1
|
Sugimura M, Seike T, Okahashi N, Izumi Y, Bamba T, Ishii J, Matsuda F. Improved 2,3-Butanediol Production Rate of Metabolically Engineered Saccharomyces cerevisiae by Deletion of RIM15 and Activation of Pyruvate Consumption Pathway. Int J Mol Sci 2023; 24:16378. [PMID: 38003568 PMCID: PMC10671664 DOI: 10.3390/ijms242216378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/31/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Saccharomyces cerevisiae is a promising host for the bioproduction of higher alcohols, such as 2,3-butanediol (2,3-BDO). Metabolically engineered S. cerevisiae strains that produce 2,3-BDO via glycolysis have been constructed. However, the specific 2,3-BDO production rates of engineered strains must be improved. To identify approaches to improving the 2,3-BDO production rate, we investigated the factors contributing to higher ethanol production rates in certain industrial strains of S. cerevisiae compared to laboratory strains. Sequence analysis of 11 industrial strains revealed the accumulation of many nonsynonymous substitutions in RIM15, a negative regulator of high fermentation capability. Comparative metabolome analysis suggested a positive correlation between the rate of ethanol production and the activity of the pyruvate-consuming pathway. Based on these findings, RIM15 was deleted, and the pyruvate-consuming pathway was activated in YHI030, a metabolically engineered S. cerevisiae strain that produces 2,3-BDO. The titer, specific production rate, and yield of 2,3-BDO in the test tube-scale culture using the YMS106 strain reached 66.4 ± 4.4 mM, 1.17 ± 0.017 mmol (g dry cell weight h)-1, and 0.70 ± 0.03 mol (mol glucose consumed)-1. These values were 2.14-, 2.92-, and 1.81-fold higher than those of the vector control, respectively. These results suggest that bioalcohol production via glycolysis can be enhanced in a metabolically engineered S. cerevisiae strain by deleting RIM15 and activating the pyruvate-consuming pathway.
Collapse
Affiliation(s)
- Masahiko Sugimura
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Taisuke Seike
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Fukuoka, Japan
| | - Takeshi Bamba
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Fukuoka, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan
| | - Fumio Matsuda
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita 565-0871, Osaka, Japan
| |
Collapse
|
2
|
Khamwachirapithak P, Sae-Tang K, Mhuantong W, Tanapongpipat S, Zhao XQ, Liu CG, Wei DQ, Champreda V, Runguphan W. Optimizing Ethanol Production in Saccharomyces cerevisiae at Ambient and Elevated Temperatures through Machine Learning-Guided Combinatorial Promoter Modifications. ACS Synth Biol 2023; 12:2897-2908. [PMID: 37681736 PMCID: PMC10594650 DOI: 10.1021/acssynbio.3c00199] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 09/09/2023]
Abstract
Bioethanol has gained popularity in recent decades as an ecofriendly alternative to fossil fuels due to increasing concerns about global climate change. However, economically viable ethanol fermentation remains a challenge. High-temperature fermentation can reduce production costs, but Saccharomyces cerevisiae yeast strains normally ferment poorly under high temperatures. In this study, we present a machine learning (ML) approach to optimize bioethanol production in S. cerevisiae by fine-tuning the promoter activities of three endogenous genes. We created 216 combinatorial strains of S. cerevisiae by replacing native promoters with five promoters of varying strengths to regulate ethanol production. Promoter replacement resulted in a 63% improvement in ethanol production at 30 °C. We created an ML-guided workflow by utilizing XGBoost to train high-performance models based on promoter strengths and cellular metabolite concentrations obtained from ethanol production of 216 combinatorial strains at 30 °C. This strategy was then applied to optimize ethanol production at 40 °C, where we selected 31 strains for experimental fermentation. This reduced experimental load led to a 7.4% increase in ethanol production in the second round of the ML-guided workflow. Our study offers a comprehensive library of promoter strength modifications for key ethanol production enzymes, showcasing how machine learning can guide yeast strain optimization and make bioethanol production more cost-effective and efficient. Furthermore, we demonstrate that metabolic engineering processes can be accelerated and optimized through this approach.
Collapse
Affiliation(s)
- Peerapat Khamwachirapithak
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Kittapong Sae-Tang
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Wuttichai Mhuantong
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sutipa Tanapongpipat
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Xin-Qing Zhao
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic & Developmental Sciences, School of Life
Sciences and Biotechnology, Shanghai Jiao
Tong University, Shanghai 200240, People’s
Republic of China
| | - Chen-Guang Liu
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic & Developmental Sciences, School of Life
Sciences and Biotechnology, Shanghai Jiao
Tong University, Shanghai 200240, People’s
Republic of China
| | - Dong-Qing Wei
- Department
of Bioinformatics and Biological Statistics, School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Verawat Champreda
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Weerawat Runguphan
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| |
Collapse
|
3
|
Ciapaite J, van Roermund CWT, Bosma M, Gerrits J, Houten SM, IJlst L, Waterham HR, van Karnebeek CDM, Wanders RJA, Zwartkruis FJT, Jans JJ, Verhoeven-Duif NM. Maintenance of cellular vitamin B 6 levels and mitochondrial oxidative function depend on pyridoxal 5'-phosphate homeostasis protein. J Biol Chem 2023; 299:105047. [PMID: 37451483 PMCID: PMC10463200 DOI: 10.1016/j.jbc.2023.105047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Recently, biallelic variants in PLPBP coding for pyridoxal 5'-phosphate homeostasis protein (PLPHP) were identified as a novel cause of early-onset vitamin B6-dependent epilepsy. The molecular function and precise role of PLPHP in vitamin B6 metabolism are not well understood. To address these questions, we used PLPHP-deficient patient skin fibroblasts and HEK293 cells and YBL036C (PLPHP ortholog)-deficient yeast. We showed that independent of extracellular B6 vitamer type (pyridoxine, pyridoxamine, or pyridoxal), intracellular pyridoxal 5'-phosphate (PLP) was lower in PLPHP-deficient fibroblasts and HEK293 cells than controls. Culturing cells with pyridoxine or pyridoxamine led to the concentration-dependent accumulation of pyridoxine 5'-phosphate and pyridoxamine 5'-phosphate (PMP), respectively, suggesting insufficient pyridox(am)ine 5'-phosphate oxidase activity. Experiments utilizing 13C4-pyridoxine confirmed lower pyridox(am)ine 5'-phosphate oxidase activity and revealed increased fractional turnovers of PLP and pyridoxal, indicating increased PLP hydrolysis to pyridoxal in PLPHP-deficient cells. This effect could be partly counteracted by inactivation of pyridoxal phosphatase. PLPHP deficiency had a distinct effect on mitochondrial PLP and PMP, suggesting impaired activity of mitochondrial transaminases. Moreover, in YBL036C-deficient yeast, PLP was depleted and PMP accumulated only with carbon sources requiring mitochondrial metabolism. Lactate and pyruvate accumulation along with the decrease of tricarboxylic acid cycle intermediates downstream of α-ketoglutarate suggested impaired mitochondrial oxidative metabolism in PLPHP-deficient HEK293 cells. We hypothesize that impaired activity of mitochondrial transaminases may contribute to this depletion. Taken together, our study provides new insights into the pathomechanisms of PLPBP deficiency and reinforces the link between PLPHP function, vitamin B6 metabolism, and mitochondrial oxidative metabolism.
Collapse
Affiliation(s)
- Jolita Ciapaite
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands; United for Metabolic Diseases, The Netherlands.
| | - Carlo W T van Roermund
- United for Metabolic Diseases, The Netherlands; Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Marjolein Bosma
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands; United for Metabolic Diseases, The Netherlands
| | - Johan Gerrits
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands; United for Metabolic Diseases, The Netherlands
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lodewijk IJlst
- United for Metabolic Diseases, The Netherlands; Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans R Waterham
- United for Metabolic Diseases, The Netherlands; Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Clara D M van Karnebeek
- United for Metabolic Diseases, The Netherlands; Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands; Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, BC Children's Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ronald J A Wanders
- United for Metabolic Diseases, The Netherlands; Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Fried J T Zwartkruis
- Department of Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Judith J Jans
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands; United for Metabolic Diseases, The Netherlands
| | - Nanda M Verhoeven-Duif
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands; United for Metabolic Diseases, The Netherlands
| |
Collapse
|
4
|
Fina A, Millard P, Albiol J, Ferrer P, Heux S. High throughput 13C-metabolic flux analysis of 3-hydroxypropionic acid producing Pichia pastoris reveals limited availability of acetyl-CoA and ATP due to tight control of the glycolytic flux. Microb Cell Fact 2023; 22:117. [PMID: 37380999 DOI: 10.1186/s12934-023-02123-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/27/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND Production of 3-hydroxypropionic acid (3-HP) through the malonyl-CoA pathway has yielded promising results in Pichia pastoris (Komagataella phaffii), demonstrating the potential of this cell factory to produce this platform chemical and other acetyl-CoA-derived products using glycerol as a carbon source. However, further metabolic engineering of the original P. pastoris 3-HP-producing strains resulted in unexpected outcomes, e.g., significantly lower product yield and/or growth rate. To gain an understanding on the metabolic constraints underlying these observations, the fluxome (metabolic flux phenotype) of ten 3-HP-producing P. pastoris strains has been characterized using a high throughput 13C-metabolic flux analysis platform. Such platform enabled the operation of an optimised workflow to obtain comprehensive maps of the carbon flux distribution in the central carbon metabolism in a parallel-automated manner, thereby accelerating the time-consuming strain characterization step in the design-build-test-learn cycle for metabolic engineering of P. pastoris. RESULTS We generated detailed maps of the carbon fluxes in the central carbon metabolism of the 3-HP producing strain series, revealing the metabolic consequences of different metabolic engineering strategies aimed at improving NADPH regeneration, enhancing conversion of pyruvate into cytosolic acetyl-CoA, or eliminating by-product (arabitol) formation. Results indicate that the expression of the POS5 NADH kinase leads to a reduction in the fluxes of the pentose phosphate pathway reactions, whereas an increase in the pentose phosphate pathway fluxes was observed when the cytosolic acetyl-CoA synthesis pathway was overexpressed. Results also show that the tight control of the glycolytic flux hampers cell growth due to limited acetyl-CoA biosynthesis. When the cytosolic acetyl-CoA synthesis pathway was overexpressed, the cell growth increased, but the product yield decreased due to higher growth-associated ATP costs. Finally, the six most relevant strains were also cultured at pH 3.5 to assess the effect of a lower pH on their fluxome. Notably, similar metabolic fluxes were observed at pH 3.5 compared to the reference condition at pH 5. CONCLUSIONS This study shows that existing fluoxomics workflows for high-throughput analyses of metabolic phenotypes can be adapted to investigate P. pastoris, providing valuable information on the impact of genetic manipulations on the metabolic phenotype of this yeast. Specifically, our results highlight the metabolic robustness of P. pastoris's central carbon metabolism when genetic modifications are made to increase the availability of NADPH and cytosolic acetyl-CoA. Such knowledge can guide further metabolic engineering of these strains. Moreover, insights into the metabolic adaptation of P. pastoris to an acidic pH have also been obtained, showing the capability of the fluoxomics workflow to assess the metabolic impact of environmental changes.
Collapse
Affiliation(s)
- Albert Fina
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, 08193, Spain
| | - Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, 31077, France
| | - Joan Albiol
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, 08193, Spain
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, 08193, Spain.
| | - Stephanie Heux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, 31077, France
| |
Collapse
|
5
|
Murata Y, Nwuche CO, Nweze JE, Ndubuisi IA, Ogbonna JC. Potentials of multi-stress tolerant yeasts, Saccharomyces cerevisiae and Pichia kudriavzevii for fuel ethanol production from industrial cassava wastes. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
6
|
Fungicidal Activity of Recombinant Javanicin against Cryptococcus neoformans Is Associated with Intracellular Target(s) Involved in Carbohydrate and Energy Metabolic Processes. Molecules 2021; 26:molecules26227011. [PMID: 34834105 PMCID: PMC8618071 DOI: 10.3390/molecules26227011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 01/06/2023] Open
Abstract
The occurrence of Cryptococcus neoformans, the human fungal pathogen that primarily infects immunocompromised individuals, has been progressing at an alarming rate. The increased incidence of infection of C. neoformans with antifungal drugs resistance has become a global concern. Potential antifungal agents with extremely low toxicity are urgently needed. Herein, the biological activities of recombinant javanicin (r-javanicin) against C. neoformans were evaluated. A time-killing assay was performed and both concentration- and time-dependent antifungal activity of r-javanicin were indicated. The inhibitory effect of the peptide was initially observed at 4 h post-treatment and ultimately eradicated within 36 to 48 h. Fungal outer surface alteration was characterized by the scanning electron microscope (SEM) whereas a negligible change with slight shrinkage of external morphology was observed in r-javanicin treated cells. Confocal laser scanning microscopic analysis implied that the target(s) of r-javanicin is conceivably resided in the cell thereby allowing the peptide to penetrate across the membrane and accumulate throughout the fungal body. Finally, cryptococcal cells coped with r-javanicin were preliminarily investigated using label-free mass spectrometry-based proteomics. Combined with microscopic and proteomics analysis, it was clearly elucidated the peptide localized in the intracellular compartment where carbohydrate metabolism and energy production associated with glycolysis pathway and mitochondrial respiration, respectively, were principally interfered. Overall, r-javanicin would be an alternative candidate for further development of antifungal agents.
Collapse
|
7
|
Elimination of aromatic fusel alcohols as by-products of Saccharomyces cerevisiae strains engineered for phenylpropanoid production by 2-oxo-acid decarboxylase replacement. Metab Eng Commun 2021; 13:e00183. [PMID: 34584841 PMCID: PMC8450241 DOI: 10.1016/j.mec.2021.e00183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/24/2021] [Accepted: 09/01/2021] [Indexed: 11/24/2022] Open
Abstract
Engineered strains of the yeast Saccharomyces cerevisiae are intensively studied as production platforms for aromatic compounds such as hydroxycinnamic acids, stilbenoids and flavonoids. Heterologous pathways for production of these compounds use l-phenylalanine and/or l-tyrosine, generated by the yeast shikimate pathway, as aromatic precursors. The Ehrlich pathway converts these precursors to aromatic fusel alcohols and acids, which are undesirable by-products of yeast strains engineered for production of high-value aromatic compounds. Activity of the Ehrlich pathway requires any of four S. cerevisiae 2-oxo-acid decarboxylases (2-OADCs): Aro10 or the pyruvate-decarboxylase isoenzymes Pdc1, Pdc5, and Pdc6. Elimination of pyruvate-decarboxylase activity from S. cerevisiae is not straightforward as it plays a key role in cytosolic acetyl-CoA biosynthesis during growth on glucose. In a search for pyruvate decarboxylases that do not decarboxylate aromatic 2-oxo acids, eleven yeast and bacterial 2-OADC-encoding genes were investigated. Homologs from Kluyveromyces lactis (KlPDC1), Kluyveromyces marxianus (KmPDC1), Yarrowia lipolytica (YlPDC1), Zymomonas mobilis (Zmpdc1) and Gluconacetobacter diazotrophicus (Gdpdc1.2 and Gdpdc1.3) complemented a Pdc− strain of S. cerevisiae for growth on glucose. Enzyme-activity assays in cell extracts showed that these genes encoded active pyruvate decarboxylases with different substrate specificities. In these in vitro assays, ZmPdc1, GdPdc1.2 or GdPdc1.3 had no substrate specificity towards phenylpyruvate. Replacing Aro10 and Pdc1,5,6 by these bacterial decarboxylases completely eliminated aromatic fusel-alcohol production in glucose-grown batch cultures of an engineered coumaric acid-producing S. cerevisiae strain. These results outline a strategy to prevent formation of an important class of by-products in ‘chassis’ yeast strains for production of non-native aromatic compounds. Identification of pyruvate decarboxylases active with pyruvate but not with aromatic 2-oxo acids. Zymomonas mobilis pyruvate decarboxylase can replace the native yeast enzymes. Expression of Z. mobilis pyruvate decarboxylase removes formation of fusel alcohols. Elimination of fusel alcohol by products improves formation of coumaric acid. Decarboxylase swapping is a beneficial strategy for production of non-native aromatics.
Collapse
|
8
|
Metabolic Regulation of Sugar Assimilation for Lipid Production in Aspergillus oryzae BCC7051 through Comparative Transcriptome Perspective. BIOLOGY 2021; 10:biology10090885. [PMID: 34571762 PMCID: PMC8467706 DOI: 10.3390/biology10090885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/27/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022]
Abstract
Simple Summary Oleaginous fungi are a promising candidate to produce microbial lipids as alternative sources for industrial applications. As lipids are intracellular metabolites with dynamic traits, the fungal ability in utilizing carbon sources for biomass and lipid production is significant in terms of production yield and economic feasibility. This study aimed to explore the metabolic regulation in lipogenesis of oleaginous Aspergillus oryzae BCC7051 at the transcriptional level. Through comparative transcriptome analysis, a set of differentially expressed genes (DEGs) between the xylose- and glucose-grown cultures (C5 and C6 cultures) at fast-growing and lipid-accumulating stages were identified and functionally categorized into transporter proteins and cellular processes. Combining with the growth and lipid phenotypes, the transcriptome results pointed to a crucial link between sugar assimilation, energy, lipid, and other metabolisms in A. oryzae for leveraging the metabolic flux from xylose to fatty acid and lipid biosynthesis in render the oleaginous features. This study provides a remarkable insight in guiding strain optimization and bioprocess development using renewable feedstocks from agroindustrial residues. Abstract Microbial lipid production with cost effectiveness is a prerequisite for the oleochemical sector. In this work, genome-wide transcriptional responses on the utilization of xylose and glucose in oleaginous Aspergillus oryzae were studied with relation to growth and lipid phenotypic traits. Comparative analysis of the active growth (t1) and lipid-accumulating (t2) stages showed that the C5 cultures efficiently consumed carbon sources for biomass and lipid production comparable to the C6 cultures. By pairwise comparison, 599 and 917 differentially expressed genes (DEGs) were identified in the t1 and t2 groups, respectively, in which the consensus DEGs were categorized into polysaccharide-degrading enzymes, membrane transports, and cellular processes. A discrimination in transcriptional responses of DEGs set was also found in various metabolic genes, mostly in carbohydrate, amino acid, lipid, cofactors, and vitamin metabolisms. Although central carbohydrate metabolism was shared among the C5 and C6 cultures, the metabolic functions in acetyl-CoA and NADPH generation, and biosynthesis of terpenoid backbone, fatty acid, sterol, and amino acids were allocated for leveraging biomass and lipid production through at least transcriptional control. This study revealed robust metabolic networks in the oleaginicity of A. oryzae governing glucose/xylose flux toward lipid biosynthesis that provides meaningful hints for further process developments of microbial lipid production using cellulosic sugar feedstocks.
Collapse
|
9
|
Otto M, Teixeira PG, Vizcaino MI, David F, Siewers V. Integration of a multi-step heterologous pathway in Saccharomyces cerevisiae for the production of abscisic acid. Microb Cell Fact 2019; 18:205. [PMID: 31767000 PMCID: PMC6876084 DOI: 10.1186/s12934-019-1257-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The sesquiterpenoid abscisic acid (ABA) is mostly known for regulating developmental processes and abiotic stress responses in higher plants. Recent studies show that ABA also exhibits a variety of pharmacological activities. Affordable and sustainable production will be required to utilize the compound in agriculture and as a potential pharmaceutical. Saccharomyces cerevisiae is an established workhorse for the biotechnological production of chemicals. In this study, we constructed and characterised an ABA-producing S. cerevisiae strain using the ABA biosynthetic pathway from Botrytis cinerea. RESULTS Expression of the B. cinerea genes bcaba1, bcaba2, bcaba3 and bcaba4 was sufficient to establish ABA production in the heterologous host. We characterised the ABA-producing strain further by monitoring ABA production over time and, since the pathway contains two cytochrome P450 enzymes, by investigating the effects of overexpressing the native S. cerevisiae or the B. cinerea cytochrome P450 reductase. Both, overexpression of the native or heterologous cytochrome P450 reductase, led to increased ABA titres. We were able to show that ABA production was not affected by precursor or NADPH supply, which suggested that the heterologous enzymes were limiting the flux towards the product. The B. cinerea cytochrome P450 monooxygenases BcABA1 and BcABA2 were identified as pathway bottlenecks and balancing the expression levels of the pathway enzymes resulted in 4.1-fold increased ABA titres while reducing by-product formation. CONCLUSION This work represents the first step towards a heterologous ABA cell factory for the commercially relevant sesquiterpenoid.
Collapse
Affiliation(s)
- Maximilian Otto
- Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Paulo Gonçalves Teixeira
- Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Maria Isabel Vizcaino
- Chalmers Mass Spectrometry Infrastructure, Chalmers University of Technology, Gothenburg, Sweden
| | - Florian David
- Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| |
Collapse
|
10
|
Abstract
Cells require energy for growth and maintenance and have evolved to have multiple pathways to produce energy in response to varying conditions. A basic question in this context is how cells organize energy metabolism, which is, however, challenging to elucidate due to its complexity, i.e., the energy-producing pathways overlap with each other and even intertwine with biomass formation pathways. Here, we propose a modeling concept that decomposes energy metabolism into biomass formation and ATP-producing pathways. The latter can be further decomposed into a high-yield and a low-yield pathway. This enables independent estimation of protein efficiency for each pathway. With this concept, we modeled energy metabolism for Escherichia coli and Saccharomyces cerevisiae and found that the high-yield pathway shows lower protein efficiency than the low-yield pathway. Taken together with a fixed protein constraint, we predict overflow metabolism in E. coli and the Crabtree effect in S. cerevisiae, meaning that energy metabolism is sufficient to explain the metabolic switches. The static protein constraint is supported by the findings that protein mass of energy metabolism is conserved across conditions based on absolute proteomics data. This also suggests that enzymes may have decreased saturation or activity at low glucose uptake rates. Finally, our analyses point out three ways to improve growth, i.e., increasing protein allocation to energy metabolism, decreasing ATP demand, or increasing activity for key enzymes.
Collapse
Affiliation(s)
- Yu Chen
- Department of Biology and Biological Engineering, 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, Technical University of Denmark, DK2800 Kgs. Lyngby, Denmark
- BioInnovation Institute, DK2200 Copenhagen N, Denmark
| |
Collapse
|
11
|
Niebel B, Leupold S, Heinemann M. An upper limit on Gibbs energy dissipation governs cellular metabolism. Nat Metab 2019; 1:125-132. [PMID: 32694810 DOI: 10.1038/s42255-018-0006-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/23/2018] [Indexed: 12/20/2022]
Abstract
The principles governing cellular metabolic operation are poorly understood. Because diverse organisms show similar metabolic flux patterns, we hypothesized that a fundamental thermodynamic constraint might shape cellular metabolism. Here, we develop a constraint-based model for Saccharomyces cerevisiae with a comprehensive description of biochemical thermodynamics including a Gibbs energy balance. Non-linear regression analyses of quantitative metabolome and physiology data reveal the existence of an upper rate limit for cellular Gibbs energy dissipation. By applying this limit in flux balance analyses with growth maximization as the objective function, our model correctly predicts the physiology and intracellular metabolic fluxes for different glucose uptake rates as well as the maximal growth rate. We find that cells arrange their intracellular metabolic fluxes in such a way that, with increasing glucose uptake rates, they can accomplish optimal growth rates but stay below the critical rate limit on Gibbs energy dissipation. Once all possibilities for intracellular flux redistribution are exhausted, cells reach their maximal growth rate. This principle also holds for Escherichia coli and different carbon sources. Our work proposes that metabolic reaction stoichiometry, a limit on the cellular Gibbs energy dissipation rate, and the objective of growth maximization shape metabolism across organisms and conditions.
Collapse
Affiliation(s)
- Bastian Niebel
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Simeon Leupold
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
12
|
Ji RY, Ding Y, Shi TQ, Lin L, Huang H, Gao Z, Ji XJ. Metabolic Engineering of Yeast for the Production of 3-Hydroxypropionic Acid. Front Microbiol 2018; 9:2185. [PMID: 30298059 PMCID: PMC6160737 DOI: 10.3389/fmicb.2018.02185] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/27/2018] [Indexed: 02/05/2023] Open
Abstract
The beta-hydroxy acid 3-hydroxypropionic acid (3-HP) is an attractive platform compound that can be used as a precursor for many commercially interesting compounds. In order to reduce the dependence on petroleum and follow sustainable development, 3-HP has been produced biologically from glucose or glycerol. It is reported that 3-HP synthesis pathways can be constructed in microbes such as Escherichia coli, Klebsiella pneumoniae and the yeast Saccharomyces cerevisiae. Among these host strains, yeast is prominent because of its strong acid tolerance which can simplify the fermentation process. Currently, the malonyl-CoA reductase pathway and the β-alanine pathway have been successfully constructed in yeast. This review presents the current developments in 3-HP production using yeast as an industrial host. By combining genome-scale engineering tools, malonyl-CoA biosensors and optimization of downstream fermentation, the production of 3-HP in yeast has the potential to reach or even exceed the yield of chemical production in the future.
Collapse
Affiliation(s)
- Rong-Yu Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Ying Ding
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Tian-Qiong Shi
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Lu Lin
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - He Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, China
| | - Zhen Gao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, China
| |
Collapse
|
13
|
Janssens S, Ciapaite J, Wolters JC, van Riel NA, Nicolay K, Prompers JJ. An In Vivo Magnetic Resonance Spectroscopy Study of the Effects of Caloric and Non-Caloric Sweeteners on Liver Lipid Metabolism in Rats. Nutrients 2017; 9:nu9050476. [PMID: 28489050 PMCID: PMC5452206 DOI: 10.3390/nu9050476] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/26/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022] Open
Abstract
We aimed to elucidate the effects of caloric and non-caloric sweeteners on liver lipid metabolism in rats using in vivo magnetic resonance spectroscopy (MRS) and to determine their roles in the development of liver steatosis. Wistar rats received normal chow and either normal drinking water, or solutions containing 13% (w/v) glucose, 13% fructose, or 0.4% aspartame. After 7 weeks, in vivo hepatic dietary lipid uptake and de novo lipogenesis were assessed with proton-observed, carbon-13-edited MRS combined with 13C-labeled lipids and 13C-labeled glucose, respectively. The molecular basis of alterations in hepatic liver metabolism was analyzed in detail ex vivo using immunoblotting and targeted quantitative proteomics. Both glucose and fructose feeding increased adiposity, but only fructose induced hepatic lipid accumulation. In vivo MRS showed that this was not caused by increased hepatic uptake of dietary lipids, but could be attributed to an increase in de novo lipogenesis. Stimulation of lipogenesis by fructose was confirmed by a strong upregulation of lipogenic enzymes, which was more potent than with glucose. The non-caloric sweetener aspartame did not significantly affect liver lipid content or metabolism. In conclusion, liquid fructose more severely affected liver lipid metabolism in rats than glucose, while aspartame had no effect.
Collapse
Affiliation(s)
- Sharon Janssens
- Biomedical Nuclear Magnetic Resonance (NMR), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Jolita Ciapaite
- Center for Liver, Digestive and Metabolic Diseases, Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands.
- Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands.
| | - Justina C Wolters
- Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands.
- Department of Pharmacy, Analytical Biochemistry, University of Groningen, Antonius Deusinglaan, 9713 AV Groningen, The Netherlands.
| | - Natal A van Riel
- Computational Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Klaas Nicolay
- Biomedical Nuclear Magnetic Resonance (NMR), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Jeanine J Prompers
- Biomedical Nuclear Magnetic Resonance (NMR), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
| |
Collapse
|
14
|
Landi C, Paciello L, de Alteriis E, Brambilla L, Parascandola P. High cell density culture with S. cerevisiae CEN.PK113-5D for IL-1β production: optimization, modeling, and physiological aspects. Bioprocess Biosyst Eng 2014; 38:251-61. [PMID: 25106469 DOI: 10.1007/s00449-014-1264-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/29/2014] [Indexed: 11/26/2022]
Abstract
Saccharomyces cerevisiae CEN.PK113-5D, a strain auxotrophic for uracil belonging to the CEN.PK family of the yeast S. cerevisiae, was cultured in aerated fed-batch reactor as such and once transformed to express human interleukin-1β (IL-1β), aiming at obtaining high cell densities and optimizing IL-1β production. Three different exponentially increasing glucose feeding profiles were tested, all of them "in theory" promoting respiratory metabolism to obtain high biomass/product yield. A non-structured non-segregated model was developed to describe the performance of S. cerevisiae CEN.PK113-5D during the fed-batch process and, in particular, its capability to metabolize simultaneously glucose and ethanol which derived from the precedent batch growth. Our study showed that the proliferative capacity of the yeast population declined along the fed-batch run, as shown by the exponentially decreasing specific growth rates on glucose. Further, a shift towards fermentative metabolism occurred. This shift took place earlier the higher was the feed rate and was more pronounced in the case of the recombinant strain. Determination of some physiological markers (acetate production, intracellular ROS accumulation, catalase activity and cell viability) showed that neither poor oxygenation nor oxidative stress was responsible for the decreased specific growth rate, nor for the shift to fermentative metabolism.
Collapse
Affiliation(s)
- Carmine Landi
- Dep. Ingegneria Industriale, Università Di Salerno, Via Giovanni Paolo II, 132 Fisciano, 84084, Salerno, Italy
| | | | | | | | | |
Collapse
|
15
|
Tarlak F, Sadıkoğlu H, Çakır T. The role of flexibility and optimality in the prediction of intracellular fluxes of microbial central carbon metabolism. MOLECULAR BIOSYSTEMS 2014; 10:2459-65. [DOI: 10.1039/c4mb00117f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
16
|
Dmytruk KV, Sibirny AA. Metabolic engineering of the yeast Hansenula polymorpha for the construction of efficient ethanol producers. CYTOL GENET+ 2013. [DOI: 10.3103/s0095452713060029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
17
|
Marc J, Feria-Gervasio D, Mouret JR, Guillouet SE. Impact of oleic acid as co-substrate of glucose on "short" and "long-term" Crabtree effect in Saccharomyces cerevisiae. Microb Cell Fact 2013; 12:83. [PMID: 24059537 PMCID: PMC3851978 DOI: 10.1186/1475-2859-12-83] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/04/2013] [Indexed: 11/16/2022] Open
Abstract
Background Optimization of industrial biomass directed processes requires the highest biomass yield as possible. Yet, some useful yeasts like Saccharomyces cerevisiae are subject to the Crabtree effect under glucose excess. This phenomenon can occur in large scale tank where heterogeneities in glucose concentrations exist. Therefore yeasts encounter local environments with glucose excess leading to ethanol production to the detriment of biomass formation. We previously demonstrated that oleic acid as a co-substrate in glucose-limited chemostat allowed to delay and modulate the “short-term” Crabtree effect in Saccharomyces cerevisiae. Here we further investigated the effect of oleic acid as a modulator of the Crabtree effect. Results The impact of oleic acid as co-substrate on the Crabtree effect was investigated in terms of i) strain specificity, ii) reversibility of the potential effect with aerobic glucose-excess batches and iii) durability and maximal capacities under high ethanol stress with glucose-excess fed-batches. First, the addition of oleic acid resulted in an increase of the critical dilution rate by 8% and the specific carbon uptake rate by 18%. Furthermore, a delay was observed for the onset of ethanol production when a batch was inoculated with cells previously grown in glucose-oleate chemostat. Finally, the culture of adapted cells in a glucose-oleate fed-batch led to a redirection of the carbon flux toward biomass production, with a 73% increase in the biomass yield. Conclusions This work demonstrated clearly that the perturbation by oleic acid as co-substrate resulted in a decrease in the “short-term” and “long-term” Crabtree effects. This impact was not strain dependent and reversible. Thus, industrial applications of this biochemical strategy could be envisaged to tackle heterogeneities issues in large scale tanks or to prepare starter yeasts for various applications.
Collapse
Affiliation(s)
- Jillian Marc
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National des Sciences Appliquées (INSA), UMR INSA/CNRS 5504, UMR INSA/INRA 792, 135 Avenue de Rangueil, 31077 Toulouse Cedex 4, France.
| | | | | | | |
Collapse
|
18
|
Hyland PB, Mun SLS, Mahadevan R. Prediction of Weak Acid Toxicity inSaccharomyces cerevisiaeUsing Genome-Scale Metabolic Models. Ind Biotechnol (New Rochelle N Y) 2013. [DOI: 10.1089/ind.2013.0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Patrick B Hyland
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Serene Lock-Sow Mun
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
- CO2 Management Mission Oriented Research, Universiti Teknologi PETRONAS, Tronoh, Malaysia
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| |
Collapse
|
19
|
Berlowska J, Kregiel D, Ambroziak W. Physiological tests for yeast brewery cells immobilized on modified chamotte carrier. Antonie Van Leeuwenhoek 2013; 104:703-14. [PMID: 23887884 PMCID: PMC3824387 DOI: 10.1007/s10482-013-9978-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 07/16/2013] [Indexed: 11/30/2022]
Abstract
In this study yeast cell physiological activity was assessed on the basis of the in situ activity of two important enzymes, succinate dehydrogenase and pyruvate decarboxylase. FUN1 dye bioconversion and cellular ATP content were also taken as important indicators of yeast cell activity. The study was conducted on six brewing yeast strains, which were either free cells or immobilized on a chamotte carrier. The experimental data obtained indicate clearly that, in most cases, the immobilized cells showed lower enzyme activity than free cells from analogous cultures. Pyruvate decarboxylase activity in immobilized cells was higher than in planktonic cell populations only in the case of the Saccharomyces pastorianus 680 strain. However, in a comparative assessment of the fermentation process, conducted with the use of free and immobilized cells, much more favorable dynamics and carbon dioxide productivity were observed in immobilized cells, especially in the case of brewing lager yeast strains. This may explain the higher total cell density per volume unit of the fermented medium and the improved resistance of immobilized cells to environmental changes.
Collapse
Affiliation(s)
- Joanna Berlowska
- Institute of Fermentation Technology and Microbiology, Technical University of Lodz, ul. Wolczanska 171/173, 90-924, Lodz, Poland,
| | | | | |
Collapse
|
20
|
Shirai T, Matsuda F, Okamoto M, Kondo A. Evaluation of control mechanisms for Saccharomyces cerevisiae central metabolic reactions using metabolome data of eight single-gene deletion mutants. Appl Microbiol Biotechnol 2012; 97:3569-77. [PMID: 23224404 DOI: 10.1007/s00253-012-4597-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 11/10/2012] [Accepted: 11/13/2012] [Indexed: 10/27/2022]
Abstract
We performed metabolome and metabolite-metabolite correlation analyses for eight single-gene deletion mutants of Saccharomyces cerevisiae to evaluate the physiology of glucose metabolism. The irreversible enzyme reactions can become bottlenecks when intracellular metabolism is perturbed by direct interference from the central metabolic pathway by gene deletions or by a deletion of transcriptional regulator. Metabolome data reveal that transcriptional factor, gcr2, regulates the reaction that converts 3-phosphoglycerate into phosphoenolpyruvate. Metabolome data also suggest that the reaction catalyzed by pyruvate kinase makes one of the rate-limiting reactions throughout the glycolytic pathway.
Collapse
Affiliation(s)
- Tomokazu Shirai
- Biomass Engineering Program, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | | | | | |
Collapse
|
21
|
Postmus J, Aardema R, de Koning LJ, de Koster CG, Brul S, Smits GJ. Isoenzyme expression changes in response to high temperature determine the metabolic regulation of increased glycolytic flux in yeast. FEMS Yeast Res 2012; 12:571-81. [PMID: 22548758 DOI: 10.1111/j.1567-1364.2012.00807.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/26/2012] [Accepted: 03/27/2012] [Indexed: 11/30/2022] Open
Abstract
Qualitative phenotypic changes are the integrated result of quantitative changes at multiple regulatory levels. To explain the temperature-induced increase of glycolytic flux in fermenting cultures of Saccharomyces cerevisiae, we quantified the contributions of changes in activity at many regulatory levels. We previously showed that a similar temperature increase in glucose-limited cultivations lead to a qualitative change from respiratory to fermentative metabolism, and this change was mainly regulated at the metabolic level. In contrast, in fermenting cells, a combination of different modes of regulation was observed. Regulation by changes in expression and the effect of temperature on enzyme activities contributed much to the increase in flux. Mass spectrometric quantification of glycolytic enzymes revealed that increased enzyme activity did not correlate with increased protein abundance, suggesting a large contribution of post-translational regulation to activity. Interestingly, the differences in the direct effect of temperature on enzyme kinetics can be explained by changes in the expression of the isoenzymes. Therefore, both the interaction of enzyme with its metabolic environment and the temperature dependence of activity are in turn regulated at the hierarchical level.
Collapse
Affiliation(s)
- Jarne Postmus
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | | | | |
Collapse
|
22
|
van Rensburg E, den Haan R, Smith J, van Zyl WH, Görgens JF. The metabolic burden of cellulase expression by recombinant Saccharomyces cerevisiae Y294 in aerobic batch culture. Appl Microbiol Biotechnol 2012; 96:197-209. [PMID: 22526794 DOI: 10.1007/s00253-012-4037-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 03/14/2012] [Accepted: 03/16/2012] [Indexed: 12/29/2022]
Abstract
Two recombinant strains of Saccharomyces cerevisiae Y294 producing cellulase using different expression strategies were compared to a reference strain in aerobic culture to evaluate the potential metabolic burden that cellulase expression imposed on the yeast metabolism. In a chemically defined mineral medium with glucose as carbon source, S. cerevisiae strain Y294[CEL5] with plasmid-borne cellulase genes produced endoglucanase and β-glucosidase activities of 0.038 and 0.30 U mg dry cell weight(-1), respectively. Chromosomal expression of these two cellulases in strain Y294[Y118p] resulted in no detectable activity, although low levels of episomally co-expressed cellobiohydrolase (CBH) activity were detected. Whereas the biomass concentration of strain Y294[CEL5] was slightly greater than that of a reference strain, CBH expression by Y294[Y118p] resulted in a 1.4-fold lower maximum specific growth rate than that of the reference. Supplementation of the growth medium with amino acids significantly improved culture growth and enzyme production, but only partially mitigated the physiological effects and metabolic burden of cellulase expression. Glycerol production was decreased significantly, up to threefold, in amino acid-supplemented cultures, apparently due to redox balancing. Disproportionately higher levels of glycerol production by Y294[CEL5] indicated a potential correlation between the redox balance of anabolism and the physiological stress of cellulase production. With the reliance on cellulase expression in yeast for the development of consolidated bioprocesses for bioethanol production, this work demonstrates the need for development of yeasts that are physiologically robust in response to burdens imposed by heterologous enzyme production.
Collapse
Affiliation(s)
- Eugéne van Rensburg
- Department of Process Engineering, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | | | | | | | | |
Collapse
|
23
|
Huberts DHEW, Niebel B, Heinemann M. A flux-sensing mechanism could regulate the switch between respiration and fermentation. FEMS Yeast Res 2011; 12:118-28. [DOI: 10.1111/j.1567-1364.2011.00767.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 10/28/2011] [Accepted: 11/16/2011] [Indexed: 12/20/2022] Open
Affiliation(s)
- Daphne H. E. W. Huberts
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
| | - Bastian Niebel
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
| |
Collapse
|
24
|
Deletion or overexpression of mitochondrial NAD+ carriers in Saccharomyces cerevisiae alters cellular NAD and ATP contents and affects mitochondrial metabolism and the rate of glycolysis. Appl Environ Microbiol 2011; 77:2239-46. [PMID: 21335394 DOI: 10.1128/aem.01703-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The modification of enzyme cofactor concentrations can be used as a method for both studying and engineering metabolism. We varied Saccharomyces cerevisiae mitochondrial NAD levels by altering expression of its specific mitochondrial carriers. Changes in mitochondrial NAD levels affected the overall cellular concentration of this coenzyme and the cellular metabolism. In batch culture, a strain with a severe NAD depletion in mitochondria succeeded in growing, albeit at a low rate, on fully respiratory media. Although the strain increased the efficiency of its oxidative phosphorylation, the ATP concentration was low. Under the same growth conditions, a strain with a mitochondrial NAD concentration higher than that of the wild type similarly displayed a low cellular ATP level, but its growth rate was not affected. In chemostat cultures, when cellular metabolism was fully respiratory, both mutants showed low biomass yields, indicative of impaired energetic efficiency. The two mutants increased their glycolytic fluxes, and as a consequence, the Crabtree effect was triggered at lower dilution rates. Strikingly, the mutants switched from a fully respiratory metabolism to a respirofermentative one at the same specific glucose flux as that of the wild type. This result seems to indicate that the specific glucose uptake rate and/or glycolytic flux should be considered one of the most important independent variables for establishing the long-term Crabtree effect. In cells growing under oxidative conditions, bioenergetic efficiency was affected by both low and high mitochondrial NAD availability, which suggests the existence of a critical mitochondrial NAD concentration in order to achieve optimal mitochondrial functionality.
Collapse
|
25
|
|
26
|
Adaptation of Saccharomyces cerevisiae expressing a heterologous protein. J Biotechnol 2008; 137:28-33. [DOI: 10.1016/j.jbiotec.2008.07.1787] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2008] [Revised: 07/01/2008] [Accepted: 07/07/2008] [Indexed: 11/19/2022]
|
27
|
Postmus J, Canelas AB, Bouwman J, Bakker BM, van Gulik W, de Mattos MJT, Brul S, Smits GJ. Quantitative analysis of the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae reveals dominant metabolic regulation. J Biol Chem 2008; 283:23524-32. [PMID: 18562308 DOI: 10.1074/jbc.m802908200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A major challenge in systems biology lies in the integration of processes occurring at different levels, such as transcription, translation, and metabolism, to understand the functioning of a living cell in its environment. We studied the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae and investigated the regulatory mechanisms underlying this increase. We used glucose-limited chemostat cultures to separate regulatory effects of temperature from effects on growth rate. Growth at increased temperature (38 degrees C versus 30 degrees C) resulted in a strongly increased glycolytic flux, accompanied by a switch from respiration to a partially fermentative metabolism. We observed an increased flux through all enzymes, ranging from 5- to 10-fold. We quantified the contributions of direct temperature effects on enzyme activities, the gene expression cascade and shifts in the metabolic network, to the increased flux through each enzyme. To do this we adapted flux regulation analysis. We show that the direct effect of temperature on enzyme kinetics can be included as a separate term. Together with hierarchical regulation and metabolic regulation, this term explains the total flux change between two steady states. Surprisingly, the effect of the cultivation temperature on enzyme catalytic capacity, both directly through the Arrhenius effect and indirectly through adapted gene expression, is only a moderate contribution to the increased glycolytic flux for most enzymes. The changes in flux are therefore largely caused by changes in the interaction of the enzymes with substrates, products, and effectors.
Collapse
Affiliation(s)
- Jarne Postmus
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Nieuwe Achtergracht 166, Amsterdam
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Conant GC, Wolfe KH. Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Mol Syst Biol 2007; 3:129. [PMID: 17667951 PMCID: PMC1943425 DOI: 10.1038/msb4100170] [Citation(s) in RCA: 161] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 06/27/2007] [Indexed: 11/08/2022] Open
Abstract
After whole-genome duplication (WGD), deletions return most loci to single copy. However, duplicate loci may survive through selection for increased dosage. Here, we show how the WGD increased copy number of some glycolytic genes could have conferred an almost immediate selective advantage to an ancestor of Saccharomyces cerevisiae, providing a rationale for the success of the WGD. We propose that the loss of other redundant genes throughout the genome resulted in incremental dosage increases for the surviving duplicated glycolytic genes. This increase gave post-WGD yeasts a growth advantage through rapid glucose fermentation; one of this lineage's many adaptations to glucose-rich environments. Our hypothesis is supported by data from enzyme kinetics and comparative genomics. Because changes in gene dosage follow directly from post-WGD deletions, dosage selection can confer an almost instantaneous benefit after WGD, unlike neofunctionalization or subfunctionalization, which require specific mutations. We also show theoretically that increased fermentative capacity is of greatest advantage when glucose resources are both large and dense, an observation potentially related to the appearance of angiosperms around the time of WGD.
Collapse
Affiliation(s)
- Gavin C Conant
- Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland.
| | | |
Collapse
|
29
|
Fonseca GG, Gombert AK, Heinzle E, Wittmann C. Physiology of the yeastKluyveromyces marxianusduring batch and chemostat cultures with glucose as the sole carbon source. FEMS Yeast Res 2007; 7:422-35. [PMID: 17233766 DOI: 10.1111/j.1567-1364.2006.00192.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Growth, substrate consumption, metabolite formation, biomass composition and respiratory parameters of Kluyveromyces marxianus ATCC 26548 were determined during aerobic batch and chemostat cultivations, using mineral medium with glucose as the sole carbon source, at 30 degrees C and pH 5.0. Carbon balances closed within 95-101% in all experiments. A maximum specific growth rate of 0.56 h(-1), a biomass yield on glucose of 0.51 g g(-1), and a maximum specific consumption of oxygen of 11.1 mmol g(-1) h(-1) were obtained during batch cultures. The concentration of excreted metabolites was very low at the culture conditions applied, representing 6% of the consumed carbon at most. Acetate and pyruvate were excreted to a larger extent than ethanol under the batch conditions, and the protein content accounted for 54.6% of the biomass dry weight. Steady states were obtained during chemostats at dilution rates of 0.1, 0.25 and 0.5 h(-1). At the two former dilution rates, cells grew at carbon limitation and the biomass yield on glucose was similar to that obtained under the batch conditions. Metabolite formation was rather low, accounting for a total of 0.005 C-mol C-mol(-1) substrate. At 0.5 h(-1), although the biomass yield on glucose was similar to the value obtained under the above-mentioned conditions, the cultivation was not under carbon limitation. Under this condition, 2-oxoglutarate, acetate, pyruvate and ethanol were the prevalent metabolites excreted. Total metabolite formation only accounted to 0.056 C-mol C-mol(-1) of substrate. A very high protein and a low carbohydrate content (71.9% and 9.6% of biomass dry weight, respectively) were measured in cells under this condition. It is concluded that K. marxianus aligns with the so-called aerobic-respiring or Crabtree-negative yeasts. Furthermore, it has one of the highest growth rates among yeasts, and a high capacity of converting sugar into biomass, even when carbon is not the limiting nutrient. These results provide useful data regarding the future application of K. marxianus in processes aimed at the production of biomass-linked compounds, with high yields and productivities.
Collapse
|
30
|
Chen AKL, Breuer M, Hauer B, Rogers PL, Rosche B. pH shift enhancement ofCandida utilis pyruvate decarboxylase production. Biotechnol Bioeng 2005; 92:183-8. [PMID: 15977252 DOI: 10.1002/bit.20588] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Pyruvate decarboxylase (PDC) catalyses the synthesis of asymmetric carbinols, e.g., chiral precursors for pharmaceuticals such as ephedrine and pseudoephedrine. The production of PDC by Candida utilis in a minimal medium was improved by manipulating the pH during fermentation in a 5 L bioreactor. At an aeration rate of 0.1 vvm with a stirrer speed of 300 rpm at constant pH 6, a specific PDC activity of 141 U/g dry cell weight (DCW) was achieved (average of two fermentations +/-13%). By allowing the yeast to acidify the growth medium from pH 6 to 2.9, the final specific PDC activity increased by a factor of 2.7 to 385 U/g DCW (average from 4 fermentations +/-16%). The effect of this pH drift on PDC production was confirmed by another experiment with a manual shift of pH from 6 to 3 by addition of 5 M sulfuric acid. The final PDC activity was 392 U/g DCW (average from two fermentations +/-5%). However, experiments with constant pH of 6, 5, 4, or 3 resulted in average specific activities of only 102 to 141 U/g DCW, suggesting that a transitional pH change rather than the absolute pH value was responsible for the increased specific PDC activity.
Collapse
Affiliation(s)
- Allen Kuan-Liang Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | | | | | | | | |
Collapse
|
31
|
Kolkman A, Olsthoorn MMA, Heeremans CEM, Heck AJR, Slijper M. Comparative Proteome Analysis of Saccharomyces cerevisiae Grown in Chemostat Cultures Limited for Glucose or Ethanol. Mol Cell Proteomics 2005; 4:1-11. [PMID: 15502163 DOI: 10.1074/mcp.m400087-mcp200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The use of chemostat culturing enables investigation of steady-state physiological characteristics and adaptations to nutrient-limited growth, while all other relevant growth conditions are kept constant. We examined and compared the proteomic response of wild-type Saccharomyces cerevisiae CEN.PK113-7D to growth in aerobic chemostat cultures limited for carbon sources being either glucose or ethanol. To obtain a global overview of changes in the proteome, we performed triplicate analyses using two-dimensional gel electrophoresis and identified proteins of interest using MS. Relative quantities of about 400 proteins were obtained and analyzed statistically to determine which protein steady-state expression levels changed significantly under glucose- or ethanol-limited conditions. Interestingly, only enzymes involved in central carbon metabolism showed a significant change in steady-state expression, whereas expression was only detected in one of both carbon source-limiting conditions for 15 of these enzymes. Side effects that were previously reported for batch cultivation conditions, such as responses to continuous variation of specific growth rate, to carbon-catabolite repression, and to accumulation of toxic substrates, were not observed. Moreover, by comparing our proteome data with corresponding mRNA data, we were able to unravel which processes in the central carbon metabolism were regulated at the level of the proteome, and which processes at the level of transcriptome. Importantly, we show here that the combined approach of chemostat cultivation and comprehensive proteome analysis allowed us to study the primary effect of single limiting conditions on the yeast proteome.
Collapse
Affiliation(s)
- Annemieke Kolkman
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, The Netherlands
| | | | | | | | | |
Collapse
|
32
|
Moreira dos Santos M, Thygesen G, Kötter P, Olsson L, Nielsen J. Aerobic physiology of redox-engineered Saccharomyces cerevisiae strains modified in the ammonium assimilation for increased NADPH availability. FEMS Yeast Res 2004; 4:59-68. [PMID: 14554197 DOI: 10.1016/s1567-1356(03)00155-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Recombinant strains altered in the ammonium assimilation pathways were constructed with the purpose of increasing NADPH availability. The NADPH-dependent glutamate dehydrogenase encoded by GDH1, which accounts for a major fraction of the NADPH consumption during growth on ammonium, was deleted, and alternative pathways for ammonium assimilation were overexpressed: GDH2 (NADH-consuming) or GLN1 and GLT1 (the GS-GOGAT system). The flux through the pentose phosphate pathway during aerobic growth on glucose decreased to about half that of the reference strain Saccharomyces cerevisiae CEN.PK113-7D, indicating a major redox alteration in the strains. The basic growth characteristics of the recombinant strains were not affected to a great extent, but the dilution rate at which the onset of aerobic fermentation occurred decreased, suggesting a relation between the onset of the Crabtree effect and the flux through the Embden-Meyerhof-Parnas pathway downstream of glucose 6-phosphate. No redox effect was observed in a strain containing a deletion of GLR1, encoding glutathione reductase, an enzyme that is NADPH-consuming.
Collapse
Affiliation(s)
- Margarida Moreira dos Santos
- Center for Process Biotechnology, BioCentrum-DTU, Building 223, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | | | | | | | | |
Collapse
|
33
|
Møller K, Sharif MZ, Olsson L. Production of fungal α-amylase by Saccharomyces kluyveri in glucose-limited cultivations. J Biotechnol 2004; 111:311-8. [PMID: 15246667 DOI: 10.1016/j.jbiotec.2004.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Revised: 04/21/2004] [Accepted: 04/22/2004] [Indexed: 10/26/2022]
Abstract
Heterologous protein production by the yeast Saccharomyces kluyveri was investigated under aerobic glucose-limited conditions. Alpha-amylase from Aspergillus oryzae was used as model protein and the gene was expressed from a S. cerevisiae 2 micro plasmid. For comparison, strains of both S. kluyveri and S. cerevisiae were transformed with the same plasmid, which led to secretion of active alpha-amylase in both cases. The S. cerevisiae 2 micro plasmid was found to be stable in S. kluyveri as evaluated by a constant alpha-amylase productivity in a continuous cultivation for more than 40 generations. S. kluyveri and S. cerevisiae secreted alpha-amylase with similar yields during continuous cultivations at dilution rates of 0.1 and 0.2 h(-1) (4.8-5.7 mg (g dry weight)(-1)). At a dilution rate of 0.3 h(-1) the metabolism of S. kluyveri was fully respiratory, whereas S. cerevisiae produced significant amounts of ethanol. A fed-batch cultivation was carried out with S. kluyveri where the biomass concentration reached 85 g l(-1) and the alpha-amylase concentration reached 320 mg l(-1). Even though S. kluyveri could be grown to high cell density, it was also observed that it has a high maintenance coefficient, which resulted in low biomass yields at the low specific growth rates prevailing towards the end of the fed-batch cultivation.
Collapse
Affiliation(s)
- Kasper Møller
- Center for Microbial Biotechnology, BioCentrum-DTU, Building 223, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | | | | |
Collapse
|
34
|
Bellaver LH, de Carvalho NMB, Abrahão-Neto J, Gombert AK. Ethanol formation and enzyme activities around glucose-6-phosphate in Kluyveromyces marxianus CBS 6556 exposed to glucose or lactose excess. FEMS Yeast Res 2004; 4:691-8. [PMID: 15093772 DOI: 10.1016/j.femsyr.2004.01.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2003] [Revised: 12/10/2003] [Accepted: 01/15/2004] [Indexed: 11/25/2022] Open
Abstract
The aim of this work was to investigate the physiology of Kluyveromyces marxianus CBS 6556 in terms of its low tendency to form ethanol under exposure to sugar excess, and the split of carbon flux which takes place at the level of glucose-6-phosphate. Measurements were performed in batch cultivations, and after a glucose or a lactose pulse applied to chemostat-grown respiring cells (with a dilution rate of 0.1 h(-1)). No ethanol formation was observed in batch cultivations or during pulse experiments, unless the oxygen supply was shut down, indicating that this organism is more strictly Crabtree-negative than its close relative K. lactis and other known Crabtree-negative yeasts. During the pulse experiments, activities of phosphoglucoisomerase, glucose-6-phosphate dehydrogenase and phosphoglucomutase in cell-free extracts remained rather constant, at higher levels than those of Saccharomyces cerevisiae grown at similar conditions. When cells were exposed to glucose concentrations as high as 26 gl(-1), the activity of phosphoglucomutase was higher than that in cells exposed to 14 gl(-1) glucose, whereas the activities of phosphoglucoisomerase and glucose-6-phosphate dehydrogenase did not change. Our results suggest that the low tendency for ethanol formation in K. marxianus might be a consequence of this yeast's capacity of keeping the glycolytic flux constant, due at least in part to the diversion of carbon flux towards the biosynthesis of carbohydrates and towards the pentose phosphate pathway.
Collapse
Affiliation(s)
- Leticia Heck Bellaver
- Department of Chemical Engineering, University of São Paulo, C.P. 61548, 05424-970 São Paulo-SP, Brazil
| | | | | | | |
Collapse
|
35
|
Duarte NC, Herrgård MJ, Palsson BØ. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 2004; 14:1298-309. [PMID: 15197165 PMCID: PMC442145 DOI: 10.1101/gr.2250904] [Citation(s) in RCA: 435] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A fully compartmentalized genome-scale metabolic model of Saccharomyces cerevisiae that accounts for 750 genes and their associated transcripts, proteins, and reactions has been reconstructed and validated. All of the 1149 reactions included in this in silico model are both elementally and charge balanced and have been assigned to one of eight cellular locations (extracellular space, cytosol, mitochondrion, peroxisome, nucleus, endoplasmic reticulum, Golgi apparatus, or vacuole). When in silico predictions of 4154 growth phenotypes were compared to two published large-scale gene deletion studies, an 83% agreement was found between iND750's predictions and the experimental studies. Analysis of the failure modes showed that false predictions were primarily caused by iND750's limited inclusion of cellular processes outside of metabolism. This study systematically identified inconsistencies in our knowledge of yeast metabolism that require specific further experimental investigation.
Collapse
Affiliation(s)
- Natalie C Duarte
- Department of Bioengineering, University of California-San Diego, La Jolla, California 92093-0412, USA
| | | | | |
Collapse
|
36
|
van Maris AJA, Geertman JMA, Vermeulen A, Groothuizen MK, Winkler AA, Piper MDW, van Dijken JP, Pronk JT. Directed evolution of pyruvate decarboxylase-negative Saccharomyces cerevisiae, yielding a C2-independent, glucose-tolerant, and pyruvate-hyperproducing yeast. Appl Environ Microbiol 2004; 70:159-66. [PMID: 14711638 PMCID: PMC321313 DOI: 10.1128/aem.70.1.159-166.2004] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The absence of alcoholic fermentation makes pyruvate decarboxylase-negative (Pdc(-)) strains of Saccharomyces cerevisiae an interesting platform for further metabolic engineering of central metabolism. However, Pdc(-) S. cerevisiae strains have two growth defects: (i) growth on synthetic medium in glucose-limited chemostat cultures requires the addition of small amounts of ethanol or acetate and (ii) even in the presence of a C(2) compound, these strains cannot grow in batch cultures on synthetic medium with glucose. We used two subsequent phenotypic selection strategies to obtain a Pdc(-) strain without these growth defects. An acetate-independent Pdc(-) mutant was obtained via (otherwise) glucose-limited chemostat cultivation by progressively lowering the acetate content in the feed. Transcriptome analysis did not reveal the mechanisms behind the C(2) independence. Further selection for glucose tolerance in shake flasks resulted in a Pdc(-) S. cerevisiae mutant (TAM) that could grow in batch cultures ( micro (max) = 0.20 h(-1)) on synthetic medium, with glucose as the sole carbon source. Although the exact molecular mechanisms underlying the glucose-tolerant phenotype were not resolved, transcriptome analysis of the TAM strain revealed increased transcript levels of many glucose-repressible genes relative to the isogenic wild type in nitrogen-limited chemostat cultures with excess glucose. In pH-controlled aerobic batch cultures, the TAM strain produced large amounts of pyruvate. By repeated glucose feeding, a pyruvate concentration of 135 g liter(-1) was obtained, with a specific pyruvate production rate of 6 to 7 mmol g of biomass(-1) h(-1) during the exponential-growth phase and an overall yield of 0.54 g of pyruvate g of glucose(-1).
Collapse
Affiliation(s)
- Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, NL-2628 BC Delft. BIRD Engineering B.V., NL-3044 CK Rotterdam, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Møller K, Langkjaer RB, Nielsen J, Piskur J, Olsson L. Pyruvate decarboxylases from the petite-negative yeast Saccharomyces kluyveri. Mol Genet Genomics 2003; 270:558-68. [PMID: 14648197 DOI: 10.1007/s00438-003-0950-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2003] [Accepted: 10/20/2003] [Indexed: 10/26/2022]
Abstract
Saccharomyces kluyveri is a petite-negative yeast, which is less prone to form ethanol under aerobic conditions than is S. cerevisiae. The first reaction on the route from pyruvate to ethanol is catalysed by pyruvate decarboxylase, and the differences observed between S. kluyveri and S. cerevisiae with respect to ethanol formation under aerobic conditions could be caused by differences in the regulation of this enzyme activity. We have identified and cloned three genes encoding functional pyruvate decarboxylase enzymes (PDCgenes) from the type strain of S. kluyveri (Sk- PDC11, Sk- PDC12 and Sk- PDC13). The regulation of pyruvate decarboxylase in S. kluyveri was studied by measuring the total level of Sk- PDC mRNA and the overall enzyme activity under various growth conditions. It was found that the level of Sk- PDC mRNA was enhanced by glucose and oxygen limitation, and that the level of enzyme activity was controlled by variations in the amount of mRNA. The mRNA level and the pyruvate decarboxylase activity responded to anaerobiosis and growth on different carbon sources in essentially the same fashion as in S. cerevisiae. This indicates that the difference in ethanol formation between these two yeasts is not due to differences in the regulation of pyruvate decarboxylase(s), but rather to differences in the regulation of the TCA cycle and the respiratory machinery. However, the PDC genes of Saccharomyces/ Kluyveromyces yeasts differ in their genetic organization and phylogenetic origin. While S. cerevisiae and S. kluyveri each have three PDC genes, these have apparently arisen by independent duplications and specializations in each of the two yeast lineages.
Collapse
Affiliation(s)
- K Møller
- Center for Process Biotechnology, BioCentrum-DTU, Technical University of Denmark, Building 223, 2800 Lyngby, Denmark.
| | | | | | | | | |
Collapse
|
38
|
Rossell S, van der Weijden CC, Kruckeberg A, Bakker BM, Westerhoff HV. Loss of fermentative capacity in baker's yeast can partly be explained by reduced glucose uptake capacity. Mol Biol Rep 2003; 29:255-7. [PMID: 12241067 DOI: 10.1023/a:1020398401293] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Initial attempts to increase fermentative capacity of baker's yeast focussed on the overproduction of single enzymes, which proved to be insufficient. Nowadays many components of the system are monitored simultaneously in a search for a correlation with fermentative capacity. However, this strategy has not yet proven fruitful either. Here we investigate an element previously neglected, the glucose transporter, and find that a loss of glucose transport capacity correlates with a decrease of fermentative capacity during nutrient starvation. However the correlation is not unique, suggesting that the loss of fermentative capacity cannot be attributed to an inactivation of glucose transport alone. Our results suggest the necessity to use a detailed kinetic model as an underlying working hypothesis and to use Metabolic Control Analysis to examine the pathway's control properties.
Collapse
Affiliation(s)
- Sergio Rossell
- BioCentrum Amsterdam, Faculty of Earth and Life Sciences, Department of Molecular Cell Physiology, The Netherlands
| | | | | | | | | |
Collapse
|
39
|
Frick T, Schuster S. An example of the prisoner's dilemma in biochemistry. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2003; 90:327-31. [PMID: 12883777 DOI: 10.1007/s00114-003-0434-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2002] [Accepted: 05/12/2003] [Indexed: 11/28/2022]
Abstract
Two strains of microorganisms that both use sugar as energy resource, but which may choose between two different pathways of ATP production, are studied from a game-theory point of view. We consider these pathways as distinct strategies to which we assign payoffs that are proportional to the expected steady-state number of individuals sustainable on the basis of these strategies. In a certain parameter range, we find that the payoffs fulfil the conditions for the prisoner's dilemma. Therefore, cooperative behaviour is unlikely to occur, unless additional factors intervene. In fact, the yeast Saccharomyces cerevisiae uses a competitive strategy by fermenting sugars even under aerobic conditions, thus wasting its own resource. The simple quantifiable structure of the model should enable access to an experimentally determined payoff matrix.
Collapse
Affiliation(s)
- Tobias Frick
- Institute of Biology, Theoretical Biophysics, Humboldt University Berlin, Invalidenstrasse 43, 10115 Berlin, Germany
| | | |
Collapse
|
40
|
Gonzalez R, Andrews BA, Molitor J, Asenjo JA. Metabolic analysis of the synthesis of high levels of intracellular human SOD in Saccharomyces cerevisiae rhSOD 2060 411 SGA122. Biotechnol Bioeng 2003; 82:152-69. [PMID: 12584757 DOI: 10.1002/bit.10556] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The synthesis of human superoxide dismutase (SOD) in batch cultures of a Saccharomyces cerevisiae strain using a glucose-limited minimal medium was studied through metabolic flux analysis. A stoichiometric model was built, which included 78 reactions, according to metabolic pathways operative in these strains during respirofermentative and oxidative metabolism. It allowed calculation of the distribution of metabolic fluxes during diauxic growth on glucose and ethanol. Fermentation profiles and metabolic fluxes were analyzed at different phases of diauxic growth for the recombinant strain (P+) and for its wild type (P-). The synthesis of SOD by the strain P+ resulted in a decrease in specific growth rate of 34 and 54% (growth on glucose and ethanol respectively) in comparison to the wild type. Both strains exhibited similar flux of glucose consumption and ethanol synthesis but important differences in carbon distribution with biomass/substrate yields and ATP production 50% higher in P-. A higher contribution of fermentative metabolism, with 64% of the energy produced at the phosphorylation level, was observed during SOD production. The flux of precursors to amino acids and nucleotides was higher in the recombinant strain, in agreement with the higher total RNA and protein levels. Lower specific growth rates in strain P+ appear to be related to the decrease in the rate of synthesis of nonrecombinant protein, as well as a decrease in the activities of the pentose phosphate (PP) pathway and TCA cycle. A very different way of entry into the stationary phase was observed for each strain: in the wild-type strain most metabolic fluxes decreased and fluxes related to energy reserve synthesis increased, while in the P+ strain the flux of 22 reactions (including PP pathway and amino acids biosynthesis) related to SOD production increased their fluxes. Changes in SOD production rates at different physiological states appear to be related to the differences in building blocks availability between respirofermentative and oxidative metabolism. Using the present expression system, ideal conditions for SOD synthesis are represented by either active growth during respirofermentative metabolism or transition from a growing to a nongrowing state. An increase in SOD flux could be achieved using an expression system nonassociated to growth and potentially eliminating part of the metabolic burden.
Collapse
Affiliation(s)
- Ramon Gonzalez
- Department of Chemical Engineering, Millennium Institute for Advanced Studies In Cell Biology and Biotechnology, University of Chile, Beauchef 861, Santiago, Chile
| | | | | | | |
Collapse
|
41
|
Quantitative analysis of the oxidative metabolism in HXK2- and REG1-deletion mutants of Saccharomyces cerevisiae. Enzyme Microb Technol 2002. [DOI: 10.1016/s0141-0229(02)00164-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
42
|
Ter Linde JJM, Steensma HY. A microarray-assisted screen for potential Hap1 and Rox1 target genes in Saccharomyces cerevisiae. Yeast 2002; 19:825-40. [PMID: 12112237 DOI: 10.1002/yea.879] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Saccharomyces cerevisiae adapts to altered oxygen availability by differentially expressing a number of genes. Under aerobic conditions oxygen control of gene expression is exerted through the activator Hap1 and the repressor Rox1. The Hap1 transcription factor senses cellular heme status and increases expression of aerobic genes in response to oxygen. The repression of hypoxic genes under normoxic conditions results from Hap1-mediated activation of ROX1 transcription. To allow the identification of additional Hap1 and Rox1 target genes, genome-wide expression was analysed in aerobically, chemostat-cultivated hap1 and rox1 null mutants. The microarray results show that deletion of HAP1 causes a lower transcript level of 51 genes. Transcription of 40 genes was increased in rox1 mutant cells compared to wild-type cells. Combining these results with our previously described transcriptome data of aerobically and anaerobically grown cells and with computational analysis of the promoters identified 24 genes that are potentially regulated by Hap1, and 38 genes satisfied the criteria of being direct targets of Rox1. In addition, this work provides further evidence that Rox1 controls transcription of anaerobic genes through repression under normoxic conditions.
Collapse
Affiliation(s)
- José J M Ter Linde
- Institute of Molecular Plant Sciences, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands.
| | | |
Collapse
|
43
|
Møller K, Bro C, Piskur J, Nielsen J, Olsson L. Steady-state and transient-state analyses of aerobic fermentation in Saccharomyces kluyveri. FEMS Yeast Res 2002; 2:233-44. [PMID: 12702311 DOI: 10.1111/j.1567-1364.2002.tb00088.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Some yeasts, such as Saccharomyces cerevisiae, produce ethanol at fully aerobic conditions, whereas other yeasts, such as Kluyveromyces lactis, do not. In this study we investigated the occurrence of aerobic alcoholic fermentation in the petite-negative yeast Saccharomyces kluyveri that is only distantly related to S. cerevisiae. In aerobic glucose-limited continuous cultures of S. kluyveri, two growth regimens were observed: at dilution rates below 0.5 h(-1) the metabolism was purely respiratory, and at dilution rates above 0.5 h(-1) the metabolism was respiro-fermentative. The dilution rate at which the switch in metabolism occurred, i.e. the critical dilution rate, was 66% higher than the typical critical dilution rate of S. cerevisiae. The maximum specific oxygen consumption rate around the critical dilution rate was found to 13.6 mmol (g dry weight)(-1) h(-1) and the capacity of the pyruvate dehydrogenase-bypass pathway was estimated to be high from in vitro enzyme activities; especially the specific activity of acetyl-CoA synthetase was much higher than in S. cerevisiae at all tested conditions. Addition of glucose to respiring cells of S. kluyveri led to ethanol formation after a delay of 20-50 min (depending on culture conditions prior to the pulse), which is in contrast to S. cerevisiae that ferments immediately after glucose addition.
Collapse
Affiliation(s)
- Kasper Møller
- Center for Process Biotechnology, BioCentrum-DTU, Technical University of Denmark, Building 223, 2800 Lyngby, Denmark
| | | | | | | | | |
Collapse
|
44
|
van Maris AJ, Bakker BM, Brandt M, Boorsma A, Teixeira de Mattos MJ, Grivell LA, Pronk JT, Blom J. Modulating the distribution of fluxes among respiration and fermentation by overexpression of HAP4 in Saccharomyces cerevisiae. FEMS Yeast Res 2001; 1:139-49. [PMID: 12702359 DOI: 10.1111/j.1567-1364.2001.tb00025.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The tendency of Saccharomyces cerevisiae to favor alcoholic fermentation over respiration is a complication in aerobic, biomass-directed applications of this yeast. Overproduction of Hap4p, a positive transcriptional regulator of genes involved in respiratory metabolism, has been reported to positively affect the balance between respiration and fermentation in aerobic glucose-grown batch cultures. In this study, the effects of HAP4 overexpression have been quantified in the prototrophic S. cerevisiae strain CEN.PK 113-7D under a variety of growth conditions. In aerobic glucose-limited chemostat cultures, overexpression of HAP4 increased the specific growth rate at which aerobic fermentation set in by about 10% relative to the isogenic wild-type. Upon relief of glucose-limited conditions, the HAP4-overexpressing strain produced slightly less ethanol than the wild-type strain. The effect of Hap4p overproduction was most drastic in aerobic, glucose-grown chemostat cultures in which ammonium was limiting. In such cultures, the biomass yield on glucose was double that of the wild-type.
Collapse
Affiliation(s)
- A J van Maris
- Kluwer Laboratory of Biotechnology, Delft University of Technology, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Toivari MH, Aristidou A, Ruohonen L, Penttilä M. Conversion of xylose to ethanol by recombinant Saccharomyces cerevisiae: importance of xylulokinase (XKS1) and oxygen availability. Metab Eng 2001; 3:236-49. [PMID: 11461146 DOI: 10.1006/mben.2000.0191] [Citation(s) in RCA: 150] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The yeast Saccharomyces cerevisiae efficiently ferments hexose sugars to ethanol, but it is unable to utilize xylose, a pentose sugar abundant in lignocellulosic materials. Recombinant strains containing genes coding for xylose reductase (XR) and xylitol dehydrogenase (XDH) from the xylose-utilizing yeast Pichia stipitis have been reported; however, such strains ferment xylose to ethanol poorly. One reason for this may be the low capacity of xylulokinase, the third enzyme in the xylose pathway. To investigate the potential limitation of the xylulokinase step, we have overexpressed the endogenous gene for this enzyme (XKS1) in S. cerevisiae that also expresses the P. stipitis genes for XR and XDH. The metabolism of this recombinant yeast was further investigated in pure xylose bioreactor cultivation at various oxygen levels. The results clearly indicated that overexpression of XKS1 significantly enhances the specific rate of xylose utilization. In addition, the XK-overexpressing strain can more efficiently convert xylose to ethanol under all aeration conditions studied. One of the important illustrations is the significant anaerobic and aerobic xylose conversion to ethanol by the recombinant Saccharomyces; moreover, this was achieved on pure xylose as a carbon. Under microaerobic conditions, 5.4 g L(-1) ethanol was produced from 47 g L(-1) xylose during 100 h. In fed-batch cultivations using a mixture of xylose and glucose as carbon sources, the specific ethanol production rate was highest at the highest aeration rate tested and declined by almost one order of magnitude at lower aeration levels. Intracellular metabolite analyses and in vitro enzyme activities suggest the following: the control of flux in a strain that overexpresses XKS1 has shifted to the nonoxidative steps of the pentose phosphate pathway (i.e., downstream of xylose 5-phosphate), and enzymatic steps in the lower part of glycolysis and ethanol formation pathways (pyruvate kinase, pyruvate decarboxylase, and alcohol dehydrogenase) do not have a high flux control in this recombinant strain. Furthermore, the intracellular ATP levels were found to be significantly lower for the XK strain compared with either the control strain under similar conditions or glucose-grown Saccharomyces. The ATP : ADP ratios were also lower for the XK strain, especially under microaerobic conditions (0.9 vs 6.4).
Collapse
Affiliation(s)
- M H Toivari
- VTT Biotechnology, P.O. Box 1500, FIN-02044 VTT, Finland.
| | | | | | | |
Collapse
|
46
|
Investigations of Multiple Steady-States in Continuous Cultivation of Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1474-6670(17)34202-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
47
|
Görgens JF, van Zyl WH, Knoetze JH, Hahn-Hägerdal B. The metabolic burden of the PGK1 and ADH2 promoter systems for heterologous xylanase production by Saccharomyces cerevisiae in defined medium. Biotechnol Bioeng 2001; 73:238-45. [PMID: 11257606 DOI: 10.1002/bit.1056] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Five recombinant S. cerevisiae strains were cultivated under identical conditions to quantify the molecular basis of the metabolic burden of heterologous gene expression, and to evaluate mechanisms for the metabolic burden. Two recombinant S. cerevisiae strains, producing Trichoderma reesei xylanase II under control of either the PGK1 or ADH2 promoters, were compared quantitatively with three references strains, where either the heterologous xylanase II (XYN2) gene, or the heterologous gene and the promoter and terminator were omitted from the recombinant plasmid. Neither the replication of multiple copies of the 2-microm-based YEp352 plasmid nor the replication the foreign XYN2 gene represented a metabolic burden to the cell, as the growth of the host organism was not affected. The inclusion of a glycolytic promoter on the recombinant plasmid, however, reduced the maximum specific growth rate (12% to 15%), biomass yield on glucose (8% to 11%), and specific glucose consumption rate (6% to 10%) of the recombinant strains. The presence of the heterologous XYN2 gene on the recombinant plasmid caused a further reduction in the maximum specific growth rate (11% to 14%), biomass yield (4%), and specific glucose consumption rate (12%) of the host strain during active gene expression, which was dictated by the regulatory characteristics of the promoter utilized. The metabolic effect of foreign gene expression was disproportionally large, with respect to on the amount of heterologous protein produced. This was most likely due to an increased energetic demand for the expression of a foreign gene and/or a competition for limiting amounts of transcription or translation factors, biosynthetic precursors or metabolic energy.
Collapse
Affiliation(s)
- J F Görgens
- Department of Applied Microbiology, Lund University, Box 124, S-221 00 Lund, Sweden
| | | | | | | |
Collapse
|
48
|
van Hoek P, de Hulster E, van Dijken JP, Pronk JT. Fermentative capacity in high-cell-density fed-batch cultures of baker's yeast. Biotechnol Bioeng 2000. [DOI: 10.1002/(sici)1097-0290(20000605)68:5<517::aid-bit5>3.0.co;2-o] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
49
|
Pronk JT. Regulation of fermentative capacity and levels of glycolytic enzymes in chemostat cultures of Saccharomyces cerevisiae. Enzyme Microb Technol 2000; 26:724-736. [PMID: 10862878 DOI: 10.1016/s0141-0229(00)00164-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Regulation of fermentative capacity was studied in chemostat cultures of two Saccharomyces cerevisiae strains: the laboratory strain CEN.PK113-7D and the industrial bakers' yeast strain DS28911. The two strains were cultivated at a fixed dilution rate of 0.10 h(-1) under various nutrient limitation regimes: aerobic and anaerobic glucose limitation, aerobic and anaerobic nitrogen limitation on glucose, and aerobic ethanol limitation. Also the effect of specific growth rate on fermentative capacity was compared in glucose-limited, aerobic cultures grown at dilution rates between 0.05 h(-1) and 0.40 h(-1). Biomass yields and metabolite formation patterns were identical for the two strains under all cultivation conditions tested. However, the way in which environmental conditions affected fermentative capacity (assayed off-line as ethanol production rate under anaerobic conditions) differed for the two strains. A different regulation of fermentative capacity in the two strains was also evident from the levels of the glycolytic enzymes, as determined by in vitro enzyme assays. With the exception of phosphofructokinase and pyruvate decarboxylase in the industrial strain, no clear-cut correlation between the activities of glycolytic enzymes and the fermentative capacity was found. These results emphasise the need for controlled cultivation conditions in studies on metabolic regulation in S. cerevisiae and demonstrate that conclusions from physiological studies cannot necessarily be extrapolated from one S. cerevisiae strain to the other.
Collapse
|
50
|
Overkamp KM, Bakker BM, Kötter P, van Tuijl A, de Vries S, van Dijken JP, Pronk JT. In vivo analysis of the mechanisms for oxidation of cytosolic NADH by Saccharomyces cerevisiae mitochondria. J Bacteriol 2000; 182:2823-30. [PMID: 10781551 PMCID: PMC101991 DOI: 10.1128/jb.182.10.2823-2830.2000] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During respiratory glucose dissimilation, eukaryotes produce cytosolic NADH via glycolysis. This NADH has to be reoxidized outside the mitochondria, because the mitochondrial inner membrane is impermeable to NADH. In Saccharomyces cerevisiae, this may involve external NADH dehydrogenases (Nde1p or Nde2p) and/or a glycerol-3-phosphate shuttle consisting of soluble (Gpd1p or Gpd2p) and membrane-bound (Gut2p) glycerol-3-phosphate dehydrogenases. This study addresses the physiological relevance of these mechanisms and the possible involvement of alternative routes for mitochondrial oxidation of cytosolic NADH. Aerobic, glucose-limited chemostat cultures of a gut2Delta mutant exhibited fully respiratory growth at low specific growth rates. Alcoholic fermentation set in at the same specific growth rate as in wild-type cultures (0.3 h(-1)). Apparently, the glycerol-3-phosphate shuttle is not essential for respiratory glucose dissimilation. An nde1Delta nde2Delta mutant already produced glycerol at specific growth rates of 0.10 h(-1) and above, indicating a requirement for external NADH dehydrogenase to sustain fully respiratory growth. An nde1Delta nde2Delta gut2Delta mutant produced even larger amounts of glycerol at specific growth rates ranging from 0.05 to 0.15 h(-1). Apparently, even at a low glycolytic flux, alternative mechanisms could not fully replace the external NADH dehydrogenases and glycerol-3-phosphate shuttle. However, at low dilution rates, the nde1Delta nde2Delta gut2Delta mutant did not produce ethanol. Since glycerol production could not account for all glycolytic NADH, another NADH-oxidizing system has to be present. Two alternative mechanisms for reoxidizing cytosolic NADH are discussed: (i) cytosolic production of ethanol followed by its intramitochondrial oxidation and (ii) a redox shuttle linking cytosolic NADH oxidation to the internal NADH dehydrogenase.
Collapse
Affiliation(s)
- K M Overkamp
- Kluyver Laboratory of Biotechnology, Delft University of Technology, NL-2628 BC Delft, The Netherlands
| | | | | | | | | | | | | |
Collapse
|