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Pozdniakova TA, Cruz JP, Silva PC, Azevedo F, Parpot P, Domingues MR, Carlquist M, Johansson B. Optimization of a hybrid bacterial/ Arabidopsis thaliana fatty acid synthase system II in Saccharomyces cerevisiae. Metab Eng Commun 2023; 17:e00224. [PMID: 37415783 PMCID: PMC10320613 DOI: 10.1016/j.mec.2023.e00224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/27/2023] [Accepted: 05/02/2023] [Indexed: 07/08/2023] Open
Abstract
Fatty acids are produced by eukaryotes like baker's yeast Saccharomyces cerevisiae mainly using a large multifunctional type I fatty acid synthase (FASI) where seven catalytic steps and a carrier domain are shared between one or two protein subunits. While this system may offer efficiency in catalysis, only a narrow range of fatty acids are produced. Prokaryotes, chloroplasts and mitochondria rely instead on a FAS type II (FASII) where each catalytic step is carried out by a monofunctional enzyme encoded by a separate gene. FASII is more flexible and capable of producing a wider range of fatty acid structures, such as the direct production of unsaturated fatty acids. An efficient FASII in the preferred industrial organism S. cerevisiae could provide a platform for developing sustainable production of specialized fatty acids. We functionally replaced either yeast FASI genes (FAS1 or FAS2) with a FASII consisting of nine genes from Escherichia coli (acpP, acpS and fab -A, -B, -D, -F, -G, -H, -Z) as well as three from Arabidopsis thaliana (MOD1, FATA1 and FATB). The genes were expressed from an autonomously replicating multicopy vector assembled using the Yeast Pathway Kit for in-vivo assembly in yeast. Two rounds of adaptation led to a strain with a maximum growth rate (μmax) of 0.19 h-1 without exogenous fatty acids, twice the growth rate previously reported for a comparable strain. Additional copies of the MOD1 or fabH genes resulted in cultures with higher final cell densities and three times higher lipid content compared to the control.
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Affiliation(s)
- Tatiana A. Pozdniakova
- CBMA - Center of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - João P. Cruz
- CBMA - Center of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Paulo César Silva
- CBMA - Center of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Flávio Azevedo
- CBMA - Center of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Pier Parpot
- CEB - C, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Maria Rosario Domingues
- Mass Spectrometry Center & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
- CESAM–Centre for Environmental and Marine Studies, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Magnus Carlquist
- Division of Applied Microbiology, Lund University, Box 124, 221 00, Lund, Sweden
| | - Björn Johansson
- CBMA - Center of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
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Co-culture fermentation characteristics of antifreeze yeast and mining of related freezing-resistant genes. Eur Food Res Technol 2023. [DOI: 10.1007/s00217-023-04204-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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An engineered non-oxidative glycolytic bypass based on Calvin-cycle enzymes enables anaerobic co-fermentation of glucose and sorbitol by Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:112. [PMID: 36253796 PMCID: PMC9578259 DOI: 10.1186/s13068-022-02200-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/17/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Saccharomyces cerevisiae is intensively used for industrial ethanol production. Its native fermentation pathway enables a maximum product yield of 2 mol of ethanol per mole of glucose. Based on conservation laws, supply of additional electrons could support even higher ethanol yields. However, this option is disallowed by the configuration of the native yeast metabolic network. To explore metabolic engineering strategies for eliminating this constraint, we studied alcoholic fermentation of sorbitol. Sorbitol cannot be fermented anaerobically by S. cerevisiae because its oxidation to pyruvate via glycolysis yields one more NADH than conversion of glucose. To enable re-oxidation of this additional NADH by alcoholic fermentation, sorbitol metabolism was studied in S. cerevisiae strains that functionally express heterologous genes for ribulose-1,5-bisphosphate carboxylase (RuBisCO) and phosphoribulokinase (PRK). Together with the yeast non-oxidative pentose-phosphate pathway, these Calvin-cycle enzymes enable a bypass of the oxidative reaction in yeast glycolysis. RESULTS Consistent with earlier reports, overproduction of the native sorbitol transporter Hxt15 and the NAD+-dependent sorbitol dehydrogenase Sor2 enabled aerobic, but not anaerobic growth of S. cerevisiae on sorbitol. In anaerobic, slow-growing chemostat cultures on glucose-sorbitol mixtures, functional expression of PRK-RuBisCO pathway genes enabled a 12-fold higher rate of sorbitol co-consumption than observed in a sorbitol-consuming reference strain. Consistent with the high Km for CO2 of the bacterial RuBisCO that was introduced in the engineered yeast strains, sorbitol consumption and increased ethanol formation depended on enrichment of the inlet gas with CO2. Prolonged chemostat cultivation on glucose-sorbitol mixtures led to loss of sorbitol co-fermentation. Whole-genome resequencing after prolonged cultivation suggested a trade-off between glucose-utilization and efficient fermentation of sorbitol via the PRK-RuBisCO pathway. CONCLUSIONS Combination of the native sorbitol assimilation pathway of S. cerevisiae and an engineered PRK-RuBisCO pathway enabled RuBisCO-dependent, anaerobic co-fermentation of sorbitol and glucose. This study demonstrates the potential for increasing the flexibility of redox-cofactor metabolism in anaerobic S. cerevisiae cultures and, thereby, to extend substrate range and improve product yields in anaerobic yeast-based processes by enabling entry of additional electrons.
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van Winden WA, Mans R, Breestraat S, Verlinden RAJ, Mielgo-Gómez A, de Hulster EAF, de Bruijn HMCJ, Noorman HJ. Towards closed carbon loop fermentations: co-feeding of Yarrowia lipolytica with glucose and formic acid. Biotechnol Bioeng 2022; 119:2142-2151. [PMID: 35451059 PMCID: PMC9540030 DOI: 10.1002/bit.28115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/24/2022] [Accepted: 04/07/2022] [Indexed: 11/26/2022]
Abstract
A novel fermentation process was developed in which renewable electricity is indirectly used as an energy source in fermentation, synergistically decreasing both the consumption of sugar as a first generation carbon source and emission of the greenhouse gas CO2. As an illustration, a glucose‐based process is co‐fed with formic acid, which can be generated by capturing CO2 from fermentation offgas followed by electrochemical reduction with renewable electricity. This “closed carbon loop” concept is demonstrated by a case study in which cofeeding formic acid is shown to significantly increase the yield of biomass on glucose of the industrially relevant yeast species Yarrowia lipolytica. First, the optimal feed ratio of formic acid to glucose is established using chemostat cultivations. Subsequently, guided by a dynamic fermentation process model, a fed‐batch protocol is developed and demonstrated on laboratory scale. Finally, the developed fed‐batch process is tested and proven to be scalable at pilot scale. Extensions of the concept are discussed to apply the concept to anaerobic fermentations, and to recycle the O2 that is co‐generated with the formic acid to aerobic fermentation processes for intensification purposes.
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Affiliation(s)
- Wouter A van Winden
- DSM Biotechnology Center, DSM N.V., Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Stefaan Breestraat
- Bioprocess Pilot Facility, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Rob A J Verlinden
- Bioprocess Pilot Facility, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Alvaro Mielgo-Gómez
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Erik A F de Hulster
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Hans M C J de Bruijn
- DSM Biotechnology Center, DSM N.V., Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Henk J Noorman
- DSM Biotechnology Center, DSM N.V., Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands.,Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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Hillman ET, Li M, Hooker CA, Englaender JA, Wheeldon I, Solomon KV. Hydrolysis of lignocellulose by anaerobic fungi produces free sugars and organic acids for two-stage fine chemical production with Kluyveromyces marxianus. Biotechnol Prog 2021; 37:e3172. [PMID: 33960738 DOI: 10.1002/btpr.3172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/06/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022]
Abstract
Development of the bioeconomy is driven by our ability to access the energy-rich carbon trapped in recalcitrant plant materials. Current strategies to release this carbon rely on expensive enzyme cocktails and physicochemical pretreatment, producing inhibitory compounds that hinder subsequent microbial bioproduction. Anaerobic fungi are an appealing solution as they hydrolyze crude, untreated biomass at ambient conditions into sugars that can be converted into value-added products by partner organisms. However, some carbon is lost to anaerobic fungal fermentation products. To improve efficiency and recapture this lost carbon, we built a two-stage bioprocessing system pairing the anaerobic fungus Piromyces indianae with the yeast Kluyveromyces marxianus, which grows on a wide range of sugars and fermentation products. In doing so we produce fine and commodity chemicals directly from untreated lignocellulose. P. indianae efficiently hydrolyzed substrates such as corn stover and poplar to generate sugars, fermentation acids, and ethanol, which K. marxianus consumed while producing 2.4 g/L ethyl acetate. An engineered strain of K. marxianus was also able to produce 550 mg/L 2-phenylethanol and 150 mg/L isoamyl alcohol from P. indianae hydrolyzed lignocellulosic biomass. Despite the use of crude untreated plant material, production yields were comparable to optimized rich yeast media due to the use of all available carbon including organic acids, which formed up to 97% of free carbon in the fungal hydrolysate. This work demonstrates that anaerobic fungal pretreatment of lignocellulose can sustain the production of fine chemicals at high efficiency by partnering organisms with broad substrate versatility.
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Affiliation(s)
- Ethan T Hillman
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, West Lafayette, Indiana, USA
| | - Mengwan Li
- Department of Chemical & Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Casey A Hooker
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Laboratory of Renewable Resources Engineering (LORRE), Purdue University, West Lafayette, Indiana, USA
| | - Jacob A Englaender
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Ian Wheeldon
- Department of Chemical & Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Kevin V Solomon
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, West Lafayette, Indiana, USA.,Laboratory of Renewable Resources Engineering (LORRE), Purdue University, West Lafayette, Indiana, USA
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Evaluating the Pathway for Co-fermentation of Glucose and Xylose for Enhanced Bioethanol Production Using Flux Balance Analysis. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-019-0026-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Wang X, Chen R, Wu Y, Wang D, Wei D. Nitrate Metabolism Decreases the Steroidal Alcohol Byproduct Compared with Ammonium in Biotransformation of Phytosterol to Androstenedione by Mycobacterium neoaurum. Appl Biochem Biotechnol 2019; 190:1553-1560. [PMID: 31792785 DOI: 10.1007/s12010-019-03175-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/11/2019] [Indexed: 11/24/2022]
Abstract
In biotransformation of phytosterol to 4-androstene-3,17-dione (AD) by Mycobacterium, the steroidal alcohol (such as 22-hydroxy-23,24-bisnorchol-4-ene-3-one, HBC) was a main byproduct. To weaken the accumulation of this byproduct in sterol biotransformation, ammonium was substituted by nitrate as nitrogen resource. The nitrate was utilized by Mycobacterium and led to metabolic flux shift towards AD production. The ratio of AD/HBC increased maximally from 2.1 to 5.5 and AD production increased correspondently. In the meanwhile, the nitrate metabolism resulted in the decreased intracellular redox level (NADH/NAD+) maximally by 59.5% and a slight descent tendency with the increase of the nitrate concentrations. It indicated that the nitrate utilization effectively decreased the steroidal alcohol production by regulating intracellular redox level in sterol biotransformation. These results gave an insight into the mechanism of the steroidal alcohol formation in sterol biodegradation and provided a simple strategy to regulate the metabolic distribution.
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Affiliation(s)
- Xuedong Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| | - Rui Chen
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yuyang Wu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Da Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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Mixed carbon substrates: a necessary nuisance or a missed opportunity? Curr Opin Biotechnol 2019; 62:15-21. [PMID: 31513988 DOI: 10.1016/j.copbio.2019.07.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 06/24/2019] [Accepted: 07/03/2019] [Indexed: 11/20/2022]
Abstract
Although fermentation with single carbon sources is the preferred mode of operation in current industrial biotechnology, the use of multiple substrates has been continuously investigated throughout the years. Generally, microbial metabolism varies significantly when cells are presented with mixed carbon substrates compared to a single carbon-energy source, as different nutrients interact in complex ways within the metabolic network. By exploiting these distinct modes of interaction, researchers have identified unique opportunities to optimize metabolism using mixed carbon sources. Here we review situations where process yield and productivity are markedly improved through the judicious introduction of substrate mixtures. Our goal is to illustrate that with proper design of the choice of substrates and the way they are introduced to cultures, metabolic optimization with mixed substrates can be a unique strategy that complements genetic engineering techniques to enhance cell performance beyond what is accomplished in single substrate fermentations.
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Zarmehrkhorshid R, Shafiei R, Delvigne F. Modified semi-continuous fermentation for resuscitating nongrowing cells during high-temperature gluconic acid production by Acetobacter senegalensis. J Appl Microbiol 2019; 127:1101-1112. [PMID: 31283860 DOI: 10.1111/jam.14371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/26/2019] [Accepted: 07/02/2019] [Indexed: 11/28/2022]
Abstract
AIMS The formation of metabolically inactive and nongrowing cells is an inevitable by-product of intensive fermentation. This study investigated whether co-feeding can be used to resuscitate nongrowing Acetobacter senegalensis cells to enable them to produce gluconic acid in successive fermentation runs at 38°C. METHODS AND RESULTS In the first fermentation cycle, 75 g l-1 of glucose were converted to gluconic acid. Subsequently, however, stationary-phase cells were unable to initiate a new fermentation cycle. The majority of stationary-phase cells (97%) were nonculturable on glucose at 38°C. In addition, 54 and 41% of cells contained non-active cellular dehydrogenases and a compromised cell envelope respectively. Co-feeding stationary-phase cells with a mixture of ethanol, glucose and acetic acid for 7 h enabled these cells to grow on 75 g l-1 of glucose and produce gluconic acid. Additionally, 74% of cells contained active forms of cellular dehydrogenases after 7 h of co-feeding. However, co-feeding did not improve cell envelope integrity. Quantification of cellular NAD content showed that stationary-phase cells contained moderately reduced levels of total NAD (NADt) as compared with exponential-phase cells. Interestingly, the analysis of stationary-phase cells showed that co-feeding resulted in higher levels of NADt and NADH, suggesting that the regeneration of NADH is one of the limiting factors of glucose consumption. Expression of catalase and superoxide dismutase was increased in stationary-phase cells, but analysis of protein carbonylation and lipid peroxidation did not confirm an extensive oxidative stress. CONCLUSIONS Co-feeding with favourable nutrients may enable resuscitation of cells and utilization of less-favourable carbon sources in successive cycles. SIGNIFICANCE AND IMPACT OF THE STUDY This study proposed a unique method for resuscitation of nongrowing cells during high-temperature fermentation. By applying this method, cells can be used for consecutive fermentation cycles.
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Affiliation(s)
- R Zarmehrkhorshid
- Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, TERRA Research and Teaching Centre, University of Liège, Gembloux, Belgium
| | - R Shafiei
- Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | - F Delvigne
- Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, TERRA Research and Teaching Centre, University of Liège, Gembloux, Belgium
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Wang G, Wang X, Wang T, Gulik W, Noorman HJ, Zhuang Y, Chu J, Zhang S. Comparative Fluxome and Metabolome Analysis of Formate as an Auxiliary Substrate for Penicillin Production in Glucose‐Limited Cultivation of
Penicillium chrysogenum. Biotechnol J 2019; 14:e1900009. [DOI: 10.1002/biot.201900009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/20/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Guan Wang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology (ECUST) 130 Meilong Road Shanghai 200237 P. R. China
| | - Xinxin Wang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology (ECUST) 130 Meilong Road Shanghai 200237 P. R. China
| | - Tong Wang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology (ECUST) 130 Meilong Road Shanghai 200237 P. R. China
| | - Walter Gulik
- Cell Systems Engineering, Department of BiotechnologyDelft University of Technology Delft The Netherlands
| | - Henk J. Noorman
- DSM Biotechnology Center Delft The Netherlands
- Department of BiotechnologyDelft University of Technology Delft The Netherlands
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology (ECUST) 130 Meilong Road Shanghai 200237 P. R. China
| | - Ju Chu
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology (ECUST) 130 Meilong Road Shanghai 200237 P. R. China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology (ECUST) 130 Meilong Road Shanghai 200237 P. R. China
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Engineering Saccharomyces cerevisiae for co-utilization of D-galacturonic acid and D-glucose from citrus peel waste. Nat Commun 2018; 9:5059. [PMID: 30498222 PMCID: PMC6265301 DOI: 10.1038/s41467-018-07589-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/19/2018] [Indexed: 11/08/2022] Open
Abstract
Pectin-rich biomasses, such as citrus peel and sugar beet pulp, hold promise as inexpensive feedstocks for microbial fermentations as enzymatic hydrolysis of their component polysaccharides can be accomplished inexpensively to yield high concentrations of fermentable sugars and D-galacturonic acid (D-galUA). In this study, we tackle a number of challenges associated with engineering a microbial strain to convert pectin-rich hydrolysates into commodity and specialty chemicals. First, we engineer D-galUA utilization into yeast, Saccharomyces cerevisiae. Second, we identify that the mechanism of D-galUA uptake into yeast is mediated by hexose transporters and that consumption of D-galUA is inhibited by D-glucose. Third, we enable co-utilization of D-galUA and D-glucose by identifying and expressing a heterologous transporter, GatA, from Aspergillus niger. Last, we demonstrate the use of this transporter for production of the platform chemical, meso-galactaric acid, directly from industrial Navel orange peel waste.
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Schwechheimer SK, Becker J, Peyriga L, Portais JC, Sauer D, Müller R, Hoff B, Haefner S, Schröder H, Zelder O, Wittmann C. Improved riboflavin production with Ashbya gossypii from vegetable oil based on 13C metabolic network analysis with combined labeling analysis by GC/MS, LC/MS, 1D, and 2D NMR. Metab Eng 2018; 47:357-373. [PMID: 29654833 DOI: 10.1016/j.ymben.2018.04.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/13/2018] [Accepted: 04/11/2018] [Indexed: 11/29/2022]
Abstract
The fungus Ashbya gossypii is an important industrial producer of riboflavin, i.e. vitamin B2. In order to meet the constantly increasing demands for improved production processes, it appears essential to better understand the underlying metabolic pathways of the vitamin. Here, we used a highly sophisticated set-up of parallel 13C tracer studies with labeling analysis by GC/MS, LC/MS, 1D, and 2D NMR to resolve carbon fluxes in the overproducing strain A. gossypii B2 during growth and subsequent riboflavin production from vegetable oil as carbon source, yeast extract, and supplemented glycine. The studies provided a detailed picture of the underlying metabolism. Glycine was exclusively used as carbon-two donor of the vitamin's pyrimidine ring, which is part of its isoalloxazine ring structure, but did not contribute to the carbon-one metabolism due to the proven absence of a functional glycine cleavage system. The pools of serine and glycine were closely connected due to a highly reversible serine hydroxymethyltransferase. Transmembrane formate flux simulations revealed that the one-carbon metabolism displayed a severe bottleneck during initial riboflavin production, which was overcome in later phases of the cultivation by intrinsic formate accumulation. The transiently limiting carbon-one pool was successfully replenished by time-resolved feeding of small amounts of formate and serine, respectively. This increased the intracellular availability of glycine, serine, and formate and resulted in a final riboflavin titer increase of 45%.
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Affiliation(s)
| | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Lindsay Peyriga
- Université de Toulouse; INSA, UPS, INP, Toulouse, France; INRA, UMR792 Ingénerie des Systèmes Biologiques et des Procédés, Toulouse, France; CNRS, UMR5504, Toulouse, France
| | - Jean-Charles Portais
- Université de Toulouse; INSA, UPS, INP, Toulouse, France; INRA, UMR792 Ingénerie des Systèmes Biologiques et des Procédés, Toulouse, France; CNRS, UMR5504, Toulouse, France
| | - Daniel Sauer
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Birgit Hoff
- BASF SE, White Biotechnology Research, Ludwigshafen, Germany
| | - Stefan Haefner
- BASF SE, White Biotechnology Research, Ludwigshafen, Germany
| | | | - Oskar Zelder
- BASF SE, White Biotechnology Research, Ludwigshafen, Germany
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Liu Z, Oyetunde T, Hollinshead WD, Hermanns A, Tang YJ, Liao W, Liu Y. Exploring eukaryotic formate metabolisms to enhance microbial growth and lipid accumulation. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:22. [PMID: 28149324 PMCID: PMC5267366 DOI: 10.1186/s13068-017-0708-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 01/12/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND C1 substrates (such as formate and methanol) are promising feedstock for biochemical/biofuel production. Numerous studies have been focusing on engineering heterologous pathways to incorporate C1 substrates into biomass, while the engineered microbial hosts often demonstrate inferior fermentation performance due to substrate toxicity, metabolic burdens from engineered pathways, and poor enzyme activities. Alternatively, exploring native C1 pathways in non-model microbes could be a better solution to address these challenges. RESULTS An oleaginous fungus, Umbelopsis isabellina, demonstrates an excellent capability of metabolizing formate to promote growth and lipid accumulation. By co-feeding formate with glucose at a mole ratio of 3.9:1, biomass and lipid productivities of the culture in 7.5 L bioreactors were improved by 20 and 70%, respectively. 13C-metabolite analysis, genome annotations, and enzyme assay further discovered that formate not only provides an auxiliary energy source [promoting NAD(P)H and ATP] for cell anabolism, but also contributes carbon backbones via folate-mediated C1 pathways. More interestingly, formate addition can tune fatty acid profile and increase the portion of medium-chain fatty acids, which would benefit conversion of fungal lipids for high-quality biofuel production. Flux balance analysis further indicates that formate co-utilization can power microbial metabolism to improve biosynthesis, particularly on glucose-limited cultures. CONCLUSION This study demonstrates Umbelopsis isabellina's strong capability for co-utilizing formate to produce biomass and enhance fatty acid production. It is a promising non-model platform that can be potentially integrated with photochemical/electrochemical processes to efficiently convert carbon dioxide into biofuels and value-added chemicals.
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Affiliation(s)
- Zhiguo Liu
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824-1323 USA
| | - Tolutola Oyetunde
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Whitney D. Hollinshead
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Anna Hermanns
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824-1323 USA
- Department of Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Yinjie J. Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Wei Liao
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824-1323 USA
| | - Yan Liu
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824-1323 USA
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Schievano A, Pepé Sciarria T, Vanbroekhoven K, De Wever H, Puig S, Andersen SJ, Rabaey K, Pant D. Electro-Fermentation – Merging Electrochemistry with Fermentation in Industrial Applications. Trends Biotechnol 2016; 34:866-878. [DOI: 10.1016/j.tibtech.2016.04.007] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 11/17/2022]
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15
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Zobel S, Kuepper J, Ebert B, Wierckx N, Blank LM. Metabolic response of Pseudomonas putida to increased NADH regeneration rates. Eng Life Sci 2016; 17:47-57. [PMID: 32624728 DOI: 10.1002/elsc.201600072] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/19/2016] [Accepted: 08/10/2016] [Indexed: 11/08/2022] Open
Abstract
Pseudomonas putida efficiently utilizes many different carbon sources without the formation of byproducts even under conditions of stress. This implies a high degree of flexibility to cope with conditions that require a significantly altered distribution of carbon to either biomass or energy in the form of NADH. In the literature, co-feeding of the reduced C1 compound formate to Escherichia coli heterologously expressing the NAD+-dependent formate dehydrogenase of the yeast Candida boidinii was demonstrated to boost various NADH-demanding applications. Pseudomonas putida as emerging biotechnological workhorse is inherently equipped with an NAD+-dependent formate dehydrogenase encouraging us to investigate the use of formate and its effect on P. putida's metabolism. Hence, this study provides a detailed insight into the co-utilization of formate and glucose by P. putida. Our results show that the addition of formate leads to a high increase in the NADH regeneration rate resulting in a very high biomass yield on glucose. Metabolic flux analysis revealed a significant flux rerouting from catabolism to anabolism. These metabolic insights argue further for P. putida as a host for redox cofactor demanding bioprocesses.
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Affiliation(s)
- Sebastian Zobel
- Institute of Applied Microbiology - iAMB RWTH Aachen University - ABBt Aachen Germany
| | - Jannis Kuepper
- Institute of Applied Microbiology - iAMB RWTH Aachen University - ABBt Aachen Germany
| | - Birgitta Ebert
- Institute of Applied Microbiology - iAMB RWTH Aachen University - ABBt Aachen Germany
| | - Nick Wierckx
- Institute of Applied Microbiology - iAMB RWTH Aachen University - ABBt Aachen Germany
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB RWTH Aachen University - ABBt Aachen Germany
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16
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Chomvong K, Bauer S, Benjamin DI, Li X, Nomura DK, Cate JHD. Bypassing the Pentose Phosphate Pathway: Towards Modular Utilization of Xylose. PLoS One 2016; 11:e0158111. [PMID: 27336308 PMCID: PMC4918971 DOI: 10.1371/journal.pone.0158111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/12/2016] [Indexed: 12/22/2022] Open
Abstract
The efficient use of hemicellulose in the plant cell wall is critical for the economic conversion of plant biomass to renewable fuels and chemicals. Previously, the yeast Saccharomyces cerevisiae has been engineered to convert the hemicellulose-derived pentose sugars xylose and arabinose to d-xylulose-5-phosphate for conversion via the pentose phosphate pathway (PPP). However, efficient pentose utilization requires PPP optimization and may interfere with its roles in NADPH and pentose production. Here, we developed an alternative xylose utilization pathway that largely bypasses the PPP. In the new pathway, d-xylulose is converted to d-xylulose-1-phosphate, a novel metabolite to S. cerevisiae, which is then cleaved to glycolaldehyde and dihydroxyacetone phosphate. This synthetic pathway served as a platform for the biosynthesis of ethanol and ethylene glycol. The use of d-xylulose-1-phosphate as an entry point for xylose metabolism opens the way for optimizing chemical conversion of pentose sugars in S. cerevisiae in a modular fashion.
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Affiliation(s)
- Kulika Chomvong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - Stefan Bauer
- Energy Biosciences Institute, Berkeley, CA, United States of America
| | - Daniel I. Benjamin
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, United States of America
| | - Xin Li
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
| | - Daniel K. Nomura
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, United States of America
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
- Department of Chemistry, University of California, Berkeley, CA, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- * E-mail:
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17
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van Rossum HM, Kozak BU, Pronk JT, van Maris AJA. Engineering cytosolic acetyl-coenzyme A supply in Saccharomyces cerevisiae: Pathway stoichiometry, free-energy conservation and redox-cofactor balancing. Metab Eng 2016; 36:99-115. [PMID: 27016336 DOI: 10.1016/j.ymben.2016.03.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/20/2016] [Accepted: 03/21/2016] [Indexed: 11/18/2022]
Abstract
Saccharomyces cerevisiae is an important industrial cell factory and an attractive experimental model for evaluating novel metabolic engineering strategies. Many current and potential products of this yeast require acetyl coenzyme A (acetyl-CoA) as a precursor and pathways towards these products are generally expressed in its cytosol. The native S. cerevisiae pathway for production of cytosolic acetyl-CoA consumes 2 ATP equivalents in the acetyl-CoA synthetase reaction. Catabolism of additional sugar substrate, which may be required to generate this ATP, negatively affects product yields. Here, we review alternative pathways that can be engineered into yeast to optimize supply of cytosolic acetyl-CoA as a precursor for product formation. Particular attention is paid to reaction stoichiometry, free-energy conservation and redox-cofactor balancing of alternative pathways for acetyl-CoA synthesis from glucose. A theoretical analysis of maximally attainable yields on glucose of four compounds (n-butanol, citric acid, palmitic acid and farnesene) showed a strong product dependency of the optimal pathway configuration for acetyl-CoA synthesis. Moreover, this analysis showed that combination of different acetyl-CoA production pathways may be required to achieve optimal product yields. This review underlines that an integral analysis of energy coupling and redox-cofactor balancing in precursor-supply and product-formation pathways is crucial for the design of efficient cell factories.
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Affiliation(s)
- Harmen M van Rossum
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Barbara U Kozak
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
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18
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Jayakody LN, Lane S, Kim H, Jin YS. Mitigating health risks associated with alcoholic beverages through metabolic engineering. Curr Opin Biotechnol 2016; 37:173-181. [PMID: 26760759 DOI: 10.1016/j.copbio.2015.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/24/2015] [Accepted: 12/01/2015] [Indexed: 10/22/2022]
Abstract
Epidemiological studies have established a positive relationship between the occurrence of cancer and consumption of alcoholic beverages. Metabolic engineering of brewing yeast to reduce potential carcinogenic compounds in alcoholic beverage is technically feasible as well as economically promising. This review presents the mechanisms of formation of potentially carcinogenic components in alcoholic beverages, such as formaldehyde, acetaldehyde, ethyl carbamate, acrylamide, and heavy metals, and introduces effective genetic perturbations to minimize the concentrations of these harmful components. As precise and effective genome editing tools for polyploid yeast are now available, we envision that yeast metabolic engineering might open up new research directions for improving brewing yeast in order to ensure product safety as well as to increase overall quality of alcoholic beverages.
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Affiliation(s)
- Lahiru N Jayakody
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephan Lane
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Heejin Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea.
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19
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Rebalancing Redox to Improve Biobutanol Production by Clostridium tyrobutyricum. Bioengineering (Basel) 2015; 3:bioengineering3010002. [PMID: 28952564 PMCID: PMC5597160 DOI: 10.3390/bioengineering3010002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/24/2015] [Accepted: 12/18/2015] [Indexed: 12/26/2022] Open
Abstract
Biobutanol is a sustainable green biofuel that can substitute for gasoline. Carbon flux has been redistributed in Clostridium tyrobutyricum via metabolic cell engineering to produce biobutanol. However, the lack of reducing power hampered the further improvement of butanol production. The objective of this study was to improve butanol production by rebalancing redox. Firstly, a metabolically-engineered mutant CTC-fdh-adhE2 was constructed by introducing heterologous formate dehydrogenase (fdh) and bifunctional aldehyde/alcohol dehydrogenase (adhE2) simultaneously into wild-type C. tyrobutyricum. The mutant evaluation indicated that the fdh-catalyzed NADH-producing pathway improved butanol titer by 2.15-fold in the serum bottle and 2.72-fold in the bioreactor. Secondly, the medium supplements that could shift metabolic flux to improve the production of butyrate or butanol were identified, including vanadate, acetamide, sodium formate, vitamin B12 and methyl viologen hydrate. Finally, the free-cell fermentation produced 12.34 g/L of butanol from glucose using the mutant CTC-fdh-adhE2, which was 3.88-fold higher than that produced by the control mutant CTC-adhE2. This study demonstrated that the redox engineering in C. tyrobutyricum could greatly increase butanol production.
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20
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Lee JY, Kang CD, Lee SH, Park YK, Cho KM. Engineering cellular redox balance inSaccharomyces cerevisiaefor improved production of L-lactic acid. Biotechnol Bioeng 2015; 112:751-8. [DOI: 10.1002/bit.25488] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/28/2014] [Accepted: 10/21/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Ju Young Lee
- Biomaterials Laboratory; Samsung Advanced Institute of Technology; Gyeonggi-do Korea
| | - Chang Duk Kang
- Biomaterials Laboratory; Samsung Advanced Institute of Technology; Gyeonggi-do Korea
| | - Seung Hyun Lee
- Biomaterials Laboratory; Samsung Advanced Institute of Technology; Gyeonggi-do Korea
| | - Young Kyoung Park
- Biomaterials Laboratory; Samsung Advanced Institute of Technology; Gyeonggi-do Korea
| | - Kwang Myung Cho
- Biomaterials Laboratory; Samsung Advanced Institute of Technology; Gyeonggi-do Korea
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21
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Xiao H, Shao Z, Jiang Y, Dole S, Zhao H. Exploiting Issatchenkia orientalis SD108 for succinic acid production. Microb Cell Fact 2014; 13:121. [PMID: 25159171 PMCID: PMC4244060 DOI: 10.1186/s12934-014-0121-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/10/2014] [Indexed: 11/23/2022] Open
Abstract
Background Recent advances in synthesizing valuable chemicals such as organic acids from low-cost renewable biomass through microbial fermentation have attracted great attention. However, the toxicity of organic acids presents a key challenge to the development of an economically viable fermentation process. Therefore, a platform organism that not only produces organic acids but also tolerates the associated toxicity is highly desirable. Results Here we report the discovery, characterization, and engineering of a yeast strain, Issatchenkia orientalis SD108, that is tolerant to low pH and high concentration of organic acids. This strain demonstrated a higher tolerance compared to I. orientalis ATCC 24210 and Classic Distiller’s Turbo yeast. In order to explore SD108 as a potential platform organism for organic acid production, we determined its draft genome sequence and use the sequencing information to guide pathway design. As proof of concept, an engineered four-gene expression cassette related to the reductive TCA cycle was assembled and integrated into the genome of a uracil auxotroph of SD108. The resulting strain was able to produce succinic acid with a titer of 11.63 g/L, yield of 0.12 g/g, and productivity of 0.11 g/L · h in batch cultures using shake flasks. Conclusions The high tolerance of I. orientalis SD108 towards multiple important organic acids makes it a highly attractive organism as a platform host for producing this group of compounds as it will reduce production cost, facilitate downstream processing, and serve as a host for construction of production strains with both pH and specific anion tolerance. Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0121-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana 61801, IL, USA.
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22
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van Heerden JH, Wortel MT, Bruggeman FJ, Heijnen JJ, Bollen YJM, Planqué R, Hulshof J, O'Toole TG, Wahl SA, Teusink B. Lost in transition: start-up of glycolysis yields subpopulations of nongrowing cells. Science 2014; 343:1245114. [PMID: 24436182 DOI: 10.1126/science.1245114] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cells need to adapt to dynamic environments. Yeast that fail to cope with dynamic changes in the abundance of glucose can undergo growth arrest. We show that this failure is caused by imbalanced reactions in glycolysis, the essential pathway in energy metabolism in most organisms. The imbalance arises largely from the fundamental design of glycolysis, making this state of glycolysis a generic risk. Cells with unbalanced glycolysis coexisted with vital cells. Spontaneous, nongenetic metabolic variability among individual cells determines which state is reached and, consequently, which cells survive. Transient ATP (adenosine 5'-triphosphate) hydrolysis through futile cycling reduces the probability of reaching the imbalanced state. Our results reveal dynamic behavior of glycolysis and indicate that cell fate can be determined by heterogeneity purely at the metabolic level.
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Affiliation(s)
- Johan H van Heerden
- Systems Bioinformatics/Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)/Netherlands Institute for Systems Biology, VU University, De Boelelaan 1085, 1081 HV Amsterdam, Netherlands
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23
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24
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Kozak BU, van Rossum HM, Benjamin KR, Wu L, Daran JMG, Pronk JT, van Maris AJA. Replacement of the Saccharomyces cerevisiae acetyl-CoA synthetases by alternative pathways for cytosolic acetyl-CoA synthesis. Metab Eng 2013; 21:46-59. [PMID: 24269999 DOI: 10.1016/j.ymben.2013.11.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 10/03/2013] [Accepted: 11/11/2013] [Indexed: 10/26/2022]
Abstract
Cytosolic acetyl-coenzyme A is a precursor for many biotechnologically relevant compounds produced by Saccharomyces cerevisiae. In this yeast, cytosolic acetyl-CoA synthesis and growth strictly depend on expression of either the Acs1 or Acs2 isoenzyme of acetyl-CoA synthetase (ACS). Since hydrolysis of ATP to AMP and pyrophosphate in the ACS reaction constrains maximum yields of acetyl-CoA-derived products, this study explores replacement of ACS by two ATP-independent pathways for acetyl-CoA synthesis. After evaluating expression of different bacterial genes encoding acetylating acetaldehyde dehydrogenase (A-ALD) and pyruvate-formate lyase (PFL), acs1Δ acs2Δ S. cerevisiae strains were constructed in which A-ALD or PFL successfully replaced ACS. In A-ALD-dependent strains, aerobic growth rates of up to 0.27 h(-1) were observed, while anaerobic growth rates of PFL-dependent S. cerevisiae (0.20 h(-1)) were stoichiometrically coupled to formate production. In glucose-limited chemostat cultures, intracellular metabolite analysis did not reveal major differences between A-ALD-dependent and reference strains. However, biomass yields on glucose of A-ALD- and PFL-dependent strains were lower than those of the reference strain. Transcriptome analysis suggested that reduced biomass yields were caused by acetaldehyde and formate in A-ALD- and PFL-dependent strains, respectively. Transcript profiles also indicated that a previously proposed role of Acs2 in histone acetylation is probably linked to cytosolic acetyl-CoA levels rather than to direct involvement of Acs2 in histone acetylation. While demonstrating that yeast ACS can be fully replaced, this study demonstrates that further modifications are needed to achieve optimal in vivo performance of the alternative reactions for supply of cytosolic acetyl-CoA as a product precursor.
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Affiliation(s)
- Barbara U Kozak
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Harmen M van Rossum
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | | | - Liang Wu
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands.
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25
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Laluce C, Schenberg ACG, Gallardo JCM, Coradello LFC, Pombeiro-Sponchiado SR. Advances and Developments in Strategies to Improve Strains of Saccharomyces cerevisiae and Processes to Obtain the Lignocellulosic Ethanol−A Review. Appl Biochem Biotechnol 2012; 166:1908-26. [DOI: 10.1007/s12010-012-9619-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
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26
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Farhana A, Guidry L, Srivastava A, Singh A, Hondalus MK, Steyn AJC. Reductive stress in microbes: implications for understanding Mycobacterium tuberculosis disease and persistence. Adv Microb Physiol 2011; 57:43-117. [PMID: 21078441 DOI: 10.1016/b978-0-12-381045-8.00002-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is a remarkably successful pathogen that is capable of persisting in host tissues for decades without causing disease. Years after initial infection, the bacilli may resume growth, the outcome of which is active tuberculosis (TB). In order to establish infection, resist host defences and re-emerge, Mtb must coordinate its metabolism with the in vivo environmental conditions and nutrient availability within the primary site of infection, the lung. Maintaining metabolic homeostasis for an intracellular pathogen such as Mtb requires a carefully orchestrated series of oxidation-reduction reactions, which, if unbalanced, generate oxidative or reductive stress. The importance of oxidative stress in microbial pathogenesis has been appreciated and well studied over the past several decades. However, the role of its counterpart, reductive stress, has been largely ignored. Reductive stress is defined as an aberrant increase in reducing equivalents, the magnitude and identity of which is determined by host carbon source utilisation and influenced by the presence of host-generated gases (e.g. NO, CO, O(2) and CO(2)). This increased reductive power must be dissipated for bacterial survival. To recycle reducing equivalents, microbes have evolved unique electron 'sinks' that are distinct for their particular environmental niche. In this review, we describe the specific mechanisms that some microbes have evolved to dispel reductive stress. The intention of this review is to introduce the concept of reductive stress, in tuberculosis research in particular, in the hope of stimulating new avenues of investigation.
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Affiliation(s)
- Aisha Farhana
- Department of Microbiology, University of Alabama at Birmingham, AL, USA
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27
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Hasunuma T, Sung KM, Sanda T, Yoshimura K, Matsuda F, Kondo A. Efficient fermentation of xylose to ethanol at high formic acid concentrations by metabolically engineered Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2011; 90:997-1004. [DOI: 10.1007/s00253-011-3085-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 12/17/2010] [Accepted: 12/22/2010] [Indexed: 01/10/2023]
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Metabolic impact of increased NADH availability in Saccharomyces cerevisiae. Appl Environ Microbiol 2009; 76:851-9. [PMID: 20023106 DOI: 10.1128/aem.02040-09] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Engineering the level of metabolic cofactors to manipulate metabolic flux is emerging as an attractive strategy for bioprocess applications. We present the metabolic consequences of increasing NADH in the cytosol and the mitochondria of Saccharomyces cerevisiae. In a strain that was disabled in formate metabolism, we either overexpressed the native NAD(+)-dependent formate dehydrogenase in the cytosol or directed it into the mitochondria by fusing it with the mitochondrial signal sequence encoded by the CYB2 gene. Upon exposure to formate, the mutant strains readily consumed formate and induced fermentative metabolism even under conditions of glucose derepression. Cytosolic overexpression of formate dehydrogenase resulted in the production of glycerol, while when this enzyme was directed into the mitochondria, we observed glycerol and ethanol production. Clearly, these results point toward different patterns of compartmental regulation of redox homeostasis. When pulsed with formate, S. cerevisiae cells growing in a steady state on glucose immediately consumed formate. However, formate consumption ceased after 20 min. Our analysis revealed that metabolites at key branch points of metabolic pathways were affected the most by the genetic perturbations and that the intracellular concentrations of sugar phosphates were specifically affected by time. In conclusion, the results have implications for the design of metabolic networks in yeast for industrial applications.
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Elimination of glycerol production in anaerobic cultures of a Saccharomyces cerevisiae strain engineered to use acetic acid as an electron acceptor. Appl Environ Microbiol 2009; 76:190-5. [PMID: 19915031 DOI: 10.1128/aem.01772-09] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In anaerobic cultures of wild-type Saccharomyces cerevisiae, glycerol production is essential to reoxidize NADH produced in biosynthetic processes. Consequently, glycerol is a major by-product during anaerobic production of ethanol by S. cerevisiae, the single largest fermentation process in industrial biotechnology. The present study investigates the possibility of completely eliminating glycerol production by engineering S. cerevisiae such that it can reoxidize NADH by the reduction of acetic acid to ethanol via NADH-dependent reactions. Acetic acid is available at significant amounts in lignocellulosic hydrolysates of agricultural residues. Consistent with earlier studies, deletion of the two genes encoding NAD-dependent glycerol-3-phosphate dehydrogenase (GPD1 and GPD2) led to elimination of glycerol production and an inability to grow anaerobically. However, when the E. coli mhpF gene, encoding the acetylating NAD-dependent acetaldehyde dehydrogenase (EC 1.2.1.10; acetaldehyde+NAD++coenzyme A<-->acetyl coenzyme A+NADH+H+), was expressed in the gpd1Delta gpd2Delta strain, anaerobic growth was restored by supplementation with 2.0 g liter(-1) acetic acid. The stoichiometry of acetate consumption and growth was consistent with the complete replacement of glycerol formation by acetate reduction to ethanol as the mechanism for NADH reoxidation. This study provides a proof of principle for the potential of this metabolic engineering strategy to improve ethanol yields, eliminate glycerol production, and partially convert acetate, which is a well-known inhibitor of yeast performance in lignocellulosic hydrolysates, to ethanol. Further research should address the kinetic aspects of acetate reduction and the effect of the elimination of glycerol production on cellular robustness (e.g., osmotolerance).
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30
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Enantioselective synthesis of ethyl (S)-2-hydroxy-4-phenylbutyrate by recombinant diketoreductase. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.10.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Hou J, Lages NF, Oldiges M, Vemuri GN. Metabolic impact of redox cofactor perturbations in Saccharomyces cerevisiae. Metab Eng 2009; 11:253-61. [PMID: 19446033 DOI: 10.1016/j.ymben.2009.05.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 04/09/2009] [Accepted: 05/05/2009] [Indexed: 01/29/2023]
Abstract
Redox cofactors play a pivotal role in coupling catabolism with anabolism and energy generation during metabolism. There exists a delicate balance in the intracellular level of these cofactors to ascertain an optimal metabolic output. Therefore, cofactors are emerging to be attractive targets to induce widespread changes in metabolism. We present a detailed analysis of the impact of perturbations in redox cofactors in the cytosol or mitochondria on glucose and energy metabolism in Saccharomyces cerevisiae to aid metabolic engineering decisions that involve cofactor engineering. We enhanced NADH oxidation by introducing NADH oxidase or alternative oxidase, its ATP-mediated conversion to NADPH using NADH kinase as well as the interconversion of NADH and NADPH independent of ATP by the soluble, non-proton-translocating bacterial transhydrogenase. Decreasing cytosolic NADH level lowered glycerol production, while decreasing mitochondrial NADH lowered ethanol production. However, when these reactions were coupled with NADPH production, the metabolic changes were more moderated. The direct consequence of these perturbations could be seen in the shift of the intracellular concentrations of the cofactors. The changes in product profile and intracellular metabolite levels were closely linked to the ATP requirement for biomass synthesis and the efficiency of oxidative phosphorylation, as estimated from a simple stoichiometric model. The results presented here will provide valuable insights for a quantitative understanding and prediction of cellular response to redox-based perturbations for metabolic engineering applications.
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Affiliation(s)
- Jin Hou
- Center for Microbial Biotechnology, BioSys, Technical University of Denmark, Lyngby 2800, Denmark
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Wu X, Liu N, He Y, Chen Y. Cloning, expression, and characterization of a novel diketoreductase from Acinetobacter baylyi. Acta Biochim Biophys Sin (Shanghai) 2009; 41:163-70. [PMID: 19204834 DOI: 10.1093/abbs/gmn019] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Reductions of carbonyl groups catalyzed by oxidoreductases are involved in all biological processes and are often a class of important biocatalyst. In this article, we report a novel enzyme designated as diketoreductase (DKR) that was able to reduce two carbonyl groups in a diketo ester to corresponding dihydroxy ester with excellent stereoselectivity. The DKR was cloned from Acinetobacter baylyi by reverse genetic method, heterogeneously expressed in Escherichia coli, and purified to homogeneity by two chromatographic steps. This novel enzyme exhibited dual cofactor specificity, with a preference of NADH over NADPH. The dihydroxy ester product catalyzed by the DKR was only 3R,5S-stereoisomer with both diastereomeric excess and enantiomeric excess values more than 99.5%. In addition, some biochemical properties of the enzyme, such as the optimal pH and temperature, were also characterized. Furthermore, sequence analysis indicated that this new enzyme was homologous to bacterial 3-hydroxyacyl coenzyme-A dehydrogenase. More importantly, based on the unique catalytic activity and excellent stereoselectivity, the DKR could be utilized in the synthesis of valuable chiral drug intermediates, such as Lipitor.
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Affiliation(s)
- Xuri Wu
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
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Engineering and analysis of a Saccharomyces cerevisiae strain that uses formaldehyde as an auxiliary substrate. Appl Environ Microbiol 2008; 74:3182-8. [PMID: 18378663 DOI: 10.1128/aem.02858-07] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We demonstrated that formaldehyde can be efficiently coutilized by an engineered Saccharomyces cerevisiae strain that expresses Hansenula polymorpha genes encoding formaldehyde dehydrogenase (FLD1) and formate dehydrogenase (FMD), in contrast to wild-type strains. Initial chemostat experiments showed that the engineered strain coutilized formaldehyde with glucose, but these mixed-substrate cultures failed to reach steady-state conditions and did not exhibit an increased biomass yield on glucose. Subsequent transcriptome analyses of chemostat cultures of the engineered strain, grown on glucose-formaldehyde mixtures, indicated that the presence of formaldehyde in the feed caused biotin limitations. Further transcriptome analysis demonstrated that this biotin inactivation was prevented by using separate formaldehyde and vitamin feeds. Using this approach, steady-state glucose-limited chemostat cultures were obtained that coutilized glucose and formaldehyde. Coutilization of formaldehyde under these conditions resulted in an enhanced biomass yield of the glucose-limited cultures. The biomass yield was quantitatively consistent with the use of formaldehyde as an auxiliary substrate that generates NADH and subsequently, via oxidative phosphorylation, ATP. On an electron pair basis, the biomass yield increase observed with formaldehyde was larger than that observed previously for formate, which is tentatively explained by different modes of formate and formaldehyde transport in S. cerevisiae.
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Harris DM, van der Krogt ZA, van Gulik WM, van Dijken JP, Pronk JT. Formate as an auxiliary substrate for glucose-limited cultivation of Penicillium chrysogenum: impact on penicillin G production and biomass yield. Appl Environ Microbiol 2007; 73:5020-5. [PMID: 17545326 PMCID: PMC1951027 DOI: 10.1128/aem.00093-07] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Production of beta-lactams by the filamentous fungus Penicillium chrysogenum requires a substantial input of ATP. During glucose-limited growth, this ATP is derived from glucose dissimilation, which reduces the product yield on glucose. The present study has investigated whether penicillin G yields on glucose can be enhanced by cofeeding of an auxiliary substrate that acts as an energy source but not as a carbon substrate. As a model system, a high-producing industrial strain of P. chrysogenum was grown in chemostat cultures on mixed substrates containing different molar ratios of formate and glucose. Up to a formate-to-glucose ratio of 4.5 mol.mol(-1), an increasing rate of formate oxidation via a cytosolic NAD(+)-dependent formate dehydrogenase increasingly replaced the dissimilatory flow of glucose. This resulted in increased biomass yields on glucose. Since at these formate-to-glucose ratios the specific penicillin G production rate remained constant, the volumetric productivity increased. Metabolic modeling studies indicated that formate transport in P. chrysogenum does not require an input of free energy. At formate-to-glucose ratios above 4.5 mol.mol(-1), the residual formate concentrations in the cultures increased, probably due to kinetic constraints in the formate-oxidizing system. The accumulation of formate coincided with a loss of the coupling between formate oxidation and the production of biomass and penicillin G. These results demonstrate that, in principle, mixed-substrate feeding can be used to increase the yield on a carbon source of assimilatory products such as beta-lactams.
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Affiliation(s)
- Diana M Harris
- Delft University of Technology, Department of Biotechnology, Julianalaan 67, Delft, The Netherlands
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Geertman JMA, van Maris AJA, van Dijken JP, Pronk JT. Physiological and genetic engineering of cytosolic redox metabolism in Saccharomyces cerevisiae for improved glycerol production. Metab Eng 2006; 8:532-42. [PMID: 16891140 DOI: 10.1016/j.ymben.2006.06.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Revised: 06/11/2006] [Accepted: 06/21/2006] [Indexed: 11/28/2022]
Abstract
Previous metabolic engineering strategies for improving glycerol production by Saccharomyces cerevisiae were constrained to a maximum theoretical glycerol yield of 1 mol.(molglucose)(-1) due to the introduction of rigid carbon, ATP or redox stoichiometries. In the present study, we sought to circumvent these constraints by (i) maintaining flexibility at fructose-1,6-bisphosphatase and triosephosphate isomerase, while (ii) eliminating reactions that compete with glycerol formation for cytosolic NADH and (iii) enabling oxidative catabolism within the mitochondrial matrix. In aerobic, glucose-grown batch cultures a S. cerevisiae strain, in which the pyruvate decarboxylases the external NADH dehydrogenases and the respiratory chain-linked glycerol-3-phosphate dehydrogenase were deleted for this purpose, produced glycerol at a yield of 0.90 mol.(molglucose)(-1). In aerobic glucose-limited chemostat cultures, the glycerol yield was ca. 25% lower, suggesting the involvement of an alternative glucose-sensitive mechanism for oxidation of cytosolic NADH. Nevertheless, in vivo generation of additional cytosolic NADH by co-feeding of formate to aerobic, glucose-limited chemostat cultures increased the glycerol yield on glucose to 1.08 mol mol(-1). To our knowledge, this is the highest glycerol yield reported for S. cerevisiae.
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Affiliation(s)
- Jan-Maarten A Geertman
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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