot.202200610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/22/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
Despite the fact that yeast is a widely used microorganism in the food, beverage, and pharmaceutical industries, the impact of viability and age distribution on cultivation performance has yet to be fully understood. For a detailed analysis of fermentation performance and physiological state, we introduced a method of magnetic batch separation to isolate daughter and mother cells from a heterogeneous culture. By binding functionalised iron oxide nanoparticles, it is possible to separate the chitin-enriched bud scars by way of a linker protein. This reveals that low viability cultures with a high daughter cell content perform similarly to a high viability culture with a low daughter cell content. Magnetic separation results in the daughter cell fraction (>95%) showing a 21% higher growth rate in aerobic conditions than mother cells and a 52% higher rate under anaerobic conditions. These findings emphasise the importance of viability and age during cultivation and are the first step towards improving the efficiency of yeast-based processes.
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Affiliation(s)
- Marco Eigenfeld
- TUM School of Life Science, Technical University of Munich, Chair of Brewing and Beverage Technology, Freising, Germany
| | - Leonie Wittmann
- TUM School of Engineering and Design, Technical University of Munich, Chair of Bioseparation Engineering, Garching, Germany
| | - Roland Kerpes
- TUM School of Life Science, Technical University of Munich, Chair of Brewing and Beverage Technology, Freising, Germany
| | - Sebastian P Schwaminger
- TUM School of Engineering and Design, Technical University of Munich, Chair of Bioseparation Engineering, Garching, Germany
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Thomas Becker
- TUM School of Life Science, Technical University of Munich, Chair of Brewing and Beverage Technology, Freising, Germany
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4
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Combes J, Imatoukene N, Couvreur J, Godon B, Fojcik C, Allais F, Lopez M. An optimized semi-defined medium for p-coumaric acid production in extractive fermentation. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Horikiri S, Harada M, Asada R, J Sakamoto J, Furuta M, Tsuchido T. Low Temperature Heating-Induced Death and Vacuole Injury in Cladosporium sphaerospermum Conidia. Biocontrol Sci 2022; 27:107-115. [PMID: 35753793 DOI: 10.4265/bio.27.107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The mechanism of thermal death of mold conidia has not been understood in detail. The purpose of this study is to analyze the death kinetics of heated conidia of Cladosporium sphaerospermum and to ascertain the expectant cell injury responsible for the death. The death of the dormant (resting) conidia of Cladosporium sphaerospermum was examined at temperatures of between 43 and 54℃ with the conventional colony count method. The death reaction apparently followed the first order kinetics, but the Arrhenius plot of the death rate constant demonstrated seemingly a break. The linearity at temperatures higher than that at the break was lost at lower temperatures, suggesting the involvement of an unusual mechanism in the latter temperatures. In the cell morphology, we observed with quinacrine staining the vacuole rupture at a lower temperature but not at a high temperature. Interestingly, the vacuole rupture by low-temperature heating was found to correlate with the viability loss. Furthermore, active protease originally locating in vacuoles was detected in the cytoplasm of the conidia after heated at a low temperature. The results obtained suggest the involvement of potent autophagic cell death induced by low temperature heating of C. sphaerospermum conidia.
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Affiliation(s)
- Shigetoshi Horikiri
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University.,Panasonic Ecology Systems Co., Ltd
| | - Mami Harada
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University
| | - Ryoko Asada
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University.,Research Center of Microorganism Control, Organization for Research Promotion
| | - Jin J Sakamoto
- Research Center of Microorganism Control, Organization for Research Promotion.,Faculty of Chemistry, Materials and Bioengineering, Kansai University
| | - Masakazu Furuta
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University.,Research Center of Microorganism Control, Organization for Research Promotion
| | - Tetsuaki Tsuchido
- Research Center of Microorganism Control, Organization for Research Promotion
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6
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Eigenfeld M, Kerpes R, Becker T. Understanding the Impact of Industrial Stress Conditions on Replicative Aging in Saccharomyces cerevisiae. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:665490. [PMID: 37744109 PMCID: PMC10512339 DOI: 10.3389/ffunb.2021.665490] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/30/2021] [Indexed: 09/26/2023]
Abstract
In yeast, aging is widely understood as the decline of physiological function and the decreasing ability to adapt to environmental changes. Saccharomyces cerevisiae has become an important model organism for the investigation of these processes. Yeast is used in industrial processes (beer and wine production), and several stress conditions can influence its intracellular aging processes. The aim of this review is to summarize the current knowledge on applied stress conditions, such as osmotic pressure, primary metabolites (e.g., ethanol), low pH, oxidative stress, heat on aging indicators, age-related physiological changes, and yeast longevity. There is clear evidence that yeast cells are exposed to many stressors influencing viability and vitality, leading to an age-related shift in age distribution. Currently, there is a lack of rapid, non-invasive methods allowing the investigation of aspects of yeast aging in real time on a single-cell basis using the high-throughput approach. Methods such as micromanipulation, centrifugal elutriator, or biotinylation do not provide real-time information on age distributions in industrial processes. In contrast, innovative approaches, such as non-invasive fluorescence coupled flow cytometry intended for high-throughput measurements, could be promising for determining the replicative age of yeast cells in fermentation and its impact on industrial stress conditions.
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Affiliation(s)
| | - Roland Kerpes
- Research Group Beverage and Cereal Biotechnology, Institute of Brewing and Beverage Technology, Technical University of Munich, Freising, Germany
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7
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Peetermans A, Foulquié-Moreno MR, Thevelein JM. Mechanisms underlying lactic acid tolerance and its influence on lactic acid production in Saccharomyces cerevisiae. MICROBIAL CELL 2021; 8:111-130. [PMID: 34055965 PMCID: PMC8144909 DOI: 10.15698/mic2021.06.751] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the major bottlenecks in lactic acid production using microbial fermentation is the detrimental influence lactic acid accumulation poses on the lactic acid producing cells. The accumulation of lactic acid results in many negative effects on the cell such as intracellular acidification, anion accumulation, membrane perturbation, disturbed amino acid trafficking, increased turgor pressure, ATP depletion, ROS accumulation, metabolic dysregulation and metal chelation. In this review, the manner in which Saccharomyces cerevisiae deals with these issues will be discussed extensively not only for lactic acid as a singular stress factor but also in combination with other stresses. In addition, different methods to improve lactic acid tolerance in S. cerevisiae using targeted and non-targeted engineering methods will be discussed.
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Affiliation(s)
- Arne Peetermans
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium
| | - María R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium.,NovelYeast bv, Open Bio-Incubator, Erasmus High School, Laarbeeklaan 121, 1090 Brussels (Jette), Belgium
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8
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Wang Z, Zhou L, Lu M, Zhang Y, Perveen S, Zhou H, Wen Z, Xu Z, Jin M. Adaptive laboratory evolution of Yarrowia lipolytica improves ferulic acid tolerance. Appl Microbiol Biotechnol 2021; 105:1745-1758. [PMID: 33523248 DOI: 10.1007/s00253-021-11130-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/26/2020] [Accepted: 01/19/2021] [Indexed: 12/17/2022]
Abstract
Yarrowia lipolytica strain is a promising cell factory for the conversion of lignocellulose to biofuels and bioproducts. Despite the inherent robustness of this strain, further improvements to lignocellulose-derived inhibitors toxicity tolerance of Y. lipolytica are also required to achieve industrial application. Here, adaptive laboratory evolution was employed with increasing concentrations of ferulic acid. The adaptive laboratory evolution experiments led to evolve Y. lipolytica strain yl-XYL + *FA*4 with increased tolerance to ferulic acid as compared to the parental strain. Specifically, the evolved strain could tolerate 1.5 g/L ferulic acid, whereas 0.5 g/L ferulic acid could cause about 90% lethality of the parental strain. Transcriptome analysis of the evolved strain revealed several targets underlying toxicity tolerance enhancements. YALI0_E25201g, YALI0_F05984g, YALI0_B18854g, and YALI0_F16731g were among the highest upregulated genes, and the beneficial contributions of these genes were verified via reverse engineering. Recombinant strains with overexpressing each of these four genes obtained enhanced tolerance to ferulic acid as compared to the control strain. Fortunately, recombinant strains with overexpression of YALI0_E25201g, YALI0_B18854g, and YALI0_F16731g individually also obtained enhanced tolerance to vanillic acid. Overall, this work demonstrated a whole strain improvement cycle by "non-rational" metabolic engineering and presented new targets to modify Y. lipolytica for microbial lignocellulose valorization. KEY POINTS: • Adaptive evolution improved the ferulic acid tolerance of Yarrowia lipolytica • Transcriptome sequence was applied to analyze the ferulic acid tolerate strain • Three genes were demonstrated for both ferulic acid and vanillic acid tolerance.
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Affiliation(s)
- Zedi Wang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Linlin Zhou
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Yuwei Zhang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Samina Perveen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Huarong Zhou
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
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9
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Coelho ALS, Arraes AA, Abreu-Lima TLDE, Carreiro SC. Hydrolysis of sweet potato (Ipomoea batatas (L.) Lam.) flour by Candida homilentoma strains: effects of pH and temperature using Central Composite Rotatable Design. AN ACAD BRAS CIENC 2020; 92:e20180410. [PMID: 32667509 DOI: 10.1590/0001-3765202020180410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 01/18/2019] [Indexed: 11/21/2022] Open
Abstract
The current study focuses on the evaluation of culture parameters on the enzymatic hydrolysis of Ipomoea batatas (L.) Lam flour by Candida homilentoma strains. A 2-factor-5-level CCRD was used to evaluate the effect of pH and temperature on the hydrolysis process. For the S-47 strain, pH and both studied parameters were significant at 48 h and 96 h, respectively. Regarding S-81 strain, temperature was the only factor affecting the process, at 96 hours. The regression models were significant, and no lack of fit was observed for them.
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Affiliation(s)
- Ana LetÍcia S Coelho
- Departamento de Engenharia Química e Engenharia de Alimentos, Universidade Federal de Santa Catarina/UFSC, Florianópolis, SC, Brazil
| | - Agelles A Arraes
- Programa de Graduação em Engenharia de Alimentos, Universidade Federal do Tocantins/UFT, Palmas, TO, Brazil
| | - Thiago Lucas DE Abreu-Lima
- Programa de Graduação em Engenharia de Alimentos, Universidade Federal do Tocantins/UFT, Palmas, TO, Brazil
| | - Solange Cristina Carreiro
- Programa de Graduação em Engenharia de Alimentos, Universidade Federal do Tocantins/UFT, Palmas, TO, Brazil
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10
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Da Ros C, Conca V, Eusebi AL, Frison N, Fatone F. Sieving of municipal wastewater and recovery of bio-based volatile fatty acids at pilot scale. WATER RESEARCH 2020; 174:115633. [PMID: 32109752 DOI: 10.1016/j.watres.2020.115633] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
This study combined at pilot scale the recovery of cellulosic primary sludge from the sieving of municipal wastewater followed by the production of bio-based VFAs through acidogenic fermentation. The sieving of municipal wastewater was accomplished by a rotating belt filter which allowed the removal of around 50% of suspended solids when operated at solids loading rates higher than 30-35 kgTSS/m2 h. The solids recovered by sieving contained around 40% of cellulose, which is a suitable raw material for the production of bio-based VFAs. Initially, fermentation batch tests of cellulosic primary sludge were carried out adjusting the initial pH of the sludge at values of 8, 9, 10 and 11, in order to evaluate the best production yields of bio-based VFAs and their composition. The highest VFAs yield achieved was 521 mgCODVFA/gVS occurring when pH was adjusted at 9, while propionic acid reached 51% of the total VFAs. Then, the optimal conditions were applied at long term in a sequencing batch fermentation reactor where the highest potential productivity of bio-based VFAs (2.57 kg COD/m3 d) was obtained by adjusting the pH feeding at 9 and operating with an hydraulic retention time of 6 days under mesophilic conditions. The cost-benefit analyses for the implementation of cellulosic primary sludge recovery was carried out consideringthe anaerobic digestion as reference scenario. The economical assessment showed that the production of bio-based VFAs from cellulosic primary sludge as carbon source and/or as chemical precursors give higher net benefits instead of the only biogas production.
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Affiliation(s)
- Cinzia Da Ros
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Vincenzo Conca
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Anna Laura Eusebi
- Department of Materials, Environmental and City Planning Science and Engineering, Faculty of Engineering, Polytechnic University of Marche, Ancona, Italy
| | - Nicola Frison
- Department of Biotechnology, University of Verona, Verona, Italy.
| | - Francesco Fatone
- Department of Materials, Environmental and City Planning Science and Engineering, Faculty of Engineering, Polytechnic University of Marche, Ancona, Italy
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11
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Tiukova IA, Jiang H, Dainat J, Hoeppner MP, Lantz H, Piskur J, Sandgren M, Nielsen J, Gu Z, Passoth V. Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540. Microorganisms 2019; 7:microorganisms7110489. [PMID: 31717754 PMCID: PMC6921048 DOI: 10.3390/microorganisms7110489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/19/2019] [Accepted: 10/23/2019] [Indexed: 01/21/2023] Open
Abstract
Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis.
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Affiliation(s)
- Ievgeniia A. Tiukova
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, SE-412 96 Göteborg, Sweden;
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007 Uppsala, Sweden; (M.S.); (V.P.)
- Correspondence: ; Tel.: +46-31-772-3801
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China;
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 752 37 Uppsala, Sweden; (J.D.); (M.P.H.); (H.L.)
- National Bioinformatics Infrastructure Sweden (NBIS), 752 37 Uppsala, Sweden
| | - Marc P. Hoeppner
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 752 37 Uppsala, Sweden; (J.D.); (M.P.H.); (H.L.)
- National Bioinformatics Infrastructure Sweden (NBIS), 752 37 Uppsala, Sweden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Henrik Lantz
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 752 37 Uppsala, Sweden; (J.D.); (M.P.H.); (H.L.)
- National Bioinformatics Infrastructure Sweden (NBIS), 752 37 Uppsala, Sweden
| | - Jure Piskur
- Department of Biology, Lund University, 223 62 Lund, Sweden;
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007 Uppsala, Sweden; (M.S.); (V.P.)
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, SE-412 96 Göteborg, Sweden;
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA;
| | - Volkmar Passoth
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007 Uppsala, Sweden; (M.S.); (V.P.)
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12
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13
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Sarawan C, Suinyuy TN, Sewsynker-Sukai Y, Gueguim Kana EB. Optimized activated charcoal detoxification of acid-pretreated lignocellulosic substrate and assessment for bioethanol production. BIORESOURCE TECHNOLOGY 2019; 286:121403. [PMID: 31078980 DOI: 10.1016/j.biortech.2019.121403] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/28/2019] [Accepted: 04/29/2019] [Indexed: 06/09/2023]
Abstract
This study optimized an activated charcoal (AC) detoxification method for the reduction of three different fermentation inhibitor compounds, while minimising the reducing sugar loss from acid-pretreated sorghum leaf (SL) wastes. Process optimization demonstrated a 98%, 88% and 37% removal efficiency for furfural, 5-hydroxymethylfurfural (HMF) and acetic acid respectively, with a 7% reducing sugar loss. Subsequently, the logistic and modified Gompertz models were used to comparatively evaluate the kinetics of Saccharomyces cerevisiae growth and ethanol production using the non-detoxified (NDF) and optimized detoxified (ODF) substrate. Yeast cell growth and bioethanol kinetic coefficients revealed that the ODF process was more effective than the NDF system. The experimental data generated from this study revealed that a suitable, cost-effective AC detoxification enhanced cell growth and bioethanol production efficiency. These findings pave the way for biomass pretreatment, detoxification and bioethanol process development using lignocellulosic wastes.
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Affiliation(s)
- Caitlyn Sarawan
- University of KwaZulu-Natal, School of Life Sciences, Pietermaritzburg, South Africa
| | - T N Suinyuy
- University of KwaZulu-Natal, School of Life Sciences, Pietermaritzburg, South Africa
| | - Y Sewsynker-Sukai
- University of KwaZulu-Natal, School of Life Sciences, Pietermaritzburg, South Africa
| | - E B Gueguim Kana
- University of KwaZulu-Natal, School of Life Sciences, Pietermaritzburg, South Africa.
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Wang Z, Wang J, Shan W, Zheng F, Niu C, Liu C, Li Q. Intracellular Adenosine Triphosphate (ATP) Content Sensitively Reflects Subtle Differences in Yeast Physiology. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2019. [DOI: 10.1080/03610470.2019.1577706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Zengmei Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jinjing Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wanxiang Shan
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Feiyun Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214000, China
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15
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Suzuki R, Sakakura M, Mori M, Fujii M, Akashi S, Takahashi H. Methyl-selective isotope labeling using α-ketoisovalerate for the yeast Pichia pastoris recombinant protein expression system. JOURNAL OF BIOMOLECULAR NMR 2018; 71:213-223. [PMID: 29869771 DOI: 10.1007/s10858-018-0192-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Methyl-detected NMR spectroscopy is a useful tool for investigating the structures and interactions of large macromolecules such as membrane proteins. The procedures for preparation of methyl-specific isotopically-labeled proteins were established for the Escherichia coli (E. coli) expression system, but typically it is not feasible to express eukaryotic proteins using E. coli. The Pichia pastoris (P. pastoris) expression system is the most common yeast expression system, and is known to be superior to the E. coli system for the expression of mammalian proteins, including secretory and membrane proteins. However, this system has not yet been optimized for methyl-specific isotope labeling, especially for Val/Leu-methyl specific isotope incorporation. To overcome this difficulty, we explored various culture conditions for the yeast cells to efficiently uptake Val/Leu precursors. Among the searched conditions, we found that the cultivation pH has a critical effect on Val/Leu precursor uptake. At an acidic cultivation pH, the uptake of the Val/Leu precursor was increased, and methyl groups of Val and Leu in the synthesized recombinant protein yielded intense 1H-13C correlation signals. Based on these results, we present optimized protocols for the Val/Leu-methyl-selective 13C incorporation by the P. pastoris expression system.
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Affiliation(s)
- Rika Suzuki
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masayoshi Sakakura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masaki Mori
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Moe Fujii
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Hideo Takahashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
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16
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Inactivation of the transcription factor mig1 (YGL035C) in Saccharomyces cerevisiae improves tolerance towards monocarboxylic weak acids: acetic, formic and levulinic acid. ACTA ACUST UNITED AC 2018; 45:735-751. [DOI: 10.1007/s10295-018-2053-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
Abstract
Abstract
Toxic concentrations of monocarboxylic weak acids present in lignocellulosic hydrolyzates affect cell integrity and fermentative performance of Saccharomyces cerevisiae. In this work, we report the deletion of the general catabolite repressor Mig1p as a strategy to improve the tolerance of S. cerevisiae towards inhibitory concentrations of acetic, formic or levulinic acid. In contrast with the wt yeast, where the growth and ethanol production were ceased in presence of acetic acid 5 g/L or formic acid 1.75 g/L (initial pH not adjusted), the m9 strain (Δmig1::kan) produced 4.06 ± 0.14 and 3.87 ± 0.06 g/L of ethanol, respectively. Also, m9 strain tolerated a higher concentration of 12.5 g/L acetic acid (initial pH adjusted to 4.5) without affecting its fermentative performance. Moreover, m9 strain produced 33% less acetic acid and 50–70% less glycerol in presence of weak acids, and consumed acetate and formate as carbon sources under aerobic conditions. Our results show that the deletion of Mig1p provides a single gene deletion target for improving the acid tolerance of yeast strains significantly.
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17
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Averesch NJH, Martínez VS, Nielsen LK, Krömer JO. Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks. ACS Synth Biol 2018; 7:490-509. [PMID: 29237121 DOI: 10.1021/acssynbio.7b00304] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adipic acid, a nylon-6,6 precursor, has recently gained popularity in synthetic biology. Here, 16 different production routes to adipic acid were evaluated using a novel tool for network-embedded thermodynamic analysis of elementary flux modes. The tool distinguishes between thermodynamically feasible and infeasible modes under determined metabolite concentrations, allowing the thermodynamic feasibility of theoretical yields to be assessed. Further, patterns that always caused infeasible flux distributions were identified, which will aid the development of tailored strain design. A review of cellular efflux mechanisms revealed that significant accumulation of extracellular product is only possible if coupled with ATP hydrolysis. A stoichiometric analysis demonstrated that the maximum theoretical product carbon yield heavily depends on the metabolic route, ranging from 32 to 99% on glucose and/or palmitate in Escherichia coli and Saccharomyces cerevisiae metabolic models. Equally important, metabolite concentrations appeared to be thermodynamically restricted in several pathways. Consequently, the number of thermodynamically feasible flux distributions was reduced, in some cases even rendering whole pathways infeasible, highlighting the importance of pathway choice. Only routes based on the shikimate pathway were thermodynamically favorable over a large concentration and pH range. The low pH capability of S. cerevisiae shifted the thermodynamic equilibrium of some pathways toward product formation. One identified infeasible-pattern revealed that the reversibility of the mitochondrial malate dehydrogenase contradicted the current state of knowledge, which imposes a major restriction on the metabolism of S. cerevisiae. Finally, the evaluation of industrially relevant constraints revealed that two shikimate pathway-based routes in E. coli were the most robust.
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Affiliation(s)
- Nils J. H. Averesch
- Centre
for Microbial Electrochemical Systems (CEMES), Advanced Water Management
Centre (AWMC), The University of Queensland, Brisbane 4072, Australia
- Universities Space Research Association at NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Verónica S. Martínez
- Systems
and Synthetic Biology Group, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- ARC
Training Centre for Biopharmaceutical Innovation (CBI), Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Lars K. Nielsen
- Systems
and Synthetic Biology Group, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- DTU
BIOSUSTAIN, Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jens O. Krömer
- Centre
for Microbial Electrochemical Systems (CEMES), Advanced Water Management
Centre (AWMC), The University of Queensland, Brisbane 4072, Australia
- Department
for Solar Materials, Helmholtz Centre of Environmental Research−UFZ, 04318 Leipzig, Germany
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18
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Valík Ľ, Ačai P, Liptáková D. Modelling the effects of lactic acid, sodium benzoate and temperature on the growth of Candida maltosa. Lett Appl Microbiol 2017; 65:453-460. [PMID: 28915310 DOI: 10.1111/lam.12803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 12/01/2022]
Abstract
The growth of the oxidatively imperfect yeast Candida maltosa Komagata, Nakase et Katsuya was studied experimentally and modelled mathematically in relation to sodium benzoate and lactic acid concentrations at different temperatures. Application of gamma models for the growth rate resulted in determination of cardinal temperature parameters for the growth environment containing lactic acid or sodium benzoate (Tmin = 0·7/1·3°C, Tmax = 45·3/45·0°C, Topt = 36·1/37·0°C, μopt = 0·88/0·96 h-1 ) as well as the maximal lactic acid concentration for growth (1·9%) or sodium benzoate (1397 mg kg-1 ). Based on the model, the times to reach the density of C. maltosa at the level of 105 CFU per ml can be determined at each combination of storage temperature and preservative concentration. The approach used in this study can broaden knowledge of the microbiological quality of fermented milk products during storage as well as the preservation efficacy of mayonnaise dressing for storage and consumption. SIGNIFICANCE AND IMPACT OF THE STUDY The strain of Candida maltosaYP1 was originally isolated from air filters that ensured clean air overpressure in yoghurt fermentation tanks. Its growth in contaminated yoghurts manifested outwardly through surface growth, assimilation lactic acid and slight production of carbon dioxide. This was the opportunity to model the effects of lactic acid and sodium benzoate on growth and predict its behaviour in foods. The approach used in this study provides knowledge about microbiological quality development during storage of the fermented milk products as well as some preserved foods for storage and consumption.
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Affiliation(s)
- Ľ Valík
- Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Bratislava, Slovakia
| | - P Ačai
- Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Bratislava, Slovakia
| | - D Liptáková
- Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Bratislava, Slovakia
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19
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Deparis Q, Claes A, Foulquié-Moreno MR, Thevelein JM. Engineering tolerance to industrially relevant stress factors in yeast cell factories. FEMS Yeast Res 2017; 17:3861662. [PMID: 28586408 PMCID: PMC5812522 DOI: 10.1093/femsyr/fox036] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/04/2017] [Indexed: 01/01/2023] Open
Abstract
The main focus in development of yeast cell factories has generally been on establishing optimal activity of heterologous pathways and further metabolic engineering of the host strain to maximize product yield and titer. Adequate stress tolerance of the host strain has turned out to be another major challenge for obtaining economically viable performance in industrial production. Although general robustness is a universal requirement for industrial microorganisms, production of novel compounds using artificial metabolic pathways presents additional challenges. Many of the bio-based compounds desirable for production by cell factories are highly toxic to the host cells in the titers required for economic viability. Artificial metabolic pathways also turn out to be much more sensitive to stress factors than endogenous pathways, likely because regulation of the latter has been optimized in evolution in myriads of environmental conditions. We discuss different environmental and metabolic stress factors with high relevance for industrial utilization of yeast cell factories and the experimental approaches used to engineer higher stress tolerance. Improving stress tolerance in a predictable manner in yeast cell factories should facilitate their widespread utilization in the bio-based economy and extend the range of products successfully produced in large scale in a sustainable and economically profitable way.
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Affiliation(s)
- Quinten Deparis
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Arne Claes
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Maria R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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20
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Mohammed R, Vyas D, Yang W, Beauchemin K. Changes in the relative population size of selected ruminal bacteria following an induced episode of acidosis in beef heifers receiving viable and non-viable active dried yeast. J Appl Microbiol 2017; 122:1483-1496. [DOI: 10.1111/jam.13451] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 02/06/2017] [Accepted: 03/15/2017] [Indexed: 10/19/2022]
Affiliation(s)
- R. Mohammed
- Lethbridge Research and Development Center; Agriculture and Agri-Food Canada; Lethbridge AB Canada
| | - D. Vyas
- Lethbridge Research and Development Center; Agriculture and Agri-Food Canada; Lethbridge AB Canada
| | - W.Z. Yang
- Lethbridge Research and Development Center; Agriculture and Agri-Food Canada; Lethbridge AB Canada
| | - K.A. Beauchemin
- Lethbridge Research and Development Center; Agriculture and Agri-Food Canada; Lethbridge AB Canada
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21
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Ou QX, Nikolic-Jaric M, Gänzle M. Mechanisms of inactivation of Candida humilis and Saccharomyces cerevisiae by pulsed electric fields. Bioelectrochemistry 2016; 115:47-55. [PMID: 28063751 DOI: 10.1016/j.bioelechem.2016.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 12/28/2016] [Accepted: 12/28/2016] [Indexed: 10/20/2022]
Abstract
AIMS This study aimed to determine how electric field strength, pulse width and shape, and specific energy input relate to the effect of pulsed electric fields (PEF) on viability and membrane permeabilization in Candida humilis and Saccharomyces cerevisiae suspended in potassium phosphate buffer. METHODS AND RESULTS Cells were treated with a micro-scale system with parallel plate electrodes. Propidium iodide was added before or after treatments to differentiate between reversible and irreversible membrane permeabilization. Treatments of C. humilis with 71kV/cm and 48kJ/kg reduced cell counts by 3.9±0.6 log (cfu/mL). Pulse shape or width had only a small influence on the treatment lethality. Variation of electric field strength (17-71kV/cm), pulse width (0.086-4μs), and specific energy input (8-46kJ/kg) demonstrated that specific energy input correlated to the membrane permeabilization (r2=0.84), while other parameters were uncorrelated. A minimum energy input of 3 and 12kJ/kg was required to achieve reversible membrane permeabilization and a reduction of cell counts, respectively, of C. humilis. CONCLUSIONS Energy input was the parameter that best described the inactivation efficiency of PEF. SIGNIFICANCE AND IMPACT OF STUDY This study is an important step to identify key process parameters and to facilitate process design for improved cost-effectiveness of commercial PEF treatment.
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Affiliation(s)
- Qi-Xing Ou
- University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, Canada
| | | | - Michael Gänzle
- University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, Canada; Hubei University of Technology, School of Food and Pharmaceutical Engineering, Wuhan, China.
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22
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Efficiency of population-dependent sulfite against Brettanomyces bruxellensis in red wine. Food Res Int 2016; 89:620-630. [DOI: 10.1016/j.foodres.2016.09.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/24/2016] [Accepted: 09/17/2016] [Indexed: 11/20/2022]
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23
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Guo ZP, Olsson L. Physiological responses to acid stress by Saccharomyces cerevisiae when applying high initial cell density. FEMS Yeast Res 2016; 16:fow072. [PMID: 27620460 PMCID: PMC5094285 DOI: 10.1093/femsyr/fow072] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2016] [Indexed: 12/20/2022] Open
Abstract
High initial cell density is used to increase volumetric productivity and shorten production time in lignocellulosic hydrolysate fermentation. Comparison of physiological parameters in high initial cell density cultivation of Saccharomyces cerevisiae in the presence of acetic, formic, levulinic and cinnamic acids demonstrated general and acid-specific responses of cells. All the acids studied impaired growth and inhibited glycolytic flux, and caused oxidative stress and accumulation of trehalose. However, trehalose may play a role other than protecting yeast cells from acid-induced oxidative stress. Unlike the other acids, cinnamic acid did not cause depletion of cellular ATP, but abolished the growth of yeast on ethanol. Compared with low initial cell density, increasing initial cell density reduced the lag phase and improved the bioconversion yield of cinnamic acid during acid adaptation. In addition, yeast cells were able to grow at elevated concentrations of acid, probable due to the increase in phenotypic cell-to-cell heterogeneity in large inoculum size. Furthermore, the specific growth rate and the specific rates of glucose consumption and metabolite production were significantly lower than at low initial cell density, which was a result of the accumulation of a large fraction of cells that persisted in a viable but non-proliferating state.
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Affiliation(s)
- Zhong-Peng Guo
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Lisbeth Olsson
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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24
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Thompson OA, Hawkins GM, Gorsich SW, Doran-Peterson J. Phenotypic characterization and comparative transcriptomics of evolved Saccharomyces cerevisiae strains with improved tolerance to lignocellulosic derived inhibitors. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:200. [PMID: 27679668 PMCID: PMC5029107 DOI: 10.1186/s13068-016-0614-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/07/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Lignocellulosic biomass continues to be investigated as a viable source for bioethanol production. However, the pretreatment process generates inhibitory compounds that impair the growth and fermentation performance of microorganisms such as Saccharomyces cerevisiae. Pinewood specifically has been shown to be challenging in obtaining industrially relevant ethanol titers. An industrial S. cerevisiae strain was subjected to directed evolution and adaptation in pretreated pine biomass and resultant strains, GHP1 and GHP4, exhibited improved growth and fermentative ability on pretreated pine in the presence of related inhibitory compounds. A comparative transcriptomic approach was applied to identify and characterize differences in phenotypic stability of evolved strains. RESULTS Evolved strains displayed different fermentative capabilities with pretreated pine that appear to be influenced by the addition or absence of 13 inhibitory compounds during pre-culturing. GHP4 performance was consistent independent of culturing conditions, while GHP1 performance was dependent on culturing with inhibitors. Comparative transcriptomics revealed 52 genes potentially associated with stress responses to multiple inhibitors simultaneously. Fluorescence microscopy revealed improved cellular integrity of both strains with mitochondria exhibiting resistance to the damaging effects of inhibitors in contrast to the parent. CONCLUSIONS Multiple potentially novel genetic targets have been discovered for understanding stress tolerance through the characterization of our evolved strains. This study specifically examines the synergistic effects of multiple inhibitors and identified targets will guide future studies in remediating effects of inhibitors and further development of robust yeast strains for multiple industrial applications.
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Affiliation(s)
| | - Gary M. Hawkins
- Department of Microbiology, University of Georgia, Athens, GA 30602 USA
| | - Steven W. Gorsich
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859 USA
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25
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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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26
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Branco P, Viana T, Albergaria H, Arneborg N. Antimicrobial peptides (AMPs) produced by Saccharomyces cerevisiae induce alterations in the intracellular pH, membrane permeability and culturability of Hanseniaspora guilliermondii cells. Int J Food Microbiol 2015; 205:112-8. [PMID: 25897995 DOI: 10.1016/j.ijfoodmicro.2015.04.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/26/2015] [Accepted: 04/07/2015] [Indexed: 11/27/2022]
Abstract
Saccharomyces cerevisiae produces antimicrobial peptides (AMPs) during alcoholic fermentation that are active against several wine-related yeasts (e.g. Hanseniaspora guilliermondii) and bacteria (e.g. Oenococcus oeni). In the present study, the physiological changes induced by those AMPs on sensitive H. guilliermondii cells were evaluated in terms of intracellular pH (pHi), membrane permeability and culturability. Membrane permeability was evaluated by staining cells with propidium iodide (PI), pHi was determined by a fluorescence ratio imaging microscopy (FRIM) technique and culturability by a classical plating method. Results showed that the average pHi of H. guilliermondii cells dropped from 6.5 (healthy cells) to 5.4 (damaged cells) after 20 min of exposure to inhibitory concentrations of AMPs, and after 24 h 77.0% of the cells completely lost their pH gradient (∆pH=pHi-pHext). After 24h of exposure to AMPs, PI-stained (dead) cells increased from 0% to 77.7% and the number of viable cells fell from 1×10(5) to 10 CFU/ml. This means that virtually all cells (99.99%) became unculturable but that a sub-population of 22.3% of the cells remained viable (as determined by PI staining). Besides, pHi results showed that after 24h, 23% of the AMP-treated cells were sub-lethally injured (with 0<∆pH<3). Taken together, these results indicated that this subpopulation was under a viable but non-culturable (VBNC) state, which was further confirmed by recuperation assays. In summary, our study reveals that these AMPs compromise the plasma membrane integrity (and possibly also the vacuole membrane) of H. guilliermondii cells, disturbing the pHi homeostasis and inducing a loss of culturability.
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Affiliation(s)
- Patrícia Branco
- Unit of Bioenergy, Laboratório Nacional de Energia e Geologia (LNEG), Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal; Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, University of Lisbon, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Tiago Viana
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, University of Lisbon, Tapada da Ajuda, 1349-017 Lisboa, Portugal; Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Helena Albergaria
- Unit of Bioenergy, Laboratório Nacional de Energia e Geologia (LNEG), Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal.
| | - Nils Arneborg
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
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Bachmann H, Pronk JT, Kleerebezem M, Teusink B. Evolutionary engineering to enhance starter culture performance in food fermentations. Curr Opin Biotechnol 2015; 32:1-7. [DOI: 10.1016/j.copbio.2014.09.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/05/2014] [Accepted: 09/12/2014] [Indexed: 01/08/2023]
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28
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The effects of extracellular pH and hydroxycinnamic acids influence the intracellular pH of Brettanomyces bruxellensis DSM 7001. Lebensm Wiss Technol 2014. [DOI: 10.1016/j.lwt.2014.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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29
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Zeng SW, Huang QL, Zhao SM. Effects of microwave irradiation dose and time on Yeast ZSM-001 growth and cell membrane permeability. Food Control 2014. [DOI: 10.1016/j.foodcont.2014.05.053] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Berlowska J, Kregiel D, Rajkowska K. Biodiversity of brewery yeast strains and their fermentative activities. Yeast 2014; 32:289-300. [PMID: 25267007 DOI: 10.1002/yea.3041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 09/11/2014] [Accepted: 09/19/2014] [Indexed: 11/08/2022] Open
Abstract
We investigated the genetic, biochemical, fermentative and physiological characteristics of brewery yeast strains and performed a hierarchical cluster analysis to evaluate their similarity. We used five different ale and lager yeast strains, originating from different European breweries and deposited at the National Collection of Yeast Cultures (UK). Ale and lager strains exhibited different genomic properties, but their assimilation profiles and pyruvate decarboxylase activities corresponded to their species classifications. The activity of another enzyme, succinate dehydrogenase, varied between different brewing strains. Our results confirmed that ATP and glycogen content, and the activity of the key metabolic enzymes succinate dehydrogenase and pyruvate decarboxylase, may be good general indicators of cell viability. However, the genetic properties, physiology and fermentation capacity of different brewery yeasts are unique to individual strains.
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Affiliation(s)
- Joanna Berlowska
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, Poland
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Khattak WA, Ul-Islam M, Ullah MW, Yu B, Khan S, Park JK. Yeast cell-free enzyme system for bio-ethanol production at elevated temperatures. Process Biochem 2014. [DOI: 10.1016/j.procbio.2013.12.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Noninvasive high-throughput single-cell analysis of the intracellular pH of Saccharomyces cerevisiae by ratiometric flow cytometry. Appl Environ Microbiol 2013; 79:7179-87. [PMID: 24038689 DOI: 10.1128/aem.02515-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of cells to maintain pH homeostasis in response to environmental changes has elicited interest in basic and applied research and has prompted the development of methods for intracellular pH measurements. Many traditional methods provide information at population level and thus the average values of the studied cell physiological phenomena, excluding the fact that cell cultures are very heterogeneous. Single-cell analysis, on the other hand, offers more detailed insight into population variability, thereby facilitating a considerably deeper understanding of cell physiology. Although microscopy methods can address this issue, they suffer from limitations in terms of the small number of individual cells that can be studied and complicated image processing. We developed a noninvasive high-throughput method that employs flow cytometry to analyze large populations of cells that express pHluorin, a genetically encoded ratiometric fluorescent probe that is sensitive to pH. The method described here enables measurement of the intracellular pH of single cells with high sensitivity and speed, which is a clear improvement compared to previously published methods that either require pretreatment of the cells, measure cell populations, or require complex data analysis. The ratios of fluorescence intensities, which correlate to the intracellular pH, are independent of the expression levels of the pH probe, making the use of transiently or extrachromosomally expressed probes possible. We conducted an experiment on the kinetics of the pH homeostasis of Saccharomyces cerevisiae cultures grown to a stationary phase after ethanol or glucose addition and after exposure to weak acid stress and glucose pulse. Minor populations with pH homeostasis behaving differently upon treatments were identified.
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Ohnuki S, Enomoto K, Yoshimoto H, Ohya Y. Dynamic changes in brewing yeast cells in culture revealed by statistical analyses of yeast morphological data. J Biosci Bioeng 2013; 117:278-84. [PMID: 24012106 DOI: 10.1016/j.jbiosc.2013.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 08/08/2013] [Accepted: 08/13/2013] [Indexed: 10/26/2022]
Abstract
The vitality of brewing yeasts has been used to monitor their physiological state during fermentation. To investigate the fermentation process, we used the image processing software, CalMorph, which generates morphological data on yeast mother cells and bud shape, nuclear shape and location, and actin distribution. We found that 248 parameters changed significantly during fermentation. Successive use of principal component analysis (PCA) revealed several important features of yeast, providing insight into the dynamic changes in the yeast population. First, PCA indicated that much of the observed variability in the experiment was summarized in just two components: a change with a peak and a change over time. Second, PCA indicated the independent and important morphological features responsible for dynamic changes: budding ratio, nucleus position, neck position, and actin organization. Thus, the large amount of data provided by imaging analysis can be used to monitor the fermentation processes involved in beer and bioethanol production.
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Affiliation(s)
- Shinsuke Ohnuki
- Department of Integrated Bioscience, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Kenichi Enomoto
- Research Laboratories for Brewing, Kirin Brewery Company, Limited, 17-1 Namamugi 1-chome, Tsurumi-ku, Yokohama, Kanagawa 230-8628, Japan
| | - Hiroyuki Yoshimoto
- Research Laboratories for Brewing, Kirin Brewery Company, Limited, 17-1 Namamugi 1-chome, Tsurumi-ku, Yokohama, Kanagawa 230-8628, Japan
| | - Yoshikazu Ohya
- Department of Integrated Bioscience, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
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Behrendorff JB, Vickers CE, Chrysanthopoulos P, Nielsen LK. 2,2-Diphenyl-1-picrylhydrazyl as a screening tool for recombinant monoterpene biosynthesis. Microb Cell Fact 2013; 12:76. [PMID: 23968454 PMCID: PMC3847554 DOI: 10.1186/1475-2859-12-76] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 08/15/2013] [Indexed: 12/03/2022] Open
Abstract
Background Monoterpenes are a class of natural C10 compounds with a range of potential applications including use as fuel additives, fragrances, and chemical feedstocks. Biosynthesis of monoterpenes in heterologous systems is yet to reach commercially-viable levels, and therefore is the subject of strain engineering and fermentation optimization studies. Detection of monoterpenes typically relies on gas chromatography/mass spectrometry; this represents a significant analytical bottleneck which limits the potential to analyse combinatorial sets of conditions. To address this, we developed a high-throughput method for pre-screening monoterpene biosynthesis. Results An optimised DPPH assay was developed for detecting monoterpenes from two-phase microbial cultures using dodecane as the extraction solvent. The assay was useful for reproducible qualitative ranking of monoterpene concentrations, and detected standard preparations of myrcene and γ-terpinene dissolved in dodecane at concentrations as low as 10 and 15 μM, respectively, and limonene as low as 200 μM. The assay could not be used quantitatively due to technical difficulties in capturing the initial reaction rate in a multi-well plate and the presence of minor DPPH-reactive contaminants. Initially, limonene biosynthesis in Saccharomyces cerevisiae was tested using two different limonene synthase enzymes and three medium compositions. The assay indicated that limonene biosynthesis was enhanced in a supplemented YP medium and that the Citrus limon limonene synthase (CLLS) was more effective than the Mentha spicata limonene synthase (MSLS). GC-MS analysis revealed that the DPPH assay had correctly identified the best limonene synthase (CLLS) and culture medium (supplemented YP medium). Because only traces of limonene were detected in SD medium, we subsequently identified medium components that improved limonene production and developed a defined medium based on these findings. The best limonene titres obtained were 1.48 ± 0.22 mg limonene per L in supplemented YP medium and 0.9 ± 0.15 mg limonene per L in a pH-adjusted supplemented SD medium. Conclusions The DPPH assay is useful for detecting biosynthesis of limonene. Although the assay cannot be used quantitatively, it proved successful in ranking limonene production conditions qualitatively and thus is suitable as a first-tier screen. The DPPH assay will likely be applicable in detecting biosynthesis of several other monoterpenes and for screening libraries of monoterpene-producing strains.
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Affiliation(s)
- James Byh Behrendorff
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia QLD 4072, Australia.
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35
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Berlowska J, Kregiel D, Ambroziak W. Physiological tests for yeast brewery cells immobilized on modified chamotte carrier. Antonie Van Leeuwenhoek 2013; 104:703-14. [PMID: 23887884 PMCID: PMC3824387 DOI: 10.1007/s10482-013-9978-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 07/16/2013] [Indexed: 11/30/2022]
Abstract
In this study yeast cell physiological activity was assessed on the basis of the in situ activity of two important enzymes, succinate dehydrogenase and pyruvate decarboxylase. FUN1 dye bioconversion and cellular ATP content were also taken as important indicators of yeast cell activity. The study was conducted on six brewing yeast strains, which were either free cells or immobilized on a chamotte carrier. The experimental data obtained indicate clearly that, in most cases, the immobilized cells showed lower enzyme activity than free cells from analogous cultures. Pyruvate decarboxylase activity in immobilized cells was higher than in planktonic cell populations only in the case of the Saccharomyces pastorianus 680 strain. However, in a comparative assessment of the fermentation process, conducted with the use of free and immobilized cells, much more favorable dynamics and carbon dioxide productivity were observed in immobilized cells, especially in the case of brewing lager yeast strains. This may explain the higher total cell density per volume unit of the fermented medium and the improved resistance of immobilized cells to environmental changes.
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Affiliation(s)
- Joanna Berlowska
- Institute of Fermentation Technology and Microbiology, Technical University of Lodz, ul. Wolczanska 171/173, 90-924, Lodz, Poland,
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36
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Theoretical considerations about usage of metabolic inhibitors as possible alternative to reduce alcohol content of wines from hot areas. Eur Food Res Technol 2013. [DOI: 10.1007/s00217-013-1992-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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37
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Zi LH, Liu CG, Xin CB, Bai FW. Stillage backset and its impact on ethanol fermentation by the flocculating yeast. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.03.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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38
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Oku M, Hoseki J, Ichiki Y, Sakai Y. A fluorescence resonance energy transfer (FRET)-based redox sensor reveals physiological role of thioredoxin in the yeast Saccharomyces cerevisiae. FEBS Lett 2013; 587:793-8. [PMID: 23416294 DOI: 10.1016/j.febslet.2013.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/24/2013] [Accepted: 02/01/2013] [Indexed: 12/31/2022]
Abstract
The physiological roles of the thioredoxin isozymes in the yeast Saccharomyces cerevisiae were investigated using a novel FRET-based redox probe, Redoxfluor. After establishing responsiveness of the probe toward thioredoxin, we followed the fluorescence signal of Redoxfluor expressed in the yeast and found that one of the thioredoxin isozymes, Trx2, was required for maintaining the redox status when stationary culture of the organism was exposed to starvation and mild-heat stresses. The failure to maintain redox balance under the tested condition preceded decreased viability of the trx2 mutants, indicating the functional importance of the cytoplasmic thioredoxin in adaptation to environmental changes.
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Affiliation(s)
- Masahide Oku
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo, Kyoto 606-8502, Japan
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39
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Kurz T, Mieleitner J, Becker T, Delgado A. A Model Based Simulation of Brewing Yeast Propagation. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2002.tb00548.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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40
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Effect of pH on potassium metabisulphite biocidic activity against yeast and human cell cultures. Food Chem 2012; 134:1327-36. [DOI: 10.1016/j.foodchem.2012.03.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 01/23/2012] [Accepted: 03/06/2012] [Indexed: 02/08/2023]
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41
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Novel endophytic yeast Rhodotorula mucilaginosa strain PTD3 II: production of xylitol and ethanol in the presence of inhibitors. ACTA ACUST UNITED AC 2012; 39:1453-63. [DOI: 10.1007/s10295-012-1154-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 05/28/2012] [Indexed: 10/28/2022]
Abstract
Abstract
A systematic study was conducted characterizing the effect of furfural, 5-hydroxymethylfurfural (5-HMF), and acetic acid concentration on the production of xylitol and ethanol by a novel endophytic yeast, Rhodotorula mucilaginosa strain PTD3. The influence of different inhibitor concentrations on the growth and fermentation abilities of PTD3 cultivated in synthetic nutrient media containing 30 g/l xylose or glucose were measured during liquid batch cultures. Concentrations of up to 5 g/l of furfural stimulated production of xylitol to 77 % of theoretical yield (10 % higher compared to the control) by PTD3. Xylitol yields produced by this yeast were not affected in the presence of 5-HMF at concentrations of up to 3 g/l. At higher concentrations of furfural and 5-HMF, xylitol and ethanol yields were negatively affected. The higher the concentration of acetic acid present in a media, the higher the ethanol yield approaching 99 % of theoretical yield (15 % higher compared to the control) was produced by the yeast. At all concentrations of acetic acid tested, xylitol yield was lowered. PTD3 was capable of metabolizing concentrations of 5, 15, and 5 g/l of furfural, 5-HMF, and acetic acid, respectively. This yeast would be a potent candidate for the bioconversion of lignocellulosic sugars to biochemicals given that in the presence of low concentrations of inhibitors, its xylitol and ethanol yields are stimulated, and it is capable of metabolizing pretreatment degradation products.
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42
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Divol B, du Toit M, Duckitt E. Surviving in the presence of sulphur dioxide: strategies developed by wine yeasts. Appl Microbiol Biotechnol 2012; 95:601-13. [PMID: 22669635 DOI: 10.1007/s00253-012-4186-x] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 05/15/2012] [Accepted: 05/15/2012] [Indexed: 11/26/2022]
Abstract
Sulphur dioxide has been used as a common preservative in wine since at least the nineteenth century. Its use has even become essential to the making of quality wines because of its antioxidant, antioxidasic and antiseptic properties. The chemistry of SO₂ in wine is fairly complex due to its dissociation into different species and its binding to other compounds produced by yeasts and bacteria during fermentation. The only antiseptic species is the minute part remaining as molecular SO₂. The latter concentration is both dependent on pH and concentration of free bisulphite. However, certain yeast species have developed cellular and molecular mechanisms as a response to SO₂ exposure. Some of these mechanisms are fairly complex and have only been investigated recently, at least for the molecular mechanisms. They include sulphite reduction, sulphite oxidation, acetaldehyde production, sulphite efflux and the entry into viable but not culturable state, as the ultimate response. In this review, the chemistry of SO₂ in wine is explained together with the impact of SO₂ on yeast cells. The different defence mechanisms are described and discussed, mostly based on current knowledge available for Saccharomyces cerevisiae.
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Affiliation(s)
- Benoit Divol
- Institute for Wine Biotechnology, Stellenbosch University, Private Bag X1, 7602 Matieland, South Africa.
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43
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Noor E, Bar-Even A, Flamholz A, Lubling Y, Davidi D, Milo R. An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. ACTA ACUST UNITED AC 2012; 28:2037-44. [PMID: 22645166 PMCID: PMC3400964 DOI: 10.1093/bioinformatics/bts317] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Motivation: The laws of thermodynamics describe a direct, quantitative relationship between metabolite concentrations and reaction directionality. Despite great efforts, thermodynamic data suffer from limited coverage, scattered accessibility and non-standard annotations. We present a framework for unifying thermodynamic data from multiple sources and demonstrate two new techniques for extrapolating the Gibbs energies of unmeasured reactions and conditions. Results: Both methods account for changes in cellular conditions (pH, ionic strength, etc.) by using linear regression over the ΔG○ of pseudoisomers and reactions. The Pseudoisomeric Reactant Contribution method systematically infers compound formation energies using measured K′ and pKa data. The Pseudoisomeric Group Contribution method extends the group contribution method and achieves a high coverage of unmeasured reactions. We define a continuous index that predicts the reversibility of a reaction under a given physiological concentration range. In the characteristic physiological range 3μM–3mM, we find that roughly half of the reactions in Escherichia coli's metabolism are reversible. These new tools can increase the accuracy of thermodynamic-based models, especially in non-standard pH and ionic strengths. The reversibility index can help modelers decide which reactions are reversible in physiological conditions. Availability: Freely available on the web at: http://equilibrator.weizmann.ac.il. Website implemented in Python, MySQL, Apache and Django, with all major browsers supported. The framework is open-source (code.google.com/p/milo-lab), implemented in pure Python and tested mainly on Linux. Contact:ron.milo@weizmann.ac.il Supplementary Information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Elad Noor
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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44
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Chlup PH, Bernard D, Stewart GG. Disc Stack Centrifuge Operating Parameters and Their Impact on Yeast Physiology. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2008.tb00305.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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45
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Bura R, Vajzovic A, Doty SL. Novel endophytic yeast Rhodotorula mucilaginosa strain PTD3 I: production of xylitol and ethanol. J Ind Microbiol Biotechnol 2012; 39:1003-11. [PMID: 22399239 DOI: 10.1007/s10295-012-1109-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 02/11/2012] [Indexed: 10/28/2022]
Abstract
An endophytic yeast, Rhodotorula mucilaginosa strain PTD3, that was isolated from stems of hybrid poplar was found to be capable of production of xylitol from xylose, of ethanol from glucose, galactose, and mannose, and of arabitol from arabinose. The utilization of 30 g/L of each of the five sugars during fermentation by PTD3 was studied in liquid batch cultures. Glucose-acclimated PTD3 produced enhanced yields of xylitol (67% of theoretical yield) from xylose and of ethanol (84, 86, and 94% of theoretical yield, respectively) from glucose, galactose, and mannose. Additionally, this yeast was capable of metabolizing high concentrations of mixed sugars (150 g/L), with high yields of xylitol (61% of theoretical yield) and ethanol (83% of theoretical yield). A 1:1 glucose:xylose ratio with 30 g/L of each during double sugar fermentation did not affect PTD3's ability to produce high yields of xylitol (65% of theoretical yield) and ethanol (92% of theoretical yield). Surprisingly, the highest yields of xylitol (76% of theoretical yield) and ethanol (100% of theoretical yield) were observed during fermentation of sugars present in the lignocellulosic hydrolysate obtained after steam pretreatment of a mixture of hybrid poplar and Douglas fir. PTD3 demonstrated an exceptional ability to ferment the hydrolysate, overcome hexose repression of xylose utilization with a short lag period of 10 h, and tolerate sugar degradation products. In direct comparison, PTD3 had higher xylitol yields from the mixed sugar hydrolysate compared with the widely studied and used xylitol producer Candida guilliermondii.
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Affiliation(s)
- Renata Bura
- University of Washington, School of Environmental and Forest Sciences, Seattle, WA 98195-2100, USA.
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46
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Buchhaupt M, Guder JC, Etschmann MMW, Schrader J. Synthesis of green note aroma compounds by biotransformation of fatty acids using yeast cells coexpressing lipoxygenase and hydroperoxide lyase. Appl Microbiol Biotechnol 2012; 93:159-68. [PMID: 21789493 DOI: 10.1007/s00253-011-3482-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 07/01/2011] [Accepted: 07/13/2011] [Indexed: 10/18/2022]
Abstract
Green notes are substances that characterize the aroma of freshly cut grass, cucumbers, green apples, and foliage. In plants, they are synthesized by conversion of linolenic or linoleic acid via the enzymes lipoxygenase (LOX) and hydroperoxide lyase (HPL) to short-chained aldehydes. Current processes for production of natural green notes rely on plant homogenates as enzyme sources but are limited by low enzyme concentration and low specificity. In an alternative approach, soybean LOX2 and watermelon HPL were overexpressed in Saccharomyces cerevisiae. After optimization of the expression constructs, a yeast strain coexpressing LOX and HPL was applied in whole cell biotransformation experiments. Whereas addition of linolenic acid to growing cultures of this strain yielded no products, we were able to identify high green note concentrations when resting cells were used. The primary biotransformation product was 3(Z)-hexenal, a small amount of which isomerized to 2(E)-hexenal. Furthermore, both aldehydes were reduced to the corresponding green note alcohols by endogenous yeast alcohol dehydrogenase to some extent. As the cosolvent ethanol was the source of reducing equivalents for green note alcohol formation, the hexenal/hexenol ratio could be influenced by the use of alternative cosolvents. Further investigations to identify the underlying mechanism of the rather low biocatalyst stability revealed a high toxicity of linolenic acid to yeast cells. The whole cell catalyst containing LOX and HPL enzyme activity described here can be a promising approach towards a highly efficient microbial green note synthesis process.
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Affiliation(s)
- Markus Buchhaupt
- Biochemical Engineering, DECHEMA eV, Karl Winnacker-Institut, Frankfurt, Germany.
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47
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Aabo T, Glückstad J, Siegumfeldt H, Arneborg N. Intracellular pH distribution as a cell health indicator in Saccharomyces cerevisiae. J R Soc Interface 2011; 8:1635-43. [PMID: 21527496 PMCID: PMC3177618 DOI: 10.1098/rsif.2011.0148] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 04/08/2011] [Indexed: 11/12/2022] Open
Abstract
Internal pH regulation is vital for many cell functions, including transport mechanisms and metabolic enzyme activity. More specifically, transport mechanisms are to a wide degree governed by internal pH distributions. We introduce the term standard deviation of the intracellular pH (s.d.(pH(int))) to describe the internal pH distributions. The cellular pH distributional response to external stress such as heat has not previously been determined. In this study, the intracellular pH (pH(i)) and the s.d.(pH(int)) of Saccharomyces cerevisiae cells exposed to supralethal temperatures were measured using fluorescence ratio imaging microscopy (FRIM). An exponential decline in pH(i) was observed after an initial small decline. For the first time, we report the use of FRIM for determining in vivo plasma membrane proton permeability coefficients in yeast. Furthermore, the exponential decay of pH(i) and the rupture of the cell plasma membrane, as measured by propidium iodide staining, at 70°C were not simultaneous but were separated by a significant temporal difference. Finally, a nonlinear relationship between the pH(i) and s.d.(pH(int)) was found; i.e. the s.d.(pH(int)) was significantly more sensitive to supralethal temperatures than pH(i). s.d.(pH(int)) is therefore proposed as an early health/vitality indicator in S. cerevisiae cells exposed to heat stress.
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Affiliation(s)
- Thomas Aabo
- Department of Food Science, University of Copenhagen, , Frederiksberg, Denmark.
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48
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Siegumfeldt H, Arneborg N. Assessment of survival of food-borne microorganisms in the food chain by fluorescence ratio imaging microscopy. Trends Food Sci Technol 2011. [DOI: 10.1016/j.tifs.2011.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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49
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Use of sugarcane molasses "B" as an alternative for ethanol production with wild-type yeast Saccharomyces cerevisiae ITV-01 at high sugar concentrations. Bioprocess Biosyst Eng 2011; 35:605-14. [PMID: 21971607 DOI: 10.1007/s00449-011-0633-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Accepted: 09/20/2011] [Indexed: 10/17/2022]
Abstract
Molasses "B" is a rich co-product of the sugarcane process. It is obtained from the second step of crystallization and is richer in fermentable sugars (50-65%) than the final molasses, with a lower non-sugar solid content (18-33%); this co-product also contains good vitamin and mineral levels. The use of molasses "B" for ethanol production could be a good option for the sugarcane industry when cane sugar prices diminish in the market. In a complex medium like molasses, osmotolerance is a desirable characteristic for ethanol producing strains. The aim of this work was to evaluate the use of molasses "B" for ethanol production using Saccharomyces cerevisiae ITV-01 (a wild-type yeast isolated from sugarcane molasses) using different initial sugar concentrations (70-291 g L(-1)), two inoculum sizes and the addition of nutrients such as yeast extract, urea, and ammonium sulphate to the culture medium. The results obtained showed that the strain was able to grow at 291 g L(-1) total sugars in molasses "B" medium; the addition of nutrients to the culture medium did not produce a statistically significant difference. This yeast exhibits high osmotolerance in this medium, producing high ethanol yields (0.41 g g(-1)). The best conditions for ethanol production were 220 g L(-1) initial total sugars in molasses "B" medium, pH 5.5, using an inoculum size of 6 × 10(6) cell mL(-1); ethanol production was 85 g L(-1), productivity 3.8 g L(-1 )h(-1) with 90% preserved cell viability.
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50
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Werner M, Merenda F, Piguet J, Salathé RP, Vogel H. Microfluidic array cytometer based on refractive optical tweezers for parallel trapping, imaging and sorting of individual cells. LAB ON A CHIP 2011; 11:2432-9. [PMID: 21655617 DOI: 10.1039/c1lc20181f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Analysis of genetic and functional variability in populations of living cells requires experimental techniques capable of monitoring cellular processes such as cell signaling of many single cells in parallel while offering the possibility to sort interesting cell phenotypes for further investigations. Although flow cytometry is able to sequentially probe and sort thousands of cells per second, dynamic processes cannot be experimentally accessed on single cells due to the sub-second sampling time. Cellular dynamics can be measured by image cytometry of surface-immobilized cells, however, cell sorting is complicated under these conditions due to cell attachment. We here developed a cytometric tool based on refractive multiple optical tweezers combined with microfluidics and optical microscopy. We demonstrate contact-free immobilization of more than 200 yeast cells into a high-density array of optical traps in a microfluidic chip. The cell array could be moved to specific locations of the chip enabling us to expose in a controlled manner the cells to reagents and to analyze the responses of individual cells in a highly parallel format using fluorescence microscopy. We further established a method to sort single cells within the microfluidic device using an additional steerable optical trap. Ratiometric fluorescence imaging of intracellular pH of trapped yeast cells allowed us on the one hand to measure the effect of the trapping laser on the cells' viability and on the other hand to probe the dynamic response of the cells upon glucose sensing.
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Affiliation(s)
- Michael Werner
- Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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