1
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Jashnsaz H, Neuert G. Phenotypic consequences of logarithmic signaling in MAPK stress response. iScience 2025; 28:111625. [PMID: 39886462 PMCID: PMC11780147 DOI: 10.1016/j.isci.2024.111625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 10/04/2024] [Accepted: 12/16/2024] [Indexed: 02/01/2025] Open
Abstract
How cells respond to dynamic environmental changes is crucial for understanding fundamental biological processes and cell physiology. In this study, we developed an experimental and quantitative analytical framework to explore how dynamic stress gradients that change over time regulate cellular volume, signaling activation, and growth phenotypes. Our findings reveal that gradual stress conditions substantially enhance cell growth compared to conventional acute stress. This growth advantage correlates with a minimal reduction in cell volume dependent on the dynamic of stress. We explain the growth phenotype with our finding of a logarithmic signal transduction mechanism in the yeast mitogen-activated protein kinase (MAPK) osmotic stress response pathway. These insights into the interplay between gradual environments, cell volume change, dynamic cell signaling, and growth, advance our understanding of fundamental cellular processes in gradual stress environments.
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Affiliation(s)
- Hossein Jashnsaz
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN 37232, USA
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2
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Xie D, Lei Y, Sun Y, Li X, Zheng J. Regulation of fructose levels on carbon flow and metabolites in yeast during food fermentation. FOOD SCI TECHNOL INT 2025; 31:69-82. [PMID: 37259509 DOI: 10.1177/10820132231179495] [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] [Indexed: 06/02/2023]
Abstract
In this study, the effects of fructose levels on yeast growth, metabolic pathways and products, and redox status were investigated by simulated dough medium. The results showed that yeast was subjected to oxidative stress and damage under both sugar-free and high-fructose conditions. Yeast has a strong ability to metabolize pentose phosphate, trehalose, and tricarboxylic acid under sugar-free conditions. In the high fructose environment, yeast preferentially produced trehalose and glycerol in the early stage and gradually increased the metabolism of pentose phosphate in the later stage. Compared with the low fructose concentration, yeast had stronger pentose phosphate and tricarboxylic acid cycle (TCA) metabolism to ensure nicotinamide adenine dinucleotide phosphate (NADPH) and adenosine triphosphate (ATP) content in higher fructose levels. Therefore, sugar-free and high fructose levels affected the growth of yeast cells and yeast responded to fructose levels by regulating the metabolic carbon flow of glycolysis, pentose phosphate, trehalose, and TCA.
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Affiliation(s)
- Dongdong Xie
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan, China
| | - Yanan Lei
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan, China
| | - Yingqi Sun
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan, China
| | - Xing Li
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan, China
| | - Jiaxin Zheng
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan, China
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3
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Attfield PV. Crucial aspects of metabolism and cell biology relating to industrial production and processing of Saccharomyces biomass. Crit Rev Biotechnol 2023; 43:920-937. [PMID: 35731243 DOI: 10.1080/07388551.2022.2072268] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/27/2022] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
The multitude of applications to which Saccharomyces spp. are put makes these yeasts the most prolific of industrial microorganisms. This review considers biological aspects pertaining to the manufacture of industrial yeast biomass. It is proposed that the production of yeast biomass can be considered in two distinct but interdependent phases. Firstly, there is a cell replication phase that involves reproduction of cells by their transitions through multiple budding and metabolic cycles. Secondly, there needs to be a cell conditioning phase that enables the accrued biomass to withstand the physicochemical challenges associated with downstream processing and storage. The production of yeast biomass is not simply a case of providing sugar, nutrients, and other growth conditions to enable multiple budding cycles to occur. In the latter stages of culturing, it is important that all cells are induced to complete their current budding cycle and subsequently enter into a quiescent state engendering robustness. Both the cell replication and conditioning phases need to be optimized and considered in concert to ensure good biomass production economics, and optimum performance of industrial yeasts in food and fermentation applications. Key features of metabolism and cell biology affecting replication and conditioning of industrial Saccharomyces are presented. Alternatives for growth substrates are discussed, along with the challenges and prospects associated with defining the genetic bases of industrially important phenotypes, and the generation of new yeast strains."I must be cruel only to be kind: Thus bad begins, and worse remains behind." William Shakespeare: Hamlet, Act 3, Scene 4.
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4
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Gančytė G, Šimonis P, Stirkė A. Investigation of osmotic shock effect on pulsed electric field treated S. cerevisiae yeast cells. Sci Rep 2023; 13:10573. [PMID: 37386124 PMCID: PMC10310692 DOI: 10.1038/s41598-023-37719-4] [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: 05/16/2023] [Accepted: 06/26/2023] [Indexed: 07/01/2023] Open
Abstract
Pulsed electric field (PEF) treatment is known to cause plasma membrane permeabilization of microorganisms, an effect known as electroporation. PEF treatment is very attractive since it can achieve permeabilization with or without lethal damage in accordance with desired results. This study aimed to expand the accomplishment of electroporation outcomes by applying sudden post-PEF osmotic composition change of the media. Changes in yeast cells' viability, size and plasma membrane regeneration rate were evaluated. However, we still have questions about the intracellular biochemical processes responsible for plasma membrane recovery after electroporation. Our suggested candidate is the high osmolarity glycerol (HOG) kinase pathway. The HOG pathway in Saccharomyces cerevisiae yeasts is responsible for volume recovery after dangerous shape modifications and intracellular water disbalance caused by environmental osmotic pressure changes. Thus, we evaluated the HOG pathway inactivation effect on S. cerevisiae's reaction to PEF treatment. Results showed that Hog1 deficient S. cerevisiae cells were considerably more sensitive to electric field treatment, confirming a link between the HOG pathway and S. cerevisiae recovery process after electroporation. By suddenly changing the osmolarity of the media after PEF we influenced the cells' plasma membrane recovery rate, severity of permeabilization and survivability of yeast cells. Studies of electroporation in combination with various treatments might improve electric field application range, efficiency, and optimization of the process.
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Affiliation(s)
- Greta Gančytė
- Laboratory of Bioelectrics, Center for Physical Sciences and Technology, State Research Institute, Sauletekio Ave. 3, 10257, Vilnius, Lithuania.
| | - Povilas Šimonis
- Laboratory of Bioelectrics, Center for Physical Sciences and Technology, State Research Institute, Sauletekio Ave. 3, 10257, Vilnius, Lithuania
| | - Arūnas Stirkė
- Laboratory of Bioelectrics, Center for Physical Sciences and Technology, State Research Institute, Sauletekio Ave. 3, 10257, Vilnius, Lithuania
- Micro and Nanodevices Laboratory, Institute of Solid State Physics, University of Latvia, Kengaraga Str. 8, Riga, 1063, Latvia
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5
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Spolaor S, Rovetta M, Nobile MS, Cazzaniga P, Tisi R, Besozzi D. Modeling Calcium Signaling in S. cerevisiae Highlights the Role and Regulation of the Calmodulin-Calcineurin Pathway in Response to Hypotonic Shock. Front Mol Biosci 2022; 9:856030. [PMID: 35664674 PMCID: PMC9158465 DOI: 10.3389/fmolb.2022.856030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/04/2022] [Indexed: 01/17/2023] Open
Abstract
Calcium homeostasis and signaling processes in Saccharomyces cerevisiae, as well as in any eukaryotic organism, depend on various transporters and channels located on both the plasma and intracellular membranes. The activity of these proteins is regulated by a number of feedback mechanisms that act through the calmodulin-calcineurin pathway. When exposed to hypotonic shock (HTS), yeast cells respond with an increased cytosolic calcium transient, which seems to be conditioned by the opening of stretch-activated channels. To better understand the role of each channel and transporter involved in the generation and recovery of the calcium transient—and of their feedback regulations—we defined and analyzed a mathematical model of the calcium signaling response to HTS in yeast cells. The model was validated by comparing the simulation outcomes with calcium concentration variations before and during the HTS response, which were observed experimentally in both wild-type and mutant strains. Our results show that calcium normally enters the cell through the High Affinity Calcium influx System and mechanosensitive channels. The increase of the plasma membrane tension, caused by HTS, boosts the opening probability of mechanosensitive channels. This event causes a sudden calcium pulse that is rapidly dissipated by the activity of the vacuolar transporter Pmc1. According to model simulations, the role of another vacuolar transporter, Vcx1, is instead marginal, unless calcineurin is inhibited or removed. Our results also suggest that the mechanosensitive channels are subject to a calcium-dependent feedback inhibition, possibly involving calmodulin. Noteworthy, the model predictions are in accordance with literature results concerning some aspects of calcium homeostasis and signaling that were not specifically addressed within the model itself, suggesting that it actually depicts all the main cellular components and interactions that constitute the HTS calcium pathway, and thus can correctly reproduce the shaping of the calcium signature by calmodulin- and calcineurin-dependent complex regulations. The model predictions also allowed to provide an interpretation of different regulatory schemes involved in calcium handling in both wild-type and mutants yeast strains. The model could be easily extended to represent different calcium signals in other eukaryotic cells.
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Affiliation(s)
- Simone Spolaor
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
| | - Mattia Rovetta
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
| | - Marco S. Nobile
- Department of Environmental Sciences, Informatics and Statistics, Ca’ Foscari University of Venice, Venice, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre—B4, Milan, Italy
- SYSBIO/ISBE.IT Centre of Systems Biology, Milan, Italy
| | - Paolo Cazzaniga
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre—B4, Milan, Italy
- SYSBIO/ISBE.IT Centre of Systems Biology, Milan, Italy
- Department of Human and Social Sciences, University of Bergamo, Bergamo, Italy
| | - Renata Tisi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- *Correspondence: Renata Tisi, ; Daniela Besozzi,
| | - Daniela Besozzi
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre—B4, Milan, Italy
- SYSBIO/ISBE.IT Centre of Systems Biology, Milan, Italy
- *Correspondence: Renata Tisi, ; Daniela Besozzi,
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6
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Reith P, Braam S, Welkenhuysen N, Lecinski S, Shepherd J, MacDonald C, Leake MC, Hohmann S, Shashkova S, Cvijovic M. The Effect of Lithium on the Budding Yeast Saccharomyces cerevisiae upon Stress Adaptation. Microorganisms 2022; 10:590. [PMID: 35336166 PMCID: PMC8953283 DOI: 10.3390/microorganisms10030590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 02/05/2023] Open
Abstract
Lithium salts are used in the treatment of mood disorders, cancer, and Alzheimer's disease. It has been shown to prolong life span in several phyla; however, not yet in budding yeast. In our study, we investigate the influence of lithium on yeast cells' viability by characterizing protein aggregate formation, cell volume, and molecular crowding in the context of stress adaptation. While our data suggest a concentration-dependent growth inhibition caused by LiCl, we show an extended long-term survival rate as an effect of lithium addition upon glucose deprivation. We show that caloric restriction mitigates the negative impact of LiCl on cellular survival. Therefore, we suggest that lithium could affect glucose metabolism upon caloric restriction, which could explain the extended long-term survival observed in our study. We find furthermore that lithium chloride did not affect an immediate salt-induced Hsp104-dependent aggregate formation but cellular adaptation to H2O2 and acute glucose starvation. We presume that different salt types and concentrations interfere with effective Hsp104 recruitment or its ATP-dependent disaggregase activity as a response to salt stress. This work provides novel details of Li+ effect on live eukaryotic cells which may also be applicable in further research on the treatment of cancer, Alzheimer's, or other age-related diseases in humans.
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Affiliation(s)
- Patrick Reith
- Department of Mathematical Sciences, University of Gothenburg, 412 96 Gothenburg, Sweden; (P.R.); (S.B.); (N.W.)
- Department of Mathematical Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
| | - Svenja Braam
- Department of Mathematical Sciences, University of Gothenburg, 412 96 Gothenburg, Sweden; (P.R.); (S.B.); (N.W.)
- Department of Mathematical Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Niek Welkenhuysen
- Department of Mathematical Sciences, University of Gothenburg, 412 96 Gothenburg, Sweden; (P.R.); (S.B.); (N.W.)
- Department of Mathematical Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Sarah Lecinski
- Department of Physics, University of York, York YO10 5DD, UK; (S.L.); (J.S.); (M.C.L.)
| | - Jack Shepherd
- Department of Physics, University of York, York YO10 5DD, UK; (S.L.); (J.S.); (M.C.L.)
- Department of Biology, University of York, York YO10 5DD, UK;
| | - Chris MacDonald
- Department of Biology, University of York, York YO10 5DD, UK;
| | - Mark C. Leake
- Department of Physics, University of York, York YO10 5DD, UK; (S.L.); (J.S.); (M.C.L.)
- Department of Biology, University of York, York YO10 5DD, UK;
| | - Stefan Hohmann
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
| | - Sviatlana Shashkova
- Department of Mathematical Sciences, University of Gothenburg, 412 96 Gothenburg, Sweden; (P.R.); (S.B.); (N.W.)
- Department of Mathematical Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, University of Gothenburg, 412 96 Gothenburg, Sweden; (P.R.); (S.B.); (N.W.)
- Department of Mathematical Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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7
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Oliver SG. From Petri Plates to Petri Nets, a revolution in yeast biology. FEMS Yeast Res 2022; 22:foac008. [PMID: 35142857 PMCID: PMC8862034 DOI: 10.1093/femsyr/foac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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8
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Yaakoub H, Sanchez NS, Ongay-Larios L, Courdavault V, Calenda A, Bouchara JP, Coria R, Papon N. The high osmolarity glycerol (HOG) pathway in fungi †. Crit Rev Microbiol 2021; 48:657-695. [PMID: 34893006 DOI: 10.1080/1040841x.2021.2011834] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
While fungi are widely occupying nature, many species are responsible for devastating mycosis in humans. Such niche diversity explains how quick fungal adaptation is necessary to endow the capacity of withstanding fluctuating environments and to cope with host-imposed conditions. Among all the molecular mechanisms evolved by fungi, the most studied one is the activation of the phosphorelay signalling pathways, of which the high osmolarity glycerol (HOG) pathway constitutes one of the key molecular apparatus underpinning fungal adaptation and virulence. In this review, we summarize the seminal knowledge of the HOG pathway with its more recent developments. We specifically described the HOG-mediated stress adaptation, with a particular focus on osmotic and oxidative stress, and point out some lags in our understanding of its involvement in the virulence of pathogenic species including, the medically important fungi Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus, compared to the model yeast Saccharomyces cerevisiae. Finally, we also highlighted some possible applications of the HOG pathway modifications to improve the fungal-based production of natural products in the industry.
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Affiliation(s)
- Hajar Yaakoub
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
| | - Norma Silvia Sanchez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Vincent Courdavault
- EA2106 "Biomolécules et Biotechnologies Végétales", Université de Tours, Tours, France
| | | | | | - Roberto Coria
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Nicolas Papon
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
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9
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O' Neill JS, Hoyle NP, Robertson JB, Edgar RS, Beale AD, Peak-Chew SY, Day J, Costa ASH, Frezza C, Causton HC. Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis. Nat Commun 2020; 11:4706. [PMID: 32943618 PMCID: PMC7499178 DOI: 10.1038/s41467-020-18330-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/13/2020] [Indexed: 12/17/2022] Open
Abstract
Yeast physiology is temporally regulated, this becomes apparent under nutrient-limited conditions and results in respiratory oscillations (YROs). YROs share features with circadian rhythms and interact with, but are independent of, the cell division cycle. Here, we show that YROs minimise energy expenditure by restricting protein synthesis until sufficient resources are stored, while maintaining osmotic homeostasis and protein quality control. Although nutrient supply is constant, cells sequester and store metabolic resources via increased transport, autophagy and biomolecular condensation. Replete stores trigger increased H+ export which stimulates TORC1 and liberates proteasomes, ribosomes, chaperones and metabolic enzymes from non-membrane bound compartments. This facilitates translational bursting, liquidation of storage carbohydrates, increased ATP turnover, and the export of osmolytes. We propose that dynamic regulation of ion transport and metabolic plasticity are required to maintain osmotic and protein homeostasis during remodelling of eukaryotic proteomes, and that bioenergetic constraints selected for temporal organisation that promotes oscillatory behaviour.
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Affiliation(s)
- John S O' Neill
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | | | | | - Rachel S Edgar
- Molecular Virology, Department of Medicine, Imperial College, London, W2 1NY, UK
| | - Andrew D Beale
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - Jason Day
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, UK
| | - Ana S H Costa
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Helen C Causton
- Columbia University Medical Center, New York, NY, 10032, USA.
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10
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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: 7] [Impact Index Per Article: 1.4] [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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11
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The Aspergillus fumigatus Phosphoproteome Reveals Roles of High-Osmolarity Glycerol Mitogen-Activated Protein Kinases in Promoting Cell Wall Damage and Caspofungin Tolerance. mBio 2020; 11:mBio.02962-19. [PMID: 32019798 PMCID: PMC7002344 DOI: 10.1128/mbio.02962-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aspergillus fumigatus is an opportunistic human pathogen causing allergic reactions or systemic infections, such as invasive pulmonary aspergillosis in immunocompromised patients. The mitogen-activated protein kinase (MAPK) signaling pathways are essential for fungal adaptation to the human host. Fungal cell survival, fungicide tolerance, and virulence are highly dependent on the organization, composition, and function of the cell wall. Upon cell wall stress, MAPKs phosphorylate multiple target proteins involved in the remodeling of the cell wall. Here, we investigate the global phosphoproteome of the ΔsakA and ΔmpkCA. fumigatus and high-osmolarity glycerol (HOG) pathway MAPK mutants upon cell wall damage. This showed the involvement of the HOG pathway and identified novel protein kinases and transcription factors, which were confirmed by fungal genetics to be involved in promoting tolerance of cell wall damage. Our results provide understanding of how fungal signal transduction networks modulate the cell wall. This may also lead to the discovery of new fungicide drug targets to impact fungal cell wall function, fungicide tolerance, and virulence. The filamentous fungus Aspergillus fumigatus can cause a distinct set of clinical disorders in humans. Invasive aspergillosis (IA) is the most common life-threatening fungal disease of immunocompromised humans. The mitogen-activated protein kinase (MAPK) signaling pathways are essential to the adaptation to the human host. Fungal cell survival is highly dependent on the organization, composition, and function of the cell wall. Here, an evaluation of the global A. fumigatus phosphoproteome under cell wall stress caused by the cell wall-damaging agent Congo red (CR) revealed 485 proteins potentially involved in the cell wall damage response. Comparative phosphoproteome analyses with the ΔsakA, ΔmpkC, and ΔsakA ΔmpkC mutant strains from the osmotic stress MAPK cascades identify their additional roles during the cell wall stress response. Our phosphoproteomics allowed the identification of novel kinases and transcription factors (TFs) involved in osmotic stress and in the cell wall integrity (CWI) pathway. Our global phosphoproteome network analysis showed an enrichment for protein kinases, RNA recognition motif domains, and the MAPK signaling pathway. In contrast to the wild-type strain, there is an overall decrease of differentially phosphorylated kinases and phosphatases in ΔsakA, ΔmpkC, and ΔsakA ΔmpkC mutants. We constructed phosphomutants for the phosphorylation sites of several proteins differentially phosphorylated in the wild-type and mutant strains. For all the phosphomutants, there is an increase in the sensitivity to cell wall-damaging agents and a reduction in the MpkA phosphorylation upon CR stress, suggesting these phosphosites could be important for the MpkA modulation and CWI pathway regulation.
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12
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Sipiczki M. Yeast two- and three-species hybrids and high-sugar fermentation. Microb Biotechnol 2019; 12:1101-1108. [PMID: 30838806 PMCID: PMC6801140 DOI: 10.1111/1751-7915.13390] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/07/2019] [Accepted: 02/12/2019] [Indexed: 12/15/2022] Open
Abstract
The dominating strains of most sugar-based natural and industrial fermentations either belong to Saccharomyces cerevisiae and Saccharomyces uvarum or are their chimeric derivatives. Osmotolerance is an essential trait of these strains for industrial applications in which typically high concentrations of sugars are used. As the ability of the cells to cope with the hyperosmotic stress is under polygenic control, significant improvement can be expected from concerted modification of the activity of multiple genes or from creating new genomes harbouring positive alleles of strains of two or more species. In this review, the application of the methods of intergeneric and interspecies hybridization to fitness improvement of strains used under high-sugar fermentation conditions is discussed. By protoplast fusion and heterospecific mating, hybrids can be obtained that outperform the parental strains in certain technological parameters including osmotolerance. Spontaneous postzygotic genome evolution during mitotic propagation (GARMi) and meiosis after the breakdown of the sterility barrier by loss of MAT heterozygosity (GARMe) can be exploited for further improvement. Both processes result in derivatives of chimeric genomes, some of which can be superior both to the parental strains and to the hybrid. Three-species hybridization represents further perspectives.
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Affiliation(s)
- Matthias Sipiczki
- Department of Genetics and Applied MicrobiologyUniversity of DebrecenDebrecenHungary
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13
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Altenburg T, Goldenbogen B, Uhlendorf J, Klipp E. Osmolyte homeostasis controls single-cell growth rate and maximum cell size of Saccharomyces cerevisiae. NPJ Syst Biol Appl 2019; 5:34. [PMID: 31583116 PMCID: PMC6763471 DOI: 10.1038/s41540-019-0111-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/23/2019] [Indexed: 11/09/2022] Open
Abstract
Cell growth is well described at the population level, but precisely how nutrient and water uptake and cell wall expansion drive the growth of single cells is poorly understood. Supported by measurements of single-cell growth trajectories and cell wall elasticity, we present a single-cell growth model for yeast. The model links the thermodynamic quantities, such as turgor pressure, osmolarity, cell wall elasto-plasticity, and cell size, applying concepts from rheology and thin shell theory. It reproduces cell size dynamics during single-cell growth, budding, and hyper-osmotic or hypo-osmotic stress. We find that single-cell growth rate and final size are primarily governed by osmolyte uptake and consumption, while bud expansion requires additionally different cell wall extensibilities between mother and bud. Based on first principles the model provides a more accurate description of size dynamics than previous attempts and its analytical simplification allows for easy combination with models for other cell processes.
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Affiliation(s)
- Tom Altenburg
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
- Robert Koch-Institut, Berlin, Germany
| | - Björn Goldenbogen
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jannis Uhlendorf
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
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14
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Stratford M, Steels H, Novodvorska M, Archer DB, Avery SV. Extreme Osmotolerance and Halotolerance in Food-Relevant Yeasts and the Role of Glycerol-Dependent Cell Individuality. Front Microbiol 2019; 9:3238. [PMID: 30687253 PMCID: PMC6333755 DOI: 10.3389/fmicb.2018.03238] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/13/2018] [Indexed: 12/19/2022] Open
Abstract
Osmotolerance or halotolerance are used to describe resistance to sugars and salt, or only salt, respectively. Here, a comprehensive screen of more than 600 different yeast isolates revealed that osmosensitive species were equally affected by NaCl and glucose. However, the relative toxicity of salt became increasingly prominent in more osmoresistant species. We confirmed that growth inhibition by glucose in a laboratory strain of Saccharomyces cerevisiae occurred at a lower water activity (Aw) than by salt (NaCl), and pre-growth in high levels of glucose or salt gave enhanced cross-resistance to either. Salt toxicity was largely due to osmotic stress but with an additive enhancement due to effects of the relevant cation. Almost all of the yeast isolates from the screen were also noted to exhibit hetero-resistance to both salt and sugar, whereby high concentrations restricted growth to a small minority of cells within the clonal populations. Rare resistant colonies required growth for up to 28 days to become visible. This cell individuality was more marked with salt than sugar, a possible further reflection of the ion toxicity effect. In both cases, heteroresistance in S. cerevisiae was strikingly dependent on the GPD1 gene product, important for glycerol synthesis. In contrast, a tps1Δ deletant impaired for trehalose showed altered MIC but no change in heteroresistance. Effects on heteroresistance were evident in chronic (but not acute) salt or glucose stress, particularly relevant to growth on low Aw foods. The study reports diverse osmotolerance and halotolerance phenotypes and heteroresistance across an extensive panel of yeast isolates, and indicates that Gpd1-dependent glycerol synthesis is a key determinant enabling growth of rare yeast subpopulations at low Aw, brought about by glucose and in particular salt.
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Affiliation(s)
- Malcolm Stratford
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Hazel Steels
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - David B Archer
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Simon V Avery
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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15
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Dunayevich P, Baltanás R, Clemente JA, Couto A, Sapochnik D, Vasen G, Colman-Lerner A. Heat-stress triggers MAPK crosstalk to turn on the hyperosmotic response pathway. Sci Rep 2018; 8:15168. [PMID: 30310096 PMCID: PMC6181916 DOI: 10.1038/s41598-018-33203-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 09/21/2018] [Indexed: 12/11/2022] Open
Abstract
Cells make decisions based on a combination of external and internal signals. In yeast, the high osmolarity response (HOG) is a mitogen-activated protein kinase (MAPK) pathway that responds to a variety of stimuli, and it is central to the general stress response. Here we studied the effect of heat-stress (HS) on HOG. Using live-cell reporters and genetics, we show that HS promotes Hog1 phosphorylation and Hog1-dependent gene expression, exclusively via the Sln1 phosphorelay branch, and that the strength of the activation is larger in yeast adapted to high external osmolarity. HS stimulation of HOG is indirect. First, we show that HS causes glycerol loss, necessary for HOG activation. Preventing glycerol efflux by deleting the glyceroporin FPS1 or its regulators RGC1 and ASK10/RGC2, or by increasing external glycerol, greatly reduced HOG activation. Second, we found that HOG stimulation by HS depended on the operation of a second MAPK pathway, the cell-wall integrity (CWI), a well-known mediator of HS, since inactivating Pkc1 or deleting the MAPK SLT2 greatly reduced HOG activation. Our data suggest that the main role of the CWI in this process is to stimulate glycerol loss. We found that in yeast expressing the constitutively open channel mutant (Fps1-Δ11), HOG activity was independent of Slt2. In summary, we suggest that HS causes a reduction in turgor due to the loss of glycerol and the accompanying water, and that this is what actually stimulates HOG. Thus, taken together, our findings highlight a central role for Fps1, and the metabolism of glycerol, in the communication between the yeast MAPK pathways, essential for survival and reproduction in changing environments.
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Affiliation(s)
- Paula Dunayevich
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
| | - Rodrigo Baltanás
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
| | - José Antonio Clemente
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
| | - Alicia Couto
- CIHIDECAR-Departamento de Química Orgánica, FCEN, UBA, Buenos Aires, Argentina
| | - Daiana Sapochnik
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
| | - Gustavo Vasen
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
| | - Alejandro Colman-Lerner
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina.
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina.
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16
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Shorthouse D, Riedel A, Kerr E, Pedro L, Bihary D, Samarajiwa S, Martins CP, Shields J, Hall BA. Exploring the role of stromal osmoregulation in cancer and disease using executable modelling. Nat Commun 2018; 9:3011. [PMID: 30069015 PMCID: PMC6070494 DOI: 10.1038/s41467-018-05414-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/29/2018] [Indexed: 02/07/2023] Open
Abstract
Osmotic regulation is a vital homoeostatic process in all cells and tissues. Cells initially respond to osmotic stresses by activating transmembrane transport proteins to move osmotically active ions. Disruption of ion and water transport is frequently observed in cellular transformations such as cancer. We report that genes involved in membrane transport are significantly deregulated in many cancers, and that their expression can distinguish cancer cells from normal cells with a high degree of accuracy. We present an executable model of osmotic regulation and membrane transport in mammalian cells, providing a mechanistic explanation for phenotype change in varied disease states, and accurately predicting behaviour from single cell expression data. We also predict key proteins involved in cellular transformation, SLC4A3 (AE3), and SLC9A1 (NHE1). Furthermore, we predict and verify a synergistic drug combination in vitro, of sodium and chloride channel inhibitors, which target the osmoregulatory network to reduce cancer-associated phenotypes in fibroblasts.
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Affiliation(s)
- David Shorthouse
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Angela Riedel
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Emma Kerr
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Luisa Pedro
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Dóra Bihary
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Shamith Samarajiwa
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Carla P Martins
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Jacqueline Shields
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
| | - Benjamin A Hall
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
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17
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Strome B, Hsu IS, Li Cheong Man M, Zarin T, Nguyen Ba A, Moses AM. Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity. BMC SYSTEMS BIOLOGY 2018; 12:75. [PMID: 29970070 PMCID: PMC6029073 DOI: 10.1186/s12918-018-0597-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 06/22/2018] [Indexed: 02/04/2023]
Abstract
Background The effort to characterize intrinsically disordered regions of signaling proteins is rapidly expanding. An important class of disordered interaction modules are ubiquitous and functionally diverse elements known as short linear motifs (SLiMs). Results To further examine the role of SLiMs in signal transduction, we used a previously devised bioinformatics method to predict evolutionarily conserved SLiMs within a well-characterized pathway in S. cerevisiae. Using a single cell, reporter-based flow cytometry assay in conjunction with a fluorescent reporter driven by a pathway-specific promoter, we quantitatively assessed pathway output via systematic deletions of individual motifs. We found that, when deleted, 34% (10/29) of predicted SLiMs displayed a significant decrease in pathway output, providing evidence that these motifs play a role in signal transduction. Assuming that mutations in SLiMs have quantitative effects on mechanisms of signaling, we show that perturbations of parameters in a previously published stochastic model of HOG signaling could reproduce the quantitative effects of 4 out of 7 mutations in previously unknown SLiMs. Conclusions Our study suggests that, even in well-characterized pathways, large numbers of functional elements remain undiscovered, and that challenges remain for application of systems biology models to interpret the effects of mutations in signaling pathways. Electronic supplementary material The online version of this article (10.1186/s12918-018-0597-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bob Strome
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Ian Shenyen Hsu
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Mitchell Li Cheong Man
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Taraneh Zarin
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Alex Nguyen Ba
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Alan M Moses
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada. .,Center for Analysis of Genome Evolution and Function, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.
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18
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Draft Genome Sequence of the Yeast Saccharomyces cerevisiae GUJ105 From Gujarat, India. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01315-16. [PMID: 27908989 PMCID: PMC5137403 DOI: 10.1128/genomea.01315-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of Saccharomyces cerevisiae strain GUJ105, isolated clinically. The size of the genome is approximately 11.5 Mb and contains 5,447 protein-coding genes.
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