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The Production of Pyruvate in Biological Technology: A Critical Review. Microorganisms 2022; 10:microorganisms10122454. [PMID: 36557706 PMCID: PMC9783380 DOI: 10.3390/microorganisms10122454] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Pyruvic acid has numerous applications in the food, chemical, and pharmaceutical industries. The high costs of chemical synthesis have prevented the extensive use of pyruvate for many applications. Metabolic engineering and traditional strategies for mutation and selection have been applied to microorganisms to enhance their ability to produce pyruvate. In the past decades, different microbial strains were generated to enhance their pyruvate production capability. In addition to the development of genetic engineering and metabolic engineering in recent years, the metabolic transformation of wild-type yeast, E. coli, and so on to produce high-yielding pyruvate strains has become a hot spot. The strategy and the understanding of the central metabolism directly related to pyruvate production could provide valuable information for improvements in fermentation products. One of the goals of this review was to collect information regarding metabolically engineered strains and the microbial fermentation processes used to produce pyruvate in high yield and productivity.
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Wang S, Yang Y, Yu K, Xu S, Liu M, Sun J, Zheng J, Zhang Y, Yuan W. Engineering of Yarrowia lipolytica for producing pyruvate from glycerol. 3 Biotech 2022; 12:98. [PMID: 35463047 PMCID: PMC8934898 DOI: 10.1007/s13205-022-03158-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/05/2022] [Indexed: 11/25/2022] Open
Abstract
The present study aims to increase pyruvate production by engineering Yarrowia lipolytica through modifying the glycerol metabolic pathway. Results: Wild-type Yarrowia lipolytica (Po1d) was engineered to produce six different strains, namely ZS099 (by over-expressing PYK1), ZS100 (by deleting DGA2), ZS101 (by over-expressing DAK1, DAK2, and GCY1), ZS102 (by over-expressing GUT1 and GUT2), ZS103 (by over-expressing GUT1) and ZSGP (by over-expressing POS5 and deleting GPD2). Production of pyruvate from engineered and control strains was determined using high-performance liquid chromatography (HPLC). Subsequently, the fermentation conditions for producing pyruvate were optimized, including the amount of initial inoculation, the addition of calcium carbonate (CaCO3), thiamine and glycerol. Finally, for scaled-up purposes, a 20-L fermentor was used. It was observed that pyruvate production increased by 136% (8.55 g/L) in ZSGP strain compared to control (3.62 g/L). Furthermore, pyruvate production by ZSGP reached up to 110.4 g/L in 96 h in the scaled-up process. We conclude that ZSGP strain of Y. lipolytica can be effectively used for pyruvate production at the industrial level. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03158-7.
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Affiliation(s)
- Songmao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No 18 of Changwang Road, Hangzhou, 310014 China
| | - Yuanyuan Yang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No 18 of Changwang Road, Hangzhou, 310014 China
| | - Kechen Yu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No 18 of Changwang Road, Hangzhou, 310014 China
| | - Shiyi Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No 18 of Changwang Road, Hangzhou, 310014 China
| | - Mengzhu Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No 18 of Changwang Road, Hangzhou, 310014 China
| | - Jie Sun
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No 18 of Changwang Road, Hangzhou, 310014 China
| | - Jianyong Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No 18 of Changwang Road, Hangzhou, 310014 China
| | - Yinjun Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No 18 of Changwang Road, Hangzhou, 310014 China
| | - Wei Yuan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No 18 of Changwang Road, Hangzhou, 310014 China
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Kocaefe-Özşen N, Yilmaz B, Alkım C, Arslan M, Topaloğlu A, Kısakesen HLB, Gülsev E, Çakar ZP. Physiological and Molecular Characterization of an Oxidative Stress-Resistant Saccharomyces cerevisiae Strain Obtained by Evolutionary Engineering. Front Microbiol 2022; 13:822864. [PMID: 35283819 PMCID: PMC8911705 DOI: 10.3389/fmicb.2022.822864] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
Oxidative stress is a major stress type observed in yeast bioprocesses, resulting in a decrease in yeast growth, viability, and productivity. Thus, robust yeast strains with increased resistance to oxidative stress are in highly demand by the industry. In addition, oxidative stress is also associated with aging and age-related complex conditions such as cancer and neurodegenerative diseases. Saccharomyces cerevisiae, as a model eukaryote, has been used to study these complex eukaryotic processes. However, the molecular mechanisms underlying oxidative stress responses and resistance are unclear. In this study, we have employed evolutionary engineering (also known as adaptive laboratory evolution – ALE) strategies to obtain an oxidative stress-resistant and genetically stable S. cerevisiae strain. Comparative physiological, transcriptomic, and genomic analyses of the evolved strain were then performed with respect to the reference strain. The results show that the oxidative stress-resistant evolved strain was also cross-resistant against other types of stressors, including heat, freeze-thaw, ethanol, cobalt, iron, and salt. It was also found to have higher levels of trehalose and glycogen production. Further, comparative transcriptomic analysis showed an upregulation of many genes associated with the stress response, transport, carbohydrate, lipid and cofactor metabolic processes, protein phosphorylation, cell wall organization, and biogenesis. Genes that were downregulated included those related to ribosome and RNA processing, nuclear transport, tRNA, and cell cycle. Whole genome re-sequencing analysis of the evolved strain identified mutations in genes related to the stress response, cell wall organization, carbohydrate metabolism/transport, which are in line with the physiological and transcriptomic results, and may give insight toward the complex molecular mechanisms of oxidative stress resistance.
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Affiliation(s)
- Nazlı Kocaefe-Özşen
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Bahtiyar Yilmaz
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ceren Alkım
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Mevlüt Arslan
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Alican Topaloğlu
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Halil L Brahim Kısakesen
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Erdinç Gülsev
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Z Petek Çakar
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
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Korn VL, Pennerman KK, Padhi S, Bennett JW. Trans-2-hexenal downregulates several pathogenicity genes of Pseudogymnoascus destructans, the causative agent of white-nose syndrome in bats. J Ind Microbiol Biotechnol 2021; 48:kuab060. [PMID: 34415032 PMCID: PMC8788850 DOI: 10.1093/jimb/kuab060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/13/2021] [Indexed: 11/29/2022]
Abstract
White-nose syndrome is an emergent wildlife disease that has killed millions of North American bats. It is caused by Pseudogymnoascus destructans, a cold-loving, invasive fungal pathogen that grows on bat tissues and disrupts normal hibernation patterns. Previous work identified trans-2-hexenal as a fungistatic volatile compound that potentially could be used as a fumigant against P. destructans in bat hibernacula. To determine the physiological responses of the fungus to trans-2-hexenal exposure, we characterized the P. destructans transcriptome in the presence and absence of trans-2-hexenal. Specifically, we analyzed the effects of sublethal concentrations (5 μmol/L, 10 μmol/L, and 20 μmol/L) of gas-phase trans-2-hexenal of the fungus grown in liquid culture. Among the three treatments, a total of 407 unique differentially expressed genes (DEGs) were identified, of which 74 were commonly affected across all three treatments, with 44 upregulated and 30 downregulated. Downregulated DEGs included several probable virulence genes including those coding for a high-affinity iron permease, a superoxide dismutase, and two protein-degrading enzymes. There was an accompanying upregulation of an ion homeostasis gene, as well as several genes involved in transcription, translation, and other essential cellular processes. These data provide insights into the mechanisms of action of trans-2-hexenal as an anti-fungal fumigant that is active at cold temperatures and will guide future studies on the molecular mechanisms by which six carbon volatiles inhibit growth of P. destructans and other pathogenic fungi.
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Affiliation(s)
| | - Kayla K Pennerman
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD 20742, USA
| | - Sally Padhi
- Department of Plant Biology, Rutgers University, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Joan W Bennett
- Department of Plant Biology, Rutgers University, The State University of New Jersey, New Brunswick, NJ 08901, USA
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Zhang C, Gu H, Ren Y, Lu L. GlcA-mediated glycerol-3-phosphate synthesis contributes to the oxidation resistance of Aspergillus fumigatus via decreasing the cellular ROS. Fungal Genet Biol 2021; 149:103531. [PMID: 33581364 DOI: 10.1016/j.fgb.2021.103531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/28/2020] [Accepted: 02/04/2021] [Indexed: 10/22/2022]
Abstract
Fungi activate corresponding metabolic pathways in response to different carbon sources to adapt to different environments. Previous studies have shown that the glycerol kinase GlcA that phosphorylates glycerol to the intermediate glycerol-3-phosphate (G3P) is required for the growth of Aspergillus fumigatus when glycerol is used as the sole carbon source. The present study identified there were two putative glycerol kinases, GlcA and GlcB, in A. fumigatus but glycerol activated only glcA promoter but not glcB promoter, although both glcA and glcB could encode glycerol kinase. Under normal culture conditions, the absence of glcA caused no detectable colony phenotypes on glucose and other tested carbon sources except glycerol, indicating dissimilation of glucose and these tested carbon sources bypassed requirement of glcA. Notably, the oxidative stress agent H2O2 on the background of glucose medium clearly induced GlcA expression and promoted G3P synthesis. Deletion and overexpression of glcA elicited sensitivity and resistance to oxidative stress agent H2O2, respectively, accompanied by decrease and increase of G3P production. In addition, the sensitivity to oxidative stress in the glcA mutant was probably associated with dysfunction of mitochondria with a decreased mitochondrial membrane potential and an abnormal accumulation of the cellular reactive oxygen species (ROS). Furthermore, overexpressing the glycerol-3-phosphate dehydrogenase GfdA thatcatalyzes the reduction of dihydroxyacetone phosphate (DHAP) to G3P rescued phenotypes of the glcA null mutant to H2O2. Therefore, the present study suggests that GlcA-involved G3P synthesis participates in oxidative stress tolerance of A. fumigatus via regulating the cellular ROS level.
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Affiliation(s)
- Chi Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Huiyu Gu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yiran Ren
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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Zhao Y, Li X, Zhang Z, Pan W, Li S, Xing Y, Xin W, Zhang Z, Hu Z, Liu C, Wu X, Qi Z, Xin D, Chen Q. GmGPDH12, a mitochondrial FAD-GPDH from soybean, increases salt and osmotic stress resistance by modulating redox state and respiration. ACTA ACUST UNITED AC 2021. [DOI: 10.1016/j.cj.2020.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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7
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Croft T, Venkatakrishnan P, Lin SJ. NAD + Metabolism and Regulation: Lessons From Yeast. Biomolecules 2020; 10:E330. [PMID: 32092906 PMCID: PMC7072712 DOI: 10.3390/biom10020330] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/15/2020] [Accepted: 02/16/2020] [Indexed: 12/13/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential metabolite involved in various cellular processes. The cellular NAD+ pool is maintained by three biosynthesis pathways, which are largely conserved from bacteria to human. NAD+ metabolism is an emerging therapeutic target for several human disorders including diabetes, cancer, and neuron degeneration. Factors regulating NAD+ homeostasis have remained incompletely understood due to the dynamic nature and complexity of NAD+ metabolism. Recent studies using the genetically tractable budding yeast Saccharomyces cerevisiae have identified novel NAD+ homeostasis factors. These findings help provide a molecular basis for how may NAD+ and NAD+ homeostasis factors contribute to the maintenance and regulation of cellular function. Here we summarize major NAD+ biosynthesis pathways, selected cellular processes that closely connect with and contribute to NAD+ homeostasis, and regulation of NAD+ metabolism by nutrient-sensing signaling pathways. We also extend the discussions to include possible implications of NAD+ homeostasis factors in human disorders. Understanding the cross-regulation and interconnections of NAD+ precursors and associated cellular pathways will help elucidate the mechanisms of the complex regulation of NAD+ homeostasis. These studies may also contribute to the development of effective NAD+-based therapeutic strategies specific for different types of NAD+ deficiency related disorders.
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Affiliation(s)
| | | | - Su-Ju Lin
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA; (T.C.); (P.V.)
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Aßkamp MR, Klein M, Nevoigt E. Involvement of the external mitochondrial NADH dehydrogenase Nde1 in glycerol metabolism by wild-type and engineered Saccharomyces cerevisiae strains. FEMS Yeast Res 2019; 19:5420478. [PMID: 30915433 DOI: 10.1093/femsyr/foz026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/20/2019] [Indexed: 12/17/2022] Open
Abstract
Glycerol is an attractive substrate for microbial fermentations due to its higher degree of reduction compared to glucose. The replacement of the native FAD-dependent glycerol catabolic pathway in Saccharomyces cerevisiae by an artificial NADH-delivering dihydroxyacetone (DHA) pathway is supposed to facilitate the capturing of electrons in fermentation products. This requires that the electrons from the cytosolic NADH are not exclusively transferred to oxygen. However, the external NADH dehydrogenases (Nde1/2) and the L-glycerol 3-phosphate shuttle (composed of Gpd1/2 and Gut2), both coupled to the respiratory chain, are known to contribute to cytosolic NAD+ regeneration during growth on non-fermentable carbon sources. In order to evaluate the role of these mechanisms during growth on glycerol, we deleted GPD1/2, GUT2 as well as NDE1/2, separately and in combinations in both the glycerol-utilizing wild-type strain CBS 6412-13A and the corresponding engineered strain CBS DHA in which glycerol is catabolized by the DHA pathway. Particularly, the nde1Δ mutants showed a significant reduction in growth rate and the nde1∆ nde2∆ double deletion mutants did not grow at all in synthetic glycerol medium. The current work also demonstrates a positive impact of deleting NDE1 on the production of the fermentation product 1,2-propanediol in an accordingly engineered S. cerevisiae strain.
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Affiliation(s)
- Maximilian R Aßkamp
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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Aßkamp MR, Klein M, Nevoigt E. Saccharomyces cerevisiae exhibiting a modified route for uptake and catabolism of glycerol forms significant amounts of ethanol from this carbon source considered as 'non-fermentable'. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:257. [PMID: 31695748 PMCID: PMC6822349 DOI: 10.1186/s13068-019-1597-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Due to its inevitable formation during biodiesel production and its relatively high degree of reduction, glycerol is an attractive carbon source for microbial fermentation processes. However, glycerol is catabolized in a fully respiratory manner by the eukaryotic platform organism Saccharomyces cerevisiae. We previously engineered S. cerevisiae strains to favor fermentative metabolism of glycerol by replacing the native FAD-dependent glycerol catabolic pathway with the NAD-dependent 'DHA pathway'. In addition, a heterologous aquaglyceroporin (Fps1 homolog) was expressed to facilitate glycerol uptake. The current study was launched to scrutinize the formation of S. cerevisiae's natural fermentation product ethanol from glycerol caused by the conducted genetic modifications. This understanding is supposed to facilitate future engineering of this yeast for fermenting glycerol into valuable products more reduced than ethanol. RESULTS A strain solely exhibiting the glycerol catabolic pathway replacement produced ethanol at concentrations close to the detection limit. The expression of the heterologous aquaglyceroporin caused significant ethanol production (8.5 g L-1 from 51.5 g L-1 glycerol consumed) in a strain catabolizing glycerol via the DHA pathway but not in the wild-type background. A reduction of oxygen availability in the shake flask cultures further increased the ethanol titer up to 15.7 g L-1 (from 45 g L-1 glycerol consumed). CONCLUSION The increased yield of cytosolic NADH caused by the glycerol catabolic pathway replacement seems to be a minimal requirement for the occurrence of alcoholic fermentation in S. cerevisiae growing in synthetic glycerol medium. The remarkable metabolic switch to ethanol formation in the DHA pathway strain with the heterologous aquaglyceroporin supports the assumption of a much stronger influx of glycerol accompanied by an increased rate of cytosolic NADH production via the DHA pathway. The fact that a reduction of oxygen supply increases ethanol production in DHA pathway strains is in line with the hypothesis that a major part of glycerol in normal shake flask cultures still enters the catabolism in a respiratory manner.
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Affiliation(s)
- Maximilian R. Aßkamp
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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10
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Wu Q, Lan Y, Cao X, Yao H, Qiao D, Xu H, Cao Y. Characterization and diverse evolution patterns of glycerol-3-phosphate dehydrogenase family genes in Dunaliella salina. Gene 2019; 710:161-169. [DOI: 10.1016/j.gene.2019.05.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/15/2019] [Accepted: 05/29/2019] [Indexed: 12/29/2022]
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Kawai K, Kanesaki Y, Yoshikawa H, Hirasawa T. Identification of metabolic engineering targets for improving glycerol assimilation ability of Saccharomyces cerevisiae based on adaptive laboratory evolution and transcriptome analysis. J Biosci Bioeng 2019; 128:162-169. [DOI: 10.1016/j.jbiosc.2019.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/01/2019] [Accepted: 02/02/2019] [Indexed: 11/29/2022]
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12
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Corcoles-Saez I, Ferat JL, Costanzo M, Boone CM, Cha RS. Functional link between mitochondria and Rnr3, the minor catalytic subunit of yeast ribonucleotide reductase. MICROBIAL CELL 2019; 6:286-294. [PMID: 31172013 PMCID: PMC6545439 DOI: 10.15698/mic2019.06.680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Ribonucleotide reductase (RNR) is an essential holoenzyme required for de novo synthesis of dNTPs. The Saccharomyces cerevisiae genome encodes for two catalytic subunits, Rnr1 and Rnr3. While Rnr1 is required for DNA replication and DNA damage repair, the function(s) of Rnr3 is unknown. Here, we show that carbon source, an essential nutrient, impacts Rnr1 and Rnr3 abundance: Non-fermentable carbon sources or limiting concentrations of glucose down regulate Rnr1 and induce Rnr3 expression. Oppositely, abundant glucose induces Rnr1 expression and down regulates Rnr3. The carbon source dependent regulation of Rnr3 is mediated by Mec1, the budding yeast ATM/ATR checkpoint response kinase. Unexpectedly, this regulation is independent of all currently known components of the Mec1 DNA damage response network, including Rad53, Dun1, and Tel1, implicating a novel Mec1 signalling axis. rnr3Δ leads to growth defects under respiratory conditions and rescues temperature sensitivity conferred by the absence of Tom6, a component of the mitochondrial TOM (translocase of outer membrane) complex responsible for mitochondrial protein import. Together, these results unveil involvement of Rnr3 in mitochondrial functions and Mec1 in mediating the carbon source dependent regulation of Rnr3.
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Affiliation(s)
- Isaac Corcoles-Saez
- School of Medical Sciences, North West Cancer Research Institute, Bangor University, Deniol Road, Bangor, LL57 2UW, United Kingdom
| | - Jean-Luc Ferat
- Institute of Integrative Biology of the Cell (I2BC), Avenue de la Terrasse, Paris, France
| | - Michael Costanzo
- University of Toronto, Donnelly Centre, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Charles M Boone
- University of Toronto, Donnelly Centre, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Rita S Cha
- School of Medical Sciences, North West Cancer Research Institute, Bangor University, Deniol Road, Bangor, LL57 2UW, United Kingdom
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Xiberras J, Klein M, Nevoigt E. Glycerol as a substrate for Saccharomyces cerevisiae based bioprocesses - Knowledge gaps regarding the central carbon catabolism of this 'non-fermentable' carbon source. Biotechnol Adv 2019; 37:107378. [PMID: 30930107 DOI: 10.1016/j.biotechadv.2019.03.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 12/14/2022]
Abstract
Glycerol is an interesting alternative carbon source in industrial bioprocesses due to its higher degree of reduction per carbon atom compared to sugars. During the last few years, significant progress has been made in improving the well-known industrial platform organism Saccharomyces cerevisiae with regard to its glycerol utilization capability, particularly in synthetic medium. This provided a basis for future metabolic engineering focusing on the production of valuable chemicals from glycerol. However, profound knowledge about the central carbon catabolism in synthetic glycerol medium is a prerequisite for such incentives. As a matter of fact, the current assumptions about the actual in vivo fluxes active on glycerol as the sole carbon source have mainly been based on omics data collected in complex media or were even deduced from studies with other non-fermentable carbon sources, such as ethanol or acetate. A number of uncertainties have been identified which particularly regard the role of the glyoxylate cycle, the subcellular localization of the respective enzymes, the contributions of mitochondrial transporters and the active anaplerotic reactions under these conditions. The review scrutinizes the current knowledge, highlights the necessity to collect novel experimental data using cells growing in synthetic glycerol medium and summarizes the current state of the art with regard to the production of valuable fermentation products from a carbon source that has been considered so far as 'non-fermentable' for the yeast S. cerevisiae.
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Affiliation(s)
- Joeline Xiberras
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany.
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14
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Ho PW, Klein M, Futschik M, Nevoigt E. Glycerol positive promoters for tailored metabolic engineering of the yeast Saccharomyces cerevisiae. FEMS Yeast Res 2018; 18:4898018. [DOI: 10.1093/femsyr/foy019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/21/2018] [Indexed: 01/27/2023] Open
Affiliation(s)
- Ping-Wei Ho
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Matthias Futschik
- School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, Devon, PL4 8AA, UK
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Faro, 8005-139, Portugal
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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15
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Ferreira R, Teixeira PG, Gossing M, David F, Siewers V, Nielsen J. Metabolic engineering of Saccharomyces cerevisiae for overproduction of triacylglycerols. Metab Eng Commun 2018; 6:22-27. [PMID: 29896445 PMCID: PMC5994799 DOI: 10.1016/j.meteno.2018.01.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/05/2018] [Accepted: 01/23/2018] [Indexed: 11/08/2022] Open
Abstract
Triacylglycerols (TAGs) are valuable versatile compounds that can be used as metabolites for nutrition and health, as well as feedstocks for biofuel production. Although Saccharomyces cerevisiae is the favored microbial cell factory for industrial production of biochemicals, it does not produce large amounts of lipids and TAGs comprise only ~1% of its cell dry weight. Here, we engineered S. cerevisiae to reorient its metabolism for overproduction of TAGs, by regulating lipid droplet associated-proteins involved in TAG synthesis and hydrolysis. We implemented a push-and-pull strategy by overexpressing genes encoding a deregulated acetyl-CoA carboxylase, ACC1S659A/S1157A(ACC1**), as well as the last two steps of TAG formation: phosphatidic phosphatase (PAH1) and diacylglycerol acyltransferase (DGA1), ultimately leading to 129 mg∙gCDW−1 of TAGs. Disruption of TAG lipase genes TGL3, TGL4, TGL5 and sterol acyltransferase gene ARE1 increased the TAG content to 218 mg∙gCDW−1. Further disruption of the beta-oxidation by deletion of POX1, as well as glycerol-3-phosphate utilization through deletion of GUT2, did not affect TAGs levels. Finally, disruption of the peroxisomal fatty acyl-CoA transporter PXA1 led to accumulation of 254 mg∙gCDW−1. The TAG levels achieved here are the highest titer reported in S. cerevisiae, reaching 27.4% of the maximum theoretical yield in minimal medium with 2% glucose. This work shows the potential of using an industrially established and robust yeast species for high level lipid production. Saccharomyces cerevisiae was engineered towards triacylglycerol (TAG) accumulation. Overexpression of TAG biosynthesis genes, and deletion of degradation pathways were targeted. Final strain reached 254 mg/gCDW TAG on 2% glucose media, achieving 27.4% of the maximum theoretical yield.
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Affiliation(s)
- Raphael Ferreira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Paulo Gonçalves Teixeira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Michael Gossing
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Florian David
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kgs Lyngby, Denmark
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16
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Shi Y, Wang H, Yan Y, Cao H, Liu X, Lin F, Lu J. Glycerol-3-Phosphate Shuttle Is Involved in Development and Virulence in the Rice Blast Fungus Pyricularia oryzae. FRONTIERS IN PLANT SCIENCE 2018; 9:687. [PMID: 29875789 PMCID: PMC5974175 DOI: 10.3389/fpls.2018.00687] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 05/04/2018] [Indexed: 05/07/2023]
Abstract
The glycerol-3-phosphate (G-3-P) shuttle is an important pathway for delivery of cytosolic reducing equivalents into mitochondrial oxidative phosphorylation, and plays essential physiological roles in yeast, plants, and animals. However, its role has been unclear in filamentous and pathogenic fungi. Here, we characterize the function of the G-3-P shuttle in Pyricularia oryzae by genetic and molecular analyses. In P. oryzae, a glycerol-3-phosphate dehydrogenase 1 (PoGpd1) is involved in NO production, conidiation, and utilization of several carbon sources (pyruvate, sodium acetate, glutamate, and glutamine). A glycerol-3-phosphate dehydrogenase 2 (PoGpd2) is essential for glycerol utilization and fungal development. Deletion of PoGPD2 led to delayed aerial hyphal formation, accelerated aerial hyphal collapse, and reduced conidiation on complete medium (CM) under a light-dark cycle. Aerial mycelial surface hydrophobicity to water and Tween 20 was decreased in ΔPogpd2. Melanin synthesis genes required for cell wall construction and two transcription factor genes (COS1 and CONx2) required for conidiation and/or aerial hyphal differentiation were down-regulated in the aerial mycelia of ΔPogpd2 and ΔPogpd1. Culturing under continuous dark could complement the defects of aerial hyphal differentiation of ΔPogpd2 observed in a light-dark cycle. Two light-sensitive protein genes (PoSIR2 encoding an NAD+-dependent deacetylase and TRX2 encoding a thioredoxin 2) were up-regulated in ΔPogpd2 cultured on CM medium in a light-dark cycle. ΔPogpd2 showed an increased intracellular NAD+/NADH ratio and total NAD content, and alteration of intracellular ATP production. Culturing on minimal medium also could restore aerial hyphal differentiation of ΔPogpd2, which is deficient on CM medium in a light-dark cycle. Two glutamate synthesis genes, GDH1 and PoGLT1, which synthesize glutamate coupled with oxidation of NADH to NAD+, were significantly up-regulated in ΔPogpd2 in a light-dark cycle. Moreover, deletion of PoGpd1 or PoGpd2 led to reduced virulence of conidia or hyphae on rice. The glycerol-3-phosphate shuttle is involved in cellular redox, fungal development, and virulence in P. oryzae.
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Affiliation(s)
- Yongkai Shi
- State Key Laboratory for Rice Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Huan Wang
- State Key Laboratory for Rice Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuxin Yan
- State Key Laboratory for Rice Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Huijuan Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaohong Liu
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou, China
| | - Fucheng Lin
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou, China
| | - Jianping Lu
- State Key Laboratory for Rice Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang University, Hangzhou, China
- *Correspondence: Jianping Lu,
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17
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Willis IM. Maf1 phenotypes and cell physiology. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:330-337. [PMID: 29248739 DOI: 10.1016/j.bbagrm.2017.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 11/27/2017] [Indexed: 01/16/2023]
Abstract
As a master regulator of transcription by RNA polymerase (Pol) III, Maf1 represses the synthesis of highly abundant non-coding RNAs as anabolic signals dissipate, as the quality or quantity of nutrients decreases, and under a wide range of cellular and environmental stress conditions. Thus, Maf1 responds to changes in cell physiology to conserve metabolic energy and to help maintain appropriate levels of tRNAs and other essential non-coding RNAs. Studies in different model organisms and cell-based systems show that perturbations of Maf1 can also impact cell physiology and metabolism. These effects are mediated by changes in Pol III transcription and/or by effects of Maf1 on the expression of select Pol II-transcribed genes. Maf1 phenotypes can vary between different systems and are sometimes conflicting as in comparisons between Maf1 KO mice and cultured mammalian cells. These studies are reviewed in an effort to better appreciate the relationship between Maf1 function and cell physiology. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
- Ian M Willis
- Departments of Biochemistry and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
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18
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Xue LL, Chen HH, Jiang JG. Implications of glycerol metabolism for lipid production. Prog Lipid Res 2017; 68:12-25. [PMID: 28778473 DOI: 10.1016/j.plipres.2017.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 07/06/2017] [Accepted: 07/31/2017] [Indexed: 12/13/2022]
Abstract
Triacylglycerol (TAG) is an important product in oil-producing organisms. Biosynthesis of TAG can be completed through either esterification of fatty acids to glycerol backbone, or through esterification of 2-monoacylglycerol. This review will focus on the former pathway in which two precursors, fatty acid and glycerol-3-phosphate (G3P), are required for TAG formation. Tremendous progress has been made about the enzymes or genes that regulate the biosynthetic pathway of TAG. However, much attention has been paid to the fatty acid provision and the esterification process, while the possible role of G3P is largely neglected. Glycerol is extensively studied on its usage as carbon source for value-added products, but the modification of glycerol metabolism, which is directly associated with G3P synthesis, is seldom recognized in lipid investigations. The relevance among glycerol metabolism, G3P synthesis and lipid production is described, and the role of G3P in glycerol metabolism and lipid production are discussed in detail with an emphasis on how G3P affects lipid production through the modulation of glycerol metabolism. Observations of lipid metabolic changes due to glycerol related disruption in mammals, plants, and microorganisms are introduced. Altering glycerol metabolism results in the changes of final lipid content. Possible regulatory mechanisms concerning the relationship between glycerol metabolism and lipid production are summarized.
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Affiliation(s)
- Lu-Lu Xue
- (a)College of Food and Bioengineering, South China University of Technology, Guangzhou 510640, China; (b)Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hao-Hong Chen
- (a)College of Food and Bioengineering, South China University of Technology, Guangzhou 510640, China
| | - Jian-Guo Jiang
- (a)College of Food and Bioengineering, South China University of Technology, Guangzhou 510640, China.
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Abstract
Fungi and fungal enzymes play important roles in the new bioeconomy. Enzymes from filamentous fungi can unlock the potential of recalcitrant lignocellulose structures of plant cell walls as a new resource, and fungi such as yeast can produce bioethanol from the sugars released after enzyme treatment. Such processes reflect inherent characteristics of the fungal way of life, namely, that fungi as heterotrophic organisms must break down complex carbon structures of organic materials to satisfy their need for carbon and nitrogen for growth and reproduction. This chapter describes major steps in the conversion of plant biomass to value-added products. These products provide a basis for substituting fossil-derived fuels, chemicals, and materials, as well as unlocking the biomass potential of the agricultural harvest to yield more food and feed. This article focuses on the mycological basis for the fungal contribution to biorefinery processes, which are instrumental for improved resource efficiency and central to the new bioeconomy. Which types of processes, inherent to fungal physiology and activities in nature, are exploited in the new industrial processes? Which families of the fungal kingdom and which types of fungal habitats and ecological specializations are hot spots for fungal biomass conversion? How can the best fungal enzymes be found and optimized for industrial use? How can they be produced most efficiently-in fungal expression hosts? How have industrial biotechnology and biomass conversion research contributed to mycology and environmental research? Future perspectives and approaches are listed, highlighting the importance of fungi in development of the bioeconomy.
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20
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Towards the exploitation of glycerol's high reducing power in Saccharomyces cerevisiae-based bioprocesses. Metab Eng 2016; 38:464-472. [DOI: 10.1016/j.ymben.2016.10.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 11/19/2022]
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21
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Genetic determinants for enhanced glycerol growth of Saccharomyces cerevisiae. Metab Eng 2016; 36:68-79. [DOI: 10.1016/j.ymben.2016.03.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/12/2016] [Accepted: 03/10/2016] [Indexed: 11/21/2022]
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22
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Sugar and Glycerol Transport in Saccharomyces cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:125-168. [PMID: 26721273 DOI: 10.1007/978-3-319-25304-6_6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In Saccharomyces cerevisiae the process of transport of sugar substrates into the cell comprises a complex network of transporters and interacting regulatory mechanisms. Members of the large family of hexose (HXT) transporters display uptake efficiencies consistent with their environmental expression and play physiological roles in addition to feeding the glycolytic pathway. Multiple glucose-inducing and glucose-independent mechanisms serve to regulate expression of the sugar transporters in yeast assuring that expression levels and transporter activity are coordinated with cellular metabolism and energy needs. The expression of sugar transport activity is modulated by other nutritional and environmental factors that may override glucose-generated signals. Transporter expression and activity is regulated transcriptionally, post-transcriptionally and post-translationally. Recent studies have expanded upon this suite of regulatory mechanisms to include transcriptional expression fine tuning mediated by antisense RNA and prion-based regulation of transcription. Much remains to be learned about cell biology from the continued analysis of this dynamic process of substrate acquisition.
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Moreno-García J, García-Martínez T, Moreno J, Mauricio JC. Proteins involved in flor yeast carbon metabolism under biofilm formation conditions. Food Microbiol 2014; 46:25-33. [PMID: 25475262 DOI: 10.1016/j.fm.2014.07.001] [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: 01/15/2014] [Revised: 06/30/2014] [Accepted: 07/02/2014] [Indexed: 10/25/2022]
Abstract
A lack of sugars during the production of biologically aged wines after fermentation of grape must causes flor yeasts to metabolize other carbon molecules formed during fermentation (ethanol and glycerol, mainly). In this work, a proteome analysis involving OFFGEL fractionation prior to LC/MS detection was used to elucidate the carbon metabolism of a flor yeast strain under biofilm formation conditions (BFC). The results were compared with those obtained under non-biofilm formation conditions (NBFC). Proteins associated to processes such as non-fermentable carbon uptake, the glyoxylate and TCA cycles, cellular respiration and inositol metabolism were detected at higher concentrations under BFC than under the reference conditions (NBFC). This study constitutes the first attempt at identifying the flor yeast proteins responsible for the peculiar sensory profile of biologically aged wines. A better metabolic knowledge of flor yeasts might facilitate the development of effective strategies for improved production of these special wines.
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Affiliation(s)
- Jaime Moreno-García
- Department of Microbiology, Agrifood Campus of International Excellence ceiA3, University of Cordoba, Severo Ochoa Building, Ctra. N-IV-A km 396, 14014 Cordoba, Spain
| | - Teresa García-Martínez
- Department of Microbiology, Agrifood Campus of International Excellence ceiA3, University of Cordoba, Severo Ochoa Building, Ctra. N-IV-A km 396, 14014 Cordoba, Spain
| | - Juan Moreno
- Department of Agricultural Chemistry, Agrifood Campus of International Excellence ceiA3, University of Cordoba, Marie Curie Building, Ctra. N-IV-A km 396, 14014 Cordoba, Spain
| | - Juan Carlos Mauricio
- Department of Microbiology, Agrifood Campus of International Excellence ceiA3, University of Cordoba, Severo Ochoa Building, Ctra. N-IV-A km 396, 14014 Cordoba, Spain.
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Bergdahl B, Gorwa-Grauslund MF, van Niel EWJ. Physiological effects of over-expressing compartment-specific components of the protein folding machinery in xylose-fermenting Saccharomyces cerevisiae. BMC Biotechnol 2014; 14:28. [PMID: 24758421 PMCID: PMC4021093 DOI: 10.1186/1472-6750-14-28] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Efficient utilization of both glucose and xylose is necessary for a competitive ethanol production from lignocellulosic materials. Although many advances have been made in the development of xylose-fermenting strains of Saccharomyces cerevisiae, the productivity remains much lower compared to glucose. Previous transcriptional analyses of recombinant xylose-fermenting strains have mainly focused on central carbon metabolism. Very little attention has been given to other fundamental cellular processes such as the folding of proteins. Analysis of previously measured transcript levels in a recombinant XR/XDH-strain showed a wide down-regulation of genes targeted by the unfolded protein response during xylose fermentation. Under anaerobic conditions the folding of proteins is directly connected with fumarate metabolism and requires two essential enzymes: FADH2-dependent fumarate reductase (FR) and Ero1p. In this study we tested whether these enzymes impair the protein folding process causing the very slow growth of recombinant yeast strains on xylose under anaerobic conditions. RESULTS Four strains over-expressing the cytosolic (FRD1) or mitochondrial (OSM1) FR genes and ERO1 in different combinations were constructed. The growth and fermentation performance was evaluated in defined medium as well as in a complex medium containing glucose and xylose. Over-expression of FRD1, alone or in combination with ERO1, did not have any significant effect on xylose fermentation in any medium used. Over-expression of OSM1, on the other hand, led to a diversion of carbon from glycerol to acetate and a decrease in growth rate by 39% in defined medium and by 25% in complex medium. Combined over-expression of OSM1 and ERO1 led to the same diversion of carbon from glycerol to acetate and had a stronger detrimental effect on the growth in complex medium. CONCLUSIONS Increasing the activities of the FR enzymes and Ero1p is not sufficient to increase the anaerobic growth on xylose. So additional components of the protein folding mechanism that were identified in transcription analysis of UPR related genes may also be limiting. This includes i) the transcription factor encoded by HAC1 ii) the activity of Pdi1p and iii) the requirement of free FAD during anaerobic growth.
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Affiliation(s)
- Basti Bergdahl
- Division of Applied Microbiology, Department of Chemistry, Lund University, P,O, Box 124, Lund SE-22100, Sweden.
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25
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Cabrera-Orefice A, Chiquete-Félix N, Espinasa-Jaramillo J, Rosas-Lemus M, Guerrero-Castillo S, Peña A, Uribe-Carvajal S. The branched mitochondrial respiratory chain from Debaryomyces hansenii: Components and supramolecular organization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:73-84. [DOI: 10.1016/j.bbabio.2013.07.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 07/23/2013] [Accepted: 07/25/2013] [Indexed: 11/29/2022]
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26
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Bühligen F, Rüdinger P, Fetzer I, Stahl F, Scheper T, Harms H, Müller S. Sustainability of industrial yeast serial repitching practice studied by gene expression and correlation analysis. J Biotechnol 2013; 168:718-28. [DOI: 10.1016/j.jbiotec.2013.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 09/12/2013] [Accepted: 09/13/2013] [Indexed: 12/24/2022]
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27
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Song XS, Li HP, Zhang JB, Song B, Huang T, Du XM, Gong AD, Liu YK, Feng YN, Agboola RS, Liao YC. Trehalose 6-phosphate phosphatase is required for development, virulence and mycotoxin biosynthesis apart from trehalose biosynthesis in Fusarium graminearum. Fungal Genet Biol 2013; 63:24-41. [PMID: 24291007 DOI: 10.1016/j.fgb.2013.11.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 12/11/2022]
Abstract
Trehalose 6-phosphate synthase (TPS1) and trehalose 6-phosphate phosphatase (TPS2) are required for trehalose biosynthesis in yeast and filamentous fungi, including Fusarium graminearum. Three null mutants Δtps1, Δtps2 and Δtps1-Δtps2, each carrying either a single deletion of TPS1 or TPS2 or a double deletion of TPS1-TPS2, were generated from a toxigenic F. graminearum strain and were not able to synthesize trehalose. In contrast to its reported function in yeasts and filamentous fungi, TPS1 appeared dispensable for development and virulence. However, deletion of TPS2 abolished sporulation and sexual reproduction; it also altered cell polarity and ultrastructure of the cell wall in association with reduced chitin biosynthesis. The cell polarity alteration was exhibited as reduced apical growth and increased lateral growth and branching with increased hyphal and cell wall widths. Moreover, the TPS2-deficient strain displayed abnormal septum development and nucleus distribution in its conidia and vegetative hyphae. The Δtps2 mutant also had 62% lower mycelial growth on potato dextrose agar and 99% lower virulence on wheat compared with the wild-type. The Δtps1, Δtps2 and Δtps1-Δtps2 mutants synthesized over 3.08-, 7.09- and 2.47-fold less mycotoxins, respectively, on rice culture compared with the wild-type. Comparative transcriptome analysis revealed that the Δtps1, Δtps2 and Δtps1-Δtps2 mutants had 486, 1885 and 146 genotype-specific genes, respectively, with significantly changed expression profiles compared with the wild-type. Further dissection of this pathway will provide new insights into regulation of fungal development, virulence and trichothecene biosynthesis.
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Affiliation(s)
- Xiu-Shi Song
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - He-Ping Li
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Jing-Bo Zhang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Bo Song
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Tao Huang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Xiao-Min Du
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - An-Dong Gong
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yi-Ke Liu
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yan-Ni Feng
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Rebecca S Agboola
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yu-Cai Liao
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; National Center of Plant Gene Research (Wuhan), Wuhan 430070, People's Republic of China.
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Swinnen S, Klein M, Carrillo M, McInnes J, Nguyen HTT, Nevoigt E. Re-evaluation of glycerol utilization in Saccharomyces cerevisiae: characterization of an isolate that grows on glycerol without supporting supplements. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:157. [PMID: 24209984 PMCID: PMC3835864 DOI: 10.1186/1754-6834-6-157] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 10/29/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND Glycerol has attracted attention as a carbon source for microbial production processes due to the large amounts of crude glycerol waste resulting from biodiesel production. The current knowledge about the genetics and physiology of glycerol uptake and catabolism in the versatile industrial biotechnology production host Saccharomyces cerevisiae has been mainly based on auxotrophic laboratory strains, and carried out in the presence of growth-supporting supplements such as amino acids and nucleic bases. The latter may have resulted in ambiguous conclusions concerning glycerol growth in this species. The purpose of this study was to re-evaluate growth of S. cerevisiae in synthetic glycerol medium without the addition of supplements. RESULTS Initial experiments showed that prototrophic versions of the laboratory strains CEN.PK, W303, and S288c did not exhibit any growth in synthetic glycerol medium without supporting supplements. However, a screening of 52 S. cerevisiae isolates for growth in the same medium revealed a high intraspecies diversity. Within this group significant variation with respect to the lag phase and maximum specific growth rate was observed. A haploid segregant of one good glycerol grower (CBS 6412-13A) was selected for detailed analysis. Single deletions of the genes encoding for the glycerol/H+ symporter (STL1), the glycerol kinase (GUT1), and the mitochondrial FAD+-dependent glycerol 3-phosphate dehydrogenase (GUT2) abolished glycerol growth in this strain, implying that it uses the same glycerol utilization pathway as previously identified in auxotrophic laboratory strains. Segregant analysis of a cross between CBS 6412-13A and CEN.PK113-1A revealed that the glycerol growth phenotype is a quantitative trait. Genetic linkage and reciprocal hemizygosity analysis demonstrated that GUT1CBS 6412-13A is one of the multiple genetic loci contributing to the glycerol growth phenotype. CONCLUSION The S. cerevisiae intraspecies diversity with regard to glycerol growth is a valuable starting point to identify the genetic and molecular basis of this phenotype. This knowledge can be applied for further rational strain improvement with the goal of using glycerol as a carbon source in industrial biotechnology processes based on S. cerevisiae as a production organism.
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Affiliation(s)
- Steve Swinnen
- School of Engineering and Science, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- School of Engineering and Science, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Martina Carrillo
- School of Engineering and Science, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Joseph McInnes
- School of Engineering and Science, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Huyen Thi Thanh Nguyen
- School of Engineering and Science, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- School of Engineering and Science, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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Molecular clone and expression of a NAD+-dependent glycerol-3-phosphate dehydrogenase isozyme gene from the halotolerant alga Dunaliella salina. PLoS One 2013; 8:e62287. [PMID: 23626797 PMCID: PMC3633914 DOI: 10.1371/journal.pone.0062287] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/19/2013] [Indexed: 11/19/2022] Open
Abstract
Glycerol is an important osmotically compatible solute in Dunaliella. Glycerol-3-phosphate dehydrogenase (G3PDH) is a key enzyme in the pathway of glycerol synthesis, which converts dihydroxyacetone phosphate (DHAP) to glycerol-3-phosphate. Generally, the glycerol-DHAP cycle pathway, which is driven by G3PDH, is considered as the rate-limiting enzyme to regulate the glycerol level under osmotic shocks. Considering the peculiarity in osmoregulation, the cDNA of a NAD+-dependent G3PDH was isolated from D. salina using RACE and RT-PCR approaches in this study. Results indicated that the length of the cDNA sequence of G3PDH was 2,100 bp encoding a 699 amino acid deduced polypeptide whose computational molecular weight was 76.6 kDa. Conserved domain analysis revealed that the G3PDH protein has two independent functional domains, SerB and G3PDH domains. It was predicted that the G3PDH was a nonsecretory protein and may be located in the chloroplast of D. salina. Phylogenetic analysis demonstrated that the D. salina G3PDH had a closer relationship with the G3PDHs from the Dunaliella genus than with those from other species. In addition, the cDNA was subsequently subcloned in the pET-32a(+) vector and was transformed into E. coli strain BL21 (DE3), a expression protein with 100 kDa was identified, which was consistent with the theoretical value.
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Vakeria D, Box W, Bird L, Mellor J. CHARACTERISATION OF AMYLOLYTIC BREWING YEAST. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1996.tb00891.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Mori K, Iwama R, Kobayashi S, Horiuchi H, Fukuda R, Ohta A. Transcriptional repression by glycerol of genes involved in the assimilation ofn-alkanes and fatty acids in yeastYarrowia lipolytica. FEMS Yeast Res 2013; 13:233-40. [DOI: 10.1111/1567-1364.12025] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 11/28/2012] [Accepted: 12/10/2012] [Indexed: 10/27/2022] Open
Affiliation(s)
- Katsuki Mori
- Department of Biotechnology; The University of Tokyo; Tokyo; Japan
| | - Ryo Iwama
- Department of Biotechnology; The University of Tokyo; Tokyo; Japan
| | | | | | - Ryouichi Fukuda
- Department of Biotechnology; The University of Tokyo; Tokyo; Japan
| | - Akinori Ohta
- Department of Biotechnology; The University of Tokyo; Tokyo; Japan
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Enhancement of xylitol production in glycerol kinase disrupted Candida tropicalis by co-expression of three genes involved in glycerol metabolic pathway. Bioprocess Biosyst Eng 2012; 36:1279-84. [PMID: 23232964 DOI: 10.1007/s00449-012-0872-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 11/29/2012] [Indexed: 10/27/2022]
Abstract
Glycerol can be used as a primary carbon source by yeasts, little is known regarding glycerol metabolism in Candida tropicalis. In this study, glycerol kinase gene (gk) was disrupted from xylitol dehydrogenase gene (XYL2) knockout C. tropicalis strain BSXDH-3. The resultant gk knockout C. tropicalis strain was incapable to grow on glycerol. The cells growth on glycerol was resumed by co-expressing Scheffersomyces stipitis gcy1, 2 and 3 genes, which respectively encode NADP(+)-dependent glycerol dehydrogenase 1, 2 and 3, under the control of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) promoter. NADPH-dependent xylitol production was higher in the engineered strain, termed "GK", than in BSXDH-3. In fermentation experiments using glycerol as co-substrate with xylose, strain GK produced xylitol 0.85 and 1.28 g l(-1) h(-1) at the time periods of 16 and 24 h, respectively, which is 30 and 18 % higher at same time intervals in BSXDH-3. This is the first report of gk gene disruption and co-expression of gcy1, 2 and 3 genes for NADPH regeneration and enhanced xylitol production in C. tropicalis.
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Jung JY, Kim TY, Ng CY, Oh MK. Characterization of GCY1 in Saccharomyces cerevisiae by metabolic profiling. J Appl Microbiol 2012; 113:1468-78. [PMID: 22979944 DOI: 10.1111/jam.12013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/29/2012] [Accepted: 09/07/2012] [Indexed: 12/20/2022]
Abstract
AIMS The analytical study of intracellular (IC) metabolites has developed with advances in chromatography-linked mass spectrometry and fast sampling procedures. We applied the IC metabolite analysis to characterize the role of GCY1 in the glycerol (GLY) catabolic pathway in Saccharomyces cerevisiae. METHODS AND RESULTS Strains with disrupted or overexpressing GLY catabolic genes such as GCY1, DAK1 and DAK2 were constructed. The strains were cultivated under different aeration conditions and quickly quenched using a novel rapid sampling port. IC concentrations of GLY, dihydroxyacetone (DHA), glycerol 3-phosphate and dihydroxyacetone phosphate were analysed in the strains by gas chromatography/mass spectrometry. DHA was not detected in the gcy1 gene-disrupted strain but accumulated 225.91 μmol g DCW(-1) in a DHA kinase gene-deficient strain under micro-aerobic conditions. Additionally, a 16.1% increase in DHA occurred by overexpressing GCY1 in the DHA kinase-deficient strain. CONCLUSIONS Metabolic profiling showed that the GCY1 gene product functions as a GLY dehydrogenase in S. cerevisiae, particularly under micro-aerobic conditions. SIGNIFICANCE AND IMPACT OF THE STUDY Metabolic profiling of the GLY dissimilation pathway was successfully demonstrated in S. cerevisiae, and the function of GCY1 was explained by the results.
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Affiliation(s)
- J-Y Jung
- Department of Chemical and Biological Engineering, Korea University, Seoul, Korea
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Jouhten P, Wiebe M, Penttilä M. Dynamic flux balance analysis of the metabolism ofSaccharomyces cerevisiaeduring the shift from fully respirative or respirofermentative metabolic states to anaerobiosis. FEBS J 2012; 279:3338-54. [DOI: 10.1111/j.1742-4658.2012.08649.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Promotion of glycerol utilization using ethanol and 1-propanol in Schizosaccharomyces pombe. Appl Microbiol Biotechnol 2012; 95:441-9. [DOI: 10.1007/s00253-012-3971-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 02/13/2012] [Accepted: 02/13/2012] [Indexed: 01/27/2023]
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36
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Herrera-Valencia VA, Macario-González LA, Casais-Molina ML, Beltran-Aguilar AG, Peraza-Echeverría S. In silico cloning and characterization of the glycerol-3-phosphate dehydrogenase (GPDH) gene family in the green microalga Chlamydomonas reinhardtii. Curr Microbiol 2012; 64:477-85. [PMID: 22358185 DOI: 10.1007/s00284-012-0095-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 01/30/2012] [Indexed: 11/25/2022]
Abstract
Glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the conversion of dihydroxyacetone phosphate (DHAP) and NADH to glycerol-3-phosphate (G3P) and NAD(+). G3P is important as a precursor for glycerol and glycerolipid synthesis in microalgae. A GPDH enzyme has been previously purified from the green microalga Chlamydomonas reinhardtii, however, no genes coding for GPDH have been characterized before. In this study, we report the in silico characterization of three putative GPDH genes from C. reinhardtii: CrGPDH1, CrGPDH2, and CrGPDH3. These sequences showed a significant similarity to characterized GPDH genes from the microalgae Dunaliella salina and Dunaliella viridis. The prediction of the three-dimensional structure of the proteins showed the characteristic fold topology of GPDH enzymes. Furthermore, the phylogenetic analysis showed that the three CrGPDHs share the same clade with characterized GPDHs from Dunaliella suggesting a common evolutionary origin and a similar catalytic function. In addition, the K(a)/K(s) ratios of these sequences suggested that they are under purifying selection. Moreover, the expression analysis showed a constitutive expression of CrGPDH1, while CrGPDH2 and CrGPDH3 were induced in response to osmotic stress, suggesting a possible role for these two sequences in the synthesis of glycerol as a compatible solute in osmoregulation, and perhaps also in lipid synthesis in C. reinhardtii. This study has provided a foundation for further biochemical and genetic studies of the GPDH family in this model microalga, and also opportunities to assess the potential of these genes to enhance the synthesis of TAGs for biodiesel production.
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Affiliation(s)
- Virginia A Herrera-Valencia
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán, Mexico
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Postmus J, Tuzun I, Bekker M, Müller WH, Teixeira de Mattos MJ, Brul S, Smits GJ. Dynamic regulation of mitochondrial respiratory chain efficiency in Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2011; 157:3500-3511. [PMID: 21964735 DOI: 10.1099/mic.0.050039-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To adapt to changes in the environment, cells have to dynamically alter their phenotype in response to, for instance, temperature and oxygen availability. Interestingly, mitochondrial function in Saccharomyces cerevisiae is inherently temperature sensitive; above 37 °C, yeast cells cannot grow on respiratory carbon sources. To investigate this phenomenon, we studied the effect of cultivation temperature on the efficiency (production of ATP per atom of oxygen consumed, or P/O) of the yeast respiratory chain in glucose-limited chemostats. We determined that even though the specific oxygen consumption rate did not change with temperature, oxygen consumption no longer contributed to mitochondrial ATP generation at temperatures higher than 37 °C. Remarkably, between 30 and 37 °C, we observed a linear increase in respiratory efficiency with growth temperature, up to a P/O of 1.4, close to the theoretical maximum that can be reached in vivo. The temperature-dependent increase in efficiency required the presence of the mitochondrial glycerol-3-phosphate dehydrogenase GUT2. Respiratory chain efficiency was also altered in response to changes in oxygen availibility. Our data show that, even in the absence of alternative oxidases or uncoupling proteins, yeast has retained the ability to dynamically regulate the efficiency of coupling of oxygen consumption to proton translocation in the respiratory chain in response to changes in the environment.
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Affiliation(s)
- Jarne Postmus
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Işil Tuzun
- Department of Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Martijn Bekker
- Department of Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Wally H Müller
- Department of Biology, Biomolecular Imaging, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - M Joost Teixeira de Mattos
- Department of Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Gertien J Smits
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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Dulermo T, Nicaud JM. Involvement of the G3P shuttle and β-oxidation pathway in the control of TAG synthesis and lipid accumulation in Yarrowia lipolytica. Metab Eng 2011; 13:482-91. [PMID: 21620992 DOI: 10.1016/j.ymben.2011.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 04/07/2011] [Accepted: 05/13/2011] [Indexed: 11/17/2022]
Abstract
The oleaginous yeast Yarrowia lipolytica can accumulate up to 38% of its dry weight (DW) as lipids. Factors involved in lipid accumulation, particularly triglycerides, are not well identified. Using different mutations in the glycerol-3-phosphate (G3P) shuttle pathway (Δgut2 affecting the anabolic dehydrogenase or overexpressing GPD1 affecting the catabolic dehydrogenase), we were able to modulate G3P concentration. We show that in a Po1d genetic background, GPD1 overexpression, GUT2 inactivation or both mutations together result in 1.5, 2.9, and 5.6-fold respective increases in the level of G3P leading to an increase of triacylglyceride (TAG) accumulation. Moreover, our results indicate that each strain with an increased concentration of G3P, also presented a decreased concentration of glycerol. Analysis of the different genes involved in glycerol metabolism indicated that Y. lipolytica does not possess a gene for glycerol-3-phosphatase. These findings suggest that Y. lipolytica has a modified and unique metabolism of glycerol that is dedicated to G3P synthesis (and also to TAG synthesis) which may contribute to its oleaginous character. Furthermore, coupling the G3P shuttle disorders to a deficient β-oxidation pathway (by inactiving POX1-6 or MFE1 genes) increased TAG and free fatty acids content. Finally, we obtained strains that accumulated up to 65-75% of their DW as lipid. Transcriptional analysis in these strains, revealed that the high levels of lipids resulted from over-expression of genes involved in TAG synthesis (SCT1, encoding a sn-1 acyltransferase; and DGA1, encoding an acylCoA diacylglycerol acyltransferase) and the repression of genes involved in the degradation of TAG (TGL3 and TGL4, encoding triacylglycerol lipases). These findings indicate that TAG synthesis is limited by the availability of G3P and fatty acids, and that the expression of genes involved in TAG homeostasis is regulated by the G3P shuttle and the β-oxidation pathway. Finally, the synergistic contribution of acyltransferase gene expression to G3P synthesis is required for high levels of TAG synthesis and lipid accumulation in Y. lipolytica.
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Affiliation(s)
- Thierry Dulermo
- INRA, Institut Micalis, INRA-AgroParisTech, UMR1319, domaine de Vilvert, Jouy-en-Josas, France
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Ochoa-Estopier A, Lesage J, Gorret N, Guillouet SE. Kinetic analysis of a Saccharomyces cerevisiae strain adapted for improved growth on glycerol: Implications for the development of yeast bioprocesses on glycerol. BIORESOURCE TECHNOLOGY 2011; 102:1521-1527. [PMID: 20869237 DOI: 10.1016/j.biortech.2010.08.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 07/30/2010] [Accepted: 08/02/2010] [Indexed: 05/29/2023]
Abstract
Glycerol is an agro-industrial residue generated in high amounts during the biodiesel production. The growing production of biodiesel is creating a worldwide glycerol surplus. Therefore, replacing sugar-based feedstock in bioprocesses by glycerol could be potentially attractive. Saccharomyces cerevisiae is one of the most commonly used microorganisms in the agri-food industry and therefore currently produced in large quantities from sugar-based feedstock. Unfortunately, growth of S. cerevisiae strains on glycerol is very low with reported μmax around 0.01 h(-1). This study demonstrates that successive growth of the S. cerevisiae CBS 8066, CEN.PK 113-7 D and Ethanol Red on glycerol as sole carbon source considerably improved the μmax from 0.01 up to 0.2 h(-1). The "adapted strain" CBS 8066-FL20 was kinetically characterized during aerobic and oxygen-limited cultivation in bioreactor and the results discussed in terms of their implication for developing glycerol-based S. cerevisiae bioprocesses.
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Affiliation(s)
- A Ochoa-Estopier
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Av. de Rangueil, F-31077 Toulouse, France
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Matsufuji Y, Nakagawa T, Fujimura S, Tani A, Nakagawa J. Transcription factor Stb5p is essential for acetaldehyde tolerance in Saccharomyces cerevisiae. J Basic Microbiol 2010; 50:494-8. [PMID: 20806246 DOI: 10.1002/jobm.200900391] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Transcription factor Stb5p, previously known as one of the multidrug resistance gene regulators in Saccharomyces cerevisiae, was shown here to play an essential role in acetaldehyde tolerance. A mutant strain, Δstb5 exhibited increased acetaldehyde sensitivity, and failed to induce genes such as GND1, TKL1 and TAL1 involved in the pentose phosphate pathway (PPP) upon acetaldehyde stress. Using this strain it was revealed that Stb5p acts as a repressor for PGI1 encoding glucose-6-phosphate isomerase under acetaldehyde stress. In reverse, over-expression of Stb5p reinforced acetaldehyde tolerance to the yeast. Furthermore, various deletion mutants of the genes involved in glycolysis showed increased acetaldehyde tolerance compared to the wild-type strain. From these results, it was suggested that Stb5p participates in acetaldehyde tolerance by regulating expression of the PPP genes and PGI1, and that down-regulation of glycolytic pathway may lead to vitalization of PPP and to increased acetaldehyde tolerance.
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Affiliation(s)
- Yoshimi Matsufuji
- Department of Food Science and Technology, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, Japan
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Alkayal F, Albion RL, Tillett RL, Hathwaik LT, Lemos MS, Cushman JC. Expressed sequence tag (EST) profiling in hyper saline shocked Dunaliella salina reveals high expression of protein synthetic apparatus components. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2010; 179:437-49. [PMID: 21802602 DOI: 10.1016/j.plantsci.2010.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 06/28/2010] [Accepted: 07/01/2010] [Indexed: 05/10/2023]
Abstract
The unicellular, halotolerant, green alga, Dunaliella salina (Chlorophyceae) has the unique ability to adapt and grow in a wide range of salt conditions from about 0.05 to 5.5M. To better understand the molecular basis of its salinity tolerance, a complementary DNA (cDNA) library was constructed from D. salina cells adapted to 2.5M NaCl, salt-shocked at 3.4M NaCl for 5h, and used to generate an expressed sequence tag (EST) database. ESTs were obtained for 2831 clones representing 1401 unique transcripts. Putative functions were assigned to 1901 (67.2%) ESTs after comparison with protein databases. An additional 154 (5.4%) ESTs had significant similarity to known sequences whose functions are unclear and 776 (27.4%) had no similarity to known sequences. For those D. salina ESTs for which functional assignments could be made, the largest functional categories included protein synthesis (35.7%), energy (photosynthesis) (21.4%), primary metabolism (13.8%) and protein fate (6.8%). Within the protein synthesis category, the vast majority of ESTs (80.3%) encoded ribosomal proteins representing about 95% of the approximately 82 subunits of the cytosolic ribosome indicating that D. salina invests substantial resources in the production and maintenance of protein synthesis. The increased mRNA expression upon salinity shock was verified for a small set of selected genes by real-time, quantitative reverse-transcription-polymerase chain reaction (qRT-PCR). This EST collection also provided important new insights into the genetic underpinnings for the biosynthesis and utilization of glycerol and other osmoprotectants, the carotenoid biosynthetic pathway, reactive oxygen-scavenging enzymes, and molecular chaperones (heat shock proteins) not described previously for D. salina. EST discovery also revealed the existence of RNA interference and signaling pathways associated with osmotic stress adaptation. The unknown ESTs described here provide a rich resource for the identification of novel genes associated with the mechanistic basis of salinity stress tolerance and other stress-adaptive traits.
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Affiliation(s)
- Fadi Alkayal
- Dasman Center for Research and Treatment of Diabetes, P.O Box 1180, Dasman, Kuwait
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Jiménez-Martí E, Gomar-Alba M, Palacios A, Ortiz-Julien A, del Olmo ML. Towards an understanding of the adaptation of wine yeasts to must: relevance of the osmotic stress response. Appl Microbiol Biotechnol 2010; 89:1551-61. [DOI: 10.1007/s00253-010-2909-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 09/03/2010] [Accepted: 09/07/2010] [Indexed: 10/19/2022]
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Generation of an evolved Saccharomyces cerevisiae strain with a high freeze tolerance and an improved ability to grow on glycerol. J Ind Microbiol Biotechnol 2010; 38:1037-44. [DOI: 10.1007/s10295-010-0878-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 09/13/2010] [Indexed: 10/19/2022]
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44
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Electron competition process in respiratory chain: Regulatory mechanisms and physiological functions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:671-7. [DOI: 10.1016/j.bbabio.2010.01.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/22/2010] [Accepted: 01/23/2010] [Indexed: 11/24/2022]
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The gld1+ gene encoding glycerol dehydrogenase is required for glycerol metabolism in Schizosaccharomyces pombe. Appl Microbiol Biotechnol 2010; 87:715-27. [PMID: 20396879 DOI: 10.1007/s00253-010-2586-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 03/23/2010] [Accepted: 03/24/2010] [Indexed: 10/19/2022]
Abstract
The budding yeast Saccharomyces cerevisiae is able to utilize glycerol as the sole carbon source via two pathways (glycerol 3-phosphate pathway and dihydroxyacetone [DHA] pathway). In contrast, the fission yeast Schizosaccharomyces pombe does not grow on media containing glycerol as the sole carbon source. However, in the presence of other carbon sources such as galactose and ethanol, S. pombe could assimilate glycerol and glycerol was preferentially utilized over ethanol and galactose. No equivalent of S. cerevisiae Gcy1/glycerol dehydrogenase has been identified in S. pombe. However, we identified a gene in S. pombe, SPAC13F5.03c (gld1 (+)), that is homologous to bacterial glycerol dehydrogenase. Deletion of gld1 caused a reduction in glycerol dehydrogenase activity and prevented glycerol assimilation. The gld1 Delta cells grew on 50 mM DHA as the sole carbon source, indicating that the glycerol dehydrogenase encoded by gld1 (+) is essential for glycerol assimilation in S. pombe. Strains of S. pombe deleted for dak1 (+) and dak2 (+) encoding DHA kinases could not grow on glycerol and showed sensitivity to a higher concentration of DHA. The dak1 Delta strain showed a more severe reduction of growth on glycerol and DHA than the dak2 Delta strain because the expression of dak1 (+) mRNA was higher than that of dak2 (+). In wild-type S. pombe, expression of the gld1 (+), dak1 (+), and dak2 (+) genes was repressed at a high concentration of glucose and was derepressed during glucose starvation. We found that gld1 (+) was regulated by glucose repression and that it was derepressed in scr1 Delta and tup12 Delta strains.
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Saliola M, D'Amici S, Sponziello M, Mancini P, Tassone P, Falcone C. The transdehydrogenase genes KlNDE1 and KlNDI1 regulate the expression of KlGUT2 in the yeast Kluyveromyces lactis. FEMS Yeast Res 2010; 10:518-26. [PMID: 20491935 DOI: 10.1111/j.1567-1364.2010.00631.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
KlNDE1 and KlNDI1 code for two inner mitochondrial membrane transdehydrogenases involved in the maintenance of the intracellular NAD(P)H redox balance. The function of these genes during the utilization of fermentative and respiratory carbon sources was studied. During growth in glucose, deletion of KlNDE1 and KlNDI1 led to an altered kinetic of ethanol and glycerol accumulation compared with the wild type; in addition, KlndiDelta was unable to grow in respiratory substrates. Northern analysis and GFP-fusion experiments showed that KlNDE1 and KlNDI1 regulate the expression of KlGUT2, a component of the glycerol-3-phosphate shuttle. Moreover, both genes seem to be involved in the biogenesis of the mitochondrial tubular network.
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Affiliation(s)
- Michele Saliola
- Department of Cell and Developmental Biology, University of Rome La Sapienza, Rome, Italy.
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47
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Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis. Mol Genet Genomics 2009; 282:571-86. [DOI: 10.1007/s00438-009-0486-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 09/13/2009] [Indexed: 11/26/2022]
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Rijken PJ, De Kruijff B, De Kroon AIPM. Phosphatidylcholine is essential for efficient functioning of the mitochondrial glycerol-3-phosphate dehydrogenase Gut2 inSaccharomyces cerevisiae. Mol Membr Biol 2009; 24:269-81. [PMID: 17520483 DOI: 10.1080/09687860701210732] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Gut2, the mitochondrial glycerol-3-phosphate dehydrogenase, was previously shown to become preferentially labelled with photoactivatable phosphatidylcholine (PC), pointing to a functional relation between these molecules. In the present study we analyzed whether Gut2 functioning depends on the PC content of yeast cells, using PC biosynthetic mutants in which the PC content was lowered. PC depletion was found to reduce growth on glycerol and to increase glycerol excretion, both indicating that PC is needed for optimal Gut2 functioning in vivo. Using several in vitro approaches the nature of the dependence of Gut2 functioning on cellular PC contents was investigated. The results of these experiments suggest that it is unlikely that the effects observed in vivo are due to changes in cellular Gut2 content, in specific activity of Gut2 in isolated mitochondria, or in the membrane association of Gut2, upon lowering the PC level. The in vivo effects are more likely an indirect result of PC depletion-induced changes in the cellular context in which Gut2 functions, that are not manifested in the in vitro systems used.
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Affiliation(s)
- Pieter J Rijken
- Department Biochemistry of Membranes, Bijvoet Institute and Institute of Biomembranes, Utrecht University, The Netherlands.
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49
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Chen H, Jiang JG. Osmotic responses ofDunaliellato the changes of salinity. J Cell Physiol 2009; 219:251-8. [DOI: 10.1002/jcp.21715] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kayingo G, Martins A, Andrie R, Neves L, Lucas C, Wong B. A permease encoded by STL1 is required for active glycerol uptake by Candida albicans. MICROBIOLOGY-SGM 2009; 155:1547-1557. [PMID: 19383674 DOI: 10.1099/mic.0.023457-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Candida albicans accumulates large amounts of the polyols glycerol and d-arabitol when the cells are exposed to physiological conditions relevant to stress and virulence in animals. Intracellular concentrations of glycerol are determined by rates of glycerol production and catabolism and of glycerol uptake and efflux through the plasma membrane. We and others have studied glycerol production in C. albicans, but glycerol uptake by C. albicans has not been studied. In the present study, we found that [(14)C]glycerol uptake by C. albicans SC5314 was (i) accumulative; (ii) dependent on proton-motive force; (iii) unaffected by carbon source; and (iv) unaffected by large molar excesses of d-arabitol or other polyols. The respective K(m) and V(max) values were 2.1 mM and 460 micromol h(-1) (g dry wt)(-1) in glucose medium and 2.6 mM and 268 micromol h(-1) (g dry wt)(-1) in glycerol medium. To identify the C. albicans glycerol uptake protein(s), we cloned the C. albicans homologues of the Saccharomyces cerevisiae genes GUP1 and STL1, both of which are known to be involved in glycerol transport. When multicopy plasmids encoding C. albicans STL1, C. albicans STL2 and C. albicans GUP1 were introduced into the corresponding S. cerevisiae null mutants, the transformants all acquired the ability to grow on minimal glycerol medium; however, only S. cerevisiae stl1 null mutants transformed with C. albicans STL1 actively took up extracellular [(14)C]glycerol. When both chromosomal alleles of C. albicans STL1 were deleted from C. albicans BWP17, the resulting stl1 null mutants grew poorly on minimal glycerol medium, and their ability to transport [(14)C]glycerol into the cell was markedly reduced. In contrast, deletion of both chromosomal alleles of C. albicans STL2 or of C. albicans GUP1 had no significant effects on [(14)C]glycerol uptake or the ability to grow on minimal glycerol medium. Northern blot analysis indicated that C. albicans STL1 was expressed in both glucose and glycerol media, conditions under which we detected wild-type active glycerol uptake. Furthermore, STL1 was highly expressed in salt-stressed cells; however, the stl1 null mutant was no more sensitive to salt stress than wild-type controls. We also detected high levels of STL2 expression in glycerol-grown cells, even though deletion of this gene did not influence glycerol uptake activity in glycerol-grown cells. We conclude from the results above that a plasma-membrane H(+) symporter encoded by C. albicans STL1 actively transports glycerol into C. albicans cells.
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Affiliation(s)
- Gerald Kayingo
- Department of Internal Medicine, Section of Infectious Diseases, Yale University and VA Connecticut Healthcare System, 950 Campbell Avenue (111-I), West Haven, CT 06516, USA
| | - António Martins
- Centro de Biologia Molecular e Ambiental (CBMA), Departamento de Biologia/Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Rachael Andrie
- Division of Infectious Diseases, Department of Medicine, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, NRC-3, Portland, OR 97239, USA
| | - Luisa Neves
- Centro de Biologia Molecular e Ambiental (CBMA), Departamento de Biologia/Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Cândida Lucas
- Centro de Biologia Molecular e Ambiental (CBMA), Departamento de Biologia/Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Brian Wong
- Division of Infectious Diseases, Department of Medicine, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, NRC-3, Portland, OR 97239, USA.,Department of Internal Medicine, Section of Infectious Diseases, Yale University and VA Connecticut Healthcare System, 950 Campbell Avenue (111-I), West Haven, CT 06516, USA
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