1
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Isoda T, Takeda E, Hosokawa S, Hotta-Ren S, Ohsumi Y. Atg45 is an autophagy receptor for glycogen, a non-preferred cargo of bulk autophagy in yeast. iScience 2024; 27:109810. [PMID: 38832010 PMCID: PMC11145338 DOI: 10.1016/j.isci.2024.109810] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/03/2023] [Accepted: 04/22/2024] [Indexed: 06/05/2024] Open
Abstract
The mechanisms governing autophagy of proteins and organelles have been well studied, but how other cytoplasmic components such as RNA and polysaccharides are degraded remains largely unknown. In this study, we examine autophagy of glycogen, a storage form of glucose. We find that cells accumulate glycogen in the cytoplasm during nitrogen starvation and that this carbohydrate is rarely observed within autophagosomes and autophagic bodies. However, sequestration of glycogen by autophagy is observed following prolonged nitrogen starvation. We identify a yet-uncharacterized open reading frame, Yil024c (herein Atg45), as encoding a cytosolic receptor protein that mediates autophagy of glycogen (glycophagy). Furthermore, we show that, during sporulation, Atg45 is highly expressed and is associated with an increase in glycophagy. Our results suggest that cells regulate glycophagic activity by controlling the expression level of Atg45.
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Affiliation(s)
- Takahiro Isoda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Frontier Research Center, POLA Chemical Industries, Inc, Yokohama 244-0812, Japan
| | - Eigo Takeda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Sachiko Hosokawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Shukun Hotta-Ren
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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2
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Molinet J, Navarrete JP, Villarroel CA, Villarreal P, Sandoval FI, Nespolo RF, Stelkens R, Cubillos FA. Wild Patagonian yeast improve the evolutionary potential of novel interspecific hybrid strains for lager brewing. PLoS Genet 2024; 20:e1011154. [PMID: 38900713 PMCID: PMC11189258 DOI: 10.1371/journal.pgen.1011154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 05/17/2024] [Indexed: 06/22/2024] Open
Abstract
Lager yeasts are limited to a few strains worldwide, imposing restrictions on flavour and aroma diversity and hindering our understanding of the complex evolutionary mechanisms during yeast domestication. The recent finding of diverse S. eubayanus lineages from Patagonia offers potential for generating new lager yeasts with different flavour profiles. Here, we leverage the natural genetic diversity of S. eubayanus and expand the lager yeast repertoire by including three distinct Patagonian S. eubayanus lineages. We used experimental evolution and selection on desirable traits to enhance the fermentation profiles of novel S. cerevisiae x S. eubayanus hybrids. Our analyses reveal an intricate interplay of pre-existing diversity, selection on species-specific mitochondria, de-novo mutations, and gene copy variations in sugar metabolism genes, resulting in high ethanol production and unique aroma profiles. Hybrids with S. eubayanus mitochondria exhibited greater evolutionary potential and superior fitness post-evolution, analogous to commercial lager hybrids. Using genome-wide screens of the parental subgenomes, we identified genetic changes in IRA2, IMA1, and MALX genes that influence maltose metabolism, and increase glycolytic flux and sugar consumption in the evolved hybrids. Functional validation and transcriptome analyses confirmed increased maltose-related gene expression, influencing greater maltotriose consumption in evolved hybrids. This study demonstrates the potential for generating industrially viable lager yeast hybrids from wild Patagonian strains. Our hybridization, evolution, and mitochondrial selection approach produced hybrids with high fermentation capacity and expands lager beer brewing options.
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Affiliation(s)
- Jennifer Molinet
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Juan P. Navarrete
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Carlos A. Villarroel
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Centro de Biotecnología de los Recursos Naturales (CENBio), Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
| | - Pablo Villarreal
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Felipe I. Sandoval
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Roberto F. Nespolo
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- ANID-Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Rike Stelkens
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Francisco A. Cubillos
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- ANID-Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
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3
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Duveau F, Cordier C, Chiron L, Le Bec M, Pouzet S, Séguin J, Llamosi A, Sorre B, Di Meglio JM, Hersen P. Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability. eLife 2024; 12:RP88750. [PMID: 38568203 PMCID: PMC10990491 DOI: 10.7554/elife.88750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Natural environments of living organisms are often dynamic and multifactorial, with multiple parameters fluctuating over time. To better understand how cells respond to dynamically interacting factors, we quantified the effects of dual fluctuations of osmotic stress and glucose deprivation on yeast cells using microfluidics and time-lapse microscopy. Strikingly, we observed that cell proliferation, survival, and signaling depend on the phasing of the two periodic stresses. Cells divided faster, survived longer, and showed decreased transcriptional response when fluctuations of hyperosmotic stress and glucose deprivation occurred in phase than when the two stresses occurred alternatively. Therefore, glucose availability regulates yeast responses to dynamic osmotic stress, showcasing the key role of metabolic fluctuations in cellular responses to dynamic stress. We also found that mutants with impaired osmotic stress response were better adapted to alternating stresses than wild-type cells, showing that genetic mechanisms of adaptation to a persistent stress factor can be detrimental under dynamically interacting conditions.
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Affiliation(s)
- Fabien Duveau
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364LyonFrance
| | - Céline Cordier
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Lionel Chiron
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Matthias Le Bec
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Sylvain Pouzet
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Julie Séguin
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
| | - Artémis Llamosi
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
| | - Benoit Sorre
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Jean-Marc Di Meglio
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
| | - Pascal Hersen
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
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4
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Plank M, Carmiol N, Mitri B, Lipinski AA, Langlais PR, Capaldi AP. Systems level analysis of time and stimuli specific signaling through PKA. Mol Biol Cell 2024; 35:ar60. [PMID: 38446618 PMCID: PMC11064662 DOI: 10.1091/mbc.e23-02-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 02/13/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
It is well known that eukaryotic cells create gradients of cAMP across space and time to regulate the cAMP dependent protein kinase (PKA) and, in turn, growth and metabolism. However, it is unclear how PKA responds to different concentrations of cAMP. Here, to address this question, we examine PKA signaling in Saccharomyces cerevisiae in different conditions, timepoints, and concentrations of the chemical inhibitor 1-NM-PP1, using phosphoproteomics. These experiments show that there are numerous proteins that are only phosphorylated when cAMP and PKA activity are at/near their maximum level, while other proteins are phosphorylated even when cAMP levels and PKA activity are low. The data also show that PKA drives cells into distinct growth states by acting on proteins with different thresholds for phosphorylation in different conditions. Analysis of the sequences surrounding the 118 PKA-dependent phosphosites suggests that the phosphorylation thresholds are set, at least in part, by the affinity of PKA for each site.
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Affiliation(s)
- Michael Plank
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
- The Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Nicole Carmiol
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
| | - Bassam Mitri
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
| | | | - Paul R. Langlais
- The Department of Medicine, University of Arizona, Tucson, AZ 85721
| | - Andrew P. Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
- The Bio5 Institute, University of Arizona, Tucson, AZ 85721
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5
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Kottom TJ, Carmona EM, Limper AH. Characterization of the Pneumocystis jirovecii and Pneumocystis murina phosphoglucomutases (Pgm2s): a potential target for Pneumocystis therapy. Antimicrob Agents Chemother 2024; 68:e0075623. [PMID: 38259086 PMCID: PMC10916394 DOI: 10.1128/aac.00756-23] [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: 06/08/2023] [Accepted: 12/03/2023] [Indexed: 01/24/2024] Open
Abstract
Pneumocystis cyst life forms contain abundant β-glucan carbohydrates, synthesized using β-1,3 and β-1,6 glucan synthase enzymes and the donor uridine diphosphate (UDP)-glucose. In yeast, phosphoglucomutase (PGM) plays a crucial role in carbohydrate metabolism by interconverting glucose 1-phosphate and glucose 6-phosphate, a vital step in UDP pools for β-glucan cell wall formation. This pathway has not yet been defined in Pneumocystis. Herein, we surveyed the Pneumocystis jirovecii and Pneumocystis murina genomes, which predicted a homolog of the Saccharomyces cerevisiae major PGM enzyme. Furthermore, we show that PjPgm2p and PmPgm2p function similarly to the yeast counterpart. When both Pneumocystis pgm2 homologs are heterologously expressed in S. cerevisiae pgm2Δ cells, both genes can restore growth and sedimentation rates to wild-type levels. Additionally, we demonstrate that yeast pgm2Δ cell lysates expressing the two Pneumocystis pgm2 transcripts individually can restore PGM activities significantly altered in the yeast pgm2Δ strain. The addition of lithium, a competitive inhibitor of yeast PGM activity, significantly reduces PGM activity. Next, we tested the effects of lithium on P. murina viability ex vivo and found the compound displays significant anti-Pneumocystis activity. Finally, we demonstrate that a para-aryl derivative (ISFP10) with known inhibitory activity against the Aspergillus fumigatus PGM protein and exhibiting 50-fold selectivity over the human PGM enzyme homolog can also significantly reduce Pmpgm2 activity in vitro. Collectively, our data genetically and functionally validate phosphoglucomutases in both P. jirovecii and P. murina and suggest the potential of this protein as a selective therapeutic target for individuals with Pneumocystis pneumonia.
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Affiliation(s)
- Theodore J. Kottom
- Department of Medicine, Thoracic Diseases Research Unit, Mayo Clinic, Rochester, Minnesota, USA
- Department of Biochemistry, Thoracic Diseases Research Unit, Mayo Clinic, Rochester, Minnesota, USA
| | - Eva M. Carmona
- Department of Medicine, Thoracic Diseases Research Unit, Mayo Clinic, Rochester, Minnesota, USA
- Department of Biochemistry, Thoracic Diseases Research Unit, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew H. Limper
- Department of Medicine, Thoracic Diseases Research Unit, Mayo Clinic, Rochester, Minnesota, USA
- Department of Biochemistry, Thoracic Diseases Research Unit, Mayo Clinic, Rochester, Minnesota, USA
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6
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Niphadkar S, Karinje L, Laxman S. The PP2A-like phosphatase Ppg1 mediates assembly of the Far complex to balance gluconeogenic outputs and enables adaptation to glucose depletion. PLoS Genet 2024; 20:e1011202. [PMID: 38452140 PMCID: PMC10950219 DOI: 10.1371/journal.pgen.1011202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/19/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
To sustain growth in changing nutrient conditions, cells reorganize outputs of metabolic networks and appropriately reallocate resources. Signaling by reversible protein phosphorylation can control such metabolic adaptations. In contrast to kinases, the functions of phosphatases that enable metabolic adaptation as glucose depletes are poorly studied. Using a Saccharomyces cerevisiae deletion screen, we identified the PP2A-like phosphatase Ppg1 as required for appropriate carbon allocations towards gluconeogenic outputs-trehalose, glycogen, UDP-glucose, UDP-GlcNAc-after glucose depletion. This Ppg1 function is mediated via regulation of the assembly of the Far complex-a multi-subunit complex that tethers to the ER and mitochondrial outer membranes forming localized signaling hubs. The Far complex assembly is Ppg1 catalytic activity-dependent. Ppg1 regulates the phosphorylation status of multiple ser/thr residues on Far11 to enable the proper assembly of the Far complex. The assembled Far complex is required to maintain gluconeogenic outputs after glucose depletion. Glucose in turn regulates Far complex amounts. This Ppg1-mediated Far complex assembly, and Ppg1-Far complex dependent control of gluconeogenic outputs enables adaptive growth under glucose depletion. Our study illustrates how protein dephosphorylation is required for the assembly of a multi-protein scaffold present in localized cytosolic pools, to thereby alter gluconeogenic flux and enable cells to metabolically adapt to nutrient fluctuations.
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Affiliation(s)
- Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lavanya Karinje
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
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7
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Čáp M, Palková Z. The characteristics of differentiated yeast subpopulations depend on their lifestyle and available nutrients. Sci Rep 2024; 14:3681. [PMID: 38355943 PMCID: PMC10866891 DOI: 10.1038/s41598-024-54300-9] [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: 12/01/2023] [Accepted: 02/11/2024] [Indexed: 02/16/2024] Open
Abstract
Yeast populations can undergo diversification during their growth and ageing, leading to the formation of different cell-types. Differentiation into two major subpopulations, differing in cell size and density and exhibiting distinct physiological and metabolic properties, was described in planktonic liquid cultures and in populations of colonies growing on semisolid surfaces. Here, we compare stress resistance, metabolism and expression of marker genes in seven differentiated cell subpopulations emerging during cultivation in liquid fermentative or respiratory media and during colony development on the same type of solid media. The results show that the more-dense cell subpopulations are more stress resistant than the less-dense subpopulations under all cultivation conditions tested. On the other hand, respiratory capacity, enzymatic activities and marker gene expression differed more between subpopulations. These characteristics are more influenced by the lifestyle of the population (colony vs. planktonic cultivation) and the medium composition. Only in the population growing in liquid respiratory medium, two subpopulations do not form as in the other conditions tested, but all cells exhibit a range of characteristics of the more-dense subpopulations. This suggests that signals for cell differentiation may be triggered by prior metabolic reprogramming or by an unknown signal from the structured environment in the colony.
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Affiliation(s)
- Michal Čáp
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic.
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic.
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Ramirez JF, Kumara U, Arulsamy N, Boothby TC. Water content, transition temperature and fragility influence protection and anhydrobiotic capacity. BBA ADVANCES 2024; 5:100115. [PMID: 38318251 PMCID: PMC10840120 DOI: 10.1016/j.bbadva.2024.100115] [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] [Indexed: 02/07/2024] Open
Abstract
Water is essential for metabolism and all life processes. Despite this, many organisms distributed across the kingdoms of life survive near-complete desiccation or anhydrobiosis. Increased intracellular viscosity, leading to the formation of a vitrified state is necessary, but not sufficient, for survival while dry. What properties of a vitrified system make it desiccation-tolerant or -sensitive are unknown. We have analyzed 18 different in vitro vitrified systems, composed of one of three protective disaccharides (trehalose, sucrose, or maltose) and glycerol, quantifying their enzyme-protective capacity and their material properties in a dry state. Protection conferred by mixtures containing maltose correlates strongly with increased water content, increased glass-transition temperature, and reduced glass former fragility, while the protection of glasses formed with sucrose correlates with increased glass transition temperature and the protection conferred by trehalose glasses correlates with reduced glass former fragility. Thus, in vitro different vitrified sugars confer protection through distinct material properties. Next, we examined the material properties of a dry desiccation tolerant and intolerant life stage from three different organisms. The dried desiccation tolerant life stage of all organisms had an increased glass transition temperature and reduced glass former fragility relative to its dried desiccation intolerant life stage. These results suggest in nature organismal desiccation tolerance relies on a combination of various material properties. This study advances our understanding of how protective and non-protective glasses differ in terms of material properties that promote anhydrobiosis. This knowledge presents avenues to develop novel stabilization technologies for pharmaceuticals that currently rely on the cold-chain. Statement of significance For the past three decades the anhydrobiosis field has lived with a paradox, while vitrification is necessary for survival in the dry state, it is not sufficient. Understanding what property(s) distinguishes a desiccation tolerant from an intolerant vitrified system and how anhydrobiotic organisms survive drying is one of the enduring mysteries of organismal physiology. Here we show in vitro the enzyme-protective capacity of different vitrifying sugars can be correlated with distinct material properties. However, in vivo, diverse desiccation tolerant organisms appear to combine these material properties to promote their survival in a dry state.
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Affiliation(s)
- John F. Ramirez
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - U.G.V.S.S. Kumara
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | | | - Thomas C. Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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Bzducha-Wróbel A, Farkaš P, Bieliková S, Čížová A, Sujkowska-Rybkowska M. How do the carbon and nitrogen sources affect the synthesis of β-(1,3/1,6)-glucan, its structure and the susceptibility of Candida utilis yeast cells to immunolabelling with β-(1,3)-glucan monoclonal antibodies? Microb Cell Fact 2024; 23:28. [PMID: 38243245 PMCID: PMC10799355 DOI: 10.1186/s12934-024-02305-4] [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: 11/16/2023] [Accepted: 01/14/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND The need to limit antibiotic therapy due to the spreading resistance of pathogenic microorganisms to these medicinal substances stimulates research on new therapeutic agents, including the treatment and prevention of animal diseases. This is one of the goals of the European Green Deal and the Farm-To-Fork strategy. Yeast biomass with an appropriate composition and exposure of cell wall polysaccharides could constitute a functional feed additive in precision animal nutrition, naturally stimulating the immune system to fight infections. RESULTS The results of the research carried out in this study showed that the composition of Candida utilis ATCC 9950 yeast biomass differed depending on growth medium, considering especially the content of β-(1,3/1,6)-glucan, α-glucan, and trehalose. The highest β-(1,3/1,6)-glucan content was observed after cultivation in deproteinated potato juice water (DPJW) as a nitrogen source and glycerol as a carbon source. Isolation of the polysaccharide from yeast biomass confirmed the highest yield of β-(1,3/1,6)-glucan after cultivation in indicated medium. The differences in the susceptibility of β-(1,3)-glucan localized in cells to interaction with specific β-(1,3)-glucan antibody was noted depending on the culture conditions. The polymer in cells from the DPJW supplemented with glycerol and galactose were labelled with monoclonal antibodies with highest intensity, interestingly being less susceptible to such an interaction after cell multiplication in medium with glycerol as carbon source and yeast extract plus peptone as a nitrogen source. CONCLUSIONS Obtained results confirmed differences in the structure of the β-(1,3/1,6)-glucan polymers considering side-chain length and branching frequency, as well as in quantity of β-(1,3)- and β-(1,6)-chains, however, no visible relationship was observed between the structural characteristics of the isolated polymers and its susceptibility to immunolabeling in whole cells. Presumably, other outer surface components and molecules can mask, shield, protect, or hide epitopes from antibodies. β-(1,3)-Glucan was more intensely recognized by monoclonal antibody in cells with lower trehalose and glycogen content. This suggests the need to cultivate yeast biomass under appropriate conditions to fulfil possible therapeutic functions. However, our in vitro findings should be confirmed in further studies using tissue or animal models.
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Affiliation(s)
- Anna Bzducha-Wróbel
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C Street, 02-787, Warsaw, Poland.
| | - Pavol Farkaš
- Department of Glycobiotechnology, Institute of Chemistry Slovak Academy of Sciences, Dúbravská Cesta 9, 84538, Bratislava, Slovakia.
| | - Sandra Bieliková
- Department of Glycomaterials, Institute of Chemistry Slovak Academy of Sciences, Dúbravská Cesta 9, 84538, Bratislava, Slovakia
| | - Alžbeta Čížová
- Department of Glycomaterials, Institute of Chemistry Slovak Academy of Sciences, Dúbravská Cesta 9, 84538, Bratislava, Slovakia
| | - Marzena Sujkowska-Rybkowska
- Department of Botany, Warsaw, Institute of Biology, University of Life Sciences, Nowoursynowska 159C Street, 02-787, Warsaw, Poland
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10
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Gulias JF, Niesi F, Arán M, Correa-García S, Bermúdez-Moretti M. Gcn4 impacts metabolic fluxes to promote yeast chronological lifespan. PLoS One 2023; 18:e0292949. [PMID: 37831681 PMCID: PMC10575530 DOI: 10.1371/journal.pone.0292949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Aging is characterized by a gradual decline in physiological integrity, which impairs functionality and increases susceptibility to mortality. Dietary restriction, mimicking nutrient scarcity without causing malnutrition, is an intervention known to decelerate the aging process. While various hypotheses have been proposed to elucidate how dietary restriction influences aging, the underlying mechanisms remain incompletely understood. This project aimed to investigate the role of the primary regulator of the general amino acid control (GAAC) pathway, the transcription factor Gcn4, in the aging process of S. cerevisiae cells. Under conditions of amino acid deprivation, which activate Gcn4, the deletion of GCN4 led to a diverse array of physiological changes in the cells. Notably, the absence of Gcn4 resulted in heightened mitochondrial activity, likely contributing to the observed increase in reactive oxygen species (ROS) accumulation. Furthermore, these mutant gcn4Δ cells exhibited reduced ethanol production despite maintaining similar glucose consumption rates, suggesting a pivotal role for Gcn4 in regulating the Crabtree effect. Additionally, there was a marked reduction in trehalose, the storage carbohydrate, within the mutant cells compared to the wild-type strain. The intracellular content of free amino acids also exhibited disparities between the wild-type and GCN4-deficient strains. Taken together, our findings indicate that the absence of GCN4 disrupts cellular homeostasis, triggering significant alterations in interconnected intracellular metabolic pathways. These disruptions have far-reaching metabolic consequences that ultimately culminate in a shortened lifespan.
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Affiliation(s)
- Juan Facundo Gulias
- Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina–CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Florencia Niesi
- Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina–CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Martín Arán
- Fundación Instituto Leloir e Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA)—CONICET, Patricias Argentinas, Buenos Aires, Argentina
| | - Susana Correa-García
- Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina–CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Mariana Bermúdez-Moretti
- Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina–CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
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11
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Sęk W, Kot AM, Rapoport A, Kieliszek M. Physiological and genetic regulation of anhydrobiosis in yeast cells. Arch Microbiol 2023; 205:348. [PMID: 37782422 PMCID: PMC10545650 DOI: 10.1007/s00203-023-03683-w] [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: 08/03/2023] [Revised: 08/28/2023] [Accepted: 09/10/2023] [Indexed: 10/03/2023]
Abstract
Anhydrobiosis is a state of living organisms during which their metabolism is reversibly delayed or suspended due to a high degree of dehydration. Yeast cells, which are widely used in the food industry, may be induced into this state. The degree of viability of yeast cells undergoing the drying process also depends on rehydration. In an attempt to explain the essence of the state of anhydrobiosis and clarify the mechanisms responsible for its course, scientists have described various cellular compounds and structures that are responsible for it. The structures discussed in this work include the cell wall and plasma membrane, vacuoles, mitochondria, and lysosomes, among others, while the most important compounds include trehalose, glycogen, glutathione, and lipid droplets. Various proteins (Stf2p; Sip18p; Hsp12p and Hsp70p) and genes (STF2; Nsip18; TRX2; TPS1 and TPS2) are also responsible for the process of anhydrobiosis. Each factor has a specific function and is irreplaceable, detailed information is presented in this overview.
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Affiliation(s)
- Wioletta Sęk
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
| | - Anna M Kot
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland.
| | - Alexander Rapoport
- Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Str., 1, Riga, 1004, Latvia
| | - Marek Kieliszek
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland.
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12
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Johnston EJ, Tallis J, Cunningham-Oakes E, Moses T, Moore SJ, Hosking S, Rosser SJ. Yeast lacking the sterol C-5 desaturase Erg3 are tolerant to the anti-inflammatory triterpenoid saponin escin. Sci Rep 2023; 13:13617. [PMID: 37604855 PMCID: PMC10442444 DOI: 10.1038/s41598-023-40308-0] [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: 05/10/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023] Open
Abstract
Escin is a mixture of over 30 glycosylated triterpenoid (saponin) structures, extracted from the dried fruit of horse chestnuts. Escin is currently used as an anti-inflammatory, and has potential applications in the treatment of arthritis and cancer. Engineered yeast would enable production of specific bioactive components of escin at industrial scale, however many saponins have been shown to be toxic to yeast. Here we report that a Saccharomyces cerevisiae strain specifically lacking the sterol C-5 desaturase gene ERG3, exhibits striking enhanced tolerance to escin treatment. Transcriptome analyses, as well as pre-mixing of escin with sterols, support the hypothesis that escin interacts directly with ergosterol, but not as strongly with the altered sterols present in erg3Δ. A diverse range of saponins are of commercial interest, and this research highlights the value of screening lipidome mutants to identify appropriate hosts for engineering the industrial production of saponins.
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Affiliation(s)
- Emily J Johnston
- Centre for Engineering Biology, University of Edinburgh, Edinburgh, EH9 3BD, UK.
| | - Jess Tallis
- Centre for Engineering Biology, University of Edinburgh, Edinburgh, EH9 3BD, UK
| | - Edward Cunningham-Oakes
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Tessa Moses
- EdinOmics, RRID:SCR_021838, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Simon J Moore
- Genetic Science Division, Thermo Fisher Scientific, 7 Kingsland Grange, Warrington, Cheshire, WA1 4SR, UK
| | - Sarah Hosking
- Unilever R&D Port Sunlight, Quarry Road East, Bebington, Wirral, CH63 3JW, UK
| | - Susan J Rosser
- Centre for Engineering Biology, University of Edinburgh, Edinburgh, EH9 3BD, UK.
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13
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Du Y, Gupta P, Qin S, Sieber M. The role of metabolism in cellular quiescence. J Cell Sci 2023; 136:jcs260787. [PMID: 37589342 PMCID: PMC10445740 DOI: 10.1242/jcs.260787] [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] [Indexed: 08/18/2023] Open
Abstract
Cellular quiescence is a dormant, non-dividing cell state characterized by significant shifts in physiology and metabolism. Quiescence plays essential roles in a wide variety of biological processes, ranging from microbial sporulation to human reproduction and wound repair. Moreover, when the regulation of quiescence is disrupted, it can drive cancer growth and compromise tissue regeneration after injury. In this Review, we examine the dynamic changes in metabolism that drive and support dormant and transiently quiescent cells, including spores, oocytes and adult stem cells. We begin by defining quiescent cells and discussing their roles in key biological processes. We then examine metabolic factors that influence cellular quiescence in both healthy and disease contexts, and how these could be leveraged in the treatment of cancer.
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Affiliation(s)
- Yipeng Du
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, MC9040 ND13.214, Dallas, TX 75390, USA
| | - Parul Gupta
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, MC9040 ND13.214, Dallas, TX 75390, USA
| | - Shenlu Qin
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, MC9040 ND13.214, Dallas, TX 75390, USA
| | - Matthew Sieber
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, MC9040 ND13.214, Dallas, TX 75390, USA
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14
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Watanabe D, Kawashima M, Yoshioka N, Sugimoto Y, Takagi H. Rational design of alcoholic fermentation targeting extracellular carbon. NPJ Sci Food 2023; 7:37. [PMID: 37479699 PMCID: PMC10361962 DOI: 10.1038/s41538-023-00215-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Breeding yeast strains for industrial alcoholic fermentation requires laborious screening due to the lack of in vivo modification strategies. Here we show that quiescence-specific cell wall thickening via synthesis of a major component, 1,3-β-glucan, critically antagonizes cellular fermentation ability by sequestering the available cytoplasmic carbon sources. This study provides insights into glycolytic control and reports an effective and reliable rational fermentation design.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
| | - Mikiya Kawashima
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Naoya Yoshioka
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Yukiko Sugimoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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15
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Nagy L, Vonk P, Künzler M, Földi C, Virágh M, Ohm R, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu X, Nan S, Pareek M, Sahu N, Szathmári B, Varga T, Wu H, Yang X, Merényi Z. Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Stud Mycol 2023; 104:1-85. [PMID: 37351542 PMCID: PMC10282164 DOI: 10.3114/sim.2022.104.01] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/02/2022] [Indexed: 01/09/2024] Open
Abstract
Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.
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Affiliation(s)
- L.G. Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - P.J. Vonk
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - M. Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland;
| | - C. Földi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - M. Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - R.A. Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - F. Hennicke
- Project Group Genetics and Genomics of Fungi, Chair Evolution of Plants and Fungi, Ruhr-University Bochum, 44780, Bochum, North Rhine-Westphalia, Germany;
| | - B. Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Á. Csernetics
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Z. Hou
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X.B. Liu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - S. Nan
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - M. Pareek
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - N. Sahu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Szathmári
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - T. Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - H. Wu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X. Yang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Z. Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
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16
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Zhang Y, van der Zee L, Barberis M. Two-way communication between cell cycle and metabolism in budding yeast: what do we know? Front Microbiol 2023; 14:1187304. [PMID: 37396387 PMCID: PMC10309209 DOI: 10.3389/fmicb.2023.1187304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Coordination of cell cycle and metabolism exists in all cells. The building of a new cell is a process that requires metabolic commitment to the provision of both Gibbs energy and building blocks for proteins, nucleic acids, and membranes. On the other hand, the cell cycle machinery will assess and regulate its metabolic environment before it makes decisions on when to enter the next cell cycle phase. Furthermore, more and more evidence demonstrate that the metabolism can be regulated by cell cycle progression, as different biosynthesis pathways are preferentially active in different cell cycle phases. Here, we review the available literature providing a critical overview on how cell cycle and metabolism may be coupled with one other, bidirectionally, in the budding yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Yanfei Zhang
- Molecular Systems Biology, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Lucas van der Zee
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Matteo Barberis
- Molecular Systems Biology, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
- Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, Surrey, United Kingdom
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17
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Miao J, Regan J, Cai C, Palmer GE, Williams DL, Kruppa MD, Peters BM. Glycogen Metabolism in Candida albicans Impacts Fitness and Virulence during Vulvovaginal and Invasive Candidiasis. mBio 2023; 14:e0004623. [PMID: 36840583 PMCID: PMC10127583 DOI: 10.1128/mbio.00046-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
The polymorphic fungus Candida albicans remains a leading cause of both invasive and superficial mycoses, including vulvovaginal candidiasis (VVC). Metabolic plasticity, including carbohydrate catabolism, confers fitness advantages at anatomical site-specific host niches. C. albicans possesses the capacity to accumulate and store carbohydrates as glycogen and can consume intracellular glycogen stores when nutrients become limited. In the vaginal environment, estrogen promotes epithelial glycogen accumulation and C. albicans colonization. However, whether these factors are mechanistically linked is unexplored. Here, we characterized the glycogen metabolism pathways in C. albicans and investigated whether these impact the long-term survival of C. albicans, both in vitro and in vivo during murine VVC, or virulence during systemic infection. SC5314 and 6 clinical isolates demonstrated impaired growth when glycogen was used as the sole carbon source, suggesting that environmental glycogen acquisition is limited. The genetic deletion and complementation of key genes involved in glycogen metabolism in Saccharomyces cerevisiae confirmed that GSY1 and GLC3, as well as GPH1 and GDB1, are essential for glycogen synthesis and catabolism in C. albicans, respectively. Potential compensatory roles for a glucoamylase encoded by SGA1 were also explored. Competitive survival assays revealed that gsy1Δ/Δ, gph1Δ/Δ, and gph1Δ/Δ sga1Δ/Δ mutants exhibited long-term survival defects in vitro under starvation conditions and in vivo during vaginal colonization. A complete inability to catabolize glycogen (gph1Δ/Δ sga1Δ/Δ) also rendered C. albicans significantly less virulent during disseminated infections. This is the first study fully validating the glycogen metabolism pathways in C. albicans, and the results further suggest that intracellular glycogen catabolism positively impacts the long-term fitness of C. albicans in nutrient deficient environments and is important for full virulence. IMPORTANCE Glycogen is a highly branched polymer of glucose and is used across the tree of life as an efficient and compact form of energy storage. Whereas glycogen metabolism pathways have been studied in model yeasts, they have not been extensively explored in pathogenic fungi. Using a combination of microbiologic, molecular genetic, and biochemical approaches, we reveal orthologous functions of glycogen metabolism genes in the fungal pathogen Candida albicans. We also provide evidence that extracellular glycogen poorly supports growth across the Candida species and clinical isolates. Competitive fitness assays reveal that the loss of glycogen synthesis or catabolism significantly impacts survival during both in vitro starvation and the colonization of the mouse vagina. Moreover, a global glycogen catabolism mutant is rendered less virulent during murine invasive candidiasis. Therefore, this work demonstrates that glycogen metabolism in C. albicans contributes to survival and virulence in the mammalian host and may be a novel antifungal target.
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Affiliation(s)
- Jian Miao
- Pharmaceutical Sciences Program, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jessica Regan
- Pharmaceutical Sciences Program, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Chun Cai
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Glen E. Palmer
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - David L. Williams
- Department of Surgery, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
- Center of Excellence in Inflammation, Infectious Disease, and Immunity, East Tennessee State University, Johnson City, Tennessee, USA
| | - Michael D. Kruppa
- Center of Excellence in Inflammation, Infectious Disease, and Immunity, East Tennessee State University, Johnson City, Tennessee, USA
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Brian M. Peters
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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18
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Ridder MD, van den Brandeler W, Altiner M, Daran-Lapujade P, Pabst M. Proteome dynamics during transition from exponential to stationary phase under aerobic and anaerobic conditions in yeast. Mol Cell Proteomics 2023; 22:100552. [PMID: 37076048 DOI: 10.1016/j.mcpro.2023.100552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/23/2023] [Accepted: 04/13/2023] [Indexed: 04/21/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is a widely used eukaryotic model organism and a promising cell factory for industry. However, despite decades of research, the regulation of its metabolism is not yet fully understood, and its complexity represents a major challenge for engineering and optimising biosynthetic routes. Recent studies have demonstrated the potential of resource and proteomic allocation data in enhancing models for metabolic processes. However, comprehensive and accurate proteome dynamics data that can be used for such approaches are still very limited. Therefore, we performed a quantitative proteome dynamics study to comprehensively cover the transition from exponential to stationary phase for both aerobically and anaerobically grown yeast cells. The combination of highly controlled reactor experiments, biological replicates and standardised sample preparation procedures ensured reproducibility and accuracy. Additionally, we selected the CEN.PK lineage for our experiments because of its relevance for both fundamental and applied research. Together with the prototrophic, standard haploid strain CEN.PK113-7D, we also investigated an engineered strain with genetic minimisation of the glycolytic pathway, resulting in the quantitative assessment of 54 proteomes. The anaerobic cultures showed remarkably less proteome-level changes compared to the aerobic cultures, during transition from the exponential to the stationary phase as a consequence of the lack of the diauxic shift in the absence of oxygen. These results support the notion that anaerobically growing cells lack resources to adequately adapt to starvation. This proteome dynamics study constitutes an important step towards better understanding of the impact of glucose exhaustion and oxygen on the complex proteome allocation process in yeast. Finally, the established proteome dynamics data provide a valuable resource for the development of resource allocation models as well as for metabolic engineering efforts.
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Affiliation(s)
- Maxime den Ridder
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wiebeke van den Brandeler
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Meryem Altiner
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Martin Pabst
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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19
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Velastegui E, Quezada J, Guerrero K, Altamirano C, Martinez JA, Berrios J, Fickers P. Is heterogeneity in large-scale bioreactors a real problem in recombinant protein synthesis by Pichia pastoris? Appl Microbiol Biotechnol 2023; 107:2223-2233. [PMID: 36843194 DOI: 10.1007/s00253-023-12434-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/28/2023]
Abstract
Culture medium heterogeneity is inherent in industrial bioreactors. The loss of mixing efficiency in a large-scale bioreactor yields to the formation of concentration gradients. Consequently, cells face oscillatory culture conditions that may deeply affect their metabolism. Herein, cell response to transient perturbations, namely high methanol concentration combined with hypoxia, has been investigated using a two stirred-tank reactor compartiments (STR-STR) scale-down system and a Pichia pastoris strain expressing the gene encoding enhanced green fluorescent protein (eGFP) under the control of the alcohol oxidase 1 (AOX1) promoter. Cell residence times under transient stressing conditions were calculated based on the typical hydraulic circulation times of bioreactors of tens and hundreds cubic metres. A significant increase in methanol and oxygen uptake rates was observed as the cell residence time was increased. Stressful culture conditions impaired biomass formation and triggered cell flocculation. More importantly, both expression levels of genes under the control of pAOX1 promoter and eGFP specific fluorescence were higher in those oscillatory culture conditions, suggesting that those a priori unfavourable culture conditions in fact benefit to recombinant protein productivity. Flocculent cells were also identified as the most productive as compared to ovoid cells. KEY POINTS: • Transient hypoxia and high methanol trigger high level of recombinant protein synthesis • In Pichia pastoris, pAOX1 induction is higher in flocculent cells • Medium heterogeneity leads to morphological diversification.
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Affiliation(s)
- Edgar Velastegui
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av Brasil 2085, Valparaiso, 2340000, Chile
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro Bio Tech, University of Liege, Gembloux, Belgium
| | - Johan Quezada
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av Brasil 2085, Valparaiso, 2340000, Chile
| | - Karlo Guerrero
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av Brasil 2085, Valparaiso, 2340000, Chile
| | - Claudia Altamirano
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av Brasil 2085, Valparaiso, 2340000, Chile
| | - Juan Andres Martinez
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro Bio Tech, University of Liege, Gembloux, Belgium
| | - Julio Berrios
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av Brasil 2085, Valparaiso, 2340000, Chile.
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro Bio Tech, University of Liege, Gembloux, Belgium
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20
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Synergistic Antifungal Interactions between Antibiotic Amphotericin B and Selected 1, 3, 4-thiadiazole Derivatives, Determined by Microbiological, Cytochemical, and Molecular Spectroscopic Studies. Int J Mol Sci 2023; 24:ijms24043430. [PMID: 36834848 PMCID: PMC9966784 DOI: 10.3390/ijms24043430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/03/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
In recent years, drug-resistant and multidrug-resistant fungal strains have been more frequently isolated in clinical practice. This phenomenon is responsible for difficulties in the treatment of infections. Therefore, the development of new antifungal drugs is an extremely important challenge. Combinations of selected 1,3,4-thiadiazole derivatives with amphotericin B showing strong synergic antifungal interactions are promising candidates for such formulas. In the study, microbiological, cytochemical, and molecular spectroscopy methods were used to investigate the antifungal synergy mechanisms associated with the aforementioned combinations. The present results indicate that two derivatives, i.e., C1 and NTBD, demonstrate strong synergistic interactions with AmB against some Candida species. The ATR-FTIR analysis showed that yeasts treated with the C1 + AmB and NTBD + AmB compositions, compared with those treated with single compounds, exhibited more pronounced abnormalities in the biomolecular content, suggesting that the main mechanism of the synergistic antifungal activity of the compounds is related to a disturbance in cell wall integrity. The analysis of the electron absorption and fluorescence spectra revealed that the biophysical mechanism underlying the observed synergy is associated with disaggregation of AmB molecules induced by the 1,3,4-thiadiazole derivatives. Such observations suggest the possibility of the successful application of thiadiazole derivatives combined with AmB in the therapy of fungal infections.
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21
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Takhaveev V, Özsezen S, Smith EN, Zylstra A, Chaillet ML, Chen H, Papagiannakis A, Milias-Argeitis A, Heinemann M. Temporal segregation of biosynthetic processes is responsible for metabolic oscillations during the budding yeast cell cycle. Nat Metab 2023; 5:294-313. [PMID: 36849832 PMCID: PMC9970877 DOI: 10.1038/s42255-023-00741-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 01/10/2023] [Indexed: 03/01/2023]
Abstract
Many cell biological and biochemical mechanisms controlling the fundamental process of eukaryotic cell division have been identified; however, the temporal dynamics of biosynthetic processes during the cell division cycle are still elusive. Here, we show that key biosynthetic processes are temporally segregated along the cell cycle. Using budding yeast as a model and single-cell methods to dynamically measure metabolic activity, we observe two peaks in protein synthesis, in the G1 and S/G2/M phase, whereas lipid and polysaccharide synthesis peaks only once, during the S/G2/M phase. Integrating the inferred biosynthetic rates into a thermodynamic-stoichiometric metabolic model, we find that this temporal segregation in biosynthetic processes causes flux changes in primary metabolism, with an acceleration of glucose-uptake flux in G1 and phase-shifted oscillations of oxygen and carbon dioxide exchanges. Through experimental validation of the model predictions, we demonstrate that primary metabolism oscillates with cell-cycle periodicity to satisfy the changing demands of biosynthetic processes exhibiting unexpected dynamics during the cell cycle.
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Affiliation(s)
- Vakil Takhaveev
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Serdar Özsezen
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, The Netherlands
| | - Edward N Smith
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Andre Zylstra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Marten L Chaillet
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Haoqi Chen
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Alexandros Papagiannakis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Biology and Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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22
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Brauer VS, Pessoni AM, Freitas MS, Cavalcanti-Neto MP, Ries LNA, Almeida F. Chitin Biosynthesis in Aspergillus Species. J Fungi (Basel) 2023; 9:jof9010089. [PMID: 36675910 PMCID: PMC9865612 DOI: 10.3390/jof9010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 01/11/2023] Open
Abstract
The fungal cell wall (FCW) is a dynamic structure responsible for the maintenance of cellular homeostasis, and is essential for modulating the interaction of the fungus with its environment. It is composed of proteins, lipids, pigments and polysaccharides, including chitin. Chitin synthesis is catalyzed by chitin synthases (CS), and up to eight CS-encoding genes can be found in Aspergillus species. This review discusses in detail the chitin synthesis and regulation in Aspergillus species, and how manipulation of chitin synthesis pathways can modulate fungal growth, enzyme production, virulence and susceptibility to antifungal agents. More specifically, the metabolic steps involved in chitin biosynthesis are described with an emphasis on how the initiation of chitin biosynthesis remains unknown. A description of the classification, localization and transport of CS was also made. Chitin biosynthesis is shown to underlie a complex regulatory network, with extensive cross-talks existing between the different signaling pathways. Furthermore, pathways and recently identified regulators of chitin biosynthesis during the caspofungin paradoxical effect (CPE) are described. The effect of a chitin on the mammalian immune system is also discussed. Lastly, interference with chitin biosynthesis may also be beneficial for biotechnological applications. Even after more than 30 years of research, chitin biosynthesis remains a topic of current interest in mycology.
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Affiliation(s)
- Veronica S. Brauer
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo 01000-000, Brazil
| | - André M. Pessoni
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo 01000-000, Brazil
| | - Mateus S. Freitas
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo 01000-000, Brazil
| | - Marinaldo P. Cavalcanti-Neto
- Integrated Laboratory of Morphofunctional Sciences, Institute of Biodiversity and Sustainability (NUPEM), Federal University of Rio de Janeiro, Rio de Janeiro 27965-045, Brazil
| | - Laure N. A. Ries
- MRC Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, UK
- Correspondence: (L.N.A.R.); (F.A.)
| | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo 01000-000, Brazil
- Correspondence: (L.N.A.R.); (F.A.)
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23
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Using Kinetic Modelling to Infer Adaptations in Saccharomyces cerevisiae Carbohydrate Storage Metabolism to Dynamic Substrate Conditions. Metabolites 2023; 13:metabo13010088. [PMID: 36677014 PMCID: PMC9862193 DOI: 10.3390/metabo13010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023] Open
Abstract
Microbial metabolism is strongly dependent on the environmental conditions. While these can be well controlled under laboratory conditions, large-scale bioreactors are characterized by inhomogeneities and consequently dynamic conditions for the organisms. How Saccharomyces cerevisiae response to frequent perturbations in industrial bioreactors is still not understood mechanistically. To study the adjustments to prolonged dynamic conditions, we used published repeated substrate perturbation regime experimental data, extended it with proteomic measurements and used both for modelling approaches. Multiple types of data were combined; including quantitative metabolome, 13C enrichment and flux quantification data. Kinetic metabolic modelling was applied to study the relevant intracellular metabolic response dynamics. An existing model of yeast central carbon metabolism was extended, and different subsets of enzymatic kinetic constants were estimated. A novel parameter estimation pipeline based on combinatorial enzyme selection supplemented by regularization was developed to identify and predict the minimum enzyme and parameter adjustments from steady-state to dynamic substrate conditions. This approach predicted proteomic changes in hexose transport and phosphorylation reactions, which were additionally confirmed by proteome measurements. Nevertheless, the modelling also hints at a yet unknown kinetic or regulation phenomenon. Some intracellular fluxes could not be reproduced by mechanistic rate laws, including hexose transport and intracellular trehalase activity during substrate perturbation cycles.
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24
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Holyavkin C, Turanlı-Yıldız B, Yılmaz Ü, Alkım C, Arslan M, Topaloğlu A, Kısakesen Hİ, de Billerbeck G, François JM, Çakar ZP. Genomic, transcriptomic, and metabolic characterization of 2-Phenylethanol-resistant Saccharomyces cerevisiae obtained by evolutionary engineering. Front Microbiol 2023; 14:1148065. [PMID: 37113225 PMCID: PMC10127108 DOI: 10.3389/fmicb.2023.1148065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/13/2023] [Indexed: 04/29/2023] Open
Abstract
2-Phenylethanol is an aromatic compound commonly used in the food, cosmetic, and pharmaceutical industries. Due to increasing demand for natural products by consumers, the production of this flavor by microbial fermentation is gaining interest, as a sustainable alternative to chemical synthesis or expensive plant extraction, both processes relying on the use of fossil resources. However, the drawback of the fermentation process is the high toxicity of 2-phenylethanol to the producing microorganism. The aim of this study was to obtain a 2-phenylethanol-resistant Saccharomyces cerevisiae strain by in vivo evolutionary engineering and characterize the adapted yeast at the genomic, transcriptomic and metabolic levels. For this purpose, the tolerance to 2-phenylethanol was developed by gradually increasing the concentration of this flavor compound through successive batch cultivations, leading to an adapted strain that could tolerate 3.4 g/L of 2-phenylethanol, which was about 3-times better than the reference strain. Genome sequencing of the adapted strain identified point mutations in several genes, notably in HOG1 that encodes the Mitogen-Activated Kinase of the high-osmolarity signaling pathway. As this mutation is localized in the phosphorylation lip of this protein, it likely resulted in a hyperactive protein kinase. Transcriptomic analysis of the adapted strain supported this suggestion by revealing a large set of upregulated stress-responsive genes that could be explained in great part by HOG1-dependent activation of the Msn2/Msn4 transcription factor. Another relevant mutation was found in PDE2 encoding the low affinity cAMP phosphodiesterase, the missense mutation of which may lead to hyperactivation of this enzyme and thereby enhance the stressful state of the 2-phenylethanol adapted strain. In addition, the mutation in CRH1 that encodes a chitin transglycosylase implicated in cell wall remodeling could account for the increased resistance of the adapted strain to the cell wall-degrading enzyme lyticase. Finally, the potent upregulation of ALD3 and ALD4 encoding NAD+ -dependent aldehyde dehydrogenase together with the observed phenylacetate resistance of the evolved strain suggest a resistance mechanism involving conversion of 2-phenylethanol into phenylacetaldehyde and phenylacetate implicating these dehydrogenases.
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Affiliation(s)
- Can Holyavkin
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Burcu Turanlı-Yıldız
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ülkü Yılmaz
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ceren Alkım
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Mevlüt Arslan
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Alican Topaloğlu
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Halil İbrahim Kısakesen
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | | | - Jean Marie François
- Toulouse Biotechnology Institute (TBI), CNRS, INRA, INSA, Université de Toulouse, Toulouse, France
- *Correspondence: Jean Marie François,
| | - Z. Petek Çakar
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
- Z. Petek Çakar,
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25
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Zhang J, Wang N, Chen W, Zhang W, Zhang H, Yu H, Yi Y. Integrated metabolomics and transcriptomics reveal metabolites difference between wild and cultivated Ophiocordyceps sinensis. Food Res Int 2023; 163:112275. [PMID: 36596185 DOI: 10.1016/j.foodres.2022.112275] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022]
Abstract
Ophiocordyceps sinensis is a traditional medicinal fungus endemic to the alpine and high-altitude areas of the Qinghai-Tibet plateau. The scarcity of the wild resource has led to increased attention to artificially cultivated O. sinensis. However, little is known about the metabolic differences and the regulatory mechanisms between cultivated and wild O. sinensis. This study exploited untargeted metabolomics and transcriptomics to uncover the differences in accumulated metabolites and expressed genes between wild and cultivated O. sinensis. Metabolomics results revealed that 368 differentially accumulated metabolites were mainly enriched in biosynthesis of amino acids, biosynthesis of plant secondary metabolites and purine nucleotide metabolism. Cultivated O. sinensis contained more amino acids and derivatives, carbohydrates and derivatives, and phenolic acids than wild O. sinensis, whereas the contents of most nucleosides and nucleotides in wild O. sinensis were significantly higher than in cultivated O. sinensis. Transcriptome analysis indicated that 4430 annotated differentially expressed genes were identified between two types. Integrated metabolomics and transcriptomics analyses suggested that IMPDH, AK, ADSS, guaA and GUK genes might be related to the synthesis of purine nucleotides and nucleosides. Our findings will provide a new insight into the molecular basis of metabolic variations of this medicinal fungus.
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Affiliation(s)
- Jianshuang Zhang
- The State Key Laboratory of Southwest Karst Mountain Biodiversity Conservation of Forestry Administration, School of life sciences, Guizhou Normal University, Guiyang 550025, China; The Key Laboratory of Plant Physiology and Development in Guizhou Province, School of life sciences, Guizhou Normal University, Guiyang 550025, China
| | - Na Wang
- The State Key Laboratory of Southwest Karst Mountain Biodiversity Conservation of Forestry Administration, School of life sciences, Guizhou Normal University, Guiyang 550025, China
| | - Wanxuan Chen
- The Key Laboratory of Plant Physiology and Development in Guizhou Province, School of life sciences, Guizhou Normal University, Guiyang 550025, China
| | - Weiping Zhang
- The State Key Laboratory of Southwest Karst Mountain Biodiversity Conservation of Forestry Administration, School of life sciences, Guizhou Normal University, Guiyang 550025, China
| | - Haoshen Zhang
- The Key Laboratory of Plant Physiology and Development in Guizhou Province, School of life sciences, Guizhou Normal University, Guiyang 550025, China
| | - Hao Yu
- The State Key Laboratory of Southwest Karst Mountain Biodiversity Conservation of Forestry Administration, School of life sciences, Guizhou Normal University, Guiyang 550025, China; The Key Laboratory of Plant Physiology and Development in Guizhou Province, School of life sciences, Guizhou Normal University, Guiyang 550025, China.
| | - Yin Yi
- The State Key Laboratory of Southwest Karst Mountain Biodiversity Conservation of Forestry Administration, School of life sciences, Guizhou Normal University, Guiyang 550025, China; The Key Laboratory of Plant Physiology and Development in Guizhou Province, School of life sciences, Guizhou Normal University, Guiyang 550025, China.
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26
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Qiu C, Tao H, Shen Y, Qi Q, Hou J. Dynamic-tuning yeast storage carbohydrate improves the production of acetyl-CoA-derived chemicals. iScience 2022; 26:105817. [PMID: 36636342 PMCID: PMC9830206 DOI: 10.1016/j.isci.2022.105817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/21/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Acetyl-coenzyme A (Acetyl-CoA) and malonyl-coenzyme A (malonyl-CoA) are important precursors for producing various chemicals, and their availability affects the production of their downstream chemicals. Storage carbohydrates are considered important carbon and energy reservoirs. Herein, we find that regulating the storage carbohydrate synthesis improves metabolic fluxes toward malonyl-CoA. Interestingly, not only directly decreasing storage carbohydrate accumulation improved malonyl-CoA availability but also increasing the storage carbohydrate by UGP1 overexpression enables an even higher production of acetyl-CoA- and malonyl-CoA-derived chemicals. We find that Ugp1p overexpression dynamically regulates the carbon flux to storage carbohydrate synthesis. In early exponential phases, Ugp1 overexpression causes more storage carbohydrate accumulation, while the carbon flux is then redirected toward acetyl-CoA and malonyl-CoA in later phases, thereby contributing to the synthesis of their derived products. Our study demonstrates the importance of storage carbohydrates rearrangement for the availability of acetyl-CoA and malonyl-CoA and therefore will facilitate the synthesis of their derived chemicals.
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Affiliation(s)
- Chenxi Qiu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong 266237, P. R. China
| | - Huilin Tao
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong 266237, P. R. China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong 266237, P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong 266237, P. R. China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong 266237, P. R. China,Corresponding author
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27
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Chen A, Smith JR, Tapia H, Gibney PA. Characterizing phenotypic diversity of trehalose biosynthesis mutants in multiple wild strains of Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2022; 12:jkac196. [PMID: 35929793 PMCID: PMC9635654 DOI: 10.1093/g3journal/jkac196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
In the yeast Saccharomyces cerevisiae, trehalose-6-phospahte synthase (Tps1) and trehalose-6-phosphate phosphatase (Tps2) are the main proteins catalyzing intracellular trehalose production. In addition to Tps1 and Tps2, 2 putative regulatory proteins with less clearly defined roles also appear to be involved with trehalose production, Tps3 and Tsl1. While this pathway has been extensively studied in laboratory strains of S. cerevisiae, we sought to examine the phenotypic consequences of disrupting these genes in wild strains. Here we deleted the TPS1, TPS2, TPS3, and TSL1 genes in 4 wild strains and 1 laboratory strain for comparison. Although some tested phenotypes were not shared between all strains, deletion of TPS1 abolished intracellular trehalose, caused inability to grow on fermentable carbon sources and resulted in severe sporulation deficiency for all 5 strains. After examining tps1 mutant strains expressing catalytically inactive variants of Tps1, our results indicate that Tps1, independent of trehalose production, is a key component for yeast survival in response to heat stress, for regulating sporulation, and growth on fermentable sugars. All tps2Δ mutants exhibited growth impairment on nonfermentable carbon sources, whereas variations were observed in trehalose synthesis, thermosensitivity and sporulation efficiency. tps3Δ and tsl1Δ mutants exhibited mild or no phenotypic disparity from their isogenic wild type although double mutants tps3Δ tsl1Δ decreased the amount of intracellular trehalose production in all 5 strains by 17-45%. Altogether, we evaluated, confirmed, and expanded the phenotypic characteristics associated trehalose biosynthesis mutants. We also identified natural phenotypic variants in multiple strains that could be used to genetically dissect the basis of these traits and then develop mechanistic models connecting trehalose metabolism to diverse cellular processes.
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Affiliation(s)
- Anqi Chen
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Jeremy R Smith
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Hugo Tapia
- Biology Program, California State University—Channel Islands, Camarillo, CA 93012, USA
| | - Patrick A Gibney
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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28
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Xie D, Sun Y, Lei Y. Effect of glucose levels on carbon flow rate, antioxidant status, and enzyme activity of yeast during fermentation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:5333-5347. [PMID: 35318660 DOI: 10.1002/jsfa.11887] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The physiological metabolism of yeast has a significant impact on the quality of fermentation products. The present study aimed to investigate yeast metabolism in response to a changing glucose content environment, especially in fermentation products, as well as the change of carbon flow rate, antioxidant status, and yeast enzyme activity. RESULTS Yeast in a 0 g L-1 glucose level was subjected to carbon starvation stress, cell growth retardation and cell proliferation was significantly inadequate; in the logarithmic growth stage of yeast, at a 30 g L-1 glucose level, the carbon source mainly flowed to tricarboxylic acid cycle and pentose phosphate metabolism, cell division, proliferation, and increased cell growth. In later logarithmic growth period and stable period, carbon flowed into glycerol and trehalose metabolism, to cope with the environmental stress; yeast in 60 and 150 g L-1 glucose levels faced high glucose stress at the beginning, the content of reactive oxygen increased, malondialdehyde content increased, cell damage was reduced through the regulation of superoxide dismutase and catalase enzyme activities, and most of the carbon flowed into the metabolic pathway of ethanol, glycerol, and trehalose to cope with high glucose stress, the pentose phosphate pathway showed a large late influx, and NADPH also started to increase rapidly after 24 h. CONCLUSION Yeast was stressed in a high-sugar environment and ensured the activity of yeast by preferentially increasing the metabolic intensity of trehalose, glycerol, and glycolytic metabolism, weakening tricarboxylic acid metabolism, and first weakening and then increasing pentose phosphate metabolism. © 2022 Society of Chemical Industry.
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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, China
| | - Yingqi Sun
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Yanan Lei
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
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29
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Leonov A, Feldman R, Piano A, Arlia-Ciommo A, Junio JAB, Orfanos E, Tafakori T, Lutchman V, Mohammad K, Elsaser S, Orfali S, Rajen H, Titorenko VI. Diverse geroprotectors differently affect a mechanism linking cellular aging to cellular quiescence in budding yeast. Oncotarget 2022; 13:918-943. [PMID: 35937500 PMCID: PMC9348708 DOI: 10.18632/oncotarget.28256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Anna Leonov
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Rachel Feldman
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Amanda Piano
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | | | | | - Emmanuel Orfanos
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Tala Tafakori
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Vicky Lutchman
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Karamat Mohammad
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Sarah Elsaser
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Sandra Orfali
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Harshvardhan Rajen
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
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30
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Bell PJL, Paras FE, Mandarakas S, Arcenal P, Robinson-Cast S, Grobler AS, Attfield PV. An Electro-Microbial Process to Uncouple Food Production from Photosynthesis for Application in Space Exploration. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071002. [PMID: 35888090 PMCID: PMC9317029 DOI: 10.3390/life12071002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/10/2022] [Accepted: 07/05/2022] [Indexed: 12/21/2022]
Abstract
Here we propose the concept of an electro–microbial route to uncouple food production from photosynthesis, thereby enabling production of nutritious food in space without the need to grow plant-based crops. In the proposed process, carbon dioxide is fixed into ethanol using either chemical catalysis or microbial carbon fixation, and the ethanol created is used as a carbon source for yeast to synthesize food for human or animal consumption. The process depends upon technologies that can utilize electrical energy to fix carbon into ethanol and uses an optimized strain of the yeast Saccharomyces cerevisiae to produce high-quality, food-grade, single-cell protein using ethanol as the sole carbon source in a minimal medium. Crops performing photosynthesis require months to mature and are challenging to grow under the conditions found in space, whereas the electro–microbial process could generate significant quantities of food on demand with potentially high yields and productivities. In this paper we explore the potential to provide yeast-based protein and other nutrients relevant to human dietary needs using only ethanol, urea, phosphate, and inorganic salts as inputs. It should be noted that as well as having potential to provide nutrition in space, this novel approach to food production has many valuable terrestrial applications too. For example, by enabling food production in climatically challenged environments, the electro–microbial process could potentially turn deserts into food bowls. Similarly, surplus electricity generated from large-scale renewable power sources could be used to supplement the human food chain.
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31
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Nagabhyru P, Dinkins RD, Schardl CL. Transcriptome analysis of Epichloë strains in tall fescue in response to drought stress. Mycologia 2022; 114:697-712. [PMID: 35671366 DOI: 10.1080/00275514.2022.2060008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Epichloë coenophiala, a systemic fungal symbiont (endophyte) of tall fescue (Lolium arundinaceum), has been documented to confer to this grass better persistence than plants lacking the endophyte, especially under stress conditions such as drought. The response, if any, of the endophyte to imposition of stress on the host plant has not been characterized previously. Therefore, we investigated effects on gene expression by E. coenophiala and a related endophyte when plant-endophyte symbiota were subjected to acute water-deficit stress. Plants harboring different endophyte strains were grown in sand in the greenhouse, then half were deprived of water for 48 h and the other half were watered controls. RNA was isolated from different plant tissues, and mRNA sequencing (RNA-seq) was conducted to identify genes that were differentially expressed comparing stress treatment with control. We compared two different plants harboring the common toxic E. coenophiala strain (CTE) and two non-ergot-alkaloid-producing Epichloë strains in tall fescue pseudostems, and in a second experiment we compared responses of E. coenophiala CTE in plant pseudostem and crown tissues. The endophytes responded to the stress with increased expression of genes involved in oxidative stress response, oxygen radical detoxification, C-compound carbohydrate metabolism, heat shock, and cellular transport pathways. The magnitude of fungal gene responses during stress varied among plant-endophyte symbiota. Responses in pseudostems and crowns involved some common pathways as well as some tissue-specific pathways. The fungal response to water-deficit stress involved gene expression changes in similar pathways that have been documented for plant stress responses, indicating that Epichloë spp. and their host plants either coordinate stress responses or separately activate similar stress response mechanisms that work together for mutual protection.
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Affiliation(s)
- Padmaja Nagabhyru
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
| | - Randy D Dinkins
- Forage-Animal Production Research Unit, Agricultural Research Service, United States Department of Agriculture, Lexington, Kentucky 40546
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Fungi are key players in extreme ecosystems. Trends Ecol Evol 2022; 37:517-528. [PMID: 35246323 DOI: 10.1016/j.tree.2022.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 12/13/2022]
Abstract
Extreme environments on Earth are typically devoid of macro life forms and are inhabited predominantly by highly adapted and specialized microorganisms. The discovery and persistence of these extremophiles provides tools to model how life arose on Earth and inform us on the limits of life. Fungi, in particular, are among the most extreme-tolerant organisms with highly versatile lifestyles and stunning ecological and morphological plasticity. Here, we overview the most notable examples of extremophilic and stress-tolerant fungi, highlighting their key roles in the functionality and balance of extreme ecosystems. The remarkable ability of fungi to tolerate and even thrive in the most extreme environments, which preclude most organisms, have reshaped current concepts regarding the limits of life on Earth.
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Tan LR, Liu JJ, Deewan A, Lee JW, Xia PF, Rao CV, Jin YS, Wang SG. Genome-wide transcriptional regulation in Saccharomyces cerevisiae in response to carbon dioxide. FEMS Yeast Res 2022; 22:6595876. [PMID: 35640892 DOI: 10.1093/femsyr/foac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 04/30/2022] [Accepted: 05/26/2022] [Indexed: 11/12/2022] Open
Abstract
Sugar metabolism by Saccharomyces cerevisiae produces ample amounts of CO2 under both aerobic and anaerobic conditions. High solubility of CO2 in fermentation media, contributing to enjoyable sensory properties of sparkling wine and beers by S. cerevisiae, might affect yeast metabolism. To elucidate the overlooked effects of CO2 on yeast metabolism, we examined glucose fermentation by S. cerevisiae under CO2 as compared to N2 and O2 limited conditions. While both CO2 and N2 conditions are considered anaerobic, less glycerol and acetate but more ethanol were produced under CO2 condition. Transcriptomic analysis revealed that significantly decreased mRNA levels of GPP1 coding for glycerol-3-phosphate phosphatase in glycerol synthesis explained the reduced glycerol production under CO2 condition. Besides, transcriptional regulations in signal transduction, carbohydrate synthesis, heme synthesis, membrane and cell wall metabolism, and respiration were detected in response to CO2. Interestingly, signal transduction was uniquely regulated under CO2 condition, where up-regulated genes (STE3, MSB2, WSC3, STE12 and TEC1) in the signal sensors and transcriptional factors suggested that MAPK signaling pathway plays a critical role in CO2 sensing and CO2-induced metabolisms in yeast. Our study identifies CO2 as an external stimulus for modulating metabolic activities in yeast and a transcriptional effector for diverse applications.
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Affiliation(s)
- Lin-Rui Tan
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, P. R. China.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jing-Jing Liu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Anshu Deewan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jae Won Lee
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, P. R. China
| | - Christopher V Rao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Shu-Guang Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, P. R. China.,Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao 266237, P. R. China
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Foster B, Tyrawa C, Ozsahin E, Lubberts M, Krogerus K, Preiss R, van der Merwe G. Kveik Brewing Yeasts Demonstrate Wide Flexibility in Beer Fermentation Temperature Tolerance and Exhibit Enhanced Trehalose Accumulation. Front Microbiol 2022; 13:747546. [PMID: 35369501 PMCID: PMC8966892 DOI: 10.3389/fmicb.2022.747546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 02/11/2022] [Indexed: 11/25/2022] Open
Abstract
Traditional Norwegian Farmhouse ale yeasts, also known as kveik, have captured the attention of the brewing community in recent years. Kveik were recently reported as fast fermenting thermo- and ethanol tolerant yeasts with the capacity to produce a variety of interesting flavor metabolites. They are a genetically distinct group of domesticated beer yeasts of admixed origin with one parent from the “Beer 1” clade and the other unknown. While kveik are known to ferment wort efficiently at warmer temperatures, their range of fermentation temperatures and corresponding fermentation efficiencies, remain uncharacterized. In addition, the characteristics responsible for their increased thermotolerance remain largely unknown. Here we demonstrate variation in kveik strains at a wide range of fermentation temperatures and show not all kveik strains are equal in fermentation performance and stress tolerance. Furthermore, we uncovered an increased capacity of kveik strains to accumulate intracellular trehalose, which likely contributes to their increased thermo- and ethanol tolerances. Taken together our results present a clearer picture of the future opportunities presented by Norwegian kveik yeasts and offer further insight into their applications in brewing.
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Affiliation(s)
- Barret Foster
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Caroline Tyrawa
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Emine Ozsahin
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Mark Lubberts
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | | | | | - George van der Merwe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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35
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Kocaefe-Özşen N, Yilmaz B, Alkım C, Arslan M, Topaloğlu A, Kısakesen HLB, Gülsev E, Çakar ZP. Physiological and Molecular Characterization of an Oxidative Stress-Resistant Saccharomyces cerevisiae Strain Obtained by Evolutionary Engineering. Front Microbiol 2022; 13:822864. [PMID: 35283819 PMCID: PMC8911705 DOI: 10.3389/fmicb.2022.822864] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
Oxidative stress is a major stress type observed in yeast bioprocesses, resulting in a decrease in yeast growth, viability, and productivity. Thus, robust yeast strains with increased resistance to oxidative stress are in highly demand by the industry. In addition, oxidative stress is also associated with aging and age-related complex conditions such as cancer and neurodegenerative diseases. Saccharomyces cerevisiae, as a model eukaryote, has been used to study these complex eukaryotic processes. However, the molecular mechanisms underlying oxidative stress responses and resistance are unclear. In this study, we have employed evolutionary engineering (also known as adaptive laboratory evolution – ALE) strategies to obtain an oxidative stress-resistant and genetically stable S. cerevisiae strain. Comparative physiological, transcriptomic, and genomic analyses of the evolved strain were then performed with respect to the reference strain. The results show that the oxidative stress-resistant evolved strain was also cross-resistant against other types of stressors, including heat, freeze-thaw, ethanol, cobalt, iron, and salt. It was also found to have higher levels of trehalose and glycogen production. Further, comparative transcriptomic analysis showed an upregulation of many genes associated with the stress response, transport, carbohydrate, lipid and cofactor metabolic processes, protein phosphorylation, cell wall organization, and biogenesis. Genes that were downregulated included those related to ribosome and RNA processing, nuclear transport, tRNA, and cell cycle. Whole genome re-sequencing analysis of the evolved strain identified mutations in genes related to the stress response, cell wall organization, carbohydrate metabolism/transport, which are in line with the physiological and transcriptomic results, and may give insight toward the complex molecular mechanisms of oxidative stress resistance.
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Affiliation(s)
- Nazlı Kocaefe-Özşen
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Bahtiyar Yilmaz
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ceren Alkım
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Mevlüt Arslan
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Alican Topaloğlu
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Halil L Brahim Kısakesen
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Erdinç Gülsev
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Z Petek Çakar
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
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Lai WC, Hsu HC, Cheng CW, Wang SH, Li WC, Hsieh PS, Tseng TL, Lin TH, Shieh JC. Filament Negative Regulator CDC4 Suppresses Glycogen Phosphorylase Encoded GPH1 that Impacts the Cell Wall-Associated Features in Candida albicans. J Fungi (Basel) 2022; 8:jof8030233. [PMID: 35330235 PMCID: PMC8949380 DOI: 10.3390/jof8030233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023] Open
Abstract
We have previously identified Candida albicans GPH1 (orf19.7021) whose protein product was associated with C. albicans Cdc4. The GPH1 gene is a putative glycogen phosphorylase because its Saccharomyces cerevisiae homolog participates in glycogen catabolism, which involves the synthesis of β-glucan of the fungal cell wall. We made a strain whose CaCDC4 expression is repressed, and GPH1 is constitutively expressed. We established a GPH1 null mutant strain and used it to conduct the in vitro virulence assays that detect cell wall function. The in vitro virulence assay is centered on biofilm formation in which analytic procedures are implemented to evaluate cell surface hydrophobicity; competence, either in stress resistance, germ tube formation, or fibronection association; and the XTT-based adhesion and biofilm formation. We showed that the constitutively expressed GPH1 partially suppresses filamentation when the CaCDC4 expression is repressed. The C. albicans Gph1 protein is reduced in the presence of CaCdc4 in comparison with the absence of CaCdc4. Compared with the wild-type strain, the gph1Δ/gph1Δ mutant displayed a reduction in the capability to form germ tubes and the cell surface hydrophobicity but an increase in binding with fibronectin. Compared with the wild-type strain, the gph1Δ/gph1Δ mutant showed a rise in adhesion, the initial stage of biofilm formation, but displayed a similar capacity to form a mature biofilm. There was no major impact on the gph1Δ/gph1Δ mutant regarding the conditions of cell wall damaging and TOR pathway-associated nutrient depletion. We conclude that GPH1, adversely regulated by the filament suppressor CDC4, contributes to cell wall function in C. albicans.
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Affiliation(s)
- Wei-Chung Lai
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan; (W.-C.L.); (H.-C.H.); (W.C.L.); (P.-S.H.); (T.-L.T.); (T.-H.L.)
| | - Hsiao-Chi Hsu
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan; (W.-C.L.); (H.-C.H.); (W.C.L.); (P.-S.H.); (T.-L.T.); (T.-H.L.)
| | - Chun-Wen Cheng
- Institute of Medicine, Chung Shan Medical University, Taichung City 40201, Taiwan;
| | - Shao-Hung Wang
- Department of Microbiology, Immunology and Biopharmaceuticals, National Chiayi University, Chiayi 60004, Taiwan;
| | - Wan Chen Li
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan; (W.-C.L.); (H.-C.H.); (W.C.L.); (P.-S.H.); (T.-L.T.); (T.-H.L.)
| | - Po-Szu Hsieh
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan; (W.-C.L.); (H.-C.H.); (W.C.L.); (P.-S.H.); (T.-L.T.); (T.-H.L.)
| | - Tzu-Ling Tseng
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan; (W.-C.L.); (H.-C.H.); (W.C.L.); (P.-S.H.); (T.-L.T.); (T.-H.L.)
| | - Ting-Hui Lin
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan; (W.-C.L.); (H.-C.H.); (W.C.L.); (P.-S.H.); (T.-L.T.); (T.-H.L.)
| | - Jia-Ching Shieh
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan; (W.-C.L.); (H.-C.H.); (W.C.L.); (P.-S.H.); (T.-L.T.); (T.-H.L.)
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung City 40201, Taiwan
- Immunology Research Center, Chung Shan Medical University, Taichung City 40201, Taiwan
- Correspondence: ; Tel.: +886-424-730-022 (ext. 11806); Fax: +886-424-757-412
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Lao-Martil D, Verhagen KJA, Schmitz JPJ, Teusink B, Wahl SA, van Riel NAW. Kinetic Modeling of Saccharomyces cerevisiae Central Carbon Metabolism: Achievements, Limitations, and Opportunities. Metabolites 2022; 12:74. [PMID: 35050196 PMCID: PMC8779790 DOI: 10.3390/metabo12010074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/23/2022] Open
Abstract
Central carbon metabolism comprises the metabolic pathways in the cell that process nutrients into energy, building blocks and byproducts. To unravel the regulation of this network upon glucose perturbation, several metabolic models have been developed for the microorganism Saccharomyces cerevisiae. These dynamic representations have focused on glycolysis and answered multiple research questions, but no commonly applicable model has been presented. This review systematically evaluates the literature to describe the current advances, limitations, and opportunities. Different kinetic models have unraveled key kinetic glycolytic mechanisms. Nevertheless, some uncertainties regarding model topology and parameter values still limit the application to specific cases. Progressive improvements in experimental measurement technologies as well as advances in computational tools create new opportunities to further extend the model scale. Notably, models need to be made more complex to consider the multiple layers of glycolytic regulation and external physiological variables regulating the bioprocess, opening new possibilities for extrapolation and validation. Finally, the onset of new data representative of individual cells will cause these models to evolve from depicting an average cell in an industrial fermenter, to characterizing the heterogeneity of the population, opening new and unseen possibilities for industrial fermentation improvement.
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Affiliation(s)
- David Lao-Martil
- Department of Biomedical Engineering, Eindhoven University of Technology, Groene Loper 5, 5612 AE Eindhoven, The Netherlands;
| | - Koen J. A. Verhagen
- Lehrstuhl für Bioverfahrenstechnik, FAU Erlangen-Nürnberg, 91052 Erlangen, Germany; (K.J.A.V.); (S.A.W.)
| | - Joep P. J. Schmitz
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands;
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands;
| | - S. Aljoscha Wahl
- Lehrstuhl für Bioverfahrenstechnik, FAU Erlangen-Nürnberg, 91052 Erlangen, Germany; (K.J.A.V.); (S.A.W.)
| | - Natal A. W. van Riel
- Department of Biomedical Engineering, Eindhoven University of Technology, Groene Loper 5, 5612 AE Eindhoven, The Netherlands;
- Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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38
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Alvarado-Fernández AM, Rodríguez-López EA, Espejo-Mojica AJ, Mosquera-Arévalo AR, Alméciga-Díaz CJ, Trespalacios-Rangel AA. Effect of two preservation methods on the viability and enzyme production of a recombinant Komagataella phaffii (Pichia pastoris) strain. Cryobiology 2021; 105:32-40. [PMID: 34951975 DOI: 10.1016/j.cryobiol.2021.12.004] [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: 06/15/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 11/18/2022]
Abstract
The methylotrophic yeast Komagataella phaffii, previously known as Pichia pastoris, has been reported as a host for producing human recombinant lysosomal enzymes intended for enzyme replacement therapy. K. phaffii has advantages such as easy genetic handling, rapid growth, cost-effective mediums, and the ability to develop mammalian-like post-translational modifications. To maintain cell viability and enzyme activity over time, it is important to consider the bioprocess optimization and the proper selection and preservation of clones. In this study, we evaluated the effect of glycerol and skim milk in cryopreservation at -80 °C, as well as the use of skim milk or its combination with NaCl, disaccharides or sorbitol in freeze-drying on the cell viability and activity of a recombinant lysosomal enzyme (i.e., human β-hexosaminidase-A) produced in K. phaffii GS115 strain. The results showed that cryopreservation with glycerol and skim milk, as well as freeze-drying using disaccharides and sorbitol with skim milk, maintained the viability above 80%. Although variations in enzyme activity among treatments were found, the use of disaccharides had a positive effect on the enzymatic activity levels. This is the first report of the evaluation of two suitable methods to preserve a recombinant K. phaffii strain, preventing the loss of viability and maintaining the activity of the recombinant protein.
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Affiliation(s)
| | - Edwin Alexander Rodríguez-López
- Institute for the Study of Inborn Errors of Metabolism. Faculty of Sciences. Pontificia Universidad Javeriana. Bogotá D.C., Colombia; Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC). Bogotá D.C., Colombia.
| | - Angela Johana Espejo-Mojica
- Institute for the Study of Inborn Errors of Metabolism. Faculty of Sciences. Pontificia Universidad Javeriana. Bogotá D.C., Colombia.
| | | | - Carlos Javier Alméciga-Díaz
- Institute for the Study of Inborn Errors of Metabolism. Faculty of Sciences. Pontificia Universidad Javeriana. Bogotá D.C., Colombia.
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Caloric restriction causes a distinct reorganization of the lipidome in quiescent and non-quiescent cells of budding yeast. Oncotarget 2021; 12:2351-2374. [PMID: 34853658 PMCID: PMC8629408 DOI: 10.18632/oncotarget.28133] [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: 10/01/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022] Open
Abstract
After budding yeast cells cultured in a nutrient-rich liquid medium with 0.2% glucose (under caloric restriction conditions) or 2% glucose (under non-caloric restriction conditions), ferment glucose to ethanol and then consume ethanol, they enter the stationary phase. The process of their chronological aging begins. At that point, the yeast culture starts to accumulate quiescent and non-quiescent cells. Here, we purified the high- and low-density populations of quiescent and non-quiescent cells from the yeast cultures limited in calorie supply or not. We then employed mass spectrometry-based quantitative lipidomics to assess the aging-associated changes in high- and low-density cells’ lipidomes. We found that caloric restriction, a geroprotective dietary intervention, alters the concentrations of many lipid classes through most of the chronological lifespan of the high- and low-density populations of quiescent and non-quiescent cells. Specifically, caloric restriction decreased triacylglycerol, increased free fatty acid, elevated phospholipid and amplified cardiolipin concentrations. Based on these findings, we propose a hypothetical model for a caloric restriction-dependent reorganization of lipid metabolism in budding yeast’s quiescent and non-quiescent cells. We also discovered that caloric restriction creates lipidomic patterns of these cells that differ from those established by two other robust geroprotectors, namely the tor1Δ mutation and lithocholic acid.
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Hollenstein DM, Gérecová G, Romanov N, Ferrari J, Veis J, Janschitz M, Beyer R, Schüller C, Ogris E, Hartl M, Ammerer G, Reiter W. A phosphatase-centric mechanism drives stress signaling response. EMBO Rep 2021; 22:e52476. [PMID: 34558777 PMCID: PMC8567219 DOI: 10.15252/embr.202152476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 12/14/2022] Open
Abstract
Changing environmental cues lead to the adjustment of cellular physiology by phosphorylation signaling networks that typically center around kinases as active effectors and phosphatases as antagonistic elements. Here, we report a signaling mechanism that reverses this principle. Using the hyperosmotic stress response in Saccharomyces cerevisiae as a model system, we find that a phosphatase-driven mechanism causes induction of phosphorylation. The key activating step that triggers this phospho-proteomic response is the Endosulfine-mediated inhibition of protein phosphatase 2A-Cdc55 (PP2ACdc55 ), while we do not observe concurrent kinase activation. In fact, many of the stress-induced phosphorylation sites appear to be direct substrates of the phosphatase, rendering PP2ACdc55 the main downstream effector of a signaling response that operates in parallel and independent of the well-established kinase-centric stress signaling pathways. This response affects multiple cellular processes and is required for stress survival. Our results demonstrate how a phosphatase can assume the role of active downstream effectors during signaling and allow re-evaluating the impact of phosphatases on shaping the phosphorylome.
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Affiliation(s)
- David Maria Hollenstein
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | - Gabriela Gérecová
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | | | - Jessica Ferrari
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | - Jiri Veis
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
- Center for Medical BiochemistryMax Perutz Labs, Vienna BioCenterMedical University of ViennaViennaAustria
| | - Marion Janschitz
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | - Reinhard Beyer
- Department of Applied Genetics and Cell Biology (DAGZ)University of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln a.d. DonauAustria
| | - Christoph Schüller
- Department of Applied Genetics and Cell Biology (DAGZ)University of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln a.d. DonauAustria
| | - Egon Ogris
- Center for Medical BiochemistryMax Perutz Labs, Vienna BioCenterMedical University of ViennaViennaAustria
| | - Markus Hartl
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
- Mass Spectrometry FacilityMax Perutz Labs, Vienna BioCenterUniversity of ViennaViennaAustria
| | - Gustav Ammerer
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | - Wolfgang Reiter
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
- Mass Spectrometry FacilityMax Perutz Labs, Vienna BioCenterUniversity of ViennaViennaAustria
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41
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Arhar S, Gogg-Fassolter G, Ogrizović M, Pačnik K, Schwaiger K, Žganjar M, Petrovič U, Natter K. Engineering of Saccharomyces cerevisiae for the accumulation of high amounts of triacylglycerol. Microb Cell Fact 2021; 20:147. [PMID: 34315498 PMCID: PMC8314538 DOI: 10.1186/s12934-021-01640-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/19/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Fatty acid-based substances play an important role in many products, from food supplements to pharmaceutical products and biofuels. The production of fatty acids, mainly in their esterified form as triacylglycerol (TAG), has been intensively studied in oleaginous yeasts, whereas much less effort has been invested into non-oleaginous species. In the present work, we engineered the model yeast Saccharomyces cerevisiae, which is commonly regarded as non-oleaginous, for the storage of high amounts of TAG, comparable to the contents achieved in oleaginous yeasts. RESULTS We investigated the effects of several mutations with regard to increased TAG accumulation and identified six of them as important for this phenotype: a point mutation in the acetyl-CoA carboxylase Acc1p, overexpression of the diacylglycerol acyltransferase Dga1p, deletions of genes coding for enzymes involved in the competing pathways glycogen and steryl ester synthesis and TAG hydrolysis, and a deletion of CKB1, the gene coding for one of the regulatory subunits of casein kinase 2. With the combination of these mutations in a S. cerevisiae strain with a relatively high neutral lipid level already in the non-engineered state, we achieved a TAG content of 65% in the dry biomass. High TAG levels were not only obtained under conditions that favor lipid accumulation, but also in defined standard carbon-limited media. CONCLUSIONS Baker's yeast, which is usually regarded as inefficient in the storage of TAG, can be converted into a highly oleaginous strain that could be useful in processes aiming at the synthesis of fatty acid-based products. This work emphasizes the importance of strain selection in combination with metabolic engineering to obtain high product levels.
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Affiliation(s)
- Simon Arhar
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
| | - Gabriela Gogg-Fassolter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
| | - Mojca Ogrizović
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Klavdija Pačnik
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
| | - Katharina Schwaiger
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
| | - Mia Žganjar
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Uroš Petrovič
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria.
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Zhou X, Li J, Tang N, Xie H, Fan X, Chen H, Tang M, Xie X. Genome-Wide Analysis of Nutrient Signaling Pathways Conserved in Arbuscular Mycorrhizal Fungi. Microorganisms 2021; 9:1557. [PMID: 34442636 PMCID: PMC8401276 DOI: 10.3390/microorganisms9081557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/03/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi form a mutualistic symbiosis with a majority of terrestrial vascular plants. To achieve an efficient nutrient trade with their hosts, AM fungi sense external and internal nutrients, and integrate different hierarchic regulations to optimize nutrient acquisition and homeostasis during mycorrhization. However, the underlying molecular networks in AM fungi orchestrating the nutrient sensing and signaling remain elusive. Based on homology search, we here found that at least 72 gene components involved in four nutrient sensing and signaling pathways, including cAMP-dependent protein kinase A (cAMP-PKA), sucrose non-fermenting 1 (SNF1) protein kinase, target of rapamycin kinase (TOR) and phosphate (PHO) signaling cascades, are well conserved in AM fungi. Based on the knowledge known in model yeast and filamentous fungi, we outlined the possible gene networks functioning in AM fungi. These pathways may regulate the expression of downstream genes involved in nutrient transport, lipid metabolism, trehalase activity, stress resistance and autophagy. The RNA-seq analysis and qRT-PCR results of some core genes further indicate that these pathways may play important roles in spore germination, appressorium formation, arbuscule longevity and sporulation of AM fungi. We hope to inspire further studies on the roles of these candidate genes involved in these nutrient sensing and signaling pathways in AM fungi and AM symbiosis.
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Affiliation(s)
- Xiaoqin Zhou
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Jiangyong Li
- Institute for Environmental and Climate Research, Jinan University, Guangzhou 511443, China;
| | - Nianwu Tang
- UMR Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280 Champenoux, France;
| | - Hongyun Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xiaoning Fan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
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43
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Casas-Godoy L, Arellano-Plaza M, Kirchmayr M, Barrera-Martínez I, Gschaedler-Mathis A. Preservation of non-Saccharomyces yeasts: Current technologies and challenges. Compr Rev Food Sci Food Saf 2021; 20:3464-3503. [PMID: 34096187 DOI: 10.1111/1541-4337.12760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/05/2021] [Accepted: 03/29/2021] [Indexed: 11/30/2022]
Abstract
There is a recent and growing interest in the study and application of non-Saccharomyces yeasts, mainly in fermented foods. Numerous publications and patents show the importance of these yeasts. However, a fundamental issue in studying and applying them is to ensure an appropriate preservation scheme that allows to the non-Saccharomyces yeasts conserve their characteristics and fermentative capabilities by long periods of time. The main objective of this review is to present and analyze the techniques available to preserve these yeasts (by conventional and non-conventional methods), in small or large quantities for laboratory or industrial applications, respectively. Wine fermentation is one of the few industrial applications of non-Saccharomyces yeasts, but the preservation stage has been a major obstacle to achieve a wider application of these yeasts. This review considers the preservation techniques, and clearly defines parameters such as culturability, viability, vitality and robustness. Several conservation strategies published in research articles as well as patents are analyzed, and the advantages and disadvantages of each technique used are discussed. Another important issue during conservation processes is the stress to which yeasts are subjected at the time of preservation (mainly oxidative stress). There is little published information on the subject for non-Saccharomyces yeast, but it is a fundamental point to consider when designing a preservation strategy.
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Affiliation(s)
- Leticia Casas-Godoy
- Industrial Biotechnology Unit, National Council for Science and Technology-Center for Research and Assistance in Technology and Design of the State of Jalisco, Zapopan, Mexico
| | - Melchor Arellano-Plaza
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Zapopan, Mexico
| | - Manuel Kirchmayr
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Zapopan, Mexico
| | - Iliana Barrera-Martínez
- Industrial Biotechnology Unit, National Council for Science and Technology-Center for Research and Assistance in Technology and Design of the State of Jalisco, Zapopan, Mexico
| | - Anne Gschaedler-Mathis
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Zapopan, Mexico
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44
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Saccharomyces cerevisiae Gene Expression during Fermentation of Pinot Noir Wines at an Industrially Relevant Scale. Appl Environ Microbiol 2021; 87:AEM.00036-21. [PMID: 33741633 PMCID: PMC8208162 DOI: 10.1128/aem.00036-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
This study characterized Saccharomyces cerevisiae RC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using industry-relevant conditions. The reported gene expression patterns of RC212 are generally similar to those observed under laboratory fermentation conditions but also contain gene expression signatures related to yeast-environment interactions found in a production setting (e.g., the presence of non-Saccharomyces microorganisms). Saccharomyces cerevisiae metabolism produces ethanol and other compounds during the fermentation of grape must into wine. Thousands of genes change expression over the course of a wine fermentation, allowing S. cerevisiae to adapt to and dominate the fermentation environment. Investigations into these gene expression patterns previously revealed genes that underlie cellular adaptation to the grape must and wine environments, involving metabolic specialization and ethanol tolerance. However, the majority of studies detailing gene expression patterns have occurred in controlled environments that may not recapitulate the biological and chemical complexity of fermentations performed at production scale. Here, an analysis of the S. cerevisiae RC212 gene expression program is presented, drawing from 40 pilot-scale fermentations (150 liters) using Pinot noir grapes from 10 California vineyards across two vintages. A core gene expression program was observed across all fermentations irrespective of vintage, similar to that of laboratory fermentations, in addition to novel gene expression patterns likely related to the presence of non-Saccharomyces microorganisms and oxygen availability during fermentation. These gene expression patterns, both common and diverse, provide insight into Saccharomyces cerevisiae biology critical to fermentation outcomes under industry-relevant conditions. IMPORTANCE This study characterized Saccharomyces cerevisiae RC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using industry-relevant conditions. The reported gene expression patterns of RC212 are generally similar to those observed under laboratory fermentation conditions but also contain gene expression signatures related to yeast-environment interactions found in a production setting (e.g., the presence of non-Saccharomyces microorganisms). Key genes and pathways highlighted by this work remain undercharacterized, indicating the need for further research to understand the roles of these genes and their impact on industrial wine fermentation outcomes.
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45
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Chen H, Chen H, Lu H, Tang X, Zhang H, Chen YQ, Chen W. Carbohydrate analysis of Mortierella alpina by colorimetry and HPLC-ELSD to reveal accumulation differences of sugar and lipid. Biotechnol Lett 2021; 43:1289-1301. [PMID: 33864523 DOI: 10.1007/s10529-021-03120-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 03/23/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES To establish reliable methods for the extraction and quantification of the total carbohydrate and intracellular saccharides from Mortierella alpina and study the changes between carbohydrate and lipid in fermentation process. RESULTS The extraction of mycelia with HCl following a photometric phenol-sulphuric acid reaction was identified as an optimal method for total carbohydrate analysis in Mortierella alpina, which the extraction efficiency performed 1.1-3.6 fold than other five methods. The total carbohydrate content increased from initial 19.26 to 25.86% during early fermentation process and declined gradually thereafter, while the fatty acid was increasing from 8.47 to 31.03%. For separation and qualitative estimation of intracellular saccharides, the acetonitrile/water freeze-thaw method for extraction and Sugar-Pak I column for separation proved to be possible. With the glucose rapidly decreasing at the beginning of growth, the trehalose accumulated rapidly from 1.63 to 5.04% and then decreased slightly but maintain above 4% of dry biomass. CONCLUSIONS This work established comprehensive carbohydrate extraction and analysis methods of Mortierella alpina and identified the main saccharide in fermentation process which indicated that the accumulation of fatty acids was related to the change of intracellular carbohydrate content.
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Affiliation(s)
- Hanqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China. .,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.
| | - Hengqian Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.,Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China
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46
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Yu R, Cao X, Sun L, Zhu JY, Wasko BM, Liu W, Crutcher E, Liu H, Jo MC, Qin L, Kaeberlein M, Han Z, Dang W. Inactivating histone deacetylase HDA promotes longevity by mobilizing trehalose metabolism. Nat Commun 2021; 12:1981. [PMID: 33790287 PMCID: PMC8012573 DOI: 10.1038/s41467-021-22257-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 03/02/2021] [Indexed: 02/01/2023] Open
Abstract
Histone acetylations are important epigenetic markers for transcriptional activation in response to metabolic changes and various stresses. Using the high-throughput SEquencing-Based Yeast replicative Lifespan screen method and the yeast knockout collection, we demonstrate that the HDA complex, a class-II histone deacetylase (HDAC), regulates aging through its target of acetylated H3K18 at storage carbohydrate genes. We find that, in addition to longer lifespan, disruption of HDA results in resistance to DNA damage and osmotic stresses. We show that these effects are due to increased promoter H3K18 acetylation and transcriptional activation in the trehalose metabolic pathway in the absence of HDA. Furthermore, we determine that the longevity effect of HDA is independent of the Cyc8-Tup1 repressor complex known to interact with HDA and coordinate transcriptional repression. Silencing the HDA homologs in C. elegans and Drosophila increases their lifespan and delays aging-associated physical declines in adult flies. Hence, we demonstrate that this HDAC controls an evolutionarily conserved longevity pathway.
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Affiliation(s)
- Ruofan Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Xiaohua Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Luyang Sun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Jun-Yi Zhu
- Center for Precision Disease Modeling, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Brian M Wasko
- Department of Pathology, University of Washington, Seattle, WA, USA
- University of Houston, Clear Lake, TX, USA
| | - Wei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Emeline Crutcher
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Haiying Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | | | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Zhe Han
- Center for Precision Disease Modeling, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Weiwei Dang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.
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47
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Gupta R, Laxman S. Cycles, sources, and sinks: Conceptualizing how phosphate balance modulates carbon flux using yeast metabolic networks. eLife 2021; 10:e63341. [PMID: 33544078 PMCID: PMC7864628 DOI: 10.7554/elife.63341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Phosphates are ubiquitous molecules that enable critical intracellular biochemical reactions. Therefore, cells have elaborate responses to phosphate limitation. Our understanding of long-term transcriptional responses to phosphate limitation is extensive. Contrastingly, a systems-level perspective presenting unifying biochemical concepts to interpret how phosphate balance is critically coupled to (and controls) metabolic information flow is missing. To conceptualize such processes, utilizing yeast metabolic networks we categorize phosphates utilized in metabolism into cycles, sources and sinks. Through this, we identify metabolic reactions leading to putative phosphate sources or sinks. With this conceptualization, we illustrate how mass action driven flux towards sources and sinks enable cells to manage phosphate availability during transient/immediate phosphate limitations. We thereby identify how intracellular phosphate availability will predictably alter specific nodes in carbon metabolism, and determine signature cellular metabolic states. Finally, we identify a need to understand intracellular phosphate pools, in order to address mechanisms of phosphate regulation and restoration.
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Affiliation(s)
- Ritu Gupta
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
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48
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Elbakush AE, Güven D. Evaluation of ethanol tolerance in relation to intracellular storage compounds of Saccharomyces cerevisiae using FT-IR spectroscopy. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.11.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Garcia-Albornoz M, Holman SW, Antonisse T, Daran-Lapujade P, Teusink B, Beynon RJ, Hubbard SJ. A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae. Mol Omics 2021; 16:59-72. [PMID: 31868867 DOI: 10.1039/c9mo00136k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Integrated regulatory networks can be powerful tools to examine and test properties of cellular systems, such as modelling environmental effects on the molecular bioeconomy, where protein levels are altered in response to changes in growth conditions. Although extensive regulatory pathways and protein interaction data sets exist which represent such networks, few have formally considered quantitative proteomics data to validate and extend them. We generate and consider such data here using a label-free proteomics strategy to quantify alterations in protein abundance for S. cerevisiae when grown on minimal media using glucose, galactose, maltose and trehalose as sole carbon sources. Using a high quality-controlled subset of proteins observed to be differentially abundant, we constructed a proteome-informed network, comprising 1850 transcription factor interactions and 37 chaperone interactions, which defines the major changes in the cellular proteome when growing under different carbon sources. Analysis of the differentially abundant proteins involved in the regulatory network pointed to their significant roles in specific metabolic pathways and function, including glucose homeostasis, amino acid biosynthesis, and carbohydrate metabolic process. We noted strong statistical enrichment in the differentially abundant proteome of targets of known transcription factors associated with stress responses and altered carbon metabolism. This shows how such integrated analysis can lend further experimental support to annotated regulatory interactions, since the proteomic changes capture both magnitude and direction of gene expression change at the level of the affected proteins. Overall this study highlights the power of quantitative proteomics to help define regulatory systems pertinent to environmental conditions.
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Affiliation(s)
- M Garcia-Albornoz
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester M13 9PT, UK.
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50
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Tourigny DS. Cooperative metabolic resource allocation in spatially-structured systems. J Math Biol 2021; 82:5. [PMID: 33479850 DOI: 10.1007/s00285-021-01558-6] [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: 12/05/2019] [Revised: 06/30/2020] [Accepted: 10/27/2020] [Indexed: 10/22/2022]
Abstract
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic metabolic resource allocation based on the maximum entropy principle to spatiotemporal models of metabolism with cooperation. Much like the maximum entropy principle encapsulates 'bet-hedging' behaviour displayed by organisms dealing with future uncertainty in a fluctuating environment, its cooperative extension describes how individuals adapt their metabolic resource allocation strategy to further accommodate limited knowledge about the welfare of others within a community. The resulting theory explains why local regulation of metabolic cross-feeding can fulfil a community-wide metabolic objective if individuals take into consideration an ensemble measure of total population performance as the only form of global information. The latter is likely supplied by quorum sensing in microbial systems or signalling molecules such as hormones in multi-cellular eukaryotic organisms.
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Affiliation(s)
- David S Tourigny
- Columbia University Irving Medical Center, 630 West 168th Street, New York, NY, 10032, USA.
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