1
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Schlarmann P, Sakuragi K, Ikeda A, Yang Y, Sasaki S, Hanaoka K, Araki M, Shibata T, Kanai M, Funato K. The tricalbin family of membrane contact site tethers is involved in the transcriptional responses of Saccharomyces cerevisiae to glucose. J Biol Chem 2024; 300:107665. [PMID: 39128724 PMCID: PMC11408865 DOI: 10.1016/j.jbc.2024.107665] [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: 03/05/2024] [Revised: 07/24/2024] [Accepted: 08/05/2024] [Indexed: 08/13/2024] Open
Abstract
Cellular organelles maintain areas of close apposition with other organelles at which the cytosolic gap in between them is reduced to a minimum. These membrane contact sites (MCS) are vital for organelle communication and are formed by molecular tethers that physically connect opposing membranes. Although many regulatory pathways are known to converge at MCS, a link between MCS and transcriptional regulation-the primary mechanism through which cells adapt their metabolism to environmental cues-remains largely elusive. In this study, we performed RNA-sequencing on Saccharomyces cerevisiae cells lacking tricalbin proteins (Tcb1, Tcb2, and Tcb3), a family of tethering proteins that connect the endoplasmic reticulum with the plasma membrane and Golgi, to investigate if gene expression is altered when MCS are disrupted. Our results indicate that in the tcb1Δ2Δ3Δ strain, pathways responsive to a high-glucose environment, including glycolysis, fermentation, amino acid synthesis, and low-affinity glucose uptake, are upregulated. Conversely, pathways crucial during glucose depletion, such as the tricarboxylic acid cycle, respiration, high-affinity glucose uptake, and amino acid uptake are downregulated. In addition, we demonstrate that the altered gene expression of tcb1Δ2Δ3Δ in glucose metabolism correlates with increased growth, glucose consumption, CO2 production, and ethanol generation. In conclusion, our findings reveal that tricalbin protein deletion induces a shift in gene expression patterns mimicking cellular responses to a high-glucose environment. This suggests that MCS play a role in sensing and signaling pathways that modulate gene transcription in response to glucose availability.
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Affiliation(s)
- Philipp Schlarmann
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Keiko Sakuragi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Atsuko Ikeda
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yujia Yang
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Saku Sasaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kazuki Hanaoka
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Misako Araki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Tomoko Shibata
- National Research Institute of Brewing, Higashi-Hiroshima, Japan
| | - Muneyoshi Kanai
- National Research Institute of Brewing, Higashi-Hiroshima, Japan
| | - Kouichi Funato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
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2
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Johansson SA, Dulermo T, Jann C, Smith JD, Pryszlak A, Pignede G, Schraivogel D, Colavizza D, Desfougères T, Rave C, Farwick A, Merten CA, Roy KR, Wei W, Steinmetz LM. Large scale microfluidic CRISPR screening for increased amylase secretion in yeast. LAB ON A CHIP 2023; 23:3704-3715. [PMID: 37483015 PMCID: PMC7614956 DOI: 10.1039/d3lc00111c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Key to our ability to increase recombinant protein production through secretion is a better understanding of the pathways that interact to translate, process and export mature proteins to the surrounding environment, including the supporting cellular machinery that supplies necessary energy and building blocks. By combining droplet microfluidic screening with large-scale CRISPR libraries that perturb the expression of the majority of coding and non-coding genes in S. cerevisiae, we identified 345 genes for which an increase or decrease in gene expression resulted in increased secretion of α-amylase. Our results show that modulating the expression of genes involved in the trafficking of vesicles, endosome to Golgi transport, the phagophore assembly site, the cell cycle and energy supply improve α-amylase secretion. Besides protein-coding genes, we also find multiple long non-coding RNAs enriched in the vicinity of genes associated with endosomal, Golgi and vacuolar processes. We validated our results by overexpressing or deleting selected genes, which resulted in significant improvements in α-amylase secretion. The advantages, in terms of precision and speed, inherent to CRISPR based perturbations, enables iterative testing of new strains for increased protein secretion.
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Affiliation(s)
- S Andreas Johansson
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Thierry Dulermo
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Cosimo Jann
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Justin D Smith
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
| | - Anna Pryszlak
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Georges Pignede
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Daniel Schraivogel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Didier Colavizza
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Thomas Desfougères
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Christophe Rave
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Alexander Farwick
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Christoph A Merten
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Kevin R Roy
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
| | - Wu Wei
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
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3
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Mukherjee S, Das S, Bedi M, Vadupu L, Ball WB, Ghosh A. Methylglyoxal-mediated Gpd1 activation restores the mitochondrial defects in a yeast model of mitochondrial DNA depletion syndrome. Biochim Biophys Acta Gen Subj 2023; 1867:130328. [PMID: 36791826 DOI: 10.1016/j.bbagen.2023.130328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Human MPV17, an evolutionarily conserved mitochondrial inner-membrane channel protein, accounts for the tissue-specific mitochondrial DNA depletion syndrome. However, the precise molecular function of the MPV17 protein is still elusive. Previous studies showed that the mitochondrial morphology and cristae organization are severely disrupted in the MPV17 knockout cells from yeast, zebrafish, and mammalian tissues. As mitochondrial cristae morphology is strictly regulated by the membrane phospholipids composition, we measured mitochondrial membrane phospholipids (PLs) levels in yeast Saccharomyces cerevisiae MPV17 ortholog, SYM1 (Stress-inducible Yeast MPV17) deleted cells. We found that Sym1 knockout decreases the mitochondrial membrane PL, phosphatidyl ethanolamine (PE), and inhibits respiratory growth at 37 ̊C on rich media. Both the oxygen consumption rate and the steady state expressions of mitochondrial complex II and super-complexes are compromised. Apart from mitochondrial PE defect a significant depletion of mitochondrial phosphatidyl-choline (PC) was noticed in the sym1∆ cells grown on synthetic media at both 30 ̊C and 37 ̊C temperatures. Surprisingly, exogenous supplementation of methylglyoxal (MG), an intrinsic side product of glycolysis, rescues the respiratory growth of Sym1 deficient yeast cells. Using a combination of molecular biology and lipid biochemistry, we uncovered that MG simultaneously restores both the mitochondrial PE/PC levels and the respiration by enhancing cytosolic NAD-dependent glycerol-3-phosphate dehydrogenase 1 (Gpd1) enzymatic activity. Further, MG is incapable to restore respiratory growth of the sym1∆gpd1∆ double knockout cells. Thus, our work provides Gpd1 activation as a novel strategy for combating Sym1 deficiency and PC/PE defects.
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Affiliation(s)
- Soumyajit Mukherjee
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata Pin-700019, India
| | - Shubhojit Das
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata Pin-700019, India
| | - Minakshi Bedi
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata Pin-700019, India
| | - Lavanya Vadupu
- Department of the Biological Sciences, SRM University- AP, Andhra Pradesh Pin- 522240, India
| | - Writoban Basu Ball
- Department of the Biological Sciences, SRM University- AP, Andhra Pradesh Pin- 522240, India
| | - Alok Ghosh
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata Pin-700019, India.
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4
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Singh K, Sethi R, Das E, Roy I. The role of the glycerol transporter channel Fps1p in cellular proteostasis during enhanced proteotoxic stress. Appl Microbiol Biotechnol 2022; 106:6169-6180. [PMID: 35945363 DOI: 10.1007/s00253-022-12118-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/23/2022] [Accepted: 07/31/2022] [Indexed: 11/29/2022]
Abstract
In response to osmotic shock, the components of high-osmolarity glycerol (HOG) pathway regulate the level of intracellular glycerol in yeast and ensure cell survival. Glycerol is a compatible solute and a stabiliser of proteins. Its role in maintaining proteostasis is less explored. We show that mild stress in the form of dietary restriction leads to increased glycerol level which increases cell viability. However, dietary restriction coupled with protein aggregation decreases intracellular glycerol level and attenuates cell viability. The transcript level of FPS1, the glycerol transporter channel, remains unchanged. However, its activity is altered under enhanced proteotoxic stress. Our results provide evidence for a probable role of the Fps1p channel in the cellular proteostasis network. KEY POINTS: • Dietary restriction led to increased accumulation of glycerol in Fps1-deleted yeast cells. • This led to lower protein aggregation in these cells. • Increased production of glycerol under dietary restriction was not linked to increased level of Fps1.
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Affiliation(s)
- Kuljit Singh
- Present Address: Infectious Diseases Division, Indian Institute of Integrative Medicine (CSIR-IIIM), Canal Road, Jammu, 180001, India.,Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Sector 67, Punjab, 160062, India
| | - Ratnika Sethi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Sector 67, Punjab, 160062, India
| | - Eshita Das
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Sector 67, Punjab, 160062, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Sector 67, Punjab, 160062, India.
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5
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Zhao X, Lian X, Liu Y, Zhou L, Wu B, Fu YV. A Peptide Derived from GAPDH Enhances Resistance to DNA Damage in Saccharomyces cerevisiae Cells. Appl Environ Microbiol 2022; 88:e0219421. [PMID: 34936834 PMCID: PMC8863060 DOI: 10.1128/aem.02194-21] [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: 11/11/2021] [Accepted: 12/16/2021] [Indexed: 11/20/2022] Open
Abstract
Social behaviors do not exist only in higher organisms but are also present in microbes that interact for the common good. Here, we report that budding yeast cells interact with their neighboring cells after exposure to DNA damage. Yeast cells irradiated with DNA-damaging UV light secrete signal peptides that can increase the survival of yeast cells exposed to DNA-damaging stress. The secreted peptide is derived from glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and it induced cell death of a fraction of yeast cells in the group. The data suggest that the GAPDH-derived peptide serves in budding yeast's social interaction in response to DNA-damaging stress. IMPORTANCE Many studies have shown that microorganisms, including bacteria and yeast, display increased tolerance to stress after exposure to the same stressor. However, the mechanism remains unknown. In this study, we report a striking finding that Saccharomyces cerevisiae cells respond to DNA damage by secreting a peptide that facilitates resistance to DNA-damaging stress. Although it has been shown that GAPDH possesses many key functions in cells aside from its well-established role in glycolysis, this study demonstrated that GAPDH is also involved in the social behaviors response to DNA-damaging stress. The study opens the gate to an interesting research field about microbial social activity for adaptation to a harsh environment.
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Affiliation(s)
- Xi Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Xianqiang Lian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Liyan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu V. Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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6
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Dekker WJC, Jürgens H, Ortiz-Merino RA, Mooiman C, van den Berg R, Kaljouw A, Mans R, Pronk JT. OUP accepted manuscript. FEMS Yeast Res 2022; 22:6523363. [PMID: 35137036 PMCID: PMC8862043 DOI: 10.1093/femsyr/foac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/26/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
While thermotolerance is an attractive trait for yeasts used in industrial ethanol production, oxygen requirements of known thermotolerant species are incompatible with process requirements. Analysis of oxygen-sufficient and oxygen-limited chemostat cultures of the facultatively fermentative, thermotolerant species Ogataea parapolymorpha showed its minimum oxygen requirements to be an order of magnitude larger than those reported for the thermotolerant yeast Kluyveromyces marxianus. High oxygen requirements of O. parapolymorpha coincided with a near absence of glycerol, a key NADH/NAD+ redox-cofactor-balancing product in many other yeasts, in oxygen-limited cultures. Genome analysis indicated absence of orthologs of the Saccharomyces cerevisiae glycerol-3-phosphate-phosphatase genes GPP1 and GPP2. Co-feeding of acetoin, whose conversion to 2,3-butanediol enables reoxidation of cytosolic NADH, supported a 2.5-fold increase of the biomass concentration in oxygen-limited cultures. An O. parapolymorpha strain in which key genes involved in mitochondrial reoxidation of NADH were inactivated did produce glycerol, but transcriptome analysis did not reveal a clear candidate for a responsible phosphatase. Expression of S. cerevisiae GPD2, which encodes NAD+-dependent glycerol-3-phosphate dehydrogenase, and GPP1 supported increased glycerol production by oxygen-limited chemostat cultures of O. parapolymorpha. These results identify dependence on respiration for NADH reoxidation as a key contributor to unexpectedly high oxygen requirements of O. parapolymorpha.
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Affiliation(s)
- Wijbrand J C Dekker
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Hannes Jürgens
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Christiaan Mooiman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Remon van den Berg
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Astrid Kaljouw
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Corresponding author: Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands. Tel: +31 15 2783214; E-mail:
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7
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BiFC Method Based on Intraorganellar Protein Crowding Detects Oleate-Dependent Peroxisomal Targeting of Pichia pastoris Malate Dehydrogenase. Int J Mol Sci 2021; 22:ijms22094890. [PMID: 34063066 PMCID: PMC8124512 DOI: 10.3390/ijms22094890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/24/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022] Open
Abstract
The maintenance of intracellular NAD+/NADH homeostasis across multiple, subcellular compartments requires the presence of NADH-shuttling proteins, which circumvent the lack of permeability of organelle membranes to these cofactors. Very little is known regarding these proteins in the methylotrophic yeast, Pichia pastoris. During the study of the subcellular locations of these shuttling proteins, which often have dual subcellular locations, it became necessary to develop new ways to detect the weak peroxisomal locations of some of these proteins. We have developed a novel variation of the traditional Bimolecular Fluorescence Complementation (BiFC), called divergent BiFC, to detect intraorganellar colocalization of two noninteracting proteins based on their proximity-based protein crowding within a small subcellular compartment, rather than on the traditional protein–protein interactions expected for BiFC. This method is used to demonstrate the partially peroxisomal location of one such P. pastoris NADH-shuttling protein, malate dehydrogenase B, only when cells are grown in oleate, but not when grown in methanol or glucose. We discuss the mode of NADH shuttling in P. pastoris and the physiological basis of the medium-dependent compartmentalization of PpMdhB.
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8
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Marchante L, Mena A, Izquierdo-Cañas PM, García-Romero E, Pérez-Coello MS, Díaz-Maroto MC. Effects of the pre-fermentative addition of chitosan on the nitrogenous fraction and the secondary fermentation products of SO 2 -free red wines. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:1143-1149. [PMID: 32789849 DOI: 10.1002/jsfa.10725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/06/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Different red winemaking were carried out to evaluate the effects of the prefermentative addition of chitosan, as an alternative to the use of SO2 , on the secondary products of alcoholic fermentation, yeast available nitrogen (YAN), biogenic amines and ethyl carbamate. RESULTS The wines made with chitosan presented higher total acidity and higher content of tartaric and succinic acids than those made only with SO2 . The use of chitosan in winemaking resulted in wines with higher glycerol and diacetyl content without increasing the concentration of ethanol, acetic acid, acetaldehyde or butanediol. YAN was lower in wines made with chitosan, which may mean an advantage for the microbial stability of the wines. Furthermore, the use of chitosan at the beginning of alcoholic fermentation did not increase the concentration of biogenic amines or the formation of ethyl carbamate in SO2 -free red wines. CONCLUSION The total or partial substitution of SO2 for chitosan at the beginning of the alcoholic fermentation gives rise to quality red wines without negatively affecting their nitrogen fraction or their very important secondary fermentation products such as acetic acid or acetaldehyde. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Lourdes Marchante
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal de Castilla La Mancha (IRIAF), IVICAM, Ciudad Real, Spain
| | - Adela Mena
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal de Castilla La Mancha (IRIAF), IVICAM, Ciudad Real, Spain
| | - Pedro M Izquierdo-Cañas
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal de Castilla La Mancha (IRIAF), IVICAM, Ciudad Real, Spain
| | - Esteban García-Romero
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal de Castilla La Mancha (IRIAF), IVICAM, Ciudad Real, Spain
| | - María Soledad Pérez-Coello
- Food Technology, Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - María Consuelo Díaz-Maroto
- Food Technology, Instituto Regional de Investigación Científica Aplicada (IRICA), Universidad de Castilla-La Mancha, Ciudad Real, Spain
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9
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Chornyi S, IJlst L, van Roermund CWT, Wanders RJA, Waterham HR. Peroxisomal Metabolite and Cofactor Transport in Humans. Front Cell Dev Biol 2021; 8:613892. [PMID: 33505966 PMCID: PMC7829553 DOI: 10.3389/fcell.2020.613892] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/10/2020] [Indexed: 12/20/2022] Open
Abstract
Peroxisomes are membrane-bound organelles involved in many metabolic pathways and essential for human health. They harbor a large number of enzymes involved in the different pathways, thus requiring transport of substrates, products and cofactors involved across the peroxisomal membrane. Although much progress has been made in understanding the permeability properties of peroxisomes, there are still important gaps in our knowledge about the peroxisomal transport of metabolites and cofactors. In this review, we discuss the different modes of transport of metabolites and essential cofactors, including CoA, NAD+, NADP+, FAD, FMN, ATP, heme, pyridoxal phosphate, and thiamine pyrophosphate across the peroxisomal membrane. This transport can be mediated by non-selective pore-forming proteins, selective transport proteins, membrane contact sites between organelles, and co-import of cofactors with proteins. We also discuss modes of transport mediated by shuttle systems described for NAD+/NADH and NADP+/NADPH. We mainly focus on current knowledge on human peroxisomal metabolite and cofactor transport, but also include knowledge from studies in plants, yeast, fruit fly, zebrafish, and mice, which has been exemplary in understanding peroxisomal transport mechanisms in general.
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Affiliation(s)
- Serhii Chornyi
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Carlo W T van Roermund
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
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10
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Long-Term Adaption to High Osmotic Stress as a Tool for Improving Enological Characteristics in Industrial Wine Yeast. Genes (Basel) 2020; 11:genes11050576. [PMID: 32443892 PMCID: PMC7288280 DOI: 10.3390/genes11050576] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/28/2022] Open
Abstract
Industrial wine yeasts owe their adaptability in constantly changing environments to a long evolutionary history that combines naturally occurring evolutionary events with human-enforced domestication. Among the many stressors associated with winemaking processes that have potentially detrimental impacts on yeast viability, growth, and fermentation performance are hyperosmolarity, high glucose concentrations at the beginning of fermentation, followed by the depletion of nutrients at the end of this process. Therefore, in this study, we subjected three widely used industrial wine yeasts to adaptive laboratory evolution under potassium chloride (KCl)-induced osmotic stress. At the end of the evolutionary experiment, we evaluated the tolerance to high osmotic stress of the evolved strains. All of the analyzed strains improved their fitness under high osmotic stress without worsening their economic characteristics, such as growth rate and viability. The evolved derivatives of two strains also gained the ability to accumulate glycogen, a readily mobilized storage form of glucose conferring enhanced viability and vitality of cells during prolonged nutrient deprivation. Moreover, laboratory-scale fermentation in grape juice showed that some of the KCl-evolved strains significantly enhanced glycerol synthesis and production of resveratrol-enriched wines, which in turn greatly improved the wine sensory profile. Altogether, these findings showed that long-term adaptations to osmotic stress can be an attractive approach to develop industrial yeasts.
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11
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Shashkova S, Andersson M, Hohmann S, Leake MC. Correlating single-molecule characteristics of the yeast aquaglyceroporin Fps1 with environmental perturbations directly in living cells. Methods 2020; 193:46-53. [PMID: 32387484 DOI: 10.1016/j.ymeth.2020.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 01/09/2023] Open
Abstract
Membrane proteins play key roles at the interface between the cell and its environment by mediating selective import and export of molecules via plasma membrane channels. Despite a multitude of studies on transmembrane channels, understanding of their dynamics directly within living systems is limited. To address this, we correlated molecular scale information from living cells with real time changes to their microenvironment. We employed super-resolved millisecond fluorescence microscopy with a single-molecule sensitivity, to track labelled molecules of interest in real time. We use as example the aquaglyceroporin Fps1 in the yeast Saccharomyces cerevisiae to dissect and correlate its stoichiometry and molecular turnover kinetics with various extracellular conditions. We show that Fps1 resides in multi tetrameric clusters while hyperosmotic and oxidative stress conditions cause Fps1 reorganization. Moreover, we demonstrate that rapid exposure to hydrogen peroxide causes Fps1 degradation. In this way we shed new light on aspects of architecture and dynamics of glycerol-permeable plasma membrane channels.
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Affiliation(s)
| | - Mikael Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden.
| | - Stefan Hohmann
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
| | - Mark C Leake
- Department of Physics, University of York, YO10 5DD York, UK.
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12
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Mitochondrial Damage Mediated by miR-1 Overexpression in Cancer Stem Cells. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 18:938-953. [PMID: 31765945 PMCID: PMC6883328 DOI: 10.1016/j.omtn.2019.10.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023]
Abstract
It is well known that cells rely on mitochondrial respiration for survival. However, the effect of microRNAs (miRNAs) on mitochondria of cells has not been extensively explored. Our results indicated that the overexpression of a miRNA (miR-1) could destroy mitochondria of cancer stem cells. miR-1 was downregulated in melanoma stem cells (MSCs) and breast cancer stem cells (BCSCs) compared with cancer non-stem cells. However, the upregulation of miR-1 in cancer non-stem cells did not induce mitochondrial damage. miR-1 overexpression caused mitochondrial damage of cancer stem cells by directly targeting the 3′ UTRs of MINOS1 (mitochondrial inner membrane organizing system 1) and GPD2 (glycerol-3-phosphate dehydrogenase 2) genes and interacting with LRPPRC (leucine-rich pentatricopeptide-repeat containing) protein, a protein localized in mitochondria. MINOS1, GPD2, and LRPPRC in mitochondria were required for mitochondrial inner membrane. The results of in vitro and in vivo assays demonstrated that miR-1 overexpression induced mitophagy of cancer stem cells. Therefore, our study contributed novel insights into the mechanism of miRNA-mediated regulation of mitochondria morphology of cancer stem cells.
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Joshua IM, Höfken T. Ste20 and Cla4 modulate the expression of the glycerol biosynthesis enzyme Gpd1 by a novel MAPK-independent pathway. Biochem Biophys Res Commun 2019; 517:611-616. [PMID: 31395335 DOI: 10.1016/j.bbrc.2019.07.072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 07/19/2019] [Indexed: 11/29/2022]
Abstract
p21-activated kinases (PAKs) are important signalling molecules with a wide range of functions. In budding yeast, the main PAKs Ste20 and Cla4 regulate the response to hyperosmotic stress, which is an excellent model for the adaptation to changing environmental conditions. In this pathway, the only known function of Ste20 and Cla4 is the activation of a mitogen-activated protein kinase (MAPK) cascade through Ste11. This eventually leads to increased transcription of glycerol biosynthesis genes, the most important response to hyperosmotic shock. Here, we show that Ste20 and Cla4 not only stimulate transcription, they also bind to the glycerol biosynthesis enzymes Gpd1, Gpp1 and Gpp2. Protein levels of Gpd1, the enzyme that catalyzes the rate limiting step in glycerol synthesis, positively correlate with glucose availability. Using a chemical genetics approach, we find that simultaneous inactivation of STE20 and CLA4 reduces the glucose-induced increase of Gpd1 levels, whereas the deletion of either STE20 or CLA4 alone has no effect. This is also observed for the hyperosmotic stress-induced increase of Gpd1 levels. Importantly, under both conditions the deletion of STE11 has no effect on Gpd1 induction. These observations suggest that Ste20 and Cla4 not only have a role in the transcriptional regulation of GPD1 through Ste11. They also seem to modulate GPD1 expression at another level such as translation or protein degradation.
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Affiliation(s)
| | - Thomas Höfken
- Division of Biosciences, Brunel University London, UK.
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14
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Zhang C, Meng X, Gu H, Ma Z, Lu L. Predicted Glycerol 3-Phosphate Dehydrogenase Homologs and the Glycerol Kinase GlcA Coordinately Adapt to Various Carbon Sources and Osmotic Stress in Aspergillus fumigatus. G3 (BETHESDA, MD.) 2018; 8:2291-2299. [PMID: 29739860 PMCID: PMC6027872 DOI: 10.1534/g3.118.200253] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 05/03/2018] [Indexed: 01/01/2023]
Abstract
Glycerol plays an important role in the adaptation of fungi to various microenvironments and stressors, including heat shock, anoxic conditions and osmotic stress. Glycerol 3-phosphate dehydrogenase (G3PDH) is able to catalyze dihydroxyacetone phosphate to glycerol 3-phosphate (G3P), which is subsequently dephosphorylated into glycerol. However, current knowledge about the functions of G3PDH homologs in glycerol biosynthesis in Aspergillus fumigatus is limited. Here, we show that the A. fumigatus G3PDH gene, gfdA, is crucial for normal colony growth in glucose media under both normoxic and hypoxic conditions. In addition, failure of the overexpression of the gfdA homolog, gfdB, to rescue the phenotype of a gfdA null mutant suggests that gfdA plays a predominant role in the synthesis of G3P and glycerol. However, in a wild-type background, overexpressing either gfdA or gfdB is able to significantly enhance biomass production of mycelia, suggesting that gfdA and gfdB have similar functions in promoting the use of glucose. Interestingly, overexpression of the gene encoding the predicted glycerol kinase, GlcA, which is capable of phosphorylating glycerol to form G3P, significantly rescues the growth defects of gfdA null mutants in glucose media, indicating that the growth defects of gfdA null mutants might be due to the absence of G3P rather than glycerol. Moreover, Western blotting analysis revealed that gfdA is inducibly expressed by osmotic mediators. However, in the absence of gfdA, osmotic stress can rescue colony growth defects and allow colonies to partially bypass the gfdA requirement in a high osmolarity glycerol pathway-dependent manner. Therefore, the findings of this study elucidate how saprophytic filamentous fungi have developed pathways distinct from those of budding yeasts to adapt to varied carbon sources and survive environmental stresses.
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Affiliation(s)
- Chi Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Xiuhua Meng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Huiyu Gu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zhihua Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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15
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Mojardín L, Vega M, Moreno F, Schmitz HP, Heinisch JJ, Rodicio R. Lack of the NAD+-dependent glycerol 3-phosphate dehydrogenase impairs the function of transcription factors Sip4 and Cat8 required for ethanol utilization in Kluyveromyces lactis. Fungal Genet Biol 2018; 111:16-29. [DOI: 10.1016/j.fgb.2017.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/19/2017] [Accepted: 11/21/2017] [Indexed: 11/25/2022]
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16
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Shi Y, Wang H, Yan Y, Cao H, Liu X, Lin F, Lu J. Glycerol-3-Phosphate Shuttle Is Involved in Development and Virulence in the Rice Blast Fungus Pyricularia oryzae. FRONTIERS IN PLANT SCIENCE 2018; 9:687. [PMID: 29875789 PMCID: PMC5974175 DOI: 10.3389/fpls.2018.00687] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 05/04/2018] [Indexed: 05/07/2023]
Abstract
The glycerol-3-phosphate (G-3-P) shuttle is an important pathway for delivery of cytosolic reducing equivalents into mitochondrial oxidative phosphorylation, and plays essential physiological roles in yeast, plants, and animals. However, its role has been unclear in filamentous and pathogenic fungi. Here, we characterize the function of the G-3-P shuttle in Pyricularia oryzae by genetic and molecular analyses. In P. oryzae, a glycerol-3-phosphate dehydrogenase 1 (PoGpd1) is involved in NO production, conidiation, and utilization of several carbon sources (pyruvate, sodium acetate, glutamate, and glutamine). A glycerol-3-phosphate dehydrogenase 2 (PoGpd2) is essential for glycerol utilization and fungal development. Deletion of PoGPD2 led to delayed aerial hyphal formation, accelerated aerial hyphal collapse, and reduced conidiation on complete medium (CM) under a light-dark cycle. Aerial mycelial surface hydrophobicity to water and Tween 20 was decreased in ΔPogpd2. Melanin synthesis genes required for cell wall construction and two transcription factor genes (COS1 and CONx2) required for conidiation and/or aerial hyphal differentiation were down-regulated in the aerial mycelia of ΔPogpd2 and ΔPogpd1. Culturing under continuous dark could complement the defects of aerial hyphal differentiation of ΔPogpd2 observed in a light-dark cycle. Two light-sensitive protein genes (PoSIR2 encoding an NAD+-dependent deacetylase and TRX2 encoding a thioredoxin 2) were up-regulated in ΔPogpd2 cultured on CM medium in a light-dark cycle. ΔPogpd2 showed an increased intracellular NAD+/NADH ratio and total NAD content, and alteration of intracellular ATP production. Culturing on minimal medium also could restore aerial hyphal differentiation of ΔPogpd2, which is deficient on CM medium in a light-dark cycle. Two glutamate synthesis genes, GDH1 and PoGLT1, which synthesize glutamate coupled with oxidation of NADH to NAD+, were significantly up-regulated in ΔPogpd2 in a light-dark cycle. Moreover, deletion of PoGpd1 or PoGpd2 led to reduced virulence of conidia or hyphae on rice. The glycerol-3-phosphate shuttle is involved in cellular redox, fungal development, and virulence in P. oryzae.
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Affiliation(s)
- Yongkai Shi
- State Key Laboratory for Rice Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Huan Wang
- State Key Laboratory for Rice Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuxin Yan
- State Key Laboratory for Rice Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Huijuan Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaohong Liu
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou, China
| | - Fucheng Lin
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou, China
| | - Jianping Lu
- State Key Laboratory for Rice Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang University, Hangzhou, China
- *Correspondence: Jianping Lu,
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17
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Guo X, Niemi NM, Coon JJ, Pagliarini DJ. Integrative proteomics and biochemical analyses define Ptc6p as the Saccharomyces cerevisiae pyruvate dehydrogenase phosphatase. J Biol Chem 2017; 292:11751-11759. [PMID: 28539364 DOI: 10.1074/jbc.m117.787341] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/12/2017] [Indexed: 01/27/2023] Open
Abstract
The pyruvate dehydrogenase complex (PDC) is the primary metabolic checkpoint connecting glycolysis and mitochondrial oxidative phosphorylation and is important for maintaining cellular and organismal glucose homeostasis. Phosphorylation of the PDC E1 subunit was identified as a key inhibitory modification in bovine tissue ∼50 years ago, and this regulatory process is now known to be conserved throughout evolution. Although Saccharomyces cerevisiae is a pervasive model organism for investigating cellular metabolism and its regulation by signaling processes, the phosphatase(s) responsible for activating the PDC in S. cerevisiae has not been conclusively defined. Here, using comparative mitochondrial phosphoproteomics, analyses of protein-protein interactions by affinity enrichment-mass spectrometry, and in vitro biochemistry, we define Ptc6p as the primary PDC phosphatase in S. cerevisiae Our analyses further suggest additional substrates for related S. cerevisiae phosphatases and describe the overall phosphoproteomic changes that accompany mitochondrial respiratory dysfunction. In summary, our quantitative proteomics and biochemical analyses have identified Ptc6p as the primary-and likely sole-S. cerevisiae PDC phosphatase, closing a key knowledge gap about the regulation of yeast mitochondrial metabolism. Our findings highlight the power of integrative omics and biochemical analyses for annotating the functions of poorly characterized signaling proteins.
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Affiliation(s)
- Xiao Guo
- Morgridge Institute for Research, Madison, Wisconsin 53715; Departments of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Natalie M Niemi
- Morgridge Institute for Research, Madison, Wisconsin 53715; Departments of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, Wisconsin 53715; Departments of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706; Genome Center of Wisconsin, Madison, Wisconsin 53706; Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, Wisconsin 53715; Departments of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706.
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18
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González Flores M, Rodríguez ME, Oteiza JM, Barbagelata RJ, Lopes CA. Physiological characterization of Saccharomyces uvarum and Saccharomyces eubayanus from Patagonia and their potential for cidermaking. Int J Food Microbiol 2017; 249:9-17. [PMID: 28271856 DOI: 10.1016/j.ijfoodmicro.2017.02.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/09/2017] [Accepted: 02/28/2017] [Indexed: 11/16/2022]
Abstract
A diversity of yeast strains belonging to the cryotolerant fermentative species S. uvarum and S. eubayanus have been recovered from natural habitats and traditional fermentations in North Patagonia. The aim of this work was to evaluate the most relevant physiological features in a set of Patagonian strains belonging to S. uvarum and S. eubayanus, in order to analyze their potentiality to be used as starter cultures for cidermaking elaborated at low temperature. We evidenced that S. uvarum strains isolated from natural habitats (Araucaria araucana bark) showed similar physiological features to S. eubayanus strains obtained from the same habitat, and different from S. uvarum strains from fermentative environments (apple chichas). We also confirm the capacity of S. uvarum to produce high glycerol levels, low acetic acid and elevated production of the higher alcohol 2-phenylethanol and 2-phenylethyl acetate and demonstrated similar properties in S. eubayanus. Finally, we evidenced for the first time the antagonistic activity of S. eubayanus and selected three strains (two S. uvarum and one S. eubayanus) bearing the best combination of features to be used as a starter culture in cidermaking.
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Affiliation(s)
- Melisa González Flores
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas, PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina - Universidad Nacional del Comahue, Buenos Aires 1400, (8300), Neuquén, Argentina
| | - María Eugenia Rodríguez
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas, PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina - Universidad Nacional del Comahue, Buenos Aires 1400, (8300), Neuquén, Argentina; Facultad de Ciencias Médicas, Universidad Nacional del Comahue, Argentina
| | - Juan Martín Oteiza
- Centro de Investigación y Asistencia Técnica a la Industria (CIATI) - CONICET, Argentina
| | - Raúl Jorge Barbagelata
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas, PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina - Universidad Nacional del Comahue, Buenos Aires 1400, (8300), Neuquén, Argentina
| | - Christian Ariel Lopes
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas, PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina - Universidad Nacional del Comahue, Buenos Aires 1400, (8300), Neuquén, Argentina; Facultad de Ciencias Agrarias, Universidad Nacional del Comahue, Argentina.
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19
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Vannini C, Carpentieri A, Salvioli A, Novero M, Marsoni M, Testa L, de Pinto MC, Amoresano A, Ortolani F, Bracale M, Bonfante P. An interdomain network: the endobacterium of a mycorrhizal fungus promotes antioxidative responses in both fungal and plant hosts. THE NEW PHYTOLOGIST 2016; 211:265-275. [PMID: 26914272 DOI: 10.1111/nph.13895] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 01/12/2016] [Indexed: 06/05/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are obligate plant biotrophs that may contain endobacteria in their cytoplasm. Genome sequencing of Candidatus Glomeribacter gigasporarum revealed a reduced genome and dependence on the fungal host. RNA-seq analysis of the AMF Gigaspora margarita in the presence and absence of the endobacterium indicated that endobacteria have an important role in the fungal pre-symbiotic phase by enhancing fungal bioenergetic capacity. To improve the understanding of fungal-endobacterial interactions, iTRAQ (isobaric tags for relative and absolute quantification) quantitative proteomics was used to identify differentially expressed proteins in G. margarita germinating spores with endobacteria (B+), without endobacteria in the cured line (B-) and after application of the synthetic strigolactone GR24. Proteomic, transcriptomic and biochemical data identified several fungal and bacterial proteins involved in interspecies interactions. Endobacteria influenced fungal growth, calcium signalling and metabolism. The greatest effects were on fungal primary metabolism and respiration, which was 50% higher in B+ than in B-. A shift towards pentose phosphate metabolism was detected in B-. Quantification of carbonylated proteins indicated that the B- line had higher oxidative stress levels, which were also observed in two host plants. This study shows that endobacteria generate a complex interdomain network that affects AMF and fungal-plant interactions.
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Affiliation(s)
- Candida Vannini
- Department of Biotechnology and Life Science, Università dell'Insubria, via J.H. Dunant 3, I-21100, Varese, Italy
| | - Andrea Carpentieri
- Department of Chemical Sciences, Università di Napoli 'Federico II', via Cintia 4, I-80126, Napoli, Italy
| | - Alessandra Salvioli
- Department of Life Sciences and Systems Biology, Università di Torino, viale Mattioli 25, I-10125, Torino, Italy
| | - Mara Novero
- Department of Life Sciences and Systems Biology, Università di Torino, viale Mattioli 25, I-10125, Torino, Italy
| | - Milena Marsoni
- Department of Biotechnology and Life Science, Università dell'Insubria, via J.H. Dunant 3, I-21100, Varese, Italy
| | - Lorenzo Testa
- Department of Biotechnology and Life Science, Università dell'Insubria, via J.H. Dunant 3, I-21100, Varese, Italy
| | - Maria Concetta de Pinto
- Department of Biology, Università di Bari 'Aldo Moro', via E. Orabona 4, I-70125, Bari, Italy
| | - Angela Amoresano
- Department of Chemical Sciences, Università di Napoli 'Federico II', via Cintia 4, I-80126, Napoli, Italy
| | - Francesca Ortolani
- Department of Biotechnology and Life Science, Università dell'Insubria, via J.H. Dunant 3, I-21100, Varese, Italy
| | - Marcella Bracale
- Department of Biotechnology and Life Science, Università dell'Insubria, via J.H. Dunant 3, I-21100, Varese, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, Università di Torino, viale Mattioli 25, I-10125, Torino, Italy
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20
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Kim J, Oh J, Sung GH. MAP Kinase Hog1 Regulates Metabolic Changes Induced by Hyperosmotic Stress. Front Microbiol 2016; 7:732. [PMID: 27242748 PMCID: PMC4870262 DOI: 10.3389/fmicb.2016.00732] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/02/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jiyoung Kim
- Institute for Bio-Medical Convergence, International St. Mary's Hospital and College of Medicine, Catholic Kwandong UniversityIncheon, Korea; Institute of Life Science and Biotechnology, Sungkyunkwan UniversitySuwon, Korea
| | - Junsang Oh
- College of Pharmacy, Chung-Ang University Seoul, Korea
| | - Gi-Ho Sung
- Institute for Bio-Medical Convergence, International St. Mary's Hospital and College of Medicine, Catholic Kwandong University Incheon, Korea
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21
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Wang ZK, Wang J, Liu J, Ying SH, Peng XJ, Feng MG. Proteomic and Phosphoproteomic Insights into a Signaling Hub Role for Cdc14 in Asexual Development and Multiple Stress Responses in Beauveria bassiana. PLoS One 2016; 11:e0153007. [PMID: 27055109 PMCID: PMC4824431 DOI: 10.1371/journal.pone.0153007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 03/22/2016] [Indexed: 11/18/2022] Open
Abstract
Cdc14 is a dual-specificity phosphatase that regulates nuclear behavior by dephosphorylating phosphotyrosine and phosphoserine/phosphothreonine in fungi. Previously, Cdc14 was shown to act as a positive regulator of cytokinesis, asexual development and multiple stress responses in Beauveria bassiana, a fungal insect pathogen. This study seeks to gain deep insight into a pivotal role of Cdc14 in the signaling network of B. bassiana by analyzing the Cdc14-specific proteome and phosphoproteome generated by the 8-plex iTRAQ labeling and MS/MS analysis of peptides and phosphopeptides. Under normal conditions, 154 proteins and 86 phosphorylation sites in 67 phosphoproteins were upregulated in Δcdc14 versus wild-type, whereas 117 proteins and 85 phosphorylation sites in 58 phosphoproteins were significantly downregulated. Co-cultivation of Δcdc14 with NaCl (1 M), H2O2 (3 mM) and Congo red (0.15 mg/ml) resulted in the upregulation / downregulation of 23/63, 41/39 and 79/79 proteins and of 127/112, 52/47 and 105/226 phosphorylation sites in 85/92, 45/36 and 79/146 phosphoproteins, respectively. Bioinformatic analyses revealed that Cdc14 could participate in many biological and cellular processes, such as carbohydrate metabolism, glycerophospholipid metabolism, the MAP Kinase signaling pathway, and DNA conformation, by regulating protein expression and key kinase phosphorylation in response to different environmental cues. These indicate that in B. bassiana, Cdc14 is a vital regulator of not only protein expression but also many phosphorylation events involved in developmental and stress-responsive pathways. Fourteen conserved and novel motifs were identified in the fungal phosphorylation events.
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Affiliation(s)
- Zhi-Kang Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jie Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jing Liu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiao-Jun Peng
- Jingjie PTM Biolabs (Hangzhou) Co., Ltd., Hangzhou, 310018, China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- * E-mail:
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22
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Xia M, Broek JAC, Jouroukhin Y, Schoenfelder J, Abazyan S, Jaaro-Peled H, Sawa A, Bahn S, Pletnikov M. Cell Type-Specific Effects of Mutant DISC1: A Proteomics Study. MOLECULAR NEUROPSYCHIATRY 2016; 2:28-36. [PMID: 27606318 DOI: 10.1159/000444587] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/08/2016] [Indexed: 12/19/2022]
Abstract
Despite the recent progress in psychiatric genetics, very few studies have focused on genetic risk factors in glial cells that, compared to neurons, can manifest different molecular pathologies underlying psychiatric disorders. In order to address this issue, we studied the effects of mutant disrupted in schizophrenia 1 (DISC1), a genetic risk factor for schizophrenia, in cultured primary neurons and astrocytes using an unbiased mass spectrometry-based proteomic approach. We found that selective expression of mutant DISC1 in neurons affects a wide variety of proteins predominantly involved in neuronal development (e.g., SOX1) and vesicular transport (Rab proteins), whereas selective expression of mutant DISC1 in astrocytes produces changes in the levels of mitochondrial (GDPM), nuclear (TMM43) and cell adhesion (ECM2) proteins. The present study demonstrates that DISC1 variants can perturb distinct molecular pathways in a cell type-specific fashion to contribute to psychiatric disorders through heterogenic effects in diverse brain cells.
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Affiliation(s)
- Meng Xia
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Md., USA; Preclinical College, Guangxi University of Chinese Medicine, Nanning, PR China
| | - Jantine A C Broek
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Yan Jouroukhin
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Jeannine Schoenfelder
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Sofya Abazyan
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Hanna Jaaro-Peled
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Akira Sawa
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Md., USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Sabine Bahn
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Mikhail Pletnikov
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Md., USA; Departments of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Md., USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Md., USA; Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md., USA
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23
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RNA binding protein Pub1p regulates glycerol production and stress tolerance by controlling Gpd1p activity during winemaking. Appl Microbiol Biotechnol 2016; 100:5017-27. [DOI: 10.1007/s00253-016-7340-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/14/2016] [Accepted: 01/17/2016] [Indexed: 12/18/2022]
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24
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Chen Z, Zheng Z, Yi C, Wang F, Niu Y, Li H. Intracellular metabolic changes in Saccharomyces cerevisiae and promotion of ethanol tolerance during the bioethanol fermentation process. RSC Adv 2016. [DOI: 10.1039/c6ra19254h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
During the batch bioethanol fermentation process, although Saccharomyces cerevisiae cells are challenged by accumulated ethanol, our previous work showed that the ethanol tolerance of S. cerevisiae increased as fermentation time increased.
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Affiliation(s)
- Ze Chen
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Zhou Zheng
- Key Laboratory of Marine Bioactive Substance
- The First Institute of Oceanography
- State Oceanic Administration (SOA)
- Qingdao 266061
- China
| | - Chenfeng Yi
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Fenglian Wang
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Yuanpu Niu
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Hao Li
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
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Effelsberg D, Cruz-Zaragoza LD, Tonillo J, Schliebs W, Erdmann R. Role of Pex21p for Piggyback Import of Gpd1p and Pnc1p into Peroxisomes of Saccharomyces cerevisiae. J Biol Chem 2015; 290:25333-42. [PMID: 26276932 DOI: 10.1074/jbc.m115.653451] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Indexed: 01/30/2023] Open
Abstract
Proteins designated for peroxisomal protein import harbor one of two common peroxisomal targeting signals (PTS). In the yeast Saccharomyces cerevisiae, the oleate-induced PTS2-dependent import of the thiolase Fox3p into peroxisomes is conducted by the soluble import receptor Pex7p in cooperation with the auxiliary Pex18p, one of two supposedly redundant PTS2 co-receptors. Here, we report on a novel function for the co-receptor Pex21p, which cannot be fulfilled by Pex18p. The data establish Pex21p as a general co-receptor in PTS2-dependent protein import, whereas Pex18p is especially important for oleate-induced import of PTS2 proteins. The glycerol-producing PTS2 protein glycerol-3-phosphate dehydrogenase Gpd1p shows a tripartite localization in peroxisomes, in the cytosol, and in the nucleus under osmotic stress conditions. We show the following: (i) Pex21p is required for peroxisomal import of Gpd1p as well as a key enzyme of the NAD(+) salvage pathway, Pnc1p; (ii) Pnc1p, a nicotinamidase without functional PTS2, is co-imported into peroxisomes by piggyback transport via Gpd1p. Moreover, the specific transport of these two enzymes into peroxisomes suggests a novel regulatory role for peroxisomes under various stress conditions.
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Affiliation(s)
- Daniel Effelsberg
- From the Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, and
| | | | - Jason Tonillo
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Wolfgang Schliebs
- From the Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, and
| | - Ralf Erdmann
- From the Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, and
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Duskova M, Borovikova D, Herynkova P, Rapoport A, Sychrova H. The role of glycerol transporters in yeast cells in various physiological and stress conditions. FEMS Microbiol Lett 2014; 362:1-8. [PMID: 25673653 DOI: 10.1093/femsle/fnu041] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Small and uncharged glycerol is an important molecule for yeast metabolism and osmoadaptation. Using a series of S. cerevisiae BY4741-derived mutants lacking genes encoding a glycerol exporter (Fps1p) and/or importer (Stl1p) and/or the last kinase of the HOG pathway (Hog1p), we studied their phenotypes and various physiological characteristics with the aim of finding new roles for glycerol transporters. Though the triple mutant hog1Δ stl1Δ fps1Δ was viable, it was highly sensitive to various stresses. Our results showed that the function of both Stl1p and Fps1p transporters contributes to the cell ability to survive during the transfer into the state of anhydrobiosis, and that the deletion of FPS1 decreases the cell's tolerance of hyperosmotic stress. The deletion of STL1 results in a slight increase in cell size and in a substantial increase in intracellular pH. Taken together, our results suggest that the fluxes of glycerol in both directions across the plasma membrane exist in yeast cells simultaneously, and the export or import predominates according to the actual specific conditions.
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Affiliation(s)
- Michala Duskova
- Department of Membrane Transport, Institute of Physiology Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 14220 Prague, Czech Republic
| | - Diana Borovikova
- Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, LV-1586 Riga, Latvia
| | - Pavla Herynkova
- Department of Membrane Transport, Institute of Physiology Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 14220 Prague, Czech Republic
| | - Alexander Rapoport
- Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, LV-1586 Riga, Latvia
| | - Hana Sychrova
- Department of Membrane Transport, Institute of Physiology Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 14220 Prague, Czech Republic
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27
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Knudsen JD, Carlquist M, Gorwa-Grauslund M. NADH-dependent biosensor in Saccharomyces cerevisiae: principle and validation at the single cell level. AMB Express 2014; 4:81. [PMID: 25401080 PMCID: PMC4230897 DOI: 10.1186/s13568-014-0081-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 10/15/2014] [Indexed: 01/28/2023] Open
Abstract
A reporter system was constructed to measure perturbations in the NADH/NAD+ co-factor balance in yeast, by using the green fluorescent protein gene under the control of the GPD2 promoter that is induced under conditions of excess of NADH. High fluorescence levels were obtained in a glycerol 3-phosphate dehydrogenase double deletion strain (gpd1Δgpd2Δ), which is deficient in the ability to regenerate NAD+ via glycerol formation. The responsiveness of the reporter system to externally induced perturbations in NADH oxidation was also evaluated in the gpd1Δgpd2Δ strain background by addition of acetoin, as well as by introduction of a set of heterologous xylose reductases (XRs) having different selectivities for NADH. Addition of acetoin during cell proliferation under oxygen-limited conditions resulted in a more than 2-fold decrease in mean fluorescence intensity as compared to the control experiment. Strains carrying XRs with different selectivities for NADH could be distinguished at the single cell level, so that the XR with the highest selectivity for NADH displayed the lowest fluorescence. In conclusion, the designed system successfully allowed for monitoring perturbations in the cellular redox metabolism caused by environmental changes, or by heterologous gene expression. The reporter system displayed high resolution in distinguishing cytosolic NADH oxidation capacity and hence has potential to be used for high-throughput screening based on the fluorescence of single cells.
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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.
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Affiliation(s)
- Carmine Landi
- Dep. Ingegneria Industriale, Università Di Salerno, Via Giovanni Paolo II, 132 Fisciano, 84084, Salerno, Italy
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Adaptive response and tolerance to sugar and salt stress in the food yeast Zygosaccharomyces rouxii. Int J Food Microbiol 2014; 185:140-57. [DOI: 10.1016/j.ijfoodmicro.2014.05.015] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 04/18/2014] [Accepted: 05/04/2014] [Indexed: 11/21/2022]
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Jordà J, de Jesus SS, Peltier S, Ferrer P, Albiol J. Metabolic flux analysis of recombinant Pichia pastoris growing on different glycerol/methanol mixtures by iterative fitting of NMR-derived 13C-labelling data from proteinogenic amino acids. N Biotechnol 2014; 31:120-32. [DOI: 10.1016/j.nbt.2013.06.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 06/25/2013] [Accepted: 06/28/2013] [Indexed: 02/06/2023]
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Abstract
Overexpression of a foreign protein may negatively affect several cell growth parameters, as well as cause cellular stress. Central (or core) metabolism plays a crucial role since it supplies energy, reduction equivalents, and precursor molecules for the recombinant product, cell's maintenance, and growth needs. However, the number of quantitative physiology studies of the impact of recombinant protein production on the central metabolic pathways of yeast cell factories has been traditionally rather limited, thereby hampering the application of rational strain engineering strategies targeting central metabolism.The development and application of quantitative physiology and modelling tools and methodologies is allowing for a systems-level understanding of the effect of bioprocess parameters such as growth rate, temperature, oxygen availability, and substrate(s) choice on metabolism, and its subsequent interactions with recombinant protein synthesis, folding, and secretion.Here, we review the recent developments and applications of (13)C-based metabolic flux analysis ((13)C-MFA) of Pichia pastoris and the gained understanding of the metabolic behavior of this yeast in recombinant protein production bioprocesses. We also discuss the potential of multilevel studies integrating (13)C-MFA with other omics analyses, as well as future perspectives on the metabolic modelling approaches to study and design metabolic engineering strategies for improved protein production.
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Affiliation(s)
- Pau Ferrer
- Escola d'Enginyeria, Edifici Q, Universitat Autònoma de Barcelona, Campus de Bellaterra, 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain,
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32
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Microbial Conversion of Waste Glycerol from Biodiesel Production into Value-Added Products. ENERGIES 2013. [DOI: 10.3390/en6094739] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Petelenz-Kurdziel E, Kuehn C, Nordlander B, Klein D, Hong KK, Jacobson T, Dahl P, Schaber J, Nielsen J, Hohmann S, Klipp E. Quantitative analysis of glycerol accumulation, glycolysis and growth under hyper osmotic stress. PLoS Comput Biol 2013; 9:e1003084. [PMID: 23762021 PMCID: PMC3677637 DOI: 10.1371/journal.pcbi.1003084] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 04/19/2013] [Indexed: 11/18/2022] Open
Abstract
We provide an integrated dynamic view on a eukaryotic osmolyte system, linking signaling with regulation of gene expression, metabolic control and growth. Adaptation to osmotic changes enables cells to adjust cellular activity and turgor pressure to an altered environment. The yeast Saccharomyces cerevisiae adapts to hyperosmotic stress by activating the HOG signaling cascade, which controls glycerol accumulation. The Hog1 kinase stimulates transcription of genes encoding enzymes required for glycerol production (Gpd1, Gpp2) and glycerol import (Stl1) and activates a regulatory enzyme in glycolysis (Pfk26/27). In addition, glycerol outflow is prevented by closure of the Fps1 glycerol facilitator. In order to better understand the contributions to glycerol accumulation of these different mechanisms and how redox and energy metabolism as well as biomass production are maintained under such conditions we collected an extensive dataset. Over a period of 180 min after hyperosmotic shock we monitored in wild type and different mutant cells the concentrations of key metabolites and proteins relevant for osmoadaptation. The dataset was used to parameterize an ODE model that reproduces the generated data very well. A detailed computational analysis using time-dependent response coefficients showed that Pfk26/27 contributes to rerouting glycolytic flux towards lower glycolysis. The transient growth arrest following hyperosmotic shock further adds to redirecting almost all glycolytic flux from biomass towards glycerol production. Osmoadaptation is robust to loss of individual adaptation pathways because of the existence and upregulation of alternative routes of glycerol accumulation. For instance, the Stl1 glycerol importer contributes to glycerol accumulation in a mutant with diminished glycerol production capacity. In addition, our observations suggest a role for trehalose accumulation in osmoadaptation and that Hog1 probably directly contributes to the regulation of the Fps1 glycerol facilitator. Taken together, we elucidated how different metabolic adaptation mechanisms cooperate and provide hypotheses for further experimental studies. Osmotic changes are common environmental challenges for cells, even in multi-cellular organisms, having led to sophisticated adaptation mechanisms. In order to adapt to hyperosmotic stress, yeast cells accumulate glycerol. This is achieved by short-term responses involving metabolic and transmembrane transport changes as well as long-term transcriptional responses. By integrating experimentation and simulation of a mathematical model we resolve the quantitative and temporal characteristics of different processes contributing to glycerol accumulation. We show that osmoadaptation prioritizes the redox and energy balance in glycolysis while rerouting flux from biomass to glycerol production. We further show that the glycerol accumulation network provides osmoadaptation with robustness by compensating for the loss of certain nodes and with the flexibility necessary for responding to different stress situations. Finally we provide novel insight into the roles of transport processes in glycerol accumulation and evidence that trehalose may play a role in yeast osmoadaptation. The present work provides for the first time an integrated dynamic view on a eukaryotic osmolyte system and links signaling with regulation of gene expression and metabolic control.
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Affiliation(s)
| | - Clemens Kuehn
- Theoretical Biophysics, Humboldt-Universität Berlin, Berlin, Germany
| | - Bodil Nordlander
- Department of Chemistry and Molecular Biology/Microbiology, University of Gothenburg, Göteborg, Sweden
| | - Dagmara Klein
- Department of Chemistry and Molecular Biology/Microbiology, University of Gothenburg, Göteborg, Sweden
| | - Kuk-Ki Hong
- Systems Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen, Göteborg, Sweden
| | - Therese Jacobson
- Department of Chemistry and Molecular Biology/Microbiology, University of Gothenburg, Göteborg, Sweden
| | - Peter Dahl
- Department of Chemistry and Molecular Biology/Microbiology, University of Gothenburg, Göteborg, Sweden
| | - Jörg Schaber
- Theoretical Biophysics, Humboldt-Universität Berlin, Berlin, Germany
- Institute for Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Jens Nielsen
- Systems Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen, Göteborg, Sweden
| | - Stefan Hohmann
- Department of Chemistry and Molecular Biology/Microbiology, University of Gothenburg, Göteborg, Sweden
- * E-mail: (SH); (EK)
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität Berlin, Berlin, Germany
- * E-mail: (SH); (EK)
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34
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Pagliardini J, Hubmann G, Alfenore S, Nevoigt E, Bideaux C, Guillouet SE. The metabolic costs of improving ethanol yield by reducing glycerol formation capacity under anaerobic conditions in Saccharomyces cerevisiae. Microb Cell Fact 2013; 12:29. [PMID: 23537043 PMCID: PMC3639890 DOI: 10.1186/1475-2859-12-29] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 02/24/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Finely regulating the carbon flux through the glycerol pathway by regulating the expression of the rate controlling enzyme, glycerol-3-phosphate dehydrogenase (GPDH), has been a promising approach to redirect carbon from glycerol to ethanol and thereby increasing the ethanol yield in ethanol production. Here, strains engineered in the promoter of GPD1 and deleted in GPD2 were used to investigate the possibility of reducing glycerol production of Saccharomyces cerevisiae without jeopardising its ability to cope with process stress during ethanol production. For this purpose, the mutant strains TEFmut7 and TEFmut2 with different GPD1 residual expression were studied in Very High Ethanol Performance (VHEP) fed-batch process under anaerobic conditions. RESULTS Both strains showed a drastic reduction of the glycerol yield by 44 and 61% while the ethanol yield improved by 2 and 7% respectively. TEFmut2 strain showing the highest ethanol yield was accompanied by a 28% reduction of the biomass yield. The modulation of the glycerol formation led to profound redox and energetic changes resulting in a reduction of the ATP yield (YATP) and a modulation of the production of organic acids (acetate, pyruvate and succinate). Those metabolic rearrangements resulted in a loss of ethanol and stress tolerance of the mutants, contrarily to what was previously observed under aerobiosis. CONCLUSIONS This work demonstrates the potential of fine-tuned pathway engineering, particularly when a compromise has to be found between high product yield on one hand and acceptable growth, productivity and stress resistance on the other hand. Previous study showed that, contrarily to anaerobiosis, the resulting gain in ethanol yield was accompanied with no loss of ethanol tolerance under aerobiosis. Moreover those mutants were still able to produce up to 90 gl-1 ethanol in an anaerobic SSF process. Fine tuning metabolic strategy may then open encouraging possibilities for further developing robust strains with improved ethanol yield.
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Affiliation(s)
- Julien Pagliardini
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Av. de Rangueil, F-31077 Toulouse, France INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, Toulouse F-31400, France
| | - Georg Hubmann
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31 - bus 2438, Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31 - bus 2438, Heverlee, Flanders B-3001, Belgium
| | - Sandrine Alfenore
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Av. de Rangueil, F-31077 Toulouse, France INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, Toulouse F-31400, France
| | - Elke Nevoigt
- School of Engineering and Science, Jacobs University gGmbH, Campus Ring 1, Bremen 28759, Germany
| | - Carine Bideaux
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Av. de Rangueil, F-31077 Toulouse, France INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, Toulouse F-31400, France
| | - Stephane E Guillouet
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Av. de Rangueil, F-31077 Toulouse, France INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, Toulouse F-31400, France
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35
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Reciprocal phosphorylation of yeast glycerol-3-phosphate dehydrogenases in adaptation to distinct types of stress. Mol Cell Biol 2012; 32:4705-17. [PMID: 22988299 DOI: 10.1128/mcb.00897-12] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic cells have evolved mechanisms for ensuring growth and survival in the face of stress caused by a fluctuating environment. Saccharomyces cerevisiae has two homologous glycerol-3-phosphate dehydrogenases, Gpd1 and Gpd2, that are required to endure various stresses, including hyperosmotic shock and hypoxia. These enzymes are only partially redundant, and their unique functions were attributed previously to differential transcriptional regulation and localization. We find that Gpd1 and Gpd2 are negatively regulated through phosphorylation by distinct kinases under reciprocal conditions. Gpd2 is phosphorylated by the AMP-activated protein kinase Snf1 to curtail glycerol production when nutrients are limiting. Gpd1, in contrast, is a target of TORC2-dependent kinases Ypk1 and Ypk2. Inactivation of Ypk1 by hyperosmotic shock results in dephosphorylation and activation of Gpd1, accelerating recovery through increased glycerol production. Gpd1 dephosphorylation acts synergistically with its transcriptional upregulation, enabling long-term growth at high osmolarity. Phosphorylation of Gpd1 and Gpd2 by distinct kinases thereby enables rapid adaptation to specific stress conditions. Introduction of phosphorylation motifs targeted by distinct kinases provides a general mechanism for functional specialization of duplicated genes during evolution.
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36
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Müller M, Mentel M, van Hellemond JJ, Henze K, Woehle C, Gould SB, Yu RY, van der Giezen M, Tielens AGM, Martin WF. Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol Mol Biol Rev 2012; 76:444-95. [PMID: 22688819 PMCID: PMC3372258 DOI: 10.1128/mmbr.05024-11] [Citation(s) in RCA: 505] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Major insights into the phylogenetic distribution, biochemistry, and evolutionary significance of organelles involved in ATP synthesis (energy metabolism) in eukaryotes that thrive in anaerobic environments for all or part of their life cycles have accrued in recent years. All known eukaryotic groups possess an organelle of mitochondrial origin, mapping the origin of mitochondria to the eukaryotic common ancestor, and genome sequence data are rapidly accumulating for eukaryotes that possess anaerobic mitochondria, hydrogenosomes, or mitosomes. Here we review the available biochemical data on the enzymes and pathways that eukaryotes use in anaerobic energy metabolism and summarize the metabolic end products that they generate in their anaerobic habitats, focusing on the biochemical roles that their mitochondria play in anaerobic ATP synthesis. We present metabolic maps of compartmentalized energy metabolism for 16 well-studied species. There are currently no enzymes of core anaerobic energy metabolism that are specific to any of the six eukaryotic supergroup lineages; genes present in one supergroup are also found in at least one other supergroup. The gene distribution across lineages thus reflects the presence of anaerobic energy metabolism in the eukaryote common ancestor and differential loss during the specialization of some lineages to oxic niches, just as oxphos capabilities have been differentially lost in specialization to anoxic niches and the parasitic life-style. Some facultative anaerobes have retained both aerobic and anaerobic pathways. Diversified eukaryotic lineages have retained the same enzymes of anaerobic ATP synthesis, in line with geochemical data indicating low environmental oxygen levels while eukaryotes arose and diversified.
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Affiliation(s)
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Jaap J. van Hellemond
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Katrin Henze
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Christian Woehle
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Sven B. Gould
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Re-Young Yu
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Mark van der Giezen
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Aloysius G. M. Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - William F. Martin
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
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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.
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Affiliation(s)
- Eugéne van Rensburg
- Department of Process Engineering, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
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Celton M, Goelzer A, Camarasa C, Fromion V, Dequin S. A constraint-based model analysis of the metabolic consequences of increased NADPH oxidation in Saccharomyces cerevisiae. Metab Eng 2012; 14:366-79. [PMID: 22709677 DOI: 10.1016/j.ymben.2012.03.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 01/22/2012] [Accepted: 03/16/2012] [Indexed: 11/28/2022]
Abstract
Controlling the amounts of redox cofactors to manipulate metabolic fluxes is emerging as a useful approach to optimizing byproduct yields in yeast biotechnological processes. Redox cofactors are extensively interconnected metabolites, so predicting metabolite patterns is challenging and requires in-depth knowledge of how the metabolic network responds to a redox perturbation. Our aim was to analyze comprehensively the metabolic consequences of increased cytosolic NADPH oxidation during yeast fermentation. Using a genetic device based on the overexpression of a modified 2,3-butanediol dehydrogenase catalyzing the NADPH-dependent reduction of acetoin into 2,3-butanediol, we increased the NADPH demand to between 8 and 40-fold the anabolic demand. We developed (i) a dedicated constraint-based model of yeast fermentation and (ii) a constraint-based modeling method based on the dynamical analysis of mass distribution to quantify the in vivo contribution of pathways producing NADPH to the maintenance of redox homeostasis. We report that yeast responds to NADPH oxidation through a gradual increase in the flux through the PP and acetate pathways, providing 80% and 20% of the NADPH demand, respectively. However, for the highest NADPH demand, the model reveals a saturation of the PP pathway and predicts an exchange between NADH and NADPH in the cytosol that may be mediated by the glycerol-DHA futile cycle. We also reveal the contribution of mitochondrial shuttles, resulting in a net production of NADH in the cytosol, to fine-tune the NADH/NAD(+) balance. This systems level study helps elucidate the physiological adaptation of yeast to NADPH perturbation. Our findings emphasize the robustness of yeast to alterations in NADPH metabolism and highlight the role of the glycerol-DHA cycle as a redox valve, providing additional NADPH from NADH under conditions of very high demand.
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Affiliation(s)
- Magalie Celton
- INRA, UMR1083, Sciences Pour l'Oenologie, 2 Place Viala, F-34060 Montpellier, France.
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Zooming in on Yeast Osmoadaptation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 736:293-310. [DOI: 10.1007/978-1-4419-7210-1_17] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Gpd1 and Gpd2 fine-tuning for sustainable reduction of glycerol formation in Saccharomyces cerevisiae. Appl Environ Microbiol 2011; 77:5857-67. [PMID: 21724879 DOI: 10.1128/aem.05338-11] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Gpd1 and Gpd2 are the two isoforms of glycerol 3-phosphate dehydrogenase (GPDH), which is the rate-controlling enzyme of glycerol formation in Saccharomyces cerevisiae. The two isoenzymes play crucial roles in osmoregulation and redox balancing. Past approaches to increase ethanol yield at the cost of reduced glycerol yield have most often been based on deletion of either one or two isogenes (GPD1 and GPD2). While single deletions of GPD1 or GPD2 reduced glycerol formation only slightly, the gpd1Δ gpd2Δ double deletion strain produced zero glycerol but showed an osmosensitive phenotype and abolished anaerobic growth. Our current approach has sought to generate "intermediate" phenotypes by reducing both isoenzyme activities without abolishing them. To this end, the GPD1 promoter was replaced in a gpd2Δ background by two lower-strength TEF1 promoter mutants. In the same manner, the activity of the GPD2 promoter was reduced in a gpd1Δ background. The resulting strains were crossed to obtain different combinations of residual GPD1 and GPD2 expression levels. Among our engineered strains we identified four candidates showing improved ethanol yields compared to the wild type. In contrast to a gpd1Δ gpd2Δ double-deletion strain, these strains were able to completely ferment the sugars under quasi-anaerobic conditions in both minimal medium and during simultaneous saccharification and fermentation (SSF) of liquefied wheat mash (wheat liquefact). This result implies that our strains can tolerate the ethanol concentration at the end of the wheat liquefact SSF (up to 90 g liter(-1)). Moreover, a few of these strains showed no significant reduction in osmotic stress tolerance compared to the wild type.
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Lenassi M, Zajc J, Gostinčar C, Gorjan A, Gunde-Cimerman N, Plemenitaš A. Adaptation of the glycerol-3-phosphate dehydrogenase Gpd1 to high salinities in the extremely halotolerant Hortaea werneckii and halophilic Wallemia ichthyophaga. Fungal Biol 2011; 115:959-70. [PMID: 21944208 DOI: 10.1016/j.funbio.2011.04.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 02/15/2011] [Accepted: 04/17/2011] [Indexed: 11/29/2022]
Abstract
We report the first identification and characterisation of the glycerol-3-phosphate dehydrogenase (GPD) genes from extremely halophilic fungi. The black ascomycetous yeast Hortaea werneckii and the non-melanised basidiomycetous fungus Wallemia ichthyophaga inhabit similar hypersaline environments, yet they have two different strategies of haloadaptation through Gpd1-regulated glycerol synthesis. The extremely halotolerant H. werneckii codes for two salt-inducible GPD1 genes that show similar gene transcription regulation and have 98% amino-acid sequence identity between paralogues; however, they have distinct effects when expressed heterologously in Saccharomyces cerevisiae gpd mutants. Only the HwGpd1B isoform complements the function of Gpd in the gpd1 mutant, whereas none of the Gpd1 isoforms can rescue the salt sensitivity of the gpd1gpd2 double mutant. The obligate halophile W. ichthyophaga codes for only one GPD1 orthologue, the transcription of which is less affected by salt when compared to the H. werneckii homologues. Heterologous expression of WiGPD1 in S. cerevisiae recovers halotolerance of the gpd1 and gpd1gpd2 mutant strains, which is probably due to the overall high amino-acid similarity of the Gpd1 protein in W. ichthyophaga and S. cerevisiae. Phylogenetic analysis of amino-acid sequences reveals that the evolutionary origins of all of these three novel enzymes correspond to the phylogeny of the fungal species from which the genes were identified.
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Affiliation(s)
- Metka Lenassi
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov Trg 2, SI-1000 Ljubljana, Slovenia.
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Qin Y, Johnson CH, Liu L, Chen J. Introduction of heterogeneous NADH reoxidation pathways into Torulopsis glabrata significantly increases pyruvate production efficiency. KOREAN J CHEM ENG 2011. [DOI: 10.1007/s11814-010-0483-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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The Dynamical Systems Properties of the HOG Signaling Cascade. JOURNAL OF SIGNAL TRANSDUCTION 2011; 2011:930940. [PMID: 21637384 PMCID: PMC3100117 DOI: 10.1155/2011/930940] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Revised: 10/19/2010] [Accepted: 11/12/2010] [Indexed: 01/06/2023]
Abstract
The High Osmolarity Glycerol (HOG) MAP kinase pathway in the budding yeast Saccharomyces cerevisiae is one of the best characterized model signaling pathways. The pathway processes external signals of increased osmolarity into appropriate physiological responses within the yeast cell. Recent advances in microfluidic technology coupled with quantitative modeling, and techniques from reverse systems engineering have allowed yet further insight into this already well-understood pathway. These new techniques are essential for understanding the dynamical processes at play when cells process external
stimuli into biological responses. They are widely applicable to other signaling pathways of interest. Here, we review the recent advances brought by these approaches in the context of understanding the dynamics of the HOG pathway signaling.
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Qin Y, Liu LM, Li CH, Xu S, Chen J. Accelerating glycolytic flux of Torulopsis glabrata CCTCC M202019 at high oxidoreduction potential created using potassium ferricyanide. Biotechnol Prog 2010; 26:1551-7. [PMID: 20886645 DOI: 10.1002/btpr.496] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Revised: 06/29/2010] [Indexed: 11/06/2022]
Abstract
This study aimed to increase the glycolytic flux of the multivitamin auxotrophic yeast Torulopsis glabrata by redirecting NADH oxidation from oxidative phosphorylation to membrane-bound ferric reductase. We added potassium ferricyanide as electron acceptor to T. glabrata culture broth at 20% dissolved oxygen (DO) concentration, which resulted in: (1) decreases in the NADH content, NADH/NAD(+) ratio, and ATP level of 45.3%, 60.3%, and 15.2%, respectively; (2) high activities of the key glycolytic enzymes hexokinase, phosphofructokinase, and pyruvate kinase, as well as high expression levels of the genes encoding these enzymes; and (3) increases in the specific glucose consumption rate and pyruvate yield of T. glabrata was by 45.5% and 23.1%, respectively. Our results showed that membrane-bound ferric reductase offers an alternative and efficient NADH oxidation pathway at lower DO concentration, which increases the glycolytic flux of T. glabrata.
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Affiliation(s)
- Yi Qin
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
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Bouwman J, Kiewiet J, Lindenbergh A, van Eunen K, Siderius M, Bakker BM. Metabolic regulation rather than de novo enzyme synthesis dominates the osmo-adaptation of yeast. Yeast 2010; 28:43-53. [DOI: 10.1002/yea.1819] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 07/19/2010] [Indexed: 11/09/2022] Open
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Xu S, Zhou J, Qin Y, Liu L, Chen J. Water-forming NADH oxidase protects Torulopsis glabrata against hyperosmotic stress. Yeast 2010; 27:207-16. [PMID: 20037925 DOI: 10.1002/yea.1745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A heterologous water-forming NADH oxidase was introduced into Torulopsis glabrata and the effect on cell growth under hyperosmotic conditions was investigated. Expression of the noxE gene from Lactococcus lactis NZ9000 in T. glabrata resulted in a marked decrease in the NADH : NAD+ ratio and higher activities of key enzymes in water-regenerating pathways, leading to an increase in intracellular water content. NaCl-induced reactive oxygen species production was also decreased by the introduction of NADH oxidase, resulting in a significant increase in the growth of T. glabrata under hyperosmotic stress conditions (3824 mOsmol/kg). The results indicated that the osmotolerance of cells can be enhanced by manipulating water-production pathways.
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Affiliation(s)
- Sha Xu
- State Key Laboratory of Food Science and School of Biotechnology and Key Technology and Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China
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Saliola M, D'Amici S, Sponziello M, Mancini P, Tassone P, Falcone C. The transdehydrogenase genes KlNDE1 and KlNDI1 regulate the expression of KlGUT2 in the yeast Kluyveromyces lactis. FEMS Yeast Res 2010; 10:518-26. [PMID: 20491935 DOI: 10.1111/j.1567-1364.2010.00631.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
KlNDE1 and KlNDI1 code for two inner mitochondrial membrane transdehydrogenases involved in the maintenance of the intracellular NAD(P)H redox balance. The function of these genes during the utilization of fermentative and respiratory carbon sources was studied. During growth in glucose, deletion of KlNDE1 and KlNDI1 led to an altered kinetic of ethanol and glycerol accumulation compared with the wild type; in addition, KlndiDelta was unable to grow in respiratory substrates. Northern analysis and GFP-fusion experiments showed that KlNDE1 and KlNDI1 regulate the expression of KlGUT2, a component of the glycerol-3-phosphate shuttle. Moreover, both genes seem to be involved in the biogenesis of the mitochondrial tubular network.
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Affiliation(s)
- Michele Saliola
- Department of Cell and Developmental Biology, University of Rome La Sapienza, Rome, Italy.
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Modulation of the glycerol and ethanol syntheses in the yeast Saccharomyces kudriavzevii differs from that exhibited by Saccharomyces cerevisiae and their hybrid. Food Microbiol 2010; 27:628-37. [PMID: 20510781 DOI: 10.1016/j.fm.2010.02.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 02/02/2010] [Accepted: 02/04/2010] [Indexed: 11/22/2022]
Abstract
In the last years there is an increasing demand to produce wines with higher glycerol levels and lower ethanol contents. The production of these compounds by yeasts is influenced by many environmental variables, and could be controlled by the choice of optimized cultivation conditions. The present work studies, in a wine model system, the effects of temperature, pH and sugar concentration on the glycerol and ethanol syntheses by yeasts Saccharomyces cerevisiae T73, the type strain of Saccharomyces kudriavzevii IFO 1802(T), and an interspecific hybrid between both species (W27), which was accomplished by the application of response surface methodology based in a central composite circumscribed design. Results show that carbon flux could be especially directed towards glycerol synthesis instead of ethanol at low pH, high sugar concentrations and low temperatures. In general, the non-wine yeast S. kudriavzevii produced higher glycerol levels and lower ethanol content than wine strains S. cerevisiae T73 and the hybrid W27, with specific and different glycerol production profiles as a function of temperature and pH. These results were congruent with the higher glycerol-3-phosphate dehydrogenase activities estimated for this species, chiefly at low temperatures (14 degrees C), which could explain why S. kudriavzevii is a cryotolerant yeast compared to S. cerevisiae.
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Jung S, Marelli M, Rachubinski RA, Goodlett DR, Aitchison JD. Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress. J Biol Chem 2009; 285:6739-49. [PMID: 20026609 DOI: 10.1074/jbc.m109.058552] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gpd1p is a cytosolic NAD(+)-dependent glycerol 3-phosphate dehydrogenase that also localizes to peroxisomes and plays an essential role in the cellular response to osmotic stress and a role in redox balance. Here, we show that Gpd1p is directed to peroxisomes by virtue of an N-terminal type 2 peroxisomal targeting signal (PTS2) in a Pex7p-dependent manner. Significantly, localization of Gpd1p to peroxisomes is dependent on the metabolic status of cells and the phosphorylation of aminoacyl residues adjacent to the targeting signal. Exposure of cells to osmotic stress induces changes in the subcellular distribution of Gpd1p to the cytosol and nucleus. This behavior is similar to Pnc1p, which is coordinately expressed with Gpd1p, and under conditions of cell stress changes its subcellular distribution from peroxisomes to the nucleus where it mediates chromatin silencing. Although peroxisomes are necessary for the beta-oxidation of fatty acids in yeast, the localization of Gpd1p to peroxisomes is not. Rather, shifts in the distribution of Gpd1p to different cellular compartments in response to changing cellular status suggests a role for Gpd1p in the spatial regulation of redox potential, a process critical to cell survival, especially under the complex stress conditions expected to occur in the wild.
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Affiliation(s)
- Sunhee Jung
- Institute for Systems Biology, Seattle, Washington 98103, USA
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CHEN XZ, FANG HY, RAO ZM, SHEN W, ZHUGE B, WANG ZX, ZHUGE J. Comparative Characterization of Genes Encoding Glycerol 3-phosphate Dehydrogenase From Candida glycerinogenes and Saccharomyces cerevisiae*. PROG BIOCHEM BIOPHYS 2009. [DOI: 10.3724/sp.j.1206.2008.00363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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