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Billingsley JM, DeNicola AB, Barber JS, Tang MC, Horecka J, Chu A, Garg NK, Tang Y. Engineering the biocatalytic selectivity of iridoid production in Saccharomyces cerevisiae. Metab Eng 2017; 44:117-125. [PMID: 28939278 DOI: 10.1016/j.ymben.2017.09.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/13/2017] [Indexed: 12/11/2022]
Abstract
Monoterpene indole alkaloids (MIAs) represent a structurally diverse, medicinally essential class of plant derived natural products. The universal MIA building block strictosidine was recently produced in the yeast Saccharomyces cerevisiae, setting the stage for optimization of microbial production. However, the irreversible reduction of pathway intermediates by yeast enzymes results in a non-recoverable loss of carbon, which has a strong negative impact on metabolic flux. In this study, we identified and engineered the determinants of biocatalytic selectivity which control flux towards the iridoid scaffold from which all MIAs are derived. Development of a bioconversion based production platform enabled analysis of the metabolic flux and interference around two critical steps in generating the iridoid scaffold: oxidation of 8-hydroxygeraniol to the dialdehyde 8-oxogeranial followed by reductive cyclization to form nepetalactol. In vitro reconstitution of previously uncharacterized shunt pathways enabled the identification of two distinct routes to a reduced shunt product including endogenous 'ene'-reduction and non-productive reduction by iridoid synthase when interfaced with endogenous alcohol dehydrogenases. Deletion of five genes involved in α,β-unsaturated carbonyl metabolism resulted in a 5.2-fold increase in biocatalytic selectivity of the desired iridoid over reduced shunt product. We anticipate that our engineering strategies will play an important role in the development of S. cerevisiae for sustainable production of iridoids and MIAs.
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Affiliation(s)
- John M Billingsley
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States
| | - Anthony B DeNicola
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States
| | - Joyann S Barber
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States
| | - Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States
| | - Joe Horecka
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, United States; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Angela Chu
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, United States; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Neil K Garg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States.
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Alvarenga N, Porto ALM. Stereoselective reduction of 2-azido-1-phenylethanone derivatives by whole cells of marine-derived fungi applied to synthesis of enantioenriched β-hydroxy-1,2,3-triazoles. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1352585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Natália Alvarenga
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - André L. M. Porto
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, Brazil
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104
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Löbs AK, Engel R, Schwartz C, Flores A, Wheeldon I. CRISPR-Cas9-enabled genetic disruptions for understanding ethanol and ethyl acetate biosynthesis in Kluyveromyces marxianus. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:164. [PMID: 28652865 PMCID: PMC5483312 DOI: 10.1186/s13068-017-0854-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/16/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND The thermotolerant yeast Kluyveromyces marxianus shows promise as an industrial host for the biochemical production of fuels and chemicals. Wild-type strains are known to ferment high titers of ethanol and can effectively convert a wide range of C5, C6, and C12 sugars into the volatile short-chain ester ethyl acetate. Strain engineering, however, has been limited due to a lack of advanced genome-editing tools and an incomplete understanding of ester and ethanol biosynthesis. RESULTS Enabled by the design of hybrid RNA polymerase III promoters, this work adapts the CRISPR-Cas9 system from Streptococcus pyogenes for use in K. marxianus. The system was used to rapidly create functional disruptions to alcohol dehydrogenase (ADH) and alcohol-O-acetyltransferase (ATF) genes with putative function in ethyl acetate and ethanol biosynthesis. Screening of the KmATF disrupted strain revealed that Atf activity contributes to ethyl acetate biosynthesis, but the knockout reduced ethyl acetate titers by only ~15%. Overexpression experiments revealed that KmAdh7 can catalyze the oxidation of hemiacetal to ethyl acetate. Finally, analysis of the KmADH2 disrupted strain showed that the knockout almost completely eliminated ethanol production and resulted in the accumulation of acetaldehyde. CONCLUSIONS Newly designed RNA polymerase III promoters for sgRNA expression in K. marxianus enable a CRISPR-Cas9 genome-editing system for the thermotolerant yeast. This system was used to disrupt genes involved in ethyl acetate biosynthesis, specifically KmADH1-7 and KmATF. KmAdh2 was found to be critical for aerobic and anaerobic ethanol production. Aerobically produced ethanol supplies the biosynthesis of ethyl acetate catalyzed by KmAtf. KmAdh7 was found to exhibit activity toward the oxidation of hemiacetal, a possible alternative route for the synthesis of ethyl acetate.
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Affiliation(s)
- Ann-Kathrin Löbs
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
| | - Ronja Engel
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
- Mannheim University of Applied Sciences, Mannheim, Germany
| | - Cory Schwartz
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
| | - Andrew Flores
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
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Metabolic pathway optimization for biosynthesis of 1,2,4-butanetriol from xylose by engineered Escherichia coli. Enzyme Microb Technol 2016; 93-94:51-58. [DOI: 10.1016/j.enzmictec.2016.07.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/16/2016] [Accepted: 07/18/2016] [Indexed: 12/22/2022]
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106
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Direct observation of redox reactions in Candida parapsilosis ATCC 7330 by Confocal microscopic studies. Sci Rep 2016; 6:34344. [PMID: 27739423 PMCID: PMC5064409 DOI: 10.1038/srep34344] [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: 05/19/2016] [Accepted: 09/13/2016] [Indexed: 11/09/2022] Open
Abstract
Confocal microscopic studies with the resting cells of yeast, Candida parapsilosis ATCC 7330, a reportedly versatile biocatalyst for redox enzyme mediated preparation of optically pure secondary alcohols in high optical purities [enantiomeric excess (ee) up to >99%] and yields, revealed that the yeast cells had large vacuoles under the experimental conditions studied where the redox reaction takes place. A novel fluorescence method was developed using 1-(6-methoxynaphthalen-2-yl)ethanol to track the site of biotransformation within the cells. This alcohol, itself non-fluorescent, gets oxidized to produce a fluorescent ketone, 1-(6-methoxynaphthalen-2-yl)ethanone. Kinetic studies showed that the reaction occurs spontaneously and the products get released out of the cells in less time [5 mins]. The biotransformation was validated using HPLC.
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Rauter M, Kasprzak J, Becker K, Riechen J, Worch S, Hartmann A, Mascher M, Scholz U, Baronian K, Bode R, Schauer F, Matthias Vorbrodt H, Kunze G. Aadh2p: an Arxula adeninivorans alcohol dehydrogenase involved in the first step of the 1-butanol degradation pathway. Microb Cell Fact 2016; 15:175. [PMID: 27733155 PMCID: PMC5062937 DOI: 10.1186/s12934-016-0573-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 09/28/2016] [Indexed: 11/24/2022] Open
Abstract
Background The non-conventional yeast Arxula adeninivorans uses 1-butanol as a carbon source and has recently attracted attention as a promising organism for 1-butanol production. Alcohol dehydrogenases (adhp) are important catalysts in 1-butanol metabolism, but only Aadh1p from Arxula has been characterized. This enzyme is involved in ethanol synthesis but has a low impact on 1-butanol degradation. Results In this study, we identified and characterized a second adhp from A. adeninivorans (Aadh2p). Compared to Saccharomyces cerevisiae ADHs’ (ScAdh) protein sequences it originates from the same ancestral node as ScAdh6p, 7p and 4p. It is also localized in the cytoplasm and uses NAD(H) as cofactor. The enzyme has its highest activity with medium chain-length alcohols and maximum activity with 1-butanol with the catalytic efficiency of the purified enzyme being 42 and 43,000 times higher than with ethanol and acetaldehyde, respectively. Arxula adeninivorans strain G1212/YRC102-AADH2, which expresses the AADH2 gene under the control of the strong constitutive TEF1 promoter was constructed. It achieved an ADH activity of up to 8000 U/L and 500 U/g dry cell weight (dcw) which is in contrast to the control strain G1212/YRC102 which had an ADH activity of up to 1400 U/L and 200 U/g dcw. Gene expression analysis showed that AADH2 derepression or induction using non-fermentable carbon-sources such as ethanol, pyruvate, glycerol or 1-butanol did occur. Compared to G1212/YRC102 AADH2 knock-out strain had a slower growth rate and lower 1-butanol consumption if 1-butanol was used as sole carbon source and AADH2-transformants did not grow at all in the same conditions. However, addition of the branched-chain amino acids leucine, isoleucine and valine allowed the transformants to use 1-butanol as carbon source. The addition of these amino acids to the control strain and Δaadh2 mutant cultures had the effect of accelerating 1-butanol consumption. Conclusions Our results confirm that Aadh2p plays a major role in A. adeninivorans 1-butanol metabolism. It is upregulated by up to 60-fold when the cells grow on 1-butanol, whereas only minor changes were found in the relative expression level for Aadh1p. Thus the constitutive overexpression of the AADH2 gene could be useful in the production of 1-butanol by A. adeninivorans, although it is likely that other ADHs will have to be knocked-out to prevent 1-butanol oxidation. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0573-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marion Rauter
- Orgentis Chemicals GmbH, Bahnhofstr. 3-5, 06466, Gatersleben, Germany
| | - Jakub Kasprzak
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Saxony-Anhalt, Germany
| | - Karin Becker
- Orgentis Chemicals GmbH, Bahnhofstr. 3-5, 06466, Gatersleben, Germany
| | - Jan Riechen
- Jäckering Mühlen-und Nährmittelwerke GmbH, Vorsterhauser Weg 46, 59007, Hamm, Germany
| | - Sebastian Worch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Saxony-Anhalt, Germany
| | - Anja Hartmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Saxony-Anhalt, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Saxony-Anhalt, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Saxony-Anhalt, Germany
| | - Kim Baronian
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Rüdiger Bode
- Institute of Microbiology, University of Greifswald, Jahnstr. 15, 17487, Greifswald, Germany
| | - Frieder Schauer
- Institute of Microbiology, University of Greifswald, Jahnstr. 15, 17487, Greifswald, Germany
| | | | - Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Saxony-Anhalt, Germany.
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108
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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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109
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Mao N, Nie S, Hong B, Li C, Shen X, Xiong T. Association between alcohol dehydrogenase-2 gene polymorphism and esophageal cancer risk: a meta-analysis. World J Surg Oncol 2016; 14:191. [PMID: 27450204 PMCID: PMC4957421 DOI: 10.1186/s12957-016-0937-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/08/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND It has been shown that gene polymorphisms may play an important role in the carcinogenesis of esophageal cancer. This study is to investigate the role of alcohol dehydrogenase 1B (ADH1B) gene Arg47His polymorphism in esophageal cancer susceptibility. METHODS Case-control studies published between January 2000 and June 2015 were searched to retrieve relevant articles. The pooled odds ratio (OR) and 95 % confidence interval (CI) were employed to calculate the strength of association. RESULTS A total of 23 relevant articles were finally selected for the analysis, including 9338 esophageal cancer patients and 14,896 matched controls. Overall, we found that the 47His allele was significant associated with the decreased risk of esophageal cancer when compared with the 47Arg allele in total populations (A vs. G: OR = 0.67, 95 % CI = 0.59-0.76, P < 0.00001). This protective relationship was observed under other genetic models as well (P < 0.00001). Subgroup analysis by ethnicity showed that ADH1B Arg47His variant was associated with the decreased esophageal cancer risk under all the genetic models (P < 0.00001) among Asians, especially in Chinese and Japanese; while in non-Asians, no significant correlation was detected in any genetic models (P > 0.05). Furthermore, Arg/Arg genotype of ADH1B Arg47His variant combined with drinking, smoking and males appeared to show a high risk in patients with esophageal cancer. CONCLUSIONS Our results suggested that ADH1B gene Arg47His variant was associated with the decreased esophageal cancer risk. Genetic-environmental interaction should be further considered in the future researches.
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Affiliation(s)
- Ning Mao
- />Department of Cardiothoracic Surgery, Yongchuan Hospital of Chongqing Medical University, No. 439 Xuanhua Road, Yongchuan District, Chongqing, 402160 China
| | - Siyao Nie
- />Department of Infectious Disease, Yongchuan Hospital of Chongqing Medical University, Chongqing, 402160 China
| | - Bin Hong
- />Department of Cardiothoracic Surgery, Yongchuan Hospital of Chongqing Medical University, No. 439 Xuanhua Road, Yongchuan District, Chongqing, 402160 China
| | - Chao Li
- />Department of Cardiothoracic Surgery, Yongchuan Hospital of Chongqing Medical University, No. 439 Xuanhua Road, Yongchuan District, Chongqing, 402160 China
| | - Xueyuan Shen
- />Department of Cardiothoracic Surgery, Yongchuan Hospital of Chongqing Medical University, No. 439 Xuanhua Road, Yongchuan District, Chongqing, 402160 China
| | - Tao Xiong
- />Department of Cardiothoracic Surgery, Yongchuan Hospital of Chongqing Medical University, No. 439 Xuanhua Road, Yongchuan District, Chongqing, 402160 China
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Yaacob N, Mohamad Ali MS, Salleh AB, Abdul Rahman NA. Effects of glucose, ethanol and acetic acid on regulation of ADH2 gene from Lachancea fermentati. PeerJ 2016; 4:e1751. [PMID: 26989608 PMCID: PMC4793307 DOI: 10.7717/peerj.1751] [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: 08/04/2015] [Accepted: 02/12/2016] [Indexed: 12/05/2022] Open
Abstract
Background. Not all yeast alcohol dehydrogenase 2 (ADH2) are repressed by glucose, as reported in Saccharomyces cerevisiae. Pichia stipitis ADH2 is regulated by oxygen instead of glucose, whereas Kluyveromyces marxianus ADH2 is regulated by neither glucose nor ethanol. For this reason, ADH2 regulation of yeasts may be species dependent, leading to a different type of expression and fermentation efficiency. Lachancea fermentati is a highly efficient ethanol producer, fast-growing cells and adapted to fermentation-related stresses such as ethanol and organic acid, but the metabolic information regarding the regulation of glucose and ethanol production is still lacking. Methods. Our investigation started with the stimulation of ADH2 activity from S. cerevisiae and L. fermentati by glucose and ethanol induction in a glucose-repressed medium. The study also embarked on the retrospective analysis of ADH2 genomic and protein level through direct sequencing and sites identification. Based on the sequence generated, we demonstrated ADH2 gene expression highlighting the conserved NAD(P)-binding domain in the context of glucose fermentation and ethanol production. Results. An increase of ADH2 activity was observed in starved L. fermentati (LfeADH2) and S. cerevisiae (SceADH2) in response to 2% (w/v) glucose induction. These suggest that in the presence of glucose, ADH2 activity was activated instead of being repressed. An induction of 0.5% (v/v) ethanol also increased LfeADH2 activity, promoting ethanol resistance, whereas accumulating acetic acid at a later stage of fermentation stimulated ADH2 activity and enhanced glucose consumption rates. The lack in upper stream activating sequence (UAS) and TATA elements hindered the possibility of Adr1 binding to LfeADH2. Transcription factors such as SP1 and RAP1 observed in LfeADH2 sequence have been implicated in the regulation of many genes including ADH2. In glucose fermentation, L. fermentati exhibited a bell-shaped ADH2 expression, showing the highest expression when glucose was depleted and ethanol-acetic acid was increased. Meanwhile, S. cerevisiae showed a constitutive ADH2 expression throughout the fermentation process. Discussion. ADH2 expression in L. fermentati may be subjected to changes in the presence of non-fermentative carbon source. The nucleotide sequence showed that ADH2 transcription could be influenced by other transcription genes of glycolysis oriented due to the lack of specific activation sites for Adr1. Our study suggests that if Adr1 is not capable of promoting LfeADH2 activation, the transcription can be controlled by Rap1 and Sp1 due to their inherent roles. Therefore in future, it is interesting to observe ADH2 gene being highly regulated by these potential transcription factors and functioned as a promoter for yeast under high volume of ethanol and organic acids.
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Affiliation(s)
- Norhayati Yaacob
- Department of Biochemistry, Universiti Putra Malaysia, Malaysia; Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Department of Biochemistry, Universiti Putra Malaysia, Malaysia; Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang, Malaysia
| | - Abu Bakar Salleh
- Department of Biochemistry, Universiti Putra Malaysia, Malaysia; Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang, Malaysia
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Varga MJ, Schwartz SD. Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations. J Chem Theory Comput 2016; 12:2047-54. [PMID: 26949835 DOI: 10.1021/acs.jctc.5b01169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, we develop and test a method to determine the rate of particle transfer and kinetic isotope effects in enzymatic reactions, specifically yeast alcohol dehydrogenase (YADH), from first-principles. Transition path sampling (TPS) and normal mode centroid dynamics (CMD) are used to simulate these enzymatic reactions without knowledge of their reaction coordinates and with the inclusion of quantum effects, such as zero-point energy and tunneling, on the transferring particle. Though previous studies have used TPS to calculate reaction rate constants in various model and real systems, it has not been applied to a system as large as YADH. The calculated primary H/D kinetic isotope effect agrees with previously reported experimental results, within experimental error. The kinetic isotope effects calculated with this method correspond to the kinetic isotope effect of the transfer event itself. The results reported here show that the kinetic isotope effects calculated from first-principles, purely for barrier passage, can be used to predict experimental kinetic isotope effects in enzymatic systems.
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Affiliation(s)
- Matthew J Varga
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
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112
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Lin JL, Zhu J, Wheeldon I. Rapid ester biosynthesis screening reveals a high activity alcohol-O-acyltransferase (AATase) from tomato fruit. Biotechnol J 2016; 11:700-7. [PMID: 26814045 DOI: 10.1002/biot.201500406] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/24/2015] [Accepted: 01/22/2016] [Indexed: 12/25/2022]
Abstract
Ethyl and acetate esters are naturally produced in various yeasts, plants, and bacteria. The biosynthetic pathways that produce these esters share a common reaction step, the condensation of acetyl/acyl-CoA with an alcohol by alcohol-O-acetyl/acyltransferase (AATase). Recent metabolic engineering efforts exploit AATase activity to produce fatty acid ethyl esters as potential diesel fuel replacements as well as short- and medium-chain volatile esters as fragrance and flavor compounds. These efforts have been limited by the lack of a rapid screen to quantify ester biosynthesis. Enzyme engineering efforts have also been limited by the lack of a high throughput screen for AATase activity. Here, we developed a high throughput assay for AATase activity and used this assay to discover a high activity AATase from tomato fruit, Solanum lycopersicum (Atf-S.l). Atf1-S.l exhibited broad specificity towards acyl-CoAs with chain length from C4 to C10 and was specific towards 1-pentanol. The AATase screen also revealed new acyl-CoA substrate specificities for Atf1, Atf2, Eht1, and Eeb1 from Saccharomyces cerevisiae, and Atf-C.m from melon fruit, Cucumis melo, thus increasing the pool of characterized AATases that can be used in ester biosynthesis of ester-based fragrance and flavor compounds as well as fatty acid ethyl ester biofuels.
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Affiliation(s)
- Jyun-Liang Lin
- Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Jie Zhu
- Biochemistry, University of California, Riverside, CA, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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113
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Yu AQ, Pratomo Juwono NK, Foo JL, Leong SSJ, Chang MW. Metabolic engineering of Saccharomyces cerevisiae for the overproduction of short branched-chain fatty acids. Metab Eng 2016; 34:36-43. [DOI: 10.1016/j.ymben.2015.12.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/14/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
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114
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Kasprzak J, Rauter M, Riechen J, Worch S, Baronian K, Bode R, Schauer F, Kunze G. Characterization of an Arxula adeninivorans alcohol dehydrogenase involved in the metabolism of ethanol and 1-butanol. FEMS Yeast Res 2016; 16:fow018. [PMID: 26912215 DOI: 10.1093/femsyr/fow018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2016] [Indexed: 01/25/2023] Open
Abstract
In this study, alcohol dehydrogenase 1 from Arxula adeninivorans (Aadh1p) was identified and characterized. Aadh1p showed activity with short and medium chain length primary alcohols in the forward reaction and their aldehydes in the reverse reaction. Aadh1p has 64% identity with Saccharomyces cerevisiae Adh1p, is localized in the cytoplasm and uses NAD(+) as cofactor. Gene expression analysis showed a low level increase in AADH1 gene expression with ethanol, pyruvate or xylose as the carbon source. Deletion of the AADH1 gene affects growth of the cells with 1-butanol, ethanol and glucose as the carbon source, and a strain which overexpressed the AADH1 gene metabolized 1-butanol more rapidly. An ADH activity assay indicated that Aadh1p is a major enzyme for the synthesis of ethanol and the degradation of 1-butanol in A. adeninivorans.
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Affiliation(s)
- Jakub Kasprzak
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correnstr. 3, D-06466 Gatersleben, Germany
| | - Marion Rauter
- Orgentis Chemicals GmbH, Bahnhofstr. 3-5, D-06466 Gatersleben, Germany
| | - Jan Riechen
- Jäckering Mühlen- und Nährmittelwerke GmbH, Vorsterhauser Weg 46, D-59007 Hamm, Germany
| | - Sebastian Worch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correnstr. 3, D-06466 Gatersleben, Germany
| | - Kim Baronian
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Rüdiger Bode
- Institute of Microbiology, University of Greifswald, Jahnstr. 15, D-17487 Greifswald, Germany
| | - Frieder Schauer
- Institute of Microbiology, University of Greifswald, Jahnstr. 15, D-17487 Greifswald, Germany
| | - Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correnstr. 3, D-06466 Gatersleben, Germany
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115
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Schifferdecker AJ, Siurkus J, Andersen MR, Joerck-Ramberg D, Ling Z, Zhou N, Blevins JE, Sibirny AA, Piškur J, Ishchuk OP. Alcohol dehydrogenase gene ADH3 activates glucose alcoholic fermentation in genetically engineered Dekkera bruxellensis yeast. Appl Microbiol Biotechnol 2016; 100:3219-31. [PMID: 26743658 PMCID: PMC4786601 DOI: 10.1007/s00253-015-7266-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/13/2015] [Accepted: 12/19/2015] [Indexed: 01/05/2023]
Abstract
Dekkera bruxellensis is a non-conventional Crabtree-positive yeast with a good ethanol production capability. Compared to Saccharomyces cerevisiae, its tolerance to acidic pH and its utilization of alternative carbon sources make it a promising organism for producing biofuel. In this study, we developed an auxotrophic transformation system and an expression vector, which enabled the manipulation of D. bruxellensis, thereby improving its fermentative performance. Its gene ADH3, coding for alcohol dehydrogenase, was cloned and overexpressed under the control of the strong and constitutive promoter TEF1. Our recombinant D. bruxellensis strain displayed 1.4 and 1.7 times faster specific glucose consumption rate during aerobic and anaerobic glucose fermentations, respectively; it yielded 1.2 times and 1.5 times more ethanol than did the parental strain under aerobic and anaerobic conditions, respectively. The overexpression of ADH3 in D. bruxellensis also reduced the inhibition of fermentation by anaerobiosis, the “Custer effect”. Thus, the fermentative capacity of D. bruxellensis could be further improved by metabolic engineering.
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Affiliation(s)
| | - Juozas Siurkus
- Department of Systems Biology, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Mikael Rørdam Andersen
- Department of Systems Biology, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Dorte Joerck-Ramberg
- Department of Systems Biology, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Zhihao Ling
- Department of Biology, Lund University, Sölvegatan 35, Lund, SE-223 62, Sweden
| | - Nerve Zhou
- Department of Biology, Lund University, Sölvegatan 35, Lund, SE-223 62, Sweden
| | - James E Blevins
- Consulting statistician, Pinnmöllevägen 48, SE-24755, Dalby, Sweden
| | - Andriy A Sibirny
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, Lviv, 79005, Ukraine.,Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowizca 4, Rzeszow, 35-601, Poland
| | - Jure Piškur
- Department of Biology, Lund University, Sölvegatan 35, Lund, SE-223 62, Sweden
| | - Olena P Ishchuk
- Department of Biology, Lund University, Sölvegatan 35, Lund, SE-223 62, Sweden.
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116
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Yin DT, Urresti S, Lafond M, Johnston EM, Derikvand F, Ciano L, Berrin JG, Henrissat B, Walton PH, Davies GJ, Brumer H. Structure-function characterization reveals new catalytic diversity in the galactose oxidase and glyoxal oxidase family. Nat Commun 2015; 6:10197. [PMID: 26680532 PMCID: PMC4703870 DOI: 10.1038/ncomms10197] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/16/2015] [Indexed: 11/09/2022] Open
Abstract
Alcohol oxidases, including carbohydrate oxidases, have a long history of research that has generated fundamental biological understanding and biotechnological applications. Despite a long history of study, the galactose 6-oxidase/glyoxal oxidase family of mononuclear copper-radical oxidases, Auxiliary Activity Family 5 (AA5), is currently represented by only very few characterized members. Here we report the recombinant production and detailed structure-function analyses of two homologues from the phytopathogenic fungi Colletotrichum graminicola and C. gloeosporioides, CgrAlcOx and CglAlcOx, respectively, to explore the wider biocatalytic potential in AA5. EPR spectroscopy and crystallographic analysis confirm a common active-site structure vis-à-vis the archetypal galactose 6-oxidase from Fusarium graminearum. Strikingly, however, CgrAlcOx and CglAlcOx are essentially incapable of oxidizing galactose and galactosides, but instead efficiently catalyse the oxidation of diverse aliphatic alcohols. The results highlight the significant potential of prospecting the evolutionary diversity of AA5 to reveal novel enzyme specificities, thereby informing both biology and applications.
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Affiliation(s)
- DeLu Tyler Yin
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Saioa Urresti
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Mickael Lafond
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada V6T 1Z4.,Institut des Sciences Moléculaires de Marseille-Team BiosCiences UMR 7313-CNRS, Aix-Marseille University, Avenue Escadrille Normandie Niemen, Marseille 13397, France
| | - Esther M Johnston
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Fatemeh Derikvand
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Luisa Ciano
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Jean-Guy Berrin
- INRA, UMR1163 Biodiversité et Biotechnologie Fongiques Marseille F-13288, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS-Aix-Marseille University, 163 Avenue de Luminy, Marseille 13288, France.,INRA, USC 1408 AFMB, Marseille 13288, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Paul H Walton
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Harry Brumer
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada V6T 1Z4
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117
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Karaoglan M, Karaoglan FE, Inan M. Functional analysis of alcohol dehydrogenase (ADH) genes in Pichia pastoris. Biotechnol Lett 2015; 38:463-9. [PMID: 26573637 DOI: 10.1007/s10529-015-1993-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/03/2015] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To characterize the genes responsible for ethanol utilization in Pichia pastoris. RESULTS ADH3 (XM_002491337) and ADH (FN392323) genes were disrupted in P. pastoris. The ADH3 mutant strain, MK115 (Δadh3), lost its ability to grow on minimal ethanol media but produced ethanol in minimal glucose medium. ADH3p was responsible for 92 % of total Adh enzyme activity in glucose media. The double knockout strain MK117 (Δadh3Δadh) also produced ethanol. The Adh activities of X33 and MK116 (Δadh) strains were not different. Thus, the ADH gene does not play a role in ethanol metabolism. CONCLUSION The PpADH3 is the only gene responsible for consumption of ethanol in P. pastoris.
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Affiliation(s)
- Mert Karaoglan
- Department of Food Engineering, Akdeniz University, Dumlupinar Bulvari Campus, 07058, Antalya, Turkey
| | - Fidan Erden Karaoglan
- Department of Food Engineering, Akdeniz University, Dumlupinar Bulvari Campus, 07058, Antalya, Turkey
| | - Mehmet Inan
- Department of Food Engineering, Akdeniz University, Dumlupinar Bulvari Campus, 07058, Antalya, Turkey.
- Food Safety and Agricultural Research Center, Akdeniz University, 07058, Antalya, Turkey.
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118
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Jin Z, Wong A, Foo JL, Ng J, Cao Y, Chang MW, Yuan Y. Engineering
Saccharomyces cerevisiae
to produce odd chain‐length fatty alcohols. Biotechnol Bioeng 2015; 113:842-51. [DOI: 10.1002/bit.25856] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 09/15/2015] [Accepted: 10/08/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Zhu Jin
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringSchool of Chemical Engineering and Technology, Tianjin UniversityTianjin300072PR China
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Adison Wong
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Jee Loon Foo
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Joey Ng
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Ying‐Xiu Cao
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringSchool of Chemical Engineering and Technology, Tianjin UniversityTianjin300072PR China
| | - Matthew Wook Chang
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Ying‐Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringSchool of Chemical Engineering and Technology, Tianjin UniversityTianjin300072PR China
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119
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Increasing anaerobic acetate consumption and ethanol yields in Saccharomyces cerevisiae with NADPH-specific alcohol dehydrogenase. Appl Environ Microbiol 2015; 81:8108-17. [PMID: 26386051 DOI: 10.1128/aem.01689-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/12/2015] [Indexed: 12/18/2022] Open
Abstract
Saccharomyces cerevisiae has recently been engineered to use acetate, a primary inhibitor in lignocellulosic hydrolysates, as a cosubstrate during anaerobic ethanolic fermentation. However, the original metabolic pathway devised to convert acetate to ethanol uses NADH-specific acetylating acetaldehyde dehydrogenase and alcohol dehydrogenase and quickly becomes constrained by limited NADH availability, even when glycerol formation is abolished. We present alcohol dehydrogenase as a novel target for anaerobic redox engineering of S. cerevisiae. Introduction of an NADPH-specific alcohol dehydrogenase (NADPH-ADH) not only reduces the NADH demand of the acetate-to-ethanol pathway but also allows the cell to effectively exchange NADPH for NADH during sugar fermentation. Unlike NADH, NADPH can be freely generated under anoxic conditions, via the oxidative pentose phosphate pathway. We show that an industrial bioethanol strain engineered with the original pathway (expressing acetylating acetaldehyde dehydrogenase from Bifidobacterium adolescentis and with deletions of glycerol-3-phosphate dehydrogenase genes GPD1 and GPD2) consumed 1.9 g liter(-1) acetate during fermentation of 114 g liter(-1) glucose. Combined with a decrease in glycerol production from 4.0 to 0.1 g liter(-1), this increased the ethanol yield by 4% over that for the wild type. We provide evidence that acetate consumption in this strain is indeed limited by NADH availability. By introducing an NADPH-ADH from Entamoeba histolytica and with overexpression of ACS2 and ZWF1, we increased acetate consumption to 5.3 g liter(-1) and raised the ethanol yield to 7% above the wild-type level.
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120
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Kim S, Hahn JS. Efficient production of 2,3-butanediol in Saccharomyces cerevisiae by eliminating ethanol and glycerol production and redox rebalancing. Metab Eng 2015; 31:94-101. [DOI: 10.1016/j.ymben.2015.07.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 06/24/2015] [Accepted: 07/17/2015] [Indexed: 12/18/2022]
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121
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Bekers KM, Heijnen JJ, van Gulik WM. Determination of the in vivo NAD:NADH ratio in Saccharomyces cerevisiae under anaerobic conditions, using alcohol dehydrogenase as sensor reaction. Yeast 2015; 32:541-57. [PMID: 26059529 DOI: 10.1002/yea.3078] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 05/11/2015] [Accepted: 05/17/2015] [Indexed: 11/07/2022] Open
Abstract
With the current quantitative metabolomics techniques, only whole-cell concentrations of NAD and NADH can be quantified. These measurements cannot provide information on the in vivo redox state of the cells, which is determined by the ratio of the free forms only. In this work we quantified free NAD:NADH ratios in yeast under anaerobic conditions, using alcohol dehydrogenase (ADH) and the lumped reaction of glyceraldehyde-3-phosphate dehydrogenase and 3-phosphoglycerate kinase as sensor reactions. We showed that, with an alternative accurate acetaldehyde determination method, based on rapid sampling, instantaneous derivatization with 2,4 diaminophenol hydrazine (DNPH) and quantification with HPLC, the ADH-catalysed oxidation of ethanol to acetaldehyde can be applied as a relatively fast and simple sensor reaction to quantify the free NAD:NADH ratio under anaerobic conditions. We evaluated the applicability of ADH as a sensor reaction in the yeast Saccharomyces cerevisiae, grown in anaerobic glucose-limited chemostats under steady-state and dynamic conditions. The results found in this study showed that the cytosolic redox status (NAD:NADH ratio) of yeast is at least one order of magnitude lower, and is thus much more reduced, under anaerobic conditions compared to aerobic glucose-limited steady-state conditions. The more reduced state of the cytosol under anaerobic conditions has major implications for (central) metabolism. Accurate determination of the free NAD:NADH ratio is therefore of importance for the unravelling of in vivo enzyme kinetics and to judge accurately the thermodynamic reversibility of each redox reaction.
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Affiliation(s)
- K M Bekers
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - J J Heijnen
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - W M van Gulik
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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122
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Andreatta ME, Levine JA, Foy SG, Guzman LD, Kosinski LJ, Cordes MHJ, Masel J. The Recent De Novo Origin of Protein C-Termini. Genome Biol Evol 2015; 7:1686-701. [PMID: 26002864 PMCID: PMC4494051 DOI: 10.1093/gbe/evv098] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Protein-coding sequences can arise either from duplication and divergence of existing sequences, or de novo from noncoding DNA. Unfortunately, recently evolved de novo genes can be hard to distinguish from false positives, making their study difficult. Here, we study a more tractable version of the process of conversion of noncoding sequence into coding: the co-option of short segments of noncoding sequence into the C-termini of existing proteins via the loss of a stop codon. Because we study recent additions to potentially old genes, we are able to apply a variety of stringent quality filters to our annotations of what is a true protein-coding gene, discarding the putative proteins of unknown function that are typical of recent fully de novo genes. We identify 54 examples of C-terminal extensions in Saccharomyces and 28 in Drosophila, all of them recent enough to still be polymorphic. We find one putative gene fusion that turns out, on close inspection, to be the product of replicated assembly errors, further highlighting the issue of false positives in the study of rare events. Four of the Saccharomyces C-terminal extensions (to ADH1, ARP8, TPM2, and PIS1) that survived our quality filters are predicted to lead to significant modification of a protein domain structure.
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Affiliation(s)
- Matthew E Andreatta
- Department of Ecology & Evolutionary Biology, University of Arizona Present address: Aegis Sciences, Nashville, TN
| | - Joshua A Levine
- Department of Ecology & Evolutionary Biology, University of Arizona
| | - Scott G Foy
- Department of Ecology & Evolutionary Biology, University of Arizona
| | - Lynette D Guzman
- Department of Ecology & Evolutionary Biology, University of Arizona Present address: Program in Mathematics Education, Michigan State University, MI
| | - Luke J Kosinski
- Biochemistry and Molecular & Cellular Biology Graduate Program, University of Arizona
| | | | - Joanna Masel
- Department of Ecology & Evolutionary Biology, University of Arizona
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123
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Iwama R, Kobayashi S, Ohta A, Horiuchi H, Fukuda R. Alcohol dehydrogenases and an alcohol oxidase involved in the assimilation of exogenous fatty alcohols in Yarrowia lipolytica. FEMS Yeast Res 2015; 15:fov014. [DOI: 10.1093/femsyr/fov014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2015] [Indexed: 01/21/2023] Open
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124
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Callejas-Negrete OA, Torres-Guzmán JC, Padilla-Guerrero IE, Esquivel-Naranjo U, Padilla-Ballesteros MF, García-Tapia A, Schrank A, Salazar-Solís E, Gutiérrez-Corona F, González-Hernández GA. The Adh1 gene of the fungus Metarhizium anisopliae is expressed during insect colonization and required for full virulence. Microbiol Res 2015; 172:57-67. [DOI: 10.1016/j.micres.2014.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/18/2014] [Accepted: 11/25/2014] [Indexed: 12/22/2022]
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125
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Michel S, Keller MA, Wamelink MMC, Ralser M. A haploproficient interaction of the transaldolase paralogue NQM1 with the transcription factor VHR1 affects stationary phase survival and oxidative stress resistance. BMC Genet 2015; 16:13. [PMID: 25887987 PMCID: PMC4331311 DOI: 10.1186/s12863-015-0171-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/21/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Studying the survival of yeast in stationary phase, known as chronological lifespan, led to the identification of molecular ageing factors conserved from yeast to higher organisms. To identify functional interactions among yeast chronological ageing genes, we conducted a haploproficiency screen on the basis of previously identified long-living mutants. For this, we created a library of heterozygous Saccharomyces cerevisiae double deletion strains and aged them in a competitive manner. RESULTS Stationary phase survival was prolonged in a double heterozygous mutant of the metabolic enzyme non-quiescent mutant 1 (NQM1), a paralogue to the pentose phosphate pathway enzyme transaldolase (TAL1), and the transcription factor vitamin H response transcription factor 1 (VHR1). We find that cells deleted for the two genes possess increased clonogenicity at late stages of stationary phase survival, but find no indication that the mutations delay initial mortality upon reaching stationary phase, canonically defined as an extension of chronological lifespan. We show that both genes influence the concentration of metabolites of glycolysis and the pentose phosphate pathway, central metabolic players in the ageing process, and affect osmolality of growth media in stationary phase cultures. Moreover, NQM1 is glucose repressed and induced in a VHR1 dependent manner upon caloric restriction, on non-fermentable carbon sources, as well as under osmotic and oxidative stress. Finally, deletion of NQM1 is shown to confer resistance to oxidizing substances. CONCLUSIONS The transaldolase paralogue NQM1 and the transcription factor VHR1 interact haploproficiently and affect yeast stationary phase survival. The glucose repressed NQM1 gene is induced under various stress conditions, affects stress resistance and this process is dependent on VHR1. While NQM1 appears not to function in the pentose phosphate pathway, the interplay of NQM1 with VHR1 influences the yeast metabolic homeostasis and stress tolerance during stationary phase, processes associated with yeast ageing.
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Affiliation(s)
- Steve Michel
- Max Planck Institute for Molecular Genetics, Ihnestr 73, Berlin, 14195, Germany.
| | - Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis, Court Road, Cambridge, CB2 1GA, UK.
| | - Mirjam M C Wamelink
- Metabolic Unit, Department of Clinical Chemistry, VU University Medical Centre Amsterdam, Amsterdam, The Netherlands.
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis, Court Road, Cambridge, CB2 1GA, UK.
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK.
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126
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Gao J, Yuan W, Li Y, Xiang R, Hou S, Zhong S, Bai F. Transcriptional analysis of Kluyveromyces marxianus for ethanol production from inulin using consolidated bioprocessing technology. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:115. [PMID: 26273319 PMCID: PMC4535673 DOI: 10.1186/s13068-015-0295-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/24/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND Ethanol production from non-crop materials, such as Jerusalem artichokes, would make a great contribution to the energy industry. The non-conventional yeast, Kluyveromyces marxianus, is able to carry out ethanol fermentation of sugar molecules obtained from inulin-containing materials by consolidated bioprocessing. Lower inulin concentrations and micro-aeration can lead to a relatively fast and ideal fermentation process; however, it is unclear what causes the inhibition of higher concentrations of inulin and the promotion effect of aeration. RESULTS Next-generation sequencing technology was used to study the global transcriptional response of K. marxianus Y179 under three fermentation conditions, including 120 g/L inulin without aeration (120-N), 230 g/L inulin without aeration (230-N), 230 g/L inulin with aeration by ORP controlling at -130 mV (230-130mV). A total of 35.55 million clean reads were generated from three samples, of which 4,820 predicted that open reading frames were annotated. For differential expression analysis, 950 and 1,452 differentially expressed genes were discovered under the conditions of 230-130mV and 120-N, respectively, and the sample 230-N was used as the control. These genes are mainly associated with the pathways of central carbon metabolism and ethanol formation. Increased expression of inulinase and the low activity of the autophagy-related gene, ATG8, ensured fast and ideal fermentation processes. CONCLUSIONS Despite being reported as the "crabtree-negative" species, K. marxianus Y179 could achieve favorable ethanol fermentation profiles under micro-aeration and high inulin concentrations. K. marxianus Y179 cells responded to inulin concentrations and micro-aeration that is involved in the whole ethanol metabolism network. These results will serve as an important foundation for further exploration of the regulatory mechanisms involved in ethanol fermentation from inulin by consolidated bioprocessing and also provide a valuable reference for future studies on optimization and reconstruction of the metabolism network in K. marxianus.
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Affiliation(s)
- Jiaoqi Gao
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Wenjie Yuan
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Yimin Li
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Ruijuan Xiang
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Shengbo Hou
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Shijun Zhong
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Fengwu Bai
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
- />School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240 China
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127
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Storage lipid synthesis is necessary for autophagy induced by nitrogen starvation. FEBS Lett 2014; 589:269-76. [PMID: 25500271 DOI: 10.1016/j.febslet.2014.11.050] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/19/2014] [Accepted: 11/21/2014] [Indexed: 11/24/2022]
Abstract
Nitrogen starvation is a universal stimulus of autophagy. At present, little is known about the relationship between carbon metabolism and autophagy under nitrogen starvation. Here, we show that yeast cells continue to consume glucose and downregulate fermentation under nitrogen starvation. Storage lipid production is increased, with concurrent proliferation of lipid droplets. Furthermore, we provide evidence that triacylglycerol synthesis is crucial for autophagosome biogenesis. It is involved in a step downstream of PAS (phagophore assembly site) scaffold assembly, and upstream of the recruitment of Atg1, Atg14, Atg5 and Atg8. Finally, we demonstrate that lipid droplets transiently interact with Atg8-containing membranes. Our study reveals a novel connection linking neutral lipid metabolism, lipid droplets and autophagy.
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128
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Orlandi I, Coppola DP, Vai M. Rewiring yeast acetate metabolism through MPC1 loss of function leads to mitochondrial damage and decreases chronological lifespan. ACTA ACUST UNITED AC 2014; 1:393-405. [PMID: 28357219 PMCID: PMC5349135 DOI: 10.15698/mic2014.12.178] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
During growth on fermentable substrates, such as glucose, pyruvate, which is the
end-product of glycolysis, can be used to generate acetyl-CoA in the cytosol via
acetaldehyde and acetate, or in mitochondria by direct oxidative
decarboxylation. In the latter case, the mitochondrial pyruvate carrier (MPC) is
responsible for pyruvate transport into mitochondrial matrix space. During
chronological aging, yeast cells which lack the major structural subunit Mpc1
display a reduced lifespan accompanied by an age-dependent loss of autophagy.
Here, we show that the impairment of pyruvate import into mitochondria linked to
Mpc1 loss is compensated by a flux redirection of TCA cycle intermediates
through the malic enzyme-dependent alternative route. In such a way, the TCA
cycle operates in a “branched” fashion to generate pyruvate and is depleted of
intermediates. Mutant cells cope with this depletion by increasing the activity
of glyoxylate cycle and of the pathway which provides the nucleocytosolic
acetyl-CoA. Moreover, cellular respiration decreases and ROS accumulate in the
mitochondria which, in turn, undergo severe damage. These acquired traits in
concert with the reduced autophagy restrict cell survival of the mpc1∆ mutant
during chronological aging. Conversely, the activation of the carnitine shuttle
by supplying acetyl-CoA to the mitochondria is sufficient to abrogate the
short-lived phenotype of the mutant.
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Affiliation(s)
- Ivan Orlandi
- SYSBIO Centre for Systems Biology Milano, Italy. ; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Damiano Pellegrino Coppola
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Marina Vai
- SYSBIO Centre for Systems Biology Milano, Italy. ; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
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129
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Tiukova IA, de Barros Pita W, Sundell D, Haddad Momeni M, Horn SJ, Ståhlberg J, de Morais MA, Passoth V. Adaptation of Dekkera bruxellensis to lignocellulose-based substrate. Biotechnol Appl Biochem 2014; 61:51-7. [PMID: 23941546 DOI: 10.1002/bab.1145] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/18/2013] [Indexed: 11/10/2022]
Abstract
Adaptation of Dekkera bruxellensis to lignocellulose hydrolysate was investigated. Cells of D. bruxellensis were grown for 72 and 192 H in batch and continuous culture, respectively (adapted cells). Cultivations in semisynthetic medium were run as controls (nonadapted cells). To test the adaptation, cells from these cultures were reinoculated in the lignocellulose medium, and growth and ethanol production characteristics were monitored. Cells adapted to lignocellulose hydrolysate had a shorter lag phase, grew faster, and produced a higher ethanol concentration as compared with nonadapted cells. A stability test showed that after cultivation in rich medium, cells partially lost the adapted phenotype but still showed faster growth and higher ethanol production as compared with nonadapted cells. Because alcohol dehydrogenase genes have been described to be involved in the adaptation to furfural in Saccharomyces cerevisiae, an analogous mechanism of adaptation to lignocelluloses hydrolysate of D. bruxellensis was hypothesized. However, gene expression analysis showed that genes homologous to S. cerevisiae ADH1 were not involved in the adaptation to lignocelluloses hydrolysate in D. bruxellensis.
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Affiliation(s)
- Ievgeniia A Tiukova
- Uppsala Biocenter, Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025750 07, Uppsala, Sweden
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Retro-biosynthetic screening of a modular pathway design achieves selective route for microbial synthesis of 4-methyl-pentanol. Nat Commun 2014; 5:5031. [PMID: 25248664 DOI: 10.1038/ncomms6031] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 08/19/2014] [Indexed: 12/20/2022] Open
Abstract
Increasingly complex metabolic pathways have been engineered by modifying natural pathways and establishing de novo pathways with enzymes from a variety of organisms. Here we apply retro-biosynthetic screening to a modular pathway design to identify a redox neutral, theoretically high yielding route to a branched C6 alcohol. Enzymes capable of converting natural E. coli metabolites into 4-methyl-pentanol (4MP) via coenzyme A (CoA)-dependent chemistry were taken from nine different organisms to form a ten-step de novo pathway. Selectivity for 4MP is enhanced through the use of key enzymes acting on acyl-CoA intermediates, a carboxylic acid reductase from Nocardia iowensis and an alcohol dehydrogenase from Leifsonia sp. strain S749. One implementation of the full pathway from glucose demonstrates selective carbon chain extension and acid reduction with 4MP constituting 81% (90±7 mg l(-1)) of the observed alcohol products. The highest observed 4MP titre is 192±23 mg l(-1). These results demonstrate the ability of modular pathway screening to facilitate de novo pathway engineering.
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131
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Choi S, Bird AJ. Zinc'ing sensibly: controlling zinc homeostasis at the transcriptional level. Metallomics 2014; 6:1198-215. [PMID: 24722954 DOI: 10.1039/c4mt00064a] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Zinc-responsive transcription factors are found in all kingdoms of life and include the transcriptional activators ZntR, SczA, Zap1, bZip19, bZip23, and MTF-1, and transcriptional repressors Zur, AdcR, Loz1, and SmtB. These factors have two defining features; their activity is regulated by zinc and they all play a central role in zinc homeostasis by controlling the expression of genes that directly affect zinc levels or its availability. This review summarizes what is known about the mechanisms by which each of these factors sense changes in intracellular zinc levels and how they control zinc homeostasis through target gene regulation. Other factors that influence zinc ion sensing are also discussed.
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Affiliation(s)
- Sangyong Choi
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA
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132
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Imamura K, Murai K, Korehisa T, Shimizu N, Yamahira R, Matsuura T, Tada H, Imanaka H, Ishida N, Nakanishi K. Characteristics of Sugar Surfactants in Stabilizing Proteins During Freeze–Thawing and Freeze–Drying. J Pharm Sci 2014; 103:1628-37. [DOI: 10.1002/jps.23988] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/03/2014] [Accepted: 04/09/2014] [Indexed: 11/11/2022]
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133
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Liang JJ, Zhang ML, Ding M, Mai ZM, Wu SX, Du Y, Feng JX. Alcohol dehydrogenases from Kluyveromyces marxianus: heterologous expression in Escherichia coli and biochemical characterization. BMC Biotechnol 2014; 14:45. [PMID: 24885162 PMCID: PMC4062290 DOI: 10.1186/1472-6750-14-45] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 05/12/2014] [Indexed: 11/20/2022] Open
Abstract
Background Kluyveromyces marxianus has recently become a species of interest for ethanol production since it can produce ethanol at high temperature and on a wide variety of substrates. However, the reason why this yeast can produce ethanol at high temperature is largely unknown. Results The ethanol fermentation capability of K. marxianus GX-UN120 at 40°С was found to be the same as that of Saccharomyces cerevisiae at 34°С. Zymogram analysis showed that alcohol dehydrogenase 1 (KmAdh1) was largely induced during ethanol production, KmAdh4 was constitutively expressed at a lower level and KmAdh2 and KmAdh3 were almost undetectable. The genes encoding the four alcohol dehydrogenases (ADHs) were cloned from strain GX-UN120. Each KmADH was expressed in Escherichia coli and each recombinant protein was digested with enterokinase to remove the fusion protein. The optimum pH of the purified recombinant KmAdh1 was 8.0 and that of KmAdh2, KmAdh3 and KmAdh4 was 7.0. The optimum temperatures of KmAdh1, KmAdh2, KmAdh3 and KmAdh4 were 50, 45, 55 and 45°C, respectively. The Km values of the recombinant KmAdh1 and KmAdh2 were 4.0 and 1.2 mM for acetaldehyde and 39.7 and 49.5 mM for ethanol, respectively. The Vmax values of the recombinant KmAdh1 and KmAdh2 were 114.9 and 21.6 μmol min-1 mg-1 for acetaldehyde and 57.5 and 1.8 μmol min-1 mg-1 for ethanol, respectively. KmAdh3 and KmAdh4 catalyze the oxidation reaction of ethanol to acetaldehyde but not the reduction reaction of acetaldehyde to ethanol, and the Km values of the recombinant KmAdh3 and KmAdh4 were 26.0 and 17.0 mM for ethanol, respectively. The Vmax values of the recombinant KmAdh3 and KmAdh4 were 12.8 and 56.2 μmol min-1 mg-1 for ethanol, respectively. Conclusion These data in this study collectively indicate that KmAdh1 is the primary ADH responsible for the production of ethanol from the reduction of acetaldehyde in K. marxianus. The relatively high optimum temperature of KmAdh1 may partially explain the ability of K. marxianus to produce ethanol at high temperature. Understanding the biochemical characteristics of KmAdhs will enhance our fundamental knowledge of the metabolism of ethanol fermentation in K. marxianus.
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Affiliation(s)
- Jing-juan Liang
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P, R, China.
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134
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Expression of soluble Saccharomyces cerevisiae alcohol dehydrogenase in Escherichia coli applicable to oxido-reduction bioconversions. Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0376-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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135
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Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation. PLoS One 2014; 9:e93560. [PMID: 24714189 PMCID: PMC3979922 DOI: 10.1371/journal.pone.0093560] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 03/07/2014] [Indexed: 12/27/2022] Open
Abstract
Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model.
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136
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Moreno-Cermeño A, Alsina D, Cabiscol E, Tamarit J, Ros J. Metabolic remodeling in frataxin-deficient yeast is mediated by Cth2 and Adr1. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1833:3326-3337. [PMID: 24100161 DOI: 10.1016/j.bbamcr.2013.09.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 09/10/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
Abstract
Frataxin is a mitochondrial protein involved in iron metabolism whose deficiency in humans causes Friedreich ataxia. We performed transcriptomic and proteomic analyses of conditional Yeast Frataxin Homologue (Yfh1) mutants (tetO7-YFH1) to investigate metabolic remodeling upon Yfh1 depletion. These studies revealed that Yfh1 depletion leads to downregulation of many glucose-repressed genes. Most of them were Adr1 targets, a key transcription factor required for growth in non-fermentable carbon sources. Using a GFP-tagged Adr1, we observed that Yfh1 depletion promotes the export of Adr1 from the nucleus to the cytosol without affecting its protein levels. This effect was also observed upon H2O2 treatment, but not by iron overload/starvation, indicating the presence of a regulatory pathway involved in Adr1 export and inactivation upon stress conditions. We also observed that CTH2, a gene involved in the mRNA degradation of several iron-containing enzymes, was induced upon Yfh1 depletion. Accordingly, decreased levels of aconitase and succinate dehydrogenase were observed. Nevertheless, their levels were maintained in a Δcth2 mutant even in the absence of Yfh1. From these results we can conclude that, in addition to altering iron homeostasis, frataxin depletion involves drastic metabolic remodeling governed by Adr1 and Cth2 that finally leads to downregulation of iron-sulfur proteins and other proteins involved in respiratory metabolism.
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Affiliation(s)
- Armando Moreno-Cermeño
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, IRB-Lleida, Universitat de Lleida, Lleida, Spain.
| | - David Alsina
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, IRB-Lleida, Universitat de Lleida, Lleida, Spain
| | - Elisa Cabiscol
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, IRB-Lleida, Universitat de Lleida, Lleida, Spain
| | - Jordi Tamarit
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, IRB-Lleida, Universitat de Lleida, Lleida, Spain
| | - Joaquim Ros
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, IRB-Lleida, Universitat de Lleida, Lleida, Spain.
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137
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Thitiprasert S, Sooksai S, Thongchul N. 1,2-Diazole and 2,2,2-Trifluoroethanol and Their Regulatory Effects on Ethanol and Lactic Acid Formation in the Living Culture of Rhizopus oryzae. Appl Biochem Biotechnol 2013; 172:1673-86. [DOI: 10.1007/s12010-013-0627-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 10/30/2013] [Indexed: 10/26/2022]
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138
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Hirasawa T, Ida Y, Furuasawa C, Shimizu H. Potential of a Saccharomyces cerevisiae recombinant strain lacking ethanol and glycerol biosynthesis pathways in efficient anaerobic bioproduction. Bioengineered 2013; 5:123-8. [PMID: 24247205 DOI: 10.4161/bioe.26569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Saccharomyces cerevisiae shows high growth activity under low pH conditions and can be used for producing acidic chemicals such as organic acids as well as fuel ethanol. However, ethanol can also be a problematic by-product in the production of chemicals except for ethanol. We have reported that a stable low-ethanol production phenotype was achieved by disrupting 6 NADH-dependent alcohol dehydrogenase genes of S. cerevisiae. Moreover, the genes encoding the NADH-dependent glycerol biosynthesis enzymes were further disrupted because the ADH-disrupted recombinant strain showed high glycerol production to maintain intracellular redox balance. The recombinant strain incapable producing ethanol and glycerol could have the potential to be a host for producing metabolite(s) whose biosynthesis is coupled with NADH oxidation. Indeed, we successfully achieved almost 100% yield for L-lactate production using this recombinant strain as a host. In addition, the potential of our constructed recombinant strain for efficient bioproduction, particularly under anaerobic conditions, is also discussed.
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Affiliation(s)
- Takashi Hirasawa
- Department of Bioengineering; Tokyo Institute of Technology; Kanagawa, Japan
| | - Yoshihiro Ida
- Department of Bioinformatic Engineering; Graduate School of Information Science and Technology; Osaka University; Osaka, Japan
| | | | - Hiroshi Shimizu
- Department of Bioinformatic Engineering; Graduate School of Information Science and Technology; Osaka University; Osaka, Japan
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139
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Harsch MJ, Benkwitz F, Frost A, Colonna-Ceccaldi B, Gardner RC, Salmon JM. New precursor of 3-mercaptohexan-1-ol in grape juice: thiol-forming potential and kinetics during early stages of must fermentation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:3703-13. [PMID: 23530468 DOI: 10.1021/jf3048753] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Two volatile thiols, 3-mercaptohexan-1-ol (3MH) and 3-mercaptohexyl acetate (3MHA), are key aroma impact compounds in many young white wines, especially of the variety Sauvignon blanc (SB). Although great effort has been invested to identify their precursors in recent years, the origin of the majority of 3MH and 3MHA generated during wine fermentation still cannot be explained. Here we demonstrate that supplying an external source of hydrogen sulfide to grape juice hugely increases its thiol-forming potential. We further describe the discovery of (E)-2-hexen-1-ol as an additional new thiol precursor and demonstrate that it possesses, together with (E)-2-hexenal, an immense thiol-forming potential during fermentation. Both C6-compounds are extremely rapidly metabolized by yeast during the first hours after inoculation, even under commercial conditions, and can be interconverted during this phase depending on their initial concentration in the grape juice. Spiking grape juice with additional acetaldehyde greatly enhanced the (E)-2-hexen-1-ol to (E)-2-hexenal conversion rate. Delaying the metabolization of the two unsaturated C6-thiol precursors by yeast, at the same time as increasing hydrogen sulfide production early in fermentation, opens up a great opportunity to tap into this enormous potential 3MH and 3MHA source in grape juice and extends the possibility of thiol production to other non-grape-based alcoholic beverages as well.
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Affiliation(s)
- Michael J Harsch
- Pernod Ricard New Zealand, Riverlands, Blenheim 7274, New Zealand.
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140
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An overview on alcohol oxidases and their potential applications. Appl Microbiol Biotechnol 2013; 97:4259-75. [DOI: 10.1007/s00253-013-4842-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/06/2013] [Accepted: 03/07/2013] [Indexed: 10/27/2022]
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141
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Utilization of Saccharomyces cerevisiae recombinant strain incapable of both ethanol and glycerol biosynthesis for anaerobic bioproduction. Appl Microbiol Biotechnol 2013; 97:4811-9. [PMID: 23435983 DOI: 10.1007/s00253-013-4760-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/08/2013] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
Abstract
The yeast Saccharomyces cerevisiae produces ethanol and glycerol as major unwanted byproducts, unless ethanol and glycerol are the target compounds. Minimizing the levels of these byproducts is important for bioproduction processes using yeast cells. In this study, we constructed a yeast strain in which both ethanol and glycerol production pathways were disrupted and examined its culture characteristics. In wild-type yeast strain, metabolic pathways that produce ethanol and glycerol play an important role in reoxidizing nicotinamide adenine dinucleotide (NADH) generated during glycolysis, particularly under anaerobic conditions. Strains in which both pathways were disrupted therefore failed to grow and consume glucose under anaerobic conditions. Introduction of desired metabolic reaction(s) coupled with NADH oxidation enabled the engineered strain to consume substrate and produce target compound(s). Here we introduced NADH-oxidization-coupled L-lactate production mechanisms into a yeast strain incapable of ethanol and glycerol biosynthesis, based on in silico simulation using a genome-scale metabolic model of S. cerevisiae. From the results of in silico simulation based on flux balance analysis, a feasible anaerobic non-growing metabolic state, in which L-lactate yield approached the theoretical maximum, was identified and this phenomenon was verified experimentally. The yeast strain incapable of both ethanol and glycerol biosynthesis is a potentially valuable host for bioproduction coupled with NADH oxidation under anaerobic conditions.
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142
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Kaya N, Aktaş Uygun D, Akgöl S, Denizli A. Purification of alcohol dehydrogenase from Saccharomyces cerevisiae using magnetic dye-ligand affinity nanostructures. Appl Biochem Biotechnol 2013; 169:2153-64. [PMID: 23408231 DOI: 10.1007/s12010-013-0130-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 01/31/2013] [Indexed: 11/25/2022]
Abstract
Reactive Green 19 was covalently immobilized onto magnetic nanostructures for purification of alcohol dehydrogenase from Saccharomyces cerevisiae. The Reactive Green 19 immobilized magnetic nanostructures were characterized by Fourier transform infrared spectroscopy, electron spin resonance, atomic force microscope, and energy dispersive X-ray analysis. Particle size of nanostructures was found to be roughly 70 nm. Alcohol dehydrogenase adsorption experiments were investigated under different conditions in batch system (i.e., medium pH, alcohol dehydrogenase concentration, temperature, and ionic strength). Maximum alcohol dehydrogenase adsorption capacity was found to be 176.09 mg/g polymer while nonspecific alcohol dehydrogenase adsorption onto plain magnetic nanostructures was negligible (19.4 mg/g polymer). Alcohol dehydrogenase molecules were desorbed by using 1.0 M NaCl with 98.4 % recovery. Alcohol dehydrogenase from S. cerevisiae was purified 45.63-fold in single step with dye-immobilized magnetic nanostructures, and purity of alcohol dehydrogenase was shown by silver-stained sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
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Affiliation(s)
- Nazife Kaya
- Faculty of Science and Arts, Chemistry Department, Adnan Menderes University, Aydin, Turkey
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143
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Development of Industrial Brewing Yeast with Low Acetaldehyde Production and Improved Flavor Stability. Appl Biochem Biotechnol 2013; 169:1016-25. [DOI: 10.1007/s12010-012-0077-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 12/27/2012] [Indexed: 11/26/2022]
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144
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Ehrensberger KM, Mason C, Corkins ME, Anderson C, Dutrow N, Cairns BR, Dalley B, Milash B, Bird AJ. Zinc-dependent regulation of the Adh1 antisense transcript in fission yeast. J Biol Chem 2012; 288:759-69. [PMID: 23223230 DOI: 10.1074/jbc.m112.406165] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In yeast, Adh1 (alcohol dehydrogenase 1) is an abundant zinc-binding protein that is required for the conversion of acetaldehyde to ethanol. Through transcriptome profiling of the Schizosaccharomyces pombe genome, we identified a natural antisense transcript at the adh1 locus that is induced in response to zinc limitation. This antisense transcript (adh1AS) shows a reciprocal expression pattern to that of the adh1 mRNA partner. In this study, we show that increased expression of the adh1AS transcript in zinc-limited cells is necessary for the repression of adh1 gene expression and that the increased level of the adh1AS transcript in zinc-limited cells is a result of two mechanisms. At the transcriptional level, the adh1AS transcript is expressed at a high level in zinc-limited cells. In addition to this transcriptional control, adh1AS transcripts preferentially accumulate in zinc-limited cells when the adh1AS transcript is expressed from a constitutive promoter. This secondary mechanism requires the simultaneous expression of adh1. Our studies reveal how multiple mechanisms can synergistically control the ratio of sense to antisense transcripts and highlight a novel mechanism by which adh1 gene expression can be controlled by cellular zinc availability.
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Affiliation(s)
- Kate M Ehrensberger
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA
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145
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Styger G, Jacobson D, Prior BA, Bauer FF. Genetic analysis of the metabolic pathways responsible for aroma metabolite production by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2012; 97:4429-42. [PMID: 23111598 DOI: 10.1007/s00253-012-4522-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 10/13/2012] [Accepted: 10/15/2012] [Indexed: 11/29/2022]
Abstract
During alcoholic fermentation, higher alcohols, esters, and acids are formed from amino acids via the Ehrlich pathway by yeast, but many of the genes encoding the enzymes have not yet been identified. When the BAT1/2 genes, encoding transaminases that deaminate amino acids in the first step of the Ehrlich pathway are deleted, higher metabolite formation is significantly decreased. Screening yeast strains with deletions of genes encoding decarboxylases, dehydrogenases, and reductases revealed nine genes whose absence had the most significant impact on higher alcohol production. The seven most promising genes (AAD6, BAT2, HOM2, PAD1, PRO2, SPE1, and THI3) were further investigated by constructing double- and triple-deletion mutants. All double-deletion strains showed a greater decrease in isobutanol, isoamyl alcohol, isobutyric, and isovaleric acid production than the corresponding single deletion strains with the double-deletion strains in combination with ∆bat2 and the ∆hom2-∆aad6 strain revealing the greatest impact. BAT2 is the dominant gene in these deletion strains and this suggests the initial transaminase step of the Ehrlich pathway is rate-limiting. The triple-deletion strains in combination with BAT2 (∆bat2-∆thi3-∆aad6 and ∆bat2-∆thi3-∆hom2) had the greatest impact on the end metabolite production with the exception of isoamyl alcohol and isovaleric acid. The strain deleted for two dehydrogenases and a reductase (∆hom2-∆pro2-∆aad6) had a greater effect on the levels of these two compounds. This study contributes to the elucidation of the Ehrlich pathway and its significance for aroma production by fermenting yeast cells.
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Affiliation(s)
- Gustav Styger
- Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch 7600, South Africa
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146
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Celton M, Sanchez I, Goelzer A, Fromion V, Camarasa C, Dequin S. A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation. BMC Genomics 2012; 13:317. [PMID: 22805527 PMCID: PMC3431268 DOI: 10.1186/1471-2164-13-317] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Accepted: 06/28/2012] [Indexed: 01/26/2023] Open
Abstract
Background Redox homeostasis is essential to sustain metabolism and growth. We recently reported that yeast cells meet a gradual increase in imposed NADPH demand by progressively increasing flux through the pentose phosphate (PP) and acetate pathways and by exchanging NADH for NADPH in the cytosol, via a transhydrogenase-like cycle. Here, we studied the mechanisms underlying this metabolic response, through a combination of gene expression profiling and analyses of extracellular and intracellular metabolites and 13 C-flux analysis. Results NADPH oxidation was increased by reducing acetoin to 2,3-butanediol in a strain overexpressing an engineered NADPH-dependent butanediol dehydrogenase cultured in the presence of acetoin. An increase in NADPH demand to 22 times the anabolic requirement for NADPH was accompanied by the intracellular accumulation of PP pathway metabolites consistent with an increase in flux through this pathway. Increases in NADPH demand were accompanied by the successive induction of several genes of the PP pathway. NADPH-consuming pathways, such as amino-acid biosynthesis, were upregulated as an indirect effect of the decrease in NADPH availability. Metabolomic analysis showed that the most extreme modification of NADPH demand resulted in an energetic problem. Our results also highlight the influence of redox status on aroma production. Conclusions Combined 13 C-flux, intracellular metabolite levels and microarrays analyses revealed that NADPH homeostasis, in response to a progressive increase in NADPH demand, was achieved by the regulation, at several levels, of the PP pathway. This pathway is principally under metabolic control, but regulation of the transcription of PP pathway genes can exert a stronger effect, by redirecting larger amounts of carbon to this pathway to satisfy the demand for NADPH. No coordinated response of genes involved in NADPH metabolism was observed, suggesting that yeast has no system for sensing NADPH/NADP+ ratio. Instead, the induction of NADPH-consuming amino-acid pathways in conditions of NADPH limitation may indirectly trigger the transcription of a set of PP pathway genes.
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147
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Gibson BR. 125th Anniversary Review: Improvement of Higher Gravity Brewery Fermentation via Wort Enrichment and Supplementation. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2011.tb00472.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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148
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Stabilization of a highly active but unstable alcohol dehydrogenase from yeast using immobilization and post-immobilization techniques. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.01.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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149
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Zhao XQ, Bai FW. Zinc and yeast stress tolerance: Micronutrient plays a big role. J Biotechnol 2012; 158:176-83. [DOI: 10.1016/j.jbiotec.2011.06.038] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 06/20/2011] [Accepted: 06/29/2011] [Indexed: 10/18/2022]
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150
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Ida Y, Furusawa C, Hirasawa T, Shimizu H. Stable disruption of ethanol production by deletion of the genes encoding alcohol dehydrogenase isozymes in Saccharomyces cerevisiae. J Biosci Bioeng 2012; 113:192-5. [DOI: 10.1016/j.jbiosc.2011.09.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/15/2011] [Accepted: 09/24/2011] [Indexed: 11/29/2022]
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