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Butanol is cytotoxic to Lactococcus lactis while ethanol and hexanol are cytostatic. Microbiology (Reading) 2017; 163:453-461. [DOI: 10.1099/mic.0.000441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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52
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Guo ZP, Duquesne S, Bozonnet S, Nicaud JM, Marty A, O’Donohue MJ. Expressing accessory proteins in cellulolytic Yarrowia lipolytica to improve the conversion yield of recalcitrant cellulose. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:298. [PMID: 29238402 PMCID: PMC5724336 DOI: 10.1186/s13068-017-0990-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 12/04/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND A recently constructed cellulolytic Yarrowia lipolytica is able to grow efficiently on an industrial organosolv cellulose pulp, but shows limited ability to degrade crystalline cellulose. In this work, we have further engineered this strain, adding accessory proteins xylanase II (XYNII), lytic polysaccharide monooxygenase (LPMO), and swollenin (SWO) from Trichoderma reesei in order to enhance the degradation of recalcitrant substrate. RESULTS The production of EG I was enhanced using a promoter engineering strategy. This provided a new cellulolytic Y. lipolytica strain, which compared to the parent strain, exhibited higher hydrolytic activity on different cellulosic substrates. Furthermore, three accessory proteins, TrXYNII, TrLPMOA and TrSWO, were individually expressed in cellulolytic and non-cellulolytic Y. lipolytica. The amount of rhTrXYNII and rhTrLPMOA secreted by non-cellulolytic Y. lipolytica in YTD medium during batch cultivation in flasks was approximately 62 and 52 mg/L, respectively. The purified rhTrXYNII showed a specific activity of 532 U/mg-protein on beechwood xylan, while rhTrLPMOA exhibited a specific activity of 14.4 U/g-protein when using the Amplex Red/horseradish peroxidase assay. Characterization of rhTrLPMOA revealed that this protein displays broad specificity against β-(1,4)-linked glucans, but is inactive on xylan. Further studies showed that the presence of TrLPMOA synergistically enhanced enzymatic hydrolysis of cellulose by cellulases, while TrSWO1 boosted cellulose hydrolysis only when it was applied before the action of cellulases. The presence of rTrXYNII enhanced enzymatic hydrolysis of an industrial cellulose pulp and of wheat straw. Co-expressing TrXYNII and TrLPMOA in cellulolytic Y. lipolytica with enhanced EG I production procured a novel engineered Y. lipolytica strain that displayed enhanced ability to degrade both amorphous (CIMV-cellulose) and recalcitrant crystalline cellulose in complex biomass (wheat straw) by 16 and 90%, respectively. CONCLUSIONS This study has provided a potent cellulose-degrading Y. lipolytica strain that co-expresses a core set of cellulolytic enzymes and some accessory proteins. Results reveal that the tuning of cellulase production and the production of accessory proteins leads to optimized performance. Accordingly, the beneficial effect of accessory proteins for cellulase-mediated degradation of cellulose is underlined, especially when crystalline cellulose and complex biomass are used as substrates. Findings specifically underline the benefits and specific properties of swollenin. Although in our study swollenin clearly promoted cellulase action, its use requires process redesign to accommodate its specific mode of action.
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Affiliation(s)
- Zhong-peng Guo
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- LISBP-Biocatalysis Group, INSA/INRA UMR 792, 135, Avenue de Rangueil, 31077 Toulouse, France
| | - Sophie Duquesne
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Sophie Bozonnet
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Alain Marty
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- LISBP-Biocatalysis Group, INSA/INRA UMR 792, 135, Avenue de Rangueil, 31077 Toulouse, France
| | - Michael Joseph O’Donohue
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- LISBP-Biocatalysis Group, INSA/INRA UMR 792, 135, Avenue de Rangueil, 31077 Toulouse, France
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Min BE, Hwang HG, Lim HG, Jung GY. Optimization of industrial microorganisms: recent advances in synthetic dynamic regulators. ACTA ACUST UNITED AC 2017; 44:89-98. [DOI: 10.1007/s10295-016-1867-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/04/2016] [Indexed: 12/27/2022]
Abstract
Abstract
Production of biochemicals by industrial fermentation using microorganisms requires maintaining cellular production capacity, because maximal productivity is economically important. High-productivity microbial strains can be developed using static engineering, but these may not maintain maximal productivity throughout the culture period as culture conditions and cell states change dynamically. Additionally, economic reasons limit heterologous protein expression using inducible promoters to prevent metabolic burden for commodity chemical and biofuel production. Recently, synthetic and systems biology has been used to design genetic circuits, precisely controlling gene expression or influencing genetic behavior toward a desired phenotype. Development of dynamic regulators can maintain cellular phenotype in a maximum production state in response to factors including cell concentration, oxygen, temperature, pH, and metabolites. Herein, we introduce dynamic regulators of industrial microorganism optimization and discuss metabolic flux fine control by dynamic regulators in response to metabolites or extracellular stimuli, robust production systems, and auto-induction systems using quorum sensing.
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Affiliation(s)
- Byung Eun Min
- grid.49100.3c 0000000107424007 Department of Chemical Engineering Pohang University of Science and Technology 77 Cheongam-ro, Nam-gu 37673 Pohang Gyeongbuk Korea
| | - Hyun Gyu Hwang
- grid.49100.3c 0000000107424007 School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology 77 Cheongam-ro, Nam-gu 37673 Pohang Gyeongbuk Korea
| | - Hyun Gyu Lim
- grid.49100.3c 0000000107424007 Department of Chemical Engineering Pohang University of Science and Technology 77 Cheongam-ro, Nam-gu 37673 Pohang Gyeongbuk Korea
| | - Gyoo Yeol Jung
- grid.49100.3c 0000000107424007 Department of Chemical Engineering Pohang University of Science and Technology 77 Cheongam-ro, Nam-gu 37673 Pohang Gyeongbuk Korea
- grid.49100.3c 0000000107424007 School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology 77 Cheongam-ro, Nam-gu 37673 Pohang Gyeongbuk Korea
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Dazzi A, Prater CB. AFM-IR: Technology and Applications in Nanoscale Infrared Spectroscopy and Chemical Imaging. Chem Rev 2016; 117:5146-5173. [DOI: 10.1021/acs.chemrev.6b00448] [Citation(s) in RCA: 532] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Alexandre Dazzi
- Laboratoire
de Chimie Physique, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Craig B. Prater
- Anasys Instruments, 325 Chapala
St., Santa Barbara, California 93101, United States
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55
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Yishai O, Lindner SN, Gonzalez de la Cruz J, Tenenboim H, Bar-Even A. The formate bio-economy. Curr Opin Chem Biol 2016; 35:1-9. [DOI: 10.1016/j.cbpa.2016.07.005] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/28/2016] [Accepted: 07/05/2016] [Indexed: 10/21/2022]
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56
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Liang M, Zhou X, Xu C. Systems biology in biofuel. PHYSICAL SCIENCES REVIEWS 2016. [DOI: 10.1515/psr-2016-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Identification of gene knockdown targets conferring enhanced isobutanol and 1-butanol tolerance to Saccharomyces cerevisiae using a tunable RNAi screening approach. Appl Microbiol Biotechnol 2016; 100:10005-10018. [DOI: 10.1007/s00253-016-7791-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/25/2016] [Accepted: 08/03/2016] [Indexed: 10/21/2022]
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The acquisition of Clostridium tyrobutyricum mutants with improved bioproduction under acidic conditions after two rounds of heavy-ion beam irradiation. Sci Rep 2016; 6:29968. [PMID: 27426447 PMCID: PMC4947956 DOI: 10.1038/srep29968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/28/2016] [Indexed: 11/17/2022] Open
Abstract
End-product inhibition is a key factor limiting the production of organic acid during
fermentation. Two rounds of heavy-ion beam irradiation may be an inexpensive,
indispensable and reliable approach to increase the production of butyric acid
during industrial fermentation processes. However, studies of the application of
heavy ion radiation for butyric acid fermentation engineering are lacking. In this
study, a second 12C6+ heavy-ion irradiation-response
curve is used to describe the effect of exposure to a given dose of heavy ions on
mutant strains of Clostridium tyrobutyricum. Versatile statistical elements
are introduced to characterize the mechanism and factors contributing to improved
butyric acid production and enhanced acid tolerance in adapted mutant strains
harvested from the fermentations. We characterized the physiological properties of
the strains over a large pH value gradient, which revealed that the mutant strains
obtained after a second round of radiation exposure were most resistant to harsh
external pH values and were better able to tolerate external pH values between 4.5
and 5.0. A customized second round of heavy-ion beam irradiation may be invaluable
in process engineering.
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59
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Koppolu V, Vasigala VK. Role of Escherichia coli in Biofuel Production. Microbiol Insights 2016; 9:29-35. [PMID: 27441002 PMCID: PMC4946582 DOI: 10.4137/mbi.s10878] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/26/2016] [Accepted: 06/28/2016] [Indexed: 12/19/2022] Open
Abstract
Increased energy consumption coupled with depleting petroleum reserves and increased greenhouse gas emissions have renewed our interest in generating fuels from renewable energy sources via microbial fermentation. Central to this problem is the choice of microorganism that catalyzes the production of fuels at high volumetric productivity and yield from cheap and abundantly available renewable energy sources. Microorganisms that are metabolically engineered to redirect renewable carbon sources into desired fuel products are contemplated as best choices to obtain high volumetric productivity and yield. Considering the availability of vast knowledge in genomic and metabolic fronts, Escherichia coli is regarded as a primary choice for the production of biofuels. Here, we reviewed the microbial production of liquid biofuels that have the potential to be used either alone or in combination with the present-day fuels. We specifically highlighted the metabolic engineering and synthetic biology approaches used to improve the production of biofuels from E. coli over the past few years. We also discussed the challenges that still exist for the biofuel production from E. coli and their possible solutions.
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Affiliation(s)
- Veerendra Koppolu
- Scientist, Department of Analytical Biotechnology, MedImmune/AstraZeneca, Gaithersburg, MD, USA.; Former affiliation: Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Veneela Kr Vasigala
- Rangaraya Medical College, NTR University of Health Sciences, Kakinada, AP, India
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Ledesma-Amaro R, Dulermo R, Niehus X, Nicaud JM. Combining metabolic engineering and process optimization to improve production and secretion of fatty acids. Metab Eng 2016; 38:38-46. [PMID: 27301328 DOI: 10.1016/j.ymben.2016.06.004] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/10/2016] [Accepted: 06/10/2016] [Indexed: 12/16/2022]
Abstract
Microbial oils are sustainable alternatives to petroleum for the production of chemicals and fuels. Oleaginous yeasts are promising source of oils and Yarrowia lipolytica is the most studied and engineered one. Nonetheless the commercial production of biolipids is so far limited to high value products due to the elevated production and extraction costs. In order to contribute to overcoming these limitations we exploited the possibility of secreting lipids to the culture broth, uncoupling production and biomass formation and facilitating the extraction. We therefore considered two synthetic approaches, Strategy I where fatty acids are produced by enhancing the flux through neutral lipid formation, as typically occurs in eukaryotic systems and Strategy II where the bacterial system to produce free fatty acids is mimicked. The engineered strains, in a coupled fermentation and extraction process using alkanes, secreted the highest titer of lipids described so far, with a content of 120% of DCW.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Remi Dulermo
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Xochitl Niehus
- Industrial Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), A.C. 44270 Guadalajara, Jalisco, Mexico
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
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Pade N, Erdmann S, Enke H, Dethloff F, Dühring U, Georg J, Wambutt J, Kopka J, Hess WR, Zimmermann R, Kramer D, Hagemann M. Insights into isoprene production using the cyanobacterium Synechocystis sp. PCC 6803. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:89. [PMID: 27096007 PMCID: PMC4836186 DOI: 10.1186/s13068-016-0503-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/01/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cyanobacteria are phototrophic prokaryotes that convert inorganic carbon as CO2 into organic compounds at the expense of light energy. They need only inorganic nutrients and can be cultivated to high densities using non-arable land and seawater. This has made cyanobacteria attractive organisms for the production of biofuels and chemical feedstock. Synechocystis sp. PCC 6803 is one of the most widely used cyanobacterial model strains. Based on its available genome sequence and genetic tools, Synechocystis has been genetically modified to produce different biotechnological products. Efficient isoprene production is an attractive goal because this compound is widely used as chemical feedstock. RESULTS Here, we report on our attempts to generate isoprene-producing strains of Synechocystis using a plasmid-based strategy. As previously reported, a codon-optimized plant isoprene synthase (IspS) was expressed under the control of different Synechocystis promoters that ensure strong constitutive or light-regulated ispS expression. The expression of the ispS gene was quantified by qPCR and Western blotting, while the amount of isoprene was quantified using GC-MS. In addition to isoprene measurements in the headspace of closed culture vessels, single photon ionization time-of-flight mass spectrometry (SPI-MS) was applied, which allowed online measurements of isoprene production in open-cultivation systems under various conditions. Under standard conditions, a good correlation existed between ispS expression and isoprene production rate. The cultivation of isoprene production strains under NaCl-supplemented conditions decreased isoprene production despite enhanced ispS mRNA levels. The characterization of the metabolome of isoprene-producing strains indicated that isoprene production might be limited by insufficient precursor levels. Transcriptomic analysis revealed the upregulation of mRNA and regulatory RNAs characteristic of acclimation to metabolic stress. CONCLUSIONS Our best production strains produced twofold higher isoprene amounts in the presence of low NaCl concentrations than previously reported strains. These results will guide future attempts to establish isoprene production in cyanobacterial hosts.
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Affiliation(s)
- Nadin Pade
- />Plant Physiology Department, Institute of Biological Science, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Sabrina Erdmann
- />Analytic Chemistry Department, University of Rostock, Dr.-Lorenz-Weg 1, 18059 Rostock, Germany
| | - Heike Enke
- />Algenol Biofuels Germany GmbH, Magnusstr. 11, 12489 Berlin, Germany
| | - Frederik Dethloff
- />Department of Molecular Physiology, Applied Metabolome Analysis, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ulf Dühring
- />Algenol Biofuels Germany GmbH, Magnusstr. 11, 12489 Berlin, Germany
| | - Jens Georg
- />Genetics & Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Juliane Wambutt
- />Algenol Biofuels Germany GmbH, Magnusstr. 11, 12489 Berlin, Germany
| | - Joachim Kopka
- />Department of Molecular Physiology, Applied Metabolome Analysis, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Wolfgang R. Hess
- />Genetics & Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Ralf Zimmermann
- />Analytic Chemistry Department, University of Rostock, Dr.-Lorenz-Weg 1, 18059 Rostock, Germany
| | - Dan Kramer
- />Algenol Biofuels Germany GmbH, Magnusstr. 11, 12489 Berlin, Germany
| | - Martin Hagemann
- />Plant Physiology Department, Institute of Biological Science, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
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Kunjapur AM, Hyun JC, Prather KLJ. Deregulation of S-adenosylmethionine biosynthesis and regeneration improves methylation in the E. coli de novo vanillin biosynthesis pathway. Microb Cell Fact 2016; 15:61. [PMID: 27067813 PMCID: PMC4828866 DOI: 10.1186/s12934-016-0459-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/28/2016] [Indexed: 12/31/2022] Open
Abstract
Background Vanillin is an industrially valuable molecule that can be produced from simple carbon sources in engineered microorganisms such as Saccharomyces cerevisiae and Escherichia coli. In E. coli, de novo production of vanillin was demonstrated previously as a proof of concept. In this study, a series of data-driven experiments were performed in order to better understand limitations associated with biosynthesis of vanillate, which is the immediate precursor to vanillin. Results Time-course experiments monitoring production of heterologous metabolites in the E. coli de novo vanillin pathway revealed a bottleneck in conversion of protocatechuate to vanillate. Perturbations in central metabolism intended to increase flux into the heterologous pathway increased average vanillate titers from 132 to 205 mg/L, but protocatechuate remained the dominant heterologous product on a molar basis. SDS-PAGE, in vitro activity measurements, and l-methionine supplementation experiments suggested that the decline in conversion rate was influenced more by limited availability of the co-substrate S-adenosyl-l-methionine (AdoMet or SAM) than by loss of activity of the heterologous O-methyltransferase. The combination of metJ deletion and overexpression of feedback-resistant variants of metA and cysE, which encode enzymes involved in SAM biosynthesis, increased average de novo vanillate titers by an additional 33 % (from 205 to 272 mg/L). An orthogonal strategy intended to improve SAM regeneration through overexpression of native mtn and luxS genes resulted in a 25 % increase in average de novo vanillate titers (from 205 to 256 mg/L). Vanillate production improved further upon supplementation with methionine (as high as 419 ± 58 mg/L), suggesting potential for additional enhancement by increasing SAM availability. Conclusions Results from this study demonstrate context dependency of engineered pathways and highlight the limited methylation capacity of E. coli. Unlike in previous efforts to improve SAM or methionine biosynthesis, we pursued two orthogonal strategies that are each aimed at deregulating multiple reactions. Our results increase the working knowledge of SAM biosynthesis engineering and provide a framework for improving titers of metabolic products dependent upon methylation reactions. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0459-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aditya M Kunjapur
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room E17-504G, Cambridge, MA, 02139, USA.,Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jason C Hyun
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room E17-504G, Cambridge, MA, 02139, USA.,Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room E17-504G, Cambridge, MA, 02139, USA. .,Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Liao P, Hemmerlin A, Bach TJ, Chye ML. The potential of the mevalonate pathway for enhanced isoprenoid production. Biotechnol Adv 2016; 34:697-713. [PMID: 26995109 DOI: 10.1016/j.biotechadv.2016.03.005] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 03/12/2016] [Accepted: 03/14/2016] [Indexed: 01/03/2023]
Abstract
The cytosol-localised mevalonic acid (MVA) pathway delivers the basic isoprene unit isopentenyl diphosphate (IPP). In higher plants, this central metabolic intermediate is also synthesised by the plastid-localised methylerythritol phosphate (MEP) pathway. Both MVA and MEP pathways conspire through exchange of intermediates and regulatory interactions. Products downstream of IPP such as phytosterols, carotenoids, vitamin E, artemisinin, tanshinone and paclitaxel demonstrate antioxidant, cholesterol-reducing, anti-ageing, anticancer, antimalarial, anti-inflammatory and antibacterial activities. Other isoprenoid precursors including isoprene, isoprenol, geraniol, farnesene and farnesol are economically valuable. An update on the MVA pathway and its interaction with the MEP pathway is presented, including the improvement in the production of phytosterols and other isoprenoid derivatives. Such attempts are for instance based on the bioengineering of microbes such as Escherichia coli and Saccharomyces cerevisiae, as well as plants. The function of relevant genes in the MVA pathway that can be utilised in metabolic engineering is reviewed and future perspectives are presented.
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Affiliation(s)
- Pan Liao
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Andréa Hemmerlin
- Centre National de la Recherche Scientifique, UPR 2357, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67083 Strasbourg, France.
| | - Thomas J Bach
- Centre National de la Recherche Scientifique, UPR 2357, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67083 Strasbourg, France.
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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Yoneda A, Henson WR, Goldner NK, Park KJ, Forsberg KJ, Kim SJ, Pesesky MW, Foston M, Dantas G, Moon TS. Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630. Nucleic Acids Res 2016; 44:2240-54. [PMID: 26837573 PMCID: PMC4797299 DOI: 10.1093/nar/gkw055] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/20/2016] [Indexed: 12/29/2022] Open
Abstract
Lignin-derived (e.g. phenolic) compounds can compromise the bioconversion of lignocellulosic biomass to fuels and chemicals due to their toxicity and recalcitrance. The lipid-accumulating bacterium Rhodococcus opacus PD630 has recently emerged as a promising microbial host for lignocellulose conversion to value-added products due to its natural ability to tolerate and utilize phenolics. To gain a better understanding of its phenolic tolerance and utilization mechanisms, we adaptively evolved R. opacus over 40 passages using phenol as its sole carbon source (up to 373% growth improvement over wild-type), and extensively characterized two strains from passages 33 and 40. The two adapted strains showed higher phenol consumption rates (∼20 mg/l/h) and ∼2-fold higher lipid production from phenol than the wild-type strain. Whole-genome sequencing and comparative transcriptomics identified highly-upregulated degradation pathways and putative transporters for phenol in both adapted strains, highlighting the important linkage between mechanisms of regulated phenol uptake, utilization, and evolved tolerance. Our study shows that the R. opacus mutants are likely to use their transporters to import phenol rather than export them, suggesting a new aromatic tolerance mechanism. The identified tolerance genes and pathways are promising candidates for future metabolic engineering in R. opacus for improved lignin conversion to lipid-based products.
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Affiliation(s)
- Aki Yoneda
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - William R Henson
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicholas K Goldner
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Kun Joo Park
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kevin J Forsberg
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Soo Ji Kim
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Mitchell W Pesesky
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Marcus Foston
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Gautam Dantas
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Tae Seok Moon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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65
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Waghmare AG, Arya SS. Utilization of unripe banana peel waste as feedstock for ethanol production. ACTA ACUST UNITED AC 2016. [DOI: 10.1515/bioeth-2016-0011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractBanana is second largest produced fruit of total world’s fruits. Cooking banana or plantains processing industry is generating enormous amount of waste in the form of unripe banana peel at one place, thus important to study waste management and utilization. Therefore, unripe banana peel was investigated for ethanol production. This study involved chemical characterization, optimization of acid hydrolysis, selection of yeast strain and optimization of fermentative production of ethanol from dried unripe banana peel powder (DUBPP). Ethanol concentration was determined using gas chromatography flame ionization detector (GC-FID). Characterization of DUBPP revealed notably amount of starch (41% w/w), cellulose (9.3% w/w) and protein (8.4% w/w). 49.2% w/w of reducing sugar was produced by acid hydrolysis of DUBPP at optimized conditions. Three yeast strains of Saccharomyces cerevisiae were screened for ethanol conversion efficiency, osmotolerance, ethanol tolerance, thermotolerance, fermentation ability at high temperature and sedimentation rate. Further, fermentation conditions were optimized for maximum ethanol production from acid hydrolysate of DUBPP. At optimized fermentation conditions, 35.5 g/l ethanol was produced using selected strain of Saccharomyces cerevisiae NCIM 3095. Hence, unripe banana peel waste can be good feedstock for ethanol production.
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66
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Yao P, Xiao Z, Chen C, Li W, Deng Q. Cell growth behaviors ofClostridium acetobutylicumin a pervaporation membrane bioreactor for butanol fermentation. Biotechnol Appl Biochem 2016; 63:101-5. [DOI: 10.1002/bab.1318] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 11/01/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Peina Yao
- Department of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Zeyi Xiao
- Department of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Chunyan Chen
- Department of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
- College of Chemistry and Chemical Engineering; Southwest Petroleum University; Chengdu People's Republic of China
| | - Weijia Li
- Department of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Qing Deng
- Department of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
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Turk SCHJ, Kloosterman WP, Ninaber DK, Kolen KPAM, Knutova J, Suir E, Schürmann M, Raemakers-Franken PC, Müller M, de Wildeman SMA, Raamsdonk LM, van der Pol R, Wu L, Temudo MF, van der Hoeven RAM, Akeroyd M, van der Stoel RE, Noorman HJ, Bovenberg RAL, Trefzer AC. Metabolic Engineering toward Sustainable Production of Nylon-6. ACS Synth Biol 2016; 5:65-73. [PMID: 26511532 DOI: 10.1021/acssynbio.5b00129] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nylon-6 is a bulk polymer used for many applications. It consists of the non-natural building block 6-aminocaproic acid, the linear form of caprolactam. Via a retro-synthetic approach, two synthetic pathways were identified for the fermentative production of 6-aminocaproic acid. Both pathways require yet unreported novel biocatalytic steps. We demonstrated proof of these bioconversions by in vitro enzyme assays with a set of selected candidate proteins expressed in Escherichia coli. One of the biosynthetic pathways starts with 2-oxoglutarate and contains bioconversions of the ketoacid elongation pathway known from methanogenic archaea. This pathway was selected for implementation in E. coli and yielded 6-aminocaproic acid at levels up to 160 mg/L in lab-scale batch fermentations. The total amount of 6-aminocaproic acid and related intermediates generated by this pathway exceeded 2 g/L in lab-scale fed-batch fermentations, indicating its potential for further optimization toward large-scale sustainable production of nylon-6.
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Affiliation(s)
| | - Wigard P. Kloosterman
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
- University Medical Center Utrecht, PO Box 85060, 3508 AB Utrecht, The Netherlands
| | - Dennis K. Ninaber
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
- Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | | | - Julia Knutova
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
| | - Erwin Suir
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
- BioscienZ, Goeseelsstraat 10, 4817 MV Breda, The Netherlands
| | - Martin Schürmann
- DSM Innovative Synthesis, PO Box 18, 6160 MD Geleen, The Netherlands
| | | | - Monika Müller
- DSM Innovative Synthesis, PO Box 18, 6160 MD Geleen, The Netherlands
| | | | | | - Ruud van der Pol
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
| | - Liang Wu
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
| | | | | | - Michiel Akeroyd
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
| | | | - Henk J. Noorman
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
| | - Roel A. L. Bovenberg
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
- Synthetic
Biology and Cell Engineering, Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Axel C. Trefzer
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
- Life Technologies, GeneArt, Im Gewerbepark B35, 93059 Regensburg, Germany
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68
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Friedlander J, Tsakraklides V, Kamineni A, Greenhagen EH, Consiglio AL, MacEwen K, Crabtree DV, Afshar J, Nugent RL, Hamilton MA, Joe Shaw A, South CR, Stephanopoulos G, Brevnova EE. Engineering of a high lipid producing Yarrowia lipolytica strain. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:77. [PMID: 27034715 PMCID: PMC4815080 DOI: 10.1186/s13068-016-0492-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/21/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Microbial lipids are produced by many oleaginous organisms including the well-characterized yeast Yarrowia lipolytica, which can be engineered for increased lipid yield by up-regulation of the lipid biosynthetic pathway and down-regulation or deletion of competing pathways. RESULTS We describe a strain engineering strategy centered on diacylglycerol acyltransferase (DGA) gene overexpression that applied combinatorial screening of overexpression and deletion genetic targets to construct a high lipid producing yeast biocatalyst. The resulting strain, NS432, combines overexpression of a heterologous DGA1 enzyme from Rhodosporidium toruloides, a heterlogous DGA2 enzyme from Claviceps purpurea, and deletion of the native TGL3 lipase regulator. These three genetic modifications, selected for their effect on lipid production, enabled a 77 % lipid content and 0.21 g lipid per g glucose yield in batch fermentation. In fed-batch glucose fermentation NS432 produced 85 g/L lipid at a productivity of 0.73 g/L/h. CONCLUSIONS The yields, productivities, and titers reported in this study may further support the applied goal of cost-effective, large -scale microbial lipid production for use as biofuels and biochemicals.
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Affiliation(s)
| | | | | | | | | | - Kyle MacEwen
- />Novogy, Inc., 85 Bolton Street, Cambridge, MA 02140 USA
| | | | | | - Rebecca L. Nugent
- />Total New Energies, 5858 Horton Street, Emeryville, CA 94610 USA
- />Twist Bioscience, 455 Mission Bay Blvd South, San Francisco, CA 94158 USA
| | | | - A. Joe Shaw
- />Novogy, Inc., 85 Bolton Street, Cambridge, MA 02140 USA
| | - Colin R. South
- />Novogy, Inc., 85 Bolton Street, Cambridge, MA 02140 USA
| | - Gregory Stephanopoulos
- />Novogy, Inc., 85 Bolton Street, Cambridge, MA 02140 USA
- />Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139 USA
| | - Elena E. Brevnova
- />Total New Energies, 5858 Horton Street, Emeryville, CA 94610 USA
- />Evelo Therapeutics, 620 Memorial Dr., Cambridge, MA 02139 USA
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69
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Kuroda K, Ueda M. Cellular and molecular engineering of yeastSaccharomyces cerevisiaefor advanced biobutanol production. FEMS Microbiol Lett 2015; 363:fnv247. [DOI: 10.1093/femsle/fnv247] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2015] [Indexed: 11/12/2022] Open
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70
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Gallardo R, Acevedo A, Quintero J, Paredes I, Conejeros R, Aroca G. In silico analysis of Clostridium acetobutylicum ATCC 824 metabolic response to an external electron supply. Bioprocess Biosyst Eng 2015; 39:295-305. [PMID: 26650720 DOI: 10.1007/s00449-015-1513-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/21/2015] [Indexed: 11/26/2022]
Abstract
The biological production of butanol has become an important research field and thanks to genome sequencing and annotation; genome-scale metabolic reconstructions have been developed for several Clostridium species. This work makes use of the iCAC490 model of Clostridium acetobutylicum ATCC 824 to analyze its metabolic capabilities and response to an external electron supply through a constraint-based approach using the Constraint-Based Reconstruction Analysis Toolbox. Several analyses were conducted, which included sensitivity, production envelope, and phenotypic phase planes. The model showed that the use of an external electron supply, which acts as co-reducing agent along with glucose-derived reducing power (electrofermentation), results in an increase in the butanol-specific productivity. However, a proportional increase in the butyrate uptake flux is required. Besides, the uptake of external butyrate leads to the coupling of butanol production and growth, which coincides with results reported in literature. Phenotypic phase planes showed that the reducing capacity becomes more limiting for growth at high butyrate uptake fluxes. An electron uptake flux allows the metabolism to reach the growth optimality line. Although the maximum butanol flux does not coincide with the growth optimality line, a butyrate uptake combined with an electron uptake flux would result in an increased butanol volumetric productivity, being a potential strategy to optimize the production of butanol by C. acetobutylicum ATCC 824.
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Affiliation(s)
- Roberto Gallardo
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil, 2085, Valparaíso, Chile
| | - Alejandro Acevedo
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil, 2085, Valparaíso, Chile
| | - Julián Quintero
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil, 2085, Valparaíso, Chile
| | - Ivan Paredes
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil, 2085, Valparaíso, Chile
| | - Raúl Conejeros
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil, 2085, Valparaíso, Chile
| | - Germán Aroca
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil, 2085, Valparaíso, Chile.
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71
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Grimaldi J, Collins CH, Belfort G. Towards cell-free isobutanol production: Development of a novel immobilized enzyme system. Biotechnol Prog 2015; 32:66-73. [DOI: 10.1002/btpr.2197] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/07/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Joseph Grimaldi
- Dept. of Chemical and Biological Engineering; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute; Troy NY 12180-3590
| | - Cynthia H. Collins
- Dept. of Chemical and Biological Engineering; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute; Troy NY 12180-3590
| | - Georges Belfort
- Dept. of Chemical and Biological Engineering; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute; Troy NY 12180-3590
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Dynamic interplay of multidrug transporters with TolC for isoprenol tolerance in Escherichia coli. Sci Rep 2015; 5:16505. [PMID: 26563610 PMCID: PMC4643228 DOI: 10.1038/srep16505] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/15/2015] [Indexed: 02/04/2023] Open
Abstract
Engineering of efflux pumps is a promising way to improve host’s tolerance to biofuels such as medium-chain alcohols (CmOHs); however, this strategy is restricted by poor understanding of the efflux pumps engaged in extrusion of solvents. In this study, several Escherichia coli mutants of multidrug transporters were evaluated for isoprenol tolerance. Susceptible phenotypes were observed in the mutants with individual deletion of six transporters, AcrD, EmrAB, MacAB, MdtBC, MdtJI and YdiM, whereas inactivation of AcrAB transporter resulted in an improved tolerance to isoprenol and other CmOHs. AcrAB is the major transporter forming tripartite transperiplasmic complex with outer membrane channel TolC for direct extrusion of toxic molecules in E. coli. The AcrAB inactivation enables to enhance TolC availability for the multidrug transporters associated with extrusion of CmOHs and increase the tolerance to CmOHs including isoprenol. It is assumed that outer membrane channel TolC plays an important role in extrusion of isoprenol and other CmOHs.
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73
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Luo H, Ge L, Zhang J, Zhao Y, Ding J, Li Z, He Z, Chen R, Shi Z. Enhancing Butanol Production under the Stress Environments of Co-Culturing Clostridium acetobutylicum/Saccharomyces cerevisiae Integrated with Exogenous Butyrate Addition. PLoS One 2015; 10:e0141160. [PMID: 26489085 PMCID: PMC4619017 DOI: 10.1371/journal.pone.0141160] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/03/2015] [Indexed: 12/28/2022] Open
Abstract
In this study, an efficient acetone-butanol-ethanol (ABE) fermentation strategy integrating Clostridium acetobutylicum/Saccharomyces cerevisiae co-culturing system with exogenous butyrate addition, was proposed and experimentally conducted. In solventogenic phase, by adding 0.2 g-DCW/L-broth viable S. cerevisiae cells and 4.0 g/L-broth concentrated butyrate solution into C. acetobutylicum culture broth, final butanol concentration and butanol/acetone ratio in a 7 L anaerobic fermentor reached the highest levels of 15.74 g/L and 2.83 respectively, with the increments of 35% and 43% as compared with those of control. Theoretical and experimental analysis revealed that, the proposed strategy could, 1) extensively induce secretion of amino acids particularly lysine, which are favorable for both C. acetobutylicum survival and butanol synthesis under high butanol concentration environment; 2) enhance the utilization ability of C. acetobutylicum on glucose and over-produce intracellular NADH for butanol synthesis in C. acetobutylicum metabolism simultaneously; 3) direct most of extra consumed glucose into butanol synthesis route. The synergetic actions of effective amino acids assimilation, high rates of substrate consumption and NADH regeneration yielded highest butanol concentration and butanol ratio in C. acetobutylicum under this stress environment. The proposed method supplies an alternative way to improve ABE fermentation performance by traditional fermentation technology.
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Affiliation(s)
- Hongzhen Luo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Laibing Ge
- China Shijiazhuang Pharmaceutical Group Co., Ltd., Shijiazhuang, Hebei, China
| | - Jingshu Zhang
- China Shijiazhuang Pharmaceutical Group Co., Ltd., Shijiazhuang, Hebei, China
| | - Yanli Zhao
- Hebei Changshan Biochemical Pharmaceutical Co., Ltd., Shijiazhuang, Hebei, China
| | - Jian Ding
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhigang Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhenni He
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Rui Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhongping Shi
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- * E-mail:
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74
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Tomko TA, Dunlop MJ. Engineering improved bio-jet fuel tolerance in Escherichia coli using a transgenic library from the hydrocarbon-degrader Marinobacter aquaeolei. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:165. [PMID: 26448785 PMCID: PMC4596283 DOI: 10.1186/s13068-015-0347-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/22/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Recent metabolic engineering efforts have generated microorganisms that can produce biofuels, including bio-jet fuels, however these fuels are often toxic to cells, limiting production yields. There are natural examples of microorganisms that have evolved mechanisms for tolerating hydrocarbon-rich environments, such as those that thrive near natural oil seeps and in oil-polluted waters. RESULTS Using genomic DNA from the hydrocarbon-degrading microbe Marinobacter aquaeolei, we constructed a transgenic library that we expressed in Escherichia coli. We exposed cells to inhibitory levels of pinene, a monoterpene that can serve as a jet fuel precursor with chemical properties similar to existing tactical fuels. Using a sequential strategy with a fosmid library followed by a plasmid library, we were able to isolate a region of DNA from the M. aquaeolei genome that conferred pinene tolerance when expressed in E. coli. We determined that a single gene, yceI, was responsible for the tolerance improvements. Overexpression of this gene placed no additional burden on the host. We also tested tolerance to other monoterpenes and showed that yceI selectively improves tolerance. CONCLUSIONS The genomes of hydrocarbon-tolerant microbes represent a rich resource for tolerance engineering. Using a transgenic library, we were able to identify a single gene that improves E. coli's tolerance to the bio-jet fuel precursor pinene.
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Affiliation(s)
- Timothy A. Tomko
- School of Engineering, University of Vermont, 33 Colchester Ave, Burlington, VT 05405 USA
| | - Mary J. Dunlop
- School of Engineering, University of Vermont, 33 Colchester Ave, Burlington, VT 05405 USA
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75
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Teoh ST, Putri S, Mukai Y, Bamba T, Fukusaki E. A metabolomics-based strategy for identification of gene targets for phenotype improvement and its application to 1-butanol tolerance in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:144. [PMID: 26379776 PMCID: PMC4570087 DOI: 10.1186/s13068-015-0330-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/28/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUND Traditional approaches to phenotype improvement include rational selection of genes for modification, and probability-driven processes such as laboratory evolution or random mutagenesis. A promising middle-ground approach is semi-rational engineering, where genetic modification targets are inferred from system-wide comparison of strains. Here, we have applied a metabolomics-based, semi-rational strategy of phenotype improvement to 1-butanol tolerance in Saccharomyces cerevisiae. RESULTS Nineteen yeast single-deletion mutant strains with varying growth rates under 1-butanol stress were subjected to non-targeted metabolome analysis by GC/MS, and a regression model was constructed using metabolite peak intensities as predictors and stress growth rates as the response. From this model, metabolites positively and negatively correlated with growth rate were identified including threonine and citric acid. Based on the assumption that these metabolites were linked to 1-butanol tolerance, new deletion strains accumulating higher threonine or lower citric acid were selected and subjected to tolerance measurement and metabolome analysis. The new strains exhibiting the predicted changes in metabolite levels also displayed significantly higher growth rate under stress over the control strain, thus validating the link between these metabolites and 1-butanol tolerance. CONCLUSIONS A strategy for semi-rational phenotype improvement using metabolomics was proposed and applied to the 1-butanol tolerance of S. cerevisiae. Metabolites correlated with growth rate under 1-butanol stress were identified, and new mutant strains showing higher growth rate under stress could be selected based on these metabolites. The results demonstrate the potential of metabolomics in semi-rational strain engineering.
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Affiliation(s)
- Shao Thing Teoh
- />Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Sastia Putri
- />Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Yukio Mukai
- />Department of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829 Japan
| | - Takeshi Bamba
- />Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Eiichiro Fukusaki
- />Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
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Liu DE, Cerretani C, Tellez R, Scheer AP, Sciamanna S, Bryan PF, Radke CJ, Prausnitz JM. Analysis of countercurrent membrane vapor extraction of a dilute aqueous biosolute. AIChE J 2015. [DOI: 10.1002/aic.14892] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- David E. Liu
- Dept. of Chemical and Biomolecular Engineering; University of California; Berkeley CA 94720
| | - Colin Cerretani
- Dept. of Chemical and Biomolecular Engineering; University of California; Berkeley CA 94720
| | - Rodrigo Tellez
- Dept. of Chemical and Biomolecular Engineering; University of California; Berkeley CA 94720
| | - Agnes P. Scheer
- Dept. of Chemical and Biomolecular Engineering; University of California; Berkeley CA 94720
| | - Steve Sciamanna
- Dept. of Chemical and Biomolecular Engineering; University of California; Berkeley CA 94720
| | - Paul F. Bryan
- Dept. of Chemical and Biomolecular Engineering; University of California; Berkeley CA 94720
| | - Clayton J. Radke
- Dept. of Chemical and Biomolecular Engineering; University of California; Berkeley CA 94720
| | - John M. Prausnitz
- Dept. of Chemical and Biomolecular Engineering; University of California; Berkeley CA 94720
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77
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Papoutsakis ET. Reassessing the Progress in the Production of Advanced Biofuels in the Current Competitive Environment and Beyond: What Are the Successes and Where Progress Eludes Us and Why. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01695] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Eleftherios T. Papoutsakis
- Molecular Biotechnology Laboratory, Department of Chemical & Biomolecular Engineering, Department of Biological Sciences & the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, United States
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78
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Meyer A, Pellaux R, Potot S, Becker K, Hohmann HP, Panke S, Held M. Optimization of a whole-cell biocatalyst by employing genetically encoded product sensors inside nanolitre reactors. Nat Chem 2015. [PMID: 26201745 DOI: 10.1038/nchem.2301] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Microcompartmentalization offers a high-throughput method for screening large numbers of biocatalysts generated from genetic libraries. Here we present a microcompartmentalization protocol for benchmarking the performance of whole-cell biocatalysts. Gel capsules served as nanolitre reactors (nLRs) for the cultivation and analysis of a library of Bacillus subtilis biocatalysts. The B. subtilis cells, which were co-confined with E. coli sensor cells inside the nLRs, converted the starting material cellobiose into the industrial product vitamin B2. Product formation triggered a sequence of reactions in the sensor cells: (1) conversion of B2 into flavin mononucleotide (FMN), (2) binding of FMN by a RNA riboswitch and (3) self-cleavage of RNA, which resulted in (4) the synthesis of a green fluorescent protein (GFP). The intensity of GFP fluorescence was then used to isolate B. subtilis variants that convert cellobiose into vitamin B2 with elevated efficiency. The underlying design principles of the assay are general and enable the development of similar protocols, which ultimately will speed up the optimization of whole-cell biocatalysts.
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Affiliation(s)
- Andreas Meyer
- 1] Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland [2] FGen GmbH, Basel 4057, Switzerland
| | - René Pellaux
- 1] Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland [2] FGen GmbH, Basel 4057, Switzerland
| | | | - Katja Becker
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | | | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Martin Held
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
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Tanaka T, Kondo A. Cell surface engineering of industrial microorganisms for biorefining applications. Biotechnol Adv 2015; 33:1403-11. [PMID: 26070720 DOI: 10.1016/j.biotechadv.2015.06.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 06/04/2015] [Accepted: 06/06/2015] [Indexed: 11/19/2022]
Abstract
In order to decrease carbon emissions and negative environmental impacts of various pollutants, biofuel/biochemical production should be promoted for replacing fossil-based industrial processes. Utilization of abundant lignocellulosic biomass as a feedstock has recently become an attractive option. In this review, we focus on recent efforts of cell surface display using industrial microorganisms such as Escherichia coli and yeast. Cell surface display is used primarily for endowing cellulolytic activity on the host cells, and enables direct fermentation to generate useful fuels and chemicals from lignocellulosic biomass. Cell surface display systems are systematically summarized, and the drawbacks/perspectives as well as successful application of surface display for industrial biotechnology are discussed.
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Affiliation(s)
- Tsutomu Tanaka
- Department of Chemical Science and Technology, Graduate School of Engineering, Kobe University, 1-1, Rokkodaicho, Nada, Kobe 657-8501 Japan
| | - Akihiko Kondo
- Department of Chemical Science and Technology, Graduate School of Engineering, Kobe University, 1-1, Rokkodaicho, Nada, Kobe 657-8501 Japan.
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80
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Metabolic engineering of Saccharomyces cerevisiae for production of butanol isomers. Curr Opin Biotechnol 2015; 33:1-7. [DOI: 10.1016/j.copbio.2014.09.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/09/2014] [Accepted: 09/17/2014] [Indexed: 11/22/2022]
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Vinayavekhin N, Mahipant G, Vangnai AS, Sangvanich P. Untargeted metabolomics analysis revealed changes in the composition of glycerolipids and phospholipids in Bacillus subtilis under 1-butanol stress. Appl Microbiol Biotechnol 2015; 99:5971-83. [PMID: 26025016 DOI: 10.1007/s00253-015-6692-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/18/2015] [Accepted: 05/15/2015] [Indexed: 01/21/2023]
Abstract
1-Butanol has been utilized widely in industry and can be produced or transformed by microbes. However, current knowledge about the mechanisms of 1-butanol tolerance in bacteria remains quite limited. Here, we applied untargeted metabolomics to study Bacillus subtilis cells under 1-butanol stress and identified 55 and 37 ions with significantly increased and decreased levels, respectively. Using accurate mass determination, tandem mass spectra, and synthetic standards, 86 % of these ions were characterized. The levels of phosphatidylethanolamine, diglucosyldiacylglycerol, and phosphatidylserine were found to be upregulated upon 1-butanol treatment, whereas those of diacylglycerol and lysyl phosphatidylglycerol were downregulated. Most lipids contained 15:0/15:0, 16:0/15:0, and 17:0/15:0 acyl chains, and all were mapped to membrane lipid biosynthetic pathways. Subsequent two-stage quantitative real-time reverse transcriptase PCR analyses of genes in the two principal membrane lipid biosynthesis pathways revealed elevated levels of ywiE transcripts in the presence of 1-butanol and reduced expression levels of cdsA, pgsA, mprF, clsA, and yfnI transcripts. Thus, the gene transcript levels showed agreement with the metabolomics data. Lastly, the cell morphology was investigated by scanning electron microscopy, which indicated that cells became almost twofold longer after 1.4 % (v/v) 1-butanol stress for 12 h. Overall, the studies uncovered changes in the composition of glycerolipids and phospholipids in B. subtilis under 1-butanol stress, emphasizing the power of untargeted metabolomics in the discovery of new biological insights.
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Affiliation(s)
- Nawaporn Vinayavekhin
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand,
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82
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Engineering lipid overproduction in the oleaginous yeast Yarrowia lipolytica. Metab Eng 2015; 29:56-65. [DOI: 10.1016/j.ymben.2015.02.005] [Citation(s) in RCA: 241] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/16/2015] [Indexed: 12/20/2022]
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83
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Acute Limonene Toxicity in Escherichia coli Is Caused by Limonene Hydroperoxide and Alleviated by a Point Mutation in Alkyl Hydroperoxidase AhpC. Appl Environ Microbiol 2015; 81:4690-6. [PMID: 25934627 DOI: 10.1128/aem.01102-15] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 04/27/2015] [Indexed: 02/07/2023] Open
Abstract
Limonene, a major component of citrus peel oil, has a number of applications related to microbiology. The antimicrobial properties of limonene make it a popular disinfectant and food preservative, while its potential as a biofuel component has made it the target of renewable production efforts through microbial metabolic engineering. For both applications, an understanding of microbial sensitivity or tolerance to limonene is crucial, but the mechanism of limonene toxicity remains enigmatic. In this study, we characterized a limonene-tolerant strain of Escherichia coli and found a mutation in ahpC, encoding alkyl hydroperoxidase, which alleviated limonene toxicity. We show that the acute toxicity previously attributed to limonene is largely due to the common oxidation product limonene hydroperoxide, which forms spontaneously in aerobic environments. The mutant AhpC protein with an L-to-Q change at position 177 (AhpC(L177Q)) was able to alleviate this toxicity by reducing the hydroperoxide to a more benign compound. We show that the degree of limonene toxicity is a function of its oxidation level and that nonoxidized limonene has relatively little toxicity to wild-type E. coli cells. Our results have implications for both the renewable production of limonene and the applications of limonene as an antimicrobial.
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84
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Smith MR, Khera E, Wen F. Engineering Novel and Improved Biocatalysts by Cell Surface Display. Ind Eng Chem Res 2015; 54:4021-4032. [PMID: 29056821 PMCID: PMC5647830 DOI: 10.1021/ie504071f] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biocatalysts, especially enzymes, have the ability to catalyze reactions with high product selectivity, utilize a broad range of substrates, and maintain activity at low temperature and pressure. Therefore, they represent a renewable, environmentally friendly alternative to conventional catalysts. Most current industrial-scale chemical production processes using biocatalysts employ soluble enzymes or whole cells expressing intracellular enzymes. Cell surface display systems differ by presenting heterologous enzymes extracellularly, overcoming some of the limitations associated with enzyme purification and substrate transport. Additionally, coupled with directed evolution, cell surface display is a powerful platform for engineering enzymes with enhanced properties. In this review, we will introduce the molecular and cellular principles of cell surface display and discuss how it has been applied to engineer enzymes with improved properties as well as to develop surface-engineered microbes as whole-cell biocatalysts.
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Affiliation(s)
- Mason R. Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Eshita Khera
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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85
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Miller DM, Gulbis JM. Engineering protocells: prospects for self-assembly and nanoscale production-lines. Life (Basel) 2015; 5:1019-53. [PMID: 25815781 PMCID: PMC4500129 DOI: 10.3390/life5021019] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 11/16/2022] Open
Abstract
The increasing ease of producing nucleic acids and proteins to specification offers potential for design and fabrication of artificial synthetic "organisms" with a myriad of possible capabilities. The prospects for these synthetic organisms are significant, with potential applications in diverse fields including synthesis of pharmaceuticals, sources of renewable fuel and environmental cleanup. Until now, artificial cell technology has been largely restricted to the modification and metabolic engineering of living unicellular organisms. This review discusses emerging possibilities for developing synthetic protocell "machines" assembled entirely from individual biological components. We describe a host of recent technological advances that could potentially be harnessed in design and construction of synthetic protocells, some of which have already been utilized toward these ends. More elaborate designs include options for building self-assembling machines by incorporating cellular transport and assembly machinery. We also discuss production in miniature, using microfluidic production lines. While there are still many unknowns in the design, engineering and optimization of protocells, current technologies are now tantalizingly close to the capabilities required to build the first prototype protocells with potential real-world applications.
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Affiliation(s)
- David M Miller
- The Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia.
| | - Jacqueline M Gulbis
- The Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia.
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86
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Hu G, Ji S, Yu Y, Wang S, Zhou G, Li F. Organisms for biofuel production: natural bioresources and methodologies for improving their biosynthetic potentials. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 147:185-224. [PMID: 24085385 DOI: 10.1007/10_2013_245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
In order to relieve the pressure of energy supply and environment contamination that humans are facing, there are now intensive worldwide efforts to explore natural bioresources for production of energy storage compounds, such as lipids, alcohols, hydrocarbons, and polysaccharides. Around the world, many plants have been evaluated and developed as feedstock for bioenergy production, among which several crops have successfully achieved industrialization. Microalgae are another group of photosynthetic autotroph of interest due to their superior growth rates, relatively high photosynthetic conversion efficiencies, and vast metabolic capabilities. Heterotrophic microorganisms, such as yeast and bacteria, can utilize carbohydrates from lignocellulosic biomass directly or after pretreatment and enzymatic hydrolysis to produce liquid biofuels such as ethanol and butanol. Although finding a suitable organism for biofuel production is not easy, many naturally occurring organisms with good traits have recently been obtained. This review mainly focuses on the new organism resources discovered in the last 5 years for production of transport fuels (biodiesel, gasoline, jet fuel, and alkanes) and hydrogen, and available methods to improve natural organisms as platforms for the production of biofuels.
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Affiliation(s)
- Guangrong Hu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
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87
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Genome Sequence of Saccharomyces cerevisiae NCIM3107, Used in Bioethanol Production. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01557-14. [PMID: 25676764 PMCID: PMC4333664 DOI: 10.1128/genomea.01557-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the genome of Saccharomyces cerevisiae strain NCIM3107, used in bioethanol production. The genome size is approximately 11.8 Mb and contains 5,435 protein-coding genes.
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88
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Sakuragi H, Morisaka H, Kuroda K, Ueda M. Enhanced butanol production by eukaryotic Saccharomyces cerevisiae engineered to contain an improved pathway. Biosci Biotechnol Biochem 2015; 79:314-20. [DOI: 10.1080/09168451.2014.972330] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Abstract
Compared with ethanol, butanol has more advantageous physical properties as a fuel, and biobutanol is thus considered a promising biofuel material. Biobutanol has often been produced by Clostridium species; however, because they are strictly anaerobic microorganisms, these species are challenging to work with. We attempted to introduce the butanol production pathway into yeast Saccharomyces cerevisiae, which is a well-known microorganism that is tolerant to organic solvents. 1-Butanol was found to be produced at very low levels when the butanol production pathway of Clostridium acetobutylicum was simply introduced into S. cerevisiae. The elimination of glycerol production pathway in the yeast contributed to the enhancement of 1-butanol production. In addition, by the use of trans-enoyl-CoA reductase in the engineered pathway, 1-butanol production was markedly enhanced to yield 14.1 mg/L after 48 h of cultivation.
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Affiliation(s)
- Hiroshi Sakuragi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hironobu Morisaka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Kyoto Industrial Science and Technology Innovation Center, Kyoto, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Kyoto Industrial Science and Technology Innovation Center, Kyoto, Japan
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89
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Designed surface residue substitutions in [NiFe] hydrogenase that improve electron transfer characteristics. Int J Mol Sci 2015; 16:2020-33. [PMID: 25603181 PMCID: PMC4307346 DOI: 10.3390/ijms16012020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 01/12/2015] [Indexed: 01/11/2023] Open
Abstract
Photobiological hydrogen production is an attractive, carbon-neutral means to convert solar energy to hydrogen. We build on previous research improving the Alteromonas macleodii “Deep Ecotype” [NiFe] hydrogenase, and report progress towards creating an artificial electron transfer pathway to supply the hydrogenase with electrons necessary for hydrogen production. Ferredoxin is the first soluble electron transfer mediator to receive high-energy electrons from photosystem I, and bears an electron with sufficient potential to efficiently reduce protons. Thus, we engineered a hydrogenase-ferredoxin fusion that also contained several other modifications. In addition to the C-terminal ferredoxin fusion, we truncated the C-terminus of the hydrogenase small subunit, identified as the available terminus closer to the electron transfer region. We also neutralized an anionic patch surrounding the interface Fe-S cluster to improve transfer kinetics with the negatively charged ferredoxin. Initial screening showed the enzyme tolerated both truncation and charge neutralization on the small subunit ferredoxin-binding face. While the enzyme activity was relatively unchanged using the substrate methyl viologen, we observed a marked improvement from both the ferredoxin fusion and surface modification using only dithionite as an electron donor. Combining ferredoxin fusion and surface charge modification showed progressively improved activity in an in vitro assay with purified enzyme.
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90
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Qiu Z, Deng Z, Tan H, Zhou S, Cao L. Engineering the robustness of Saccharomyces cerevisiae by introducing bifunctional glutathione synthase gene. J Ind Microbiol Biotechnol 2015; 42:537-42. [PMID: 25561319 DOI: 10.1007/s10295-014-1573-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 12/18/2014] [Indexed: 11/24/2022]
Abstract
Robust, high-yielding Saccharomyces cerevisiae is highly desirable for cost-effective cellulosic ethanol production. In this study, the bifunctional glutathione (GSH) synthetase genes GCSGS at high copy number was integrated into ribosomal DNA of S. cerevisiae by Cre-LoxP system. Threefold higher GSH contents (54.9 μmol/g dry weight) accumulated in the engineered strain BY-G compared to the reference strain. Tolerance of BY-G to H2O2 (3 mM), temperature (40 °C), furfural (10 mM), hydroxymethylfurfural (HMF, 10 mM) and 0.5 mM Cd(2+) increased compared to reference strain. Twofold higher ethanol concentration was obtained by BY-G in simultaneous saccharification and fermentation of corn stover compared to the reference strain. The results showed that intracellular GSH content of S. cerevisiae has an influence on robustness. The strategy is used to engineer S. cerevisiae strains adaptive to a combination of tolerance to inhibitors and raised temperature that may occur in high solid simultaneous saccharification and fermentation of lignocellulosic feedstocks.
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Affiliation(s)
- Zhiqi Qiu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
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91
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Köhler KAK, Rühl J, Blank LM, Schmid A. Integration of biocatalyst and process engineering for sustainable and efficientn-butanol production. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400041] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
| | - Jana Rühl
- Laboratory of Chemical Biotechnology; TU Dortmund University; Dortmund Germany
| | - Lars M. Blank
- Institute of Applied Microbiology (iAMB); Aachen Biology and Biotechnology (ABBt); RWTH Aachen University; Aachen Germany
| | - Andreas Schmid
- Department Solar Materials; Helmholtz Centre for Environmental Research (UFZ); Leipzig Germany
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92
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Lee S, J. Mitchell R. Perspectives on the use of transcriptomics to advance biofuels. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.4.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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93
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Integrated Automation for Continuous High-Throughput Synthetic Chromosome Assembly and Transformation to Identify Improved Yeast Strains for Industrial Production of Biofuels and Bio-based Chemicals. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10503-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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94
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Wang H, Wang F, Wang W, Yao X, Wei D, Cheng H, Deng Z. Improving the expression of recombinant proteins in E. coli BL21 (DE3) under acetate stress: an alkaline pH shift approach. PLoS One 2014; 9:e112777. [PMID: 25402470 PMCID: PMC4234529 DOI: 10.1371/journal.pone.0112777] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 10/20/2014] [Indexed: 11/23/2022] Open
Abstract
Excess acetate has long been an issue for the production of recombinant proteins in E. coli cells. Recently, improvements in acetate tolerance have been achieved through the use of genetic strategies and medium supplementation with certain amino acids and pyrimidines. The aim of our study was to evaluate an alternative to improve the acetate tolerance of E. coli BL21 (DE3), a popular strain used to express recombinant proteins. In this work we reported the cultivation of BL21 (DE3) in complex media containing acetate at high concentrations. In the presence of 300 mM acetate, compared with pH 6.5, pH 7.5 improved cell growth by approximately 71%, reduced intracellular acetate by approximately 50%, and restored the expression of glutathione S-transferase (GST), green fluorescent protein (GFP) and cytochrome P450 monooxygenase (CYP). Further experiments showed that alkaline pHs up to 8.5 had little inhibition in the expression of GST, GFP and CYP. In addition, the detrimental effect of acetate on the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) by the cell membrane, an index of cellular metabolic capacity, was substantially alleviated by a shift to alkaline pH values of 7.5–8.0. Thus, we suggest an approach of cultivating E. coli BL21 (DE3) at pH 8.0±0.5 to minimize the effects caused by acetate stress. The proposed strategy of an alkaline pH shift is a simple approach to solving similar bioprocessing problems in the production of biofuels and biochemicals from sugars.
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Affiliation(s)
- Hengwei Wang
- Innovation & Application Institute (IAI), Zhejiang Ocean University, Zhoushan, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fengqing Wang
- New World Institute of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Wei Wang
- New World Institute of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xueling Yao
- New World Institute of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Dongzhi Wei
- New World Institute of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hairong Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail:
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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95
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Jia H, Fan Y, Feng X, Li C. Enhancing stress-resistance for efficient microbial biotransformations by synthetic biology. Front Bioeng Biotechnol 2014; 2:44. [PMID: 25368869 PMCID: PMC4202804 DOI: 10.3389/fbioe.2014.00044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 10/04/2014] [Indexed: 12/23/2022] Open
Abstract
Chemical conversions mediated by microorganisms, otherwise known as microbial biotransformations, are playing an increasingly important role within the biotechnology industry. Unfortunately, the growth and production of microorganisms are often hampered by a number of stressful conditions emanating from environment fluctuations and/or metabolic imbalances such as high temperature, high salt condition, strongly acidic solution, and presence of toxic metabolites. Therefore, exploring methods to improve the stress tolerance of host organisms could significantly improve the biotransformation process. With the help of synthetic biology, it is now becoming feasible to implement strategies to improve the stress-resistance of the existing hosts. This review summarizes synthetic biology efforts to enhance the efficiency of biotransformations by improving the robustness of microbes. Particular attention will be given to strategies at the cellular and the microbial community levels.
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Affiliation(s)
- Haiyang Jia
- Department of Biological Engineering, School of Life Science, Beijing Institute of Technology , Beijing , China
| | - Yanshuang Fan
- Department of Biological Engineering, School of Life Science, Beijing Institute of Technology , Beijing , China
| | - Xudong Feng
- Department of Biological Engineering, School of Life Science, Beijing Institute of Technology , Beijing , China
| | - Chun Li
- Department of Biological Engineering, School of Life Science, Beijing Institute of Technology , Beijing , China
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96
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Perspective and prospective of pretreatment of corn straw for butanol production. Appl Biochem Biotechnol 2014; 172:840-53. [PMID: 24122704 DOI: 10.1007/s12010-013-0548-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
Corn straw, lignocellulosic biomass, is a potential substrate for microbial production of bio-butanol. Bio-butanol is a superior second generation biofuel among its kinds. Present researches are focused on the selection of butanol tolerant clostridium strain(s) to optimize butanol yield in the fermentation broth because of toxicity of bio-butanol to the clostridium strain(s) itself. However, whatever the type of the strain(s) used, pretreatment process always affects not only the total sugar yield before fermentation but also the performance and growth of microbes during fermentation due to the formation of hydroxyl-methyl furfural, furfural and phenolic compounds. In addition, the lignocellulosic biomasses also resist physical and biological attacks. Thus, selection of best pretreatment process and its parameters is crucial. In this context, worldwide research efforts are increased in past 12 years and researchers are tried to identify the best pretreatment method, pretreatment conditions for the actual biomass. In this review, effect of particle size, status of most common pretreatment method and enzymatic hydrolysis particularly for corn straw as a substrate is presented. This paper also highlights crucial parameters necessary to consider during most common pretreatment processes such as hydrothermal, steam explosion, ammonia explosion, sulfuric acid, and sodium hydroxide pretreatment. Moreover, the prospective of pretreatment methods and challenges is discussed.
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97
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Coconi-Linares N, Magaña-Ortíz D, Guzmán-Ortiz DA, Fernández F, Loske AM, Gómez-Lim MA. High-yield production of manganese peroxidase, lignin peroxidase, and versatile peroxidase in Phanerochaete chrysosporium. Appl Microbiol Biotechnol 2014; 98:9283-94. [PMID: 25269601 DOI: 10.1007/s00253-014-6105-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/09/2014] [Accepted: 09/15/2014] [Indexed: 11/30/2022]
Abstract
The white-rot fungus Phanerochaete chrysosporium secretes extracellular oxidative enzymes during secondary metabolism, but lacks versatile peroxidase, an enzyme important in ligninolysis and diverse biotechnology processes. In this study, we report the genetic modification of a P. chrysosporium strain capable of co-expressing two endogenous genes constitutively, manganese peroxidase (mnp1) and lignin peroxidase (lipH8), and the codon-optimized vpl2 gene from Pleurotus eryngii. For this purpose, we employed a highly efficient transformation method based on the use of shock waves developed by our group. The expression of recombinant genes was verified by PCR, Southern blot, quantitative real-time PCR (qRT-PCR), and assays of enzymatic activity. The production yield of ligninolytic enzymes was up to four times higher in comparison to previously published reports. These results may represent significant progress toward the stable production of ligninolytic enzymes and the development of an effective fungal strain with promising biotechnological applications.
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Affiliation(s)
- Nancy Coconi-Linares
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Km. 9.6 Carretera Irapuato-León, 36821, Irapuato, Gto, Mexico
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98
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Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metab Eng 2014; 25:140-58. [DOI: 10.1016/j.ymben.2014.07.009] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 11/17/2022]
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99
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Kasavi C, Eraslan S, Arga KY, Oner ET, Kirdar B. A system based network approach to ethanol tolerance in Saccharomyces cerevisiae. BMC SYSTEMS BIOLOGY 2014; 8:90. [PMID: 25103914 PMCID: PMC4236716 DOI: 10.1186/s12918-014-0090-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/15/2014] [Indexed: 01/23/2023]
Abstract
Background Saccharomyces cerevisiae has been widely used for bio-ethanol production and development of rational genetic engineering strategies leading both to the improvement of productivity and ethanol tolerance is very important for cost-effective bio-ethanol production. Studies on the identification of the genes that are up- or down-regulated in the presence of ethanol indicated that the genes may be involved to protect the cells against ethanol stress, but not necessarily required for ethanol tolerance. Results In the present study, a novel network based approach was developed to identify candidate genes involved in ethanol tolerance. Protein-protein interaction (PPI) network associated with ethanol tolerance (tETN) was reconstructed by integrating PPI data with Gene Ontology (GO) terms. Modular analysis of the constructed networks revealed genes with no previously reported experimental evidence related to ethanol tolerance and resulted in the identification of 17 genes with previously unknown biological functions. We have randomly selected four of these genes and deletion strains of two genes (YDR307W and YHL042W) were found to exhibit improved tolerance to ethanol when compared to wild type strain. The genome-wide transcriptomic response of yeast cells to the deletions of YDR307W and YHL042W in the absence of ethanol revealed that the deletion of YDR307W and YHL042W genes resulted in the transcriptional re-programming of the metabolism resulting from a mis-perception of the nutritional environment. Yeast cells perceived an excess amount of glucose and a deficiency of methionine or sulfur in the absence of YDR307W and YHL042W, respectively, possibly resulting from a defect in the nutritional sensing and signaling or transport mechanisms. Mutations leading to an increase in ribosome biogenesis were found to be important for the improvement of ethanol tolerance. Modulations of chronological life span were also identified to contribute to ethanol tolerance in yeast. Conclusions The system based network approach developed allows the identification of novel gene targets for improved ethanol tolerance and supports the highly complex nature of ethanol tolerance in yeast.
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Affiliation(s)
| | | | | | | | - Betul Kirdar
- Department of Chemical Engineering, Boğaziçi University, Istanbul, Turkey.
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100
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Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria. Proc Natl Acad Sci U S A 2014; 111:E2576-85. [PMID: 24927582 DOI: 10.1073/pnas.1401853111] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The molecular mechanisms of ethanol toxicity and tolerance in bacteria, although important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and have revealed multiple mechanisms of tolerance, but it remains difficult to separate the direct and indirect effects of ethanol. We used adaptive evolution to generate spontaneous ethanol-tolerant strains of Escherichia coli, and then characterized mechanisms of toxicity and resistance using genome-scale DNAseq, RNAseq, and ribosome profiling coupled with specific assays of ribosome and RNA polymerase function. Evolved alleles of metJ, rho, and rpsQ recapitulated most of the observed ethanol tolerance, implicating translation and transcription as key processes affected by ethanol. Ethanol induced miscoding errors during protein synthesis, from which the evolved rpsQ allele protected cells by increasing ribosome accuracy. Ribosome profiling and RNAseq analyses established that ethanol negatively affects transcriptional and translational processivity. Ethanol-stressed cells exhibited ribosomal stalling at internal AUG codons, which may be ameliorated by the adaptive inactivation of the MetJ repressor of methionine biosynthesis genes. Ethanol also caused aberrant intragenic transcription termination for mRNAs with low ribosome density, which was reduced in a strain with the adaptive rho mutation. Furthermore, ethanol inhibited transcript elongation by RNA polymerase in vitro. We propose that ethanol-induced inhibition and uncoupling of mRNA and protein synthesis through direct effects on ribosomes and RNA polymerase conformations are major contributors to ethanol toxicity in E. coli, and that adaptive mutations in metJ, rho, and rpsQ help protect these central dogma processes in the presence of ethanol.
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