1
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Walker RM, Sanabria VC, Youk H. Microbial life in slow and stopped lanes. Trends Microbiol 2024; 32:650-662. [PMID: 38123400 PMCID: PMC11187706 DOI: 10.1016/j.tim.2023.11.014] [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: 10/16/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Microbes in nature often lack nutrients and face extreme or widely fluctuating temperatures, unlike microbes in growth-optimized settings in laboratories that much of the literature examines. Slowed or suspended lives are the norm for microbes. Studying them is important for understanding the consequences of climate change and for addressing fundamental questions about life: are there limits to how slowly a cell's life can progress, and how long cells can remain viable without self-replicating? Recent studies began addressing these questions with single-cell-level measurements and mathematical models. Emerging principles that govern slowed or suspended lives of cells - including lives of dormant spores and microbes at extreme temperatures - are re-defining discrete cellular states as continuums and revealing intracellular dynamics at new timescales. Nearly inactive, lifeless-appearing microbes are transforming our understanding of life.
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Affiliation(s)
- Rachel M Walker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Valeria C Sanabria
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hyun Youk
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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2
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Sakai K, Kondo Y, Goto Y, Aoki K. Cytoplasmic fluidization contributes to breaking spore dormancy in fission yeast. Proc Natl Acad Sci U S A 2024; 121:e2405553121. [PMID: 38889144 PMCID: PMC11214080 DOI: 10.1073/pnas.2405553121] [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: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/20/2024] Open
Abstract
The cytoplasm is a complex, crowded environment that influences myriad cellular processes including protein folding and metabolic reactions. Recent studies have suggested that changes in the biophysical properties of the cytoplasm play a key role in cellular homeostasis and adaptation. However, it still remains unclear how cells control their cytoplasmic properties in response to environmental cues. Here, we used fission yeast spores as a model system of dormant cells to elucidate the mechanisms underlying regulation of the cytoplasmic properties. By tracking fluorescent tracer particles, we found that particle mobility decreased in spores compared to vegetative cells and rapidly increased at the onset of dormancy breaking upon glucose addition. This cytoplasmic fluidization depended on glucose-sensing via the cyclic adenosine monophosphate-protein kinase A pathway. PKA activation led to trehalose degradation through trehalase Ntp1, thereby increasing particle mobility as the amount of trehalose decreased. In contrast, the rapid cytoplasmic fluidization did not require de novo protein synthesis, cytoskeletal dynamics, or cell volume increase. Furthermore, the measurement of diffusion coefficients with tracer particles of different sizes suggests that the spore cytoplasm impedes the movement of larger protein complexes (40 to 150 nm) such as ribosomes, while allowing free diffusion of smaller molecules (~3 nm) such as second messengers and signaling proteins. Our experiments have thus uncovered a series of signaling events that enable cells to quickly fluidize the cytoplasm at the onset of dormancy breaking.
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Affiliation(s)
- Keiichiro Sakai
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
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3
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Chen R, Qiu K, Leong DCY, Kundu BK, Zhang C, Srivastava P, White KE, Li G, Han G, Guo Z, Elles CG, Diao J, Sun Y. A general design of pyridinium-based fluorescent probes for enhancing two-photon microscopy. Biosens Bioelectron 2023; 239:115604. [PMID: 37607448 PMCID: PMC10529004 DOI: 10.1016/j.bios.2023.115604] [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: 06/14/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023]
Abstract
Two-photon absorbing fluorescent probes have emerged as powerful imaging tools for subcellular-level monitoring of biological substances and processes, offering advantages such as deep light penetration, minimal photodamage, low autofluorescence, and high spatial resolution. However, existing two-photon absorbing probes still face several limitations, such as small two-photon absorption cross-section, poor water solubility, low membrane permeability, and potentially high toxicity. Herein, we report three small-molecule probes, namely MSP-1arm, Lyso-2arm, and Mito-3arm, composed of a pyridinium center (electron-acceptor) and various methoxystyrene "arms" (electron-donor). These probes exhibit excellent fluorescence quantum yield and decent aqueous solubility. Leveraging the inherent intramolecular charge transfer and excitonic coupling effect, these complexes demonstrate excellent two-photon absorption in the near-infrared region. Notably, Lyso-2arm and Mito-3arm exhibit distinct targeting abilities for lysosomes and mitochondria, respectively. In two-photon microscopy experiments, Mito-3arm outperforms a commercial two-photon absorbing dye in 2D monolayer HeLa cells, delivering enhanced resolution, broader NIR light excitation window, and higher signal-to-noise ratio. Moreover, the two-photon bioimaging of 3D human forebrain organoids confirms the successful deep tissue imaging capabilities of both Lyso-2arm and Mito-3arm. Overall, this work presents a rational design strategy in developing competent two-photon-absorbing probes by varying the number of conjugated "arms" for bioimaging applications.
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Affiliation(s)
- Rui Chen
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Kangqiang Qiu
- Department of Cancer Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Daniel C Y Leong
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Bidyut Kumar Kundu
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Chengying Zhang
- Department of Cancer Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | | | - Katie E White
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Guodong Li
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Guanqun Han
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Ziyuan Guo
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | | | - Jiajie Diao
- Department of Cancer Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA.
| | - Yujie Sun
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA.
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4
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Chen R, Qiu K, Han G, Kundu BK, Ding G, Sun Y, Diao J. Quantifying cell viability through organelle ratiometric probing. Chem Sci 2023; 14:10236-10248. [PMID: 37772119 PMCID: PMC10530868 DOI: 10.1039/d3sc01537h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/06/2023] [Indexed: 09/30/2023] Open
Abstract
Detecting cell viability is crucial in research involving the precancerous discovery of abnormal cells, the evaluation of treatments, and drug toxicity testing. Although conventional methods afford cumulative results regarding cell viability based on a great number of cells, they do not permit investigating cell viability at the single-cell level. In response, we rationally designed and synthesized a fluorescent probe, PCV-1, to visualize cell viability under the super-resolution technology of structured illumination microscopy. Given its sensitivity to mitochondrial membrane potential and affinity to DNA, PCV-1's ability to stain mitochondria and nucleoli was observed in live and dead cells, respectively. During cell injury induced by drug treatment, PCV-1's migration from mitochondria to the nucleolus was dynamically visualized at the single-cell level. By extension, harnessing PCV-1's excellent photostability and signal-to-noise ratio and by comparing the fluorescence intensity of the two organelles, mitochondria and nucleoli, we developed a powerful analytical assay named organelle ratiometric probing (ORP) that we applied to quantitatively analyze and efficiently assess the viability of individual cells, thereby enabling deeper insights into the potential mechanisms of cell death. In ORP analysis with PCV-1, we identified 0.3 as the cutoff point for assessing whether adding a given drug will cause apparent cytotoxicity, which greatly expands the probe's applicability. To the best of our knowledge, PCV-1 is the first probe to allow visualizing cell death and cell injury under super-resolution imaging, and our proposed analytical assay using it paves the way for quantifying cell viability at the single-cell level.
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Affiliation(s)
- Rui Chen
- Department of Chemistry, University of Cincinnati Cincinnati OH 45221 USA
| | - Kangqiang Qiu
- Department of Cancer Biology, College of Medicine, University of Cincinnati Cincinnati OH 45267 USA
| | - Guanqun Han
- Department of Chemistry, University of Cincinnati Cincinnati OH 45221 USA
| | - Bidyut Kumar Kundu
- Department of Chemistry, University of Cincinnati Cincinnati OH 45221 USA
| | - Guodong Ding
- Department of Chemistry, University of Cincinnati Cincinnati OH 45221 USA
| | - Yujie Sun
- Department of Chemistry, University of Cincinnati Cincinnati OH 45221 USA
| | - Jiajie Diao
- Department of Cancer Biology, College of Medicine, University of Cincinnati Cincinnati OH 45267 USA
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5
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Segers FJ, Dijksterhuis J, Giesbers M, Debets AJ. Natural folding of airborne fungal spores: a mechanism for dispersal and long-term survival? FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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Chen R, Qiu K, Han G, Kundu BK, Ding G, Sun Y, Diao J. Quantifying cell viability through organelle ratiometric probing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538448. [PMID: 37163053 PMCID: PMC10168353 DOI: 10.1101/2023.04.26.538448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Detecting cell viability is crucial in research involving the precancerous discovery of abnormal cells, the evaluation of treatments, and drug toxicity testing. Although conventional methods afford cumulative results regarding cell viability based on a great number of cells, they do not permit investigating cell viability at the single-cell level. In response, we rationally designed and synthesized a fluorescent probe, PCV-1, to visualize cell viability under the super-resolution technology of structured illumination microscopy. Given its sensitivity to mitochondrial membrane potential and affinity to DNA, PCV-1's ability to stain mitochondria and nucleoli was observed in live and dead cells, respectively. During cell injury induced by drug treatment, PCV-1's migration from mitochondria to the nucleolus was dynamically visualized at the single-cell level. By extension, harnessing PCV-1's excellent photostability and signal-to-noise ratio and by comparing the fluorescence intensity of the two organelles, mitochondria and nucleoli, we developed a powerful analytical assay named organelle ratiometric probing (ORP) that we applied to quantitatively analyze and efficiently assess the viability of individual cells, thereby enabling deeper insights into the potential mechanisms of cell death. In ORP analysis with PCV-1, we identified 0.3 as the cutoff point for assessing whether adding a given drug will cause apparent cytotoxicity, which greatly expands the probe's applicability. To the best of our knowledge, PCV-1 is the first probe to allow visualizing cell death and cell injury under super-resolution imaging, and our proposed analytical assay using it paves the way for quantifying cell viability at the single-cell level.
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7
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Contreras‐Llano LE, Liu Y, Henson T, Meyer CC, Baghdasaryan O, Khan S, Lin C, Wang A, Hu CJ, Tan C. Engineering Cyborg Bacteria Through Intracellular Hydrogelation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204175. [PMID: 36628538 PMCID: PMC10037956 DOI: 10.1002/advs.202204175] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/18/2022] [Indexed: 05/06/2023]
Abstract
Natural and artificial cells are two common chassis in synthetic biology. Natural cells can perform complex tasks through synthetic genetic constructs, but their autonomous replication often causes safety concerns for biomedical applications. In contrast, artificial cells based on nonreplicating materials, albeit possessing reduced biochemical complexity, provide more defined and controllable functions. Here, for the first time, the authors create hybrid material-cell entities termed Cyborg Cells. To create Cyborg Cells, a synthetic polymer network is assembled inside each bacterium, rendering them incapable of dividing. Cyborg Cells preserve essential functions, including cellular metabolism, motility, protein synthesis, and compatibility with genetic circuits. Cyborg Cells also acquire new abilities to resist stressors that otherwise kill natural cells. Finally, the authors demonstrate the therapeutic potential by showing invasion into cancer cells. This work establishes a new paradigm in cellular bioengineering by exploiting a combination of intracellular man-made polymers and their interaction with the protein networks of living cells.
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Affiliation(s)
| | - Yu‐Han Liu
- Institute of Biomedical SciencesAcademia SinicaTaipei11529Taiwan
| | - Tanner Henson
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
- Department of SurgeryUniversity of CaliforniaDavis School of MedicineSacramentoCA95817USA
| | - Conary C. Meyer
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
| | | | - Shahid Khan
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
| | - Chi‐Long Lin
- Institute of Biomedical SciencesAcademia SinicaTaipei11529Taiwan
| | - Aijun Wang
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
- Department of SurgeryUniversity of CaliforniaDavis School of MedicineSacramentoCA95817USA
| | - Che‐Ming J. Hu
- Institute of Biomedical SciencesAcademia SinicaTaipei11529Taiwan
| | - Cheemeng Tan
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
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8
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Veling MT, Nguyen DT, Thadani NN, Oster ME, Rollins NJ, Brock KP, Bethel NP, Lim S, Baker D, Way JC, Marks DS, Chang RL, Silver PA. Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells. ACS Synth Biol 2022; 11:1292-1302. [PMID: 35176859 DOI: 10.1021/acssynbio.1c00572] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Many organisms can survive extreme conditions and successfully recover to normal life. This extremotolerant behavior has been attributed in part to repetitive, amphipathic, and intrinsically disordered proteins that are upregulated in the protected state. Here, we assemble a library of approximately 300 naturally occurring and designed extremotolerance-associated proteins to assess their ability to protect human cells from chemically induced apoptosis. We show that several proteins from tardigrades, nematodes, and the Chinese giant salamander are apoptosis-protective. Notably, we identify a region of the human ApoE protein with similarity to extremotolerance-associated proteins that also protects against apoptosis. This region mirrors the phase separation behavior seen with such proteins, like the tardigrade protein CAHS2. Moreover, we identify a synthetic protein, DHR81, that shares this combination of elevated phase separation propensity and apoptosis protection. Finally, we demonstrate that driving protective proteins into the condensate state increases apoptosis protection, and highlights the ability of DHR81 condensates to sequester caspase-7. Taken together, this work draws a link between extremotolerance-associated proteins, condensate formation, and designing human cellular protection.
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Affiliation(s)
- Mike T. Veling
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Dan T. Nguyen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Nicole N. Thadani
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Michela E. Oster
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Nathan J. Rollins
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Kelly P. Brock
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Neville P. Bethel
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
| | - Jeffrey C. Way
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Debora S. Marks
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Roger L. Chang
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
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9
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Van den Bergh B, Schramke H, Michiels JE, Kimkes TEP, Radzikowski JL, Schimpf J, Vedelaar SR, Burschel S, Dewachter L, Lončar N, Schmidt A, Meijer T, Fauvart M, Friedrich T, Michiels J, Heinemann M. Mutations in respiratory complex I promote antibiotic persistence through alterations in intracellular acidity and protein synthesis. Nat Commun 2022; 13:546. [PMID: 35087069 PMCID: PMC8795404 DOI: 10.1038/s41467-022-28141-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 01/04/2022] [Indexed: 11/28/2022] Open
Abstract
Antibiotic persistence describes the presence of phenotypic variants within an isogenic bacterial population that are transiently tolerant to antibiotic treatment. Perturbations of metabolic homeostasis can promote antibiotic persistence, but the precise mechanisms are not well understood. Here, we use laboratory evolution, population-wide sequencing and biochemical characterizations to identify mutations in respiratory complex I and discover how they promote persistence in Escherichia coli. We show that persistence-inducing perturbations of metabolic homeostasis are associated with cytoplasmic acidification. Such cytoplasmic acidification is further strengthened by compromised proton pumping in the complex I mutants. While RpoS regulon activation induces persistence in the wild type, the aggravated cytoplasmic acidification in the complex I mutants leads to increased persistence via global shutdown of protein synthesis. Thus, we propose that cytoplasmic acidification, amplified by a compromised complex I, can act as a signaling hub for perturbed metabolic homeostasis in antibiotic persisters.
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Affiliation(s)
- Bram Van den Bergh
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Hannah Schramke
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Joran Elie Michiels
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
| | - Tom E P Kimkes
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Jakub Leszek Radzikowski
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Johannes Schimpf
- Molecular Bioenergetics, Institute of Biochemistry, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany
| | - Silke R Vedelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Sabrina Burschel
- Molecular Bioenergetics, Institute of Biochemistry, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany
| | - Liselot Dewachter
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
| | - Nikola Lončar
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Tim Meijer
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Thorsten Friedrich
- Molecular Bioenergetics, Institute of Biochemistry, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium.
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium.
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands.
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10
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Abundant Small Protein ICARUS Inside the Cell Wall of Stress-Resistant Ascospores of Talaromyces macrosporus Suggests a Novel Mechanism of Constitutive Dormancy. J Fungi (Basel) 2021; 7:jof7030216. [PMID: 33802751 PMCID: PMC8002430 DOI: 10.3390/jof7030216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 01/01/2023] Open
Abstract
Ascospores of Talaromyces.macrosporus belong to the most stress resistant eukaryotic cells and show a constitutive dormancy, i.e., no germination occurs in the presence of rich growth medium. Only an extreme trigger as very high temperature or pressure is able to evoke synchronized germination. In this study, several changes within the thick cell wall of these cells are observed after a heat treatment: (i.) a change in its structure as shown with EPR and X-ray diffraction; (ii.) a release of an abundant protein into the supernatant, which is proportional to the extent of heat activation; (iii.) a change in the permeability of the cell wall as judged by fluorescence studies in which staining of the interior of the cell wall correlates with germination of individual ascospores. The gene encoding the protein, dubbed ICARUS, was studied in detail and was expressed under growth conditions that showed intense ascomata (fruit body) and ascospore formation. It encodes a small 7–14 kD protein. Blast search exhibits that different Talaromyces species show a similar sequence, indicating that the protein also occurs in other species of the genus. Deletion strains show delayed ascomata formation, release of pigments into the growth medium, higher permeability of the cell wall and a markedly shorter heat activation needed for activation. Further, wild type ascospores are more heat-resistant. All these observations suggest that the protein plays a role in dormancy and is related to the structure and permeability of the ascospore cell wall. However, more research on this topic is needed to study constitutive dormancy in other fungal species that form stress-resistant ascospores.
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11
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Wylot M, Whittaker DTE, Wren SAC, Bothwell JH, Hughes L, Griffin JL. Monitoring apoptosis in intact cells by high-resolution magic angle spinning 1 H NMR spectroscopy. NMR IN BIOMEDICINE 2021; 34:e4456. [PMID: 33398876 DOI: 10.1002/nbm.4456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/09/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
Apoptosis maintains an equilibrium between cell proliferation and cell death. Many diseases, including cancer, develop because of defects in apoptosis. A known metabolic marker of apoptosis is a notable increase in 1 H NMR-observable resonances associated with lipids stored in lipid droplets. However, standard one-dimensional NMR experiments allow the quantification of lipid concentration only, without providing information about physical characteristics such as the size of lipid droplets, viscosity of the cytosol, or cytoskeletal rigidity. This additional information can improve monitoring of apoptosis-based cancer treatments in intact cells and provide us with mechanistic insight into why these changes occur. In this paper, we use high-resolution magic angle spinning (HRMAS) 1 H NMR spectroscopy to monitor lipid concentrations and apparent diffusion coefficients of mobile lipid in intact cells treated with the apoptotic agents cisplatin or etoposide. We also use solution-state NMR spectroscopy to study changes in lipid profiles of organic solvent cell extracts. Both NMR techniques show an increase in the concentration of lipids but the relative changes are 10 times larger by HRMAS 1 H NMR spectroscopy. Moreover, the apparent diffusion rates of lipids in apoptotic cells measured by HRMAS 1 H NMR spectroscopy decrease significantly as compared with control cells. Slower diffusion rates of mobile lipids in apoptotic cells correlate well with the formation of larger lipid droplets as observed by microscopy. We also compared the mean lipid droplet displacement values calculated from the two methods. Both methods showed shorter displacements of lipid droplets in apoptotic cells. Our results demonstrate that the NMR-based diffusion experiments on intact cells discriminate between control and apoptotic cells. Apparent diffusion measurements in conjunction with 1 H NMR spectroscopy-derived lipid signals provide a novel means of following apoptosis in intact cells. This method could have potential application in enhancing drug discovery by monitoring drug treatments in vitro, particularly for agents that cause portioning of lipids such as apoptosis.
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Affiliation(s)
- Marta Wylot
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - David T E Whittaker
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Stephen A C Wren
- New Modalities & Parenteral Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK
| | | | - Leslie Hughes
- New Modalities & Parenteral Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK
| | - Julian L Griffin
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
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12
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Jain K, Khetan N, Yadav SA, Palani S, Athale CA. Collective dynein transport of the nucleus by pulling on astral microtubules during Saccharomyces cerevisiae mitosis. Yeast 2021; 38:352-366. [PMID: 33547820 DOI: 10.1002/yea.3552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 11/06/2022] Open
Abstract
Positioning the nucleus at the bud neck during Saccharomyces cerevisiae mitosis involves pulling forces of cytoplasmic dynein localized in the daughter cell. Although genetic analysis has revealed a complex network positioning the nucleus, quantification of the forces acting on the nucleus and the number of dyneins driving the process has remained difficult. To better understand the collective forces involved in nuclear positioning, we compare a model of dyneins-driven microtubule (MT) pulling, MT pushing, and cytoplasmic drag to experiments. During S. cerevisiae mitosis, MTs interacting with the cortex nucleated by the daughter spindle pole body (SPB) (SPB-D) are longer than the mother SPB (SPB-M), increasing further during spindle elongation in anaphase. Interphasic SPB mobility is effectively diffusive, while the mitotic mobility is directed. By optimizing a computational model of the mobility of the nucleus due to diffusion and MTs pushing at the cell membrane to experiment, we estimate the viscosity governing the drag force on nuclei during positioning. A force balance model of mitotic SPB mobility compared to experimental mobility suggests that even one or two dynein dimers are sufficient to move the nucleus in the bud neck. Using stochastic computer simulations of a budding cell, we find that punctate dynein localization can generate sufficient force to reel in the nucleus to the bud neck. Compared to uniform motor localization, puncta involve fewer motors suggesting a functional role for motor clustering. Stochastic simulations also suggest that a higher number of force generators than predicted by force balance may be required to ensure the robustness of spindle positioning.
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Affiliation(s)
- Kunalika Jain
- Division of Biology, IISER Pune, Dr. Homi Bhabha Road, Pune, Maharashtra, 411008, India
| | - Neha Khetan
- Division of Biology, IISER Pune, Dr. Homi Bhabha Road, Pune, Maharashtra, 411008, India
| | - Shivani A Yadav
- Division of Biology, IISER Pune, Dr. Homi Bhabha Road, Pune, Maharashtra, 411008, India
| | - Saravanan Palani
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK.,Department of Biochemistry, Indian Institute of Science (IISc), C.V. Raman Road, Bangalore, Karnataka, 560012, India
| | - Chaitanya A Athale
- Division of Biology, IISER Pune, Dr. Homi Bhabha Road, Pune, Maharashtra, 411008, India
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13
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M Raj J, Kenjar A, Bhandary J, Girisha B, Chakraborty G, Karunasagar I. Development of a rapid and low-cost method for the extraction of dermatophyte DNA. Indian J Dermatol 2021; 66:668-673. [PMID: 35283499 PMCID: PMC8906329 DOI: 10.4103/ijd.ijd_19_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background: Polymerase chain reaction (PCR) is the most optimized method for the rapid detection and analysis of any environmental or clinically significant organism. While PCR amplification directly from samples has been shown effective for several bacteria and viruses, for filamentous fungus and yeast, extraction of genomic DNA is a must. The extraction of DNA from fungal cultures is often reported using user-friendly commercially available kits, which are designed to decrease the time, extensive manual work in extraction procedures but are often expensive. Dermatophytes pose an added drawback to efficient DNA extraction due to their poor recovery on culture media and slow growth rate. Aims and Objectives: In the present study, we developed and validated a method for effective genomic DNA extraction from dermatophytes. Materials and Methods: DNA yield from standard dermatophytes extracted from spore suspensions and mycelia mat by commercially available kits was compared. A modified method using lyticase buffer and phenol-chloroform extraction was developed. The yield obtained was compared with the existing methods (kit-based method and cetyl trimethyl ammonium bromide method). The yield and quality of the total genomic DNA were estimated spectrophotometrically and by successful PCR amplification of the ITS region. The results were validated using 21 clinical isolates from recalcitrant dermatophytosis. Results: Minimal fungal DNA was obtained from the spores compared to that obtained from mycelial mat. Commercially available kits yielded lower amounts of DNA compared to the CATB method. The modified method developed in this study yielded better quality and quantity of DNA. Conclusion: Of the three extraction methods evaluated, the developed method gave significantly higher total genomic DNA yield and better purity than the reference methods. In addition, the turnaround time for DNA extraction was reduced to half based on modifications in culture conditions.
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14
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Maire T, Allertz T, Betjes MA, Youk H. Dormancy-to-death transition in yeast spores occurs due to gradual loss of gene-expressing ability. Mol Syst Biol 2020; 16:e9245. [PMID: 33206464 PMCID: PMC7673291 DOI: 10.15252/msb.20199245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 11/28/2022] Open
Abstract
Dormancy is colloquially considered as extending lifespan by being still. Starved yeasts form dormant spores that wake-up (germinate) when nutrients reappear but cannot germinate (die) after some time. What sets their lifespans and how they age are open questions because what processes occur-and by how much-within each dormant spore remains unclear. With single-cell-level measurements, we discovered how dormant yeast spores age and die: spores have a quantifiable gene-expressing ability during dormancy that decreases over days to months until it vanishes, causing death. Specifically, each spore has a different probability of germinating that decreases because its ability to-without nutrients-express genes decreases, as revealed by a synthetic circuit that forces GFP expression during dormancy. Decreasing amounts of molecules required for gene expression-including RNA polymerases-decreases gene-expressing ability which then decreases chances of germinating. Spores gradually lose these molecules because they are produced too slowly compared with their degradations, causing gene-expressing ability to eventually vanish and, thus, death. Our work provides a systems-level view of dormancy-to-death transition.
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Affiliation(s)
- Théo Maire
- Kavli Institute of NanoscienceDelftThe Netherlands
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
| | - Tim Allertz
- Kavli Institute of NanoscienceDelftThe Netherlands
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
| | - Max A Betjes
- Kavli Institute of NanoscienceDelftThe Netherlands
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
| | - Hyun Youk
- Kavli Institute of NanoscienceDelftThe Netherlands
- CIFARCIFAR Azrieli Global Scholars ProgramTorontoONCanada
- Program in Molecular MedicineUniversity of Massachusetts Medical SchoolWorcesterMAUSA
- Program in Systems BiologyUniversity of Massachusetts Medical SchoolWorcesterMAUSA
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15
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Bakalis E, Parent LR, Vratsanos M, Park C, Gianneschi NC, Zerbetto F. Complex Nanoparticle Diffusional Motion in Liquid-Cell Transmission Electron Microscopy. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2020; 124:14881-14890. [PMID: 33841603 PMCID: PMC8023318 DOI: 10.1021/acs.jpcc.0c03203] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/10/2020] [Indexed: 06/01/2023]
Abstract
Liquid-cell transmission electron microscopy (LCTEM) is a powerful in situ videography technique that has the potential to allow us to observe solution-phase dynamic processes at the nanoscale, including imaging the diffusion and interaction of nanoparticles. Artefactual effects imposed by the irradiated and confined liquid-cell vessel alter the system from normal "bulk-like" behavior in multiple ways. These artefactual LCTEM effects will leave their fingerprints in the motion behavior of the diffusing objects, which can be revealed through careful analysis of the object-motion trajectories. Improper treatment of the motion data can lead to erroneous descriptions of the LCTEM system's conditions. Here, we advance our anomalous diffusion object-motion analysis (ADOMA) method to extract a detailed description of the liquid-cell system conditions during any LCTEM experiment by applying a multistep analysis of the data and treating the x/y vectors of motion independently and in correlation with each other and with the object's orientation/angle.
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Affiliation(s)
- Evangelos Bakalis
- Dipartimento
di Chimica “G. Ciamician”, Universita di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
| | - Lucas R. Parent
- Innovation
Partnership Building, The University of
Connecticut, Storrs, Connecticut 06269, United States
| | - Maria Vratsanos
- Department
of Materials Science & Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Chiwoo Park
- Department
of Industrial and Manufacturing Engineering, Florida State University, Tallahassee, Florida 32306, United States
| | - Nathan C. Gianneschi
- Department
of Chemistry, Department of Materials Science & Engineering, and
Department of Biomedical Engineering, Northwestern
University, Evanston, Illinois 60208, United States
| | - Francesco Zerbetto
- Dipartimento
di Chimica “G. Ciamician”, Universita di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
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16
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Wang X, Law J, Luo M, Gong Z, Yu J, Tang W, Zhang Z, Mei X, Huang Z, You L, Sun Y. Magnetic Measurement and Stimulation of Cellular and Intracellular Structures. ACS NANO 2020; 14:3805-3821. [PMID: 32223274 DOI: 10.1021/acsnano.0c00959] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
From single-pole magnetic tweezers to robotic magnetic-field generation systems, the development of magnetic micromanipulation systems, using electromagnets or permanent magnets, has enabled a multitude of applications for cellular and intracellular measurement and stimulation. Controlled by different configurations of magnetic-field generation systems, magnetic particles have been actuated by an external magnetic field to exert forces/torques and perform mechanical measurements on the cell membrane, cytoplasm, cytoskeleton, nucleus, intracellular motors, etc. The particles have also been controlled to generate aggregations to trigger cell signaling pathways and produce heat to cause cancer cell apoptosis for hyperthermia treatment. Magnetic micromanipulation has become an important tool in the repertoire of toolsets for cell measurement and stimulation and will continue to be used widely for further explorations of cellular/intracellular structures and their functions. Existing review papers in the literature focus on fabrication and position control of magnetic particles/structures (often termed micronanorobots) and the synthesis and functionalization of magnetic particles. Differently, this paper reviews the principles and systems of magnetic micromanipulation specifically for cellular and intracellular measurement and stimulation. Discoveries enabled by magnetic measurement and stimulation of cellular and intracellular structures are also summarized. This paper ends with discussions on future opportunities and challenges of magnetic micromanipulation in the exploration of cellular biophysics, mechanotransduction, and disease therapeutics.
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Affiliation(s)
- Xian Wang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Junhui Law
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Mengxi Luo
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Zheyuan Gong
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Jiangfan Yu
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Wentian Tang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Zhuoran Zhang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Xueting Mei
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Zongjie Huang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Lidan You
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Yu Sun
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada
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17
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Pinto CA, Moreira SA, Fidalgo LG, Inácio RS, Barba FJ, Saraiva JA. Effects of high-pressure processing on fungi spores: Factors affecting spore germination and inactivation and impact on ultrastructure. Compr Rev Food Sci Food Saf 2020; 19:553-573. [PMID: 33325178 DOI: 10.1111/1541-4337.12534] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 12/10/2019] [Accepted: 12/16/2019] [Indexed: 12/12/2022]
Abstract
Food contamination with heat-resistant fungi (HRF), and their spores, is a major issue among fruit processors, being frequently found in fruit juices and concentrates, among other products, leading to considerable economic losses and food safety issues. Several strategies were developed to minimize the contamination with HRF, with improvements from harvesting to the final product, including sanitizers and new processing techniques. Considering consumers' demands for minimally processed, fresh-like food products, nonthermal food-processing technologies, such as high-pressure processing (HPP), among others, are emerging as alternatives to the conventional thermal processing techniques. As no heat is applied to foods, vitamins, proteins, aromas, and taste are better kept when compared to thermal processes. Nevertheless, HPP is only able to destroy pathogenic and spoilage vegetative microorganisms to levels of pertinence for food safety, while bacterial spores remain. Regarding HRF spores (both ascospores and conidiospores), these seem to be more pressure-sensible than bacterial spores, despite a few cases, such as the ascospores of Byssochlamys spp., Neosartorya spp., and Talaromyces spp. that are resistant to high pressures and high temperatures, requiring the combination of both variables to be inactivated. This review aims to cover the literature available concerning the effects of HPP at room-like temperatures, and its combination with high temperatures, and high-pressure cycling, to inactivate fungi spores, including the main factors affecting spores' resistance to high-pressure, such as pH, water activity, nutritional composition of the food matrix and ascospore age, as well as the changes in the spore ultrastructure, and the parameters to consider regarding their inactivation by HPP.
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Affiliation(s)
- Carlos A Pinto
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Sílvia A Moreira
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Liliana G Fidalgo
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal.,Escola Superior Agrária, Instituto Politécnico de Beja, Beja, Portugal
| | - Rita S Inácio
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Francisco J Barba
- Area de Nutrición y Bromatología, Facultat de Farmàcia, Universitat de València, Burjassot, Spain
| | - Jorge A Saraiva
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
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18
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Relevance and Regulation of Cell Density. Trends Cell Biol 2020; 30:213-225. [PMID: 31980346 DOI: 10.1016/j.tcb.2019.12.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 01/05/2023]
Abstract
Cell density shows very little variation within a given cell type. For example, in humans variability in cell density among cells of a given cell type is 100 times smaller than variation in cell mass. This tight control indicates that maintenance of a cell type-specific cell density is important for cell function. Indeed, pathological conditions such as cellular senescence are accompanied by changes in cell density. Despite the apparent importance of cell-type-specific density, we know little about how cell density affects cell function, how it is controlled, and how it sometimes changes as part of a developmental process or in response to changes in the environment. The recent development of new technologies to accurately measure the cell density of single cells in suspension and in tissues is likely to provide answers to these important questions.
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19
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Abstract
Aspergillus fumigatus is a saprotrophic fungus; its primary habitat is the soil. In its ecological niche, the fungus has learned how to adapt and proliferate in hostile environments. This capacity has helped the fungus to resist and survive against human host defenses and, further, to be responsible for one of the most devastating lung infections in terms of morbidity and mortality. In this review, we will provide (i) a description of the biological cycle of A. fumigatus; (ii) a historical perspective of the spectrum of aspergillus disease and the current epidemiological status of these infections; (iii) an analysis of the modes of immune response against Aspergillus in immunocompetent and immunocompromised patients; (iv) an understanding of the pathways responsible for fungal virulence and their host molecular targets, with a specific focus on the cell wall; (v) the current status of the diagnosis of different clinical syndromes; and (vi) an overview of the available antifungal armamentarium and the therapeutic strategies in the clinical context. In addition, the emergence of new concepts, such as nutritional immunity and the integration and rewiring of multiple fungal metabolic activities occurring during lung invasion, has helped us to redefine the opportunistic pathogenesis of A. fumigatus.
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Affiliation(s)
- Jean-Paul Latgé
- School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Georgios Chamilos
- School of Medicine, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
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20
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Heimlicher MB, Bächler M, Liu M, Ibeneche-Nnewihe C, Florin EL, Hoenger A, Brunner D. Reversible solidification of fission yeast cytoplasm after prolonged nutrient starvation. J Cell Sci 2019; 132:jcs.231688. [PMID: 31558680 PMCID: PMC6857596 DOI: 10.1242/jcs.231688] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022] Open
Abstract
Cells depend on a highly ordered organisation of their content and must develop strategies to maintain the anisotropic distribution of organelles during periods of nutrient shortage. One of these strategies is to solidify the cytoplasm, which was observed in bacteria and yeast cells with acutely interrupted energy production. Here, we describe a different type of cytoplasm solidification fission yeast cells switch to, after having run out of nutrients during multiple days in culture. It provides the most profound reversible cytoplasmic solidification of yeast cells described to date. Our data exclude the previously proposed mechanisms for cytoplasm solidification in yeasts and suggest a mechanism that immobilises cellular components in a size-dependent manner. We provide experimental evidence that, in addition to time, cells use intrinsic nutrients and energy sources to reach this state. Such cytoplasmic solidification may provide a robust means to protect cellular architecture in dormant cells. Summary: After prolonged quiescence, fission yeast cell populations switch state to immobilise subcellular components much more profoundly than cells experiencing acute energy depletion.
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Affiliation(s)
- Maria B Heimlicher
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Mirjam Bächler
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Minghua Liu
- Dept. of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, UCB-0347, Boulder, CO 80309, USA
| | - Chieze Ibeneche-Nnewihe
- Center for Nonlinear Dynamics and Department of Physics, University of Texas at Austin, Austin, TX 78712, USA
| | - Ernst-Ludwig Florin
- Center for Nonlinear Dynamics and Department of Physics, University of Texas at Austin, Austin, TX 78712, USA
| | - Andreas Hoenger
- Dept. of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, UCB-0347, Boulder, CO 80309, USA
| | - Damian Brunner
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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21
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de Ruiter J, Arnbjerg-Nielsen SF, Herren P, Høier F, De Fine Licht HH, Jensen KH. Fungal artillery of zombie flies: infectious spore dispersal using a soft water cannon. J R Soc Interface 2019; 16:20190448. [PMID: 31662074 DOI: 10.1098/rsif.2019.0448] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Dead sporulating female fly cadavers infected by the house fly-pathogenic fungus Entomophthora muscae are attractive to healthy male flies, which by their physical inspection may mechanically trigger spore release and by their movement create whirlwind airflows that covers them in infectious conidia. The fungal artillery of E. muscae protrudes outward from the fly cadaver, and consists of a plethora of micrometric stalks that each uses a liquid-based turgor pressure build-up to eject a jet of protoplasm and the initially attached spore. The biophysical processes that regulate the release and range of spores, however, are unknown. To study the physics of ejection, we design a biomimetic 'soft cannon' that consists of a millimetric elastomeric barrel filled with fluid and plugged with a projectile. We precisely control the maximum pressure leading up to the ejection, and study the cannon efficiency as a function of its geometry and wall elasticity. In particular, we predict that ejection velocity decreases with spore size. The calculated flight trajectories under aerodynamic drag predict that the minimum spore size required to traverse a quiescent layer of a few millimetres around the fly cadaver is approximately 10 µm. This corroborates with the natural size of E. muscae conidia (approx. 27 µm) being large enough to traverse the boundary layer but small enough (less than 40 µm) to be lifted by air currents. Based on this understanding, we show how the fungal spores are able to reach a new host.
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Affiliation(s)
- Jolet de Ruiter
- Department of Physics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.,Agrotechnology and Food Sciences Group, Wageningen University and Research, 6700AA Wageningen, The Netherlands
| | | | - Pascal Herren
- Department of Plant and Environmental Sciences, University of Copenhagen, 1971 Frederiksberg, Denmark
| | - Freja Høier
- Department of Physics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Henrik H De Fine Licht
- Department of Plant and Environmental Sciences, University of Copenhagen, 1971 Frederiksberg, Denmark
| | - Kaare H Jensen
- Department of Physics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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22
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23
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Snyder AB, Biango-Daniels MN, Hodge KT, Worobo RW. Nature Abhors a Vacuum: Highly Diverse Mechanisms Enable Spoilage Fungi to Disperse, Survive, and Propagate in Commercially Processed and Preserved Foods. Compr Rev Food Sci Food Saf 2018; 18:286-304. [DOI: 10.1111/1541-4337.12403] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Abigail B. Snyder
- the Dept. of Extension; The Ohio State Univ.; 1680 Madison Ave. Wooster OH 44691 USA
| | - Megan N. Biango-Daniels
- the Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science; Cornell Univ.; Ithaca NY 14850 USA
| | - Kathie T. Hodge
- the Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science; Cornell Univ.; Ithaca NY 14850 USA
| | - Randy W. Worobo
- the Dept. of Food Science; Cornell Univ.; 411 Tower Rd. Ithaca NY 14850 USA
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24
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Fungal spores: Highly variable and stress-resistant vehicles for distribution and spoilage. Food Microbiol 2018; 81:2-11. [PMID: 30910084 DOI: 10.1016/j.fm.2018.11.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 11/21/2022]
Abstract
This review highlights the variability of fungal spores with respect to cell type, mode of formation and stress resistance. The function of spores is to disperse fungi to new areas and to get them through difficult periods. This also makes them important vehicles for food contamination. Formation of spores is a complex process that is regulated by the cooperation of different transcription factors. The discussion of the biology of spore formation, with the genus Aspergillus as an example, points to possible novel ways to eradicate fungal spore production in food. Fungi can produce different types of spores, sexual and asexually, within the same colony. The absence or presence of sexual spore formation has led to a dual nomenclature for fungi. Molecular techniques have led to a revision of this nomenclature. A number of fungal species form sexual spores, which are exceptionally stress-resistant and survive pasteurization and other treatments. A meta-analysis is provided of numerous D-values of heat-resistant ascospores generated during the years. The relevance of fungal spores for food microbiology has been discussed.
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25
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Dijksterhuis J, Meijer M, van Doorn T, Samson R, Rico-Munoz E. Inactivation of stress-resistant ascospores of Eurotiales by industrial sanitizers. Int J Food Microbiol 2018; 285:27-33. [DOI: 10.1016/j.ijfoodmicro.2018.06.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/18/2018] [Accepted: 06/22/2018] [Indexed: 10/28/2022]
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26
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Sephton-Clark PCS, Voelz K. Spore Germination of Pathogenic Filamentous Fungi. ADVANCES IN APPLIED MICROBIOLOGY 2017; 102:117-157. [PMID: 29680124 DOI: 10.1016/bs.aambs.2017.10.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Fungi, algae, plants, protozoa, and bacteria are all known to form spores, especially hardy and ubiquitous propagation structures that are also often the infectious agents of diseases. Spores can survive for thousands of years, frozen in the permafrost (Kochkina et al., 2012), with the oldest viable spores extracted after 250 million years from salt crystals (Vreeland, Rosenzweig, & Powers, 2000). Their resistance to high levels of UV, desiccation, pressure, heat, and cold enables the survival of spores in the harshest conditions (Setlow, 2016). For example, Bacillus subtilis spores can survive and remain viable after experiencing conditions similar to those on Mars (Horneck et al., 2012). Spores are disseminated through environmental factors. Wind, water, or animal carriage allow spores to be spread ubiquitously throughout the environment. Spores will break dormancy and begin to germinate once exposed to favorable conditions. Germination is the mechanism that converts the spore from a dormant biological organism to one that grows vegetatively and is capable of either sexual or asexual reproduction. The process of germination has been well studied in plants, moss, bacteria, and many fungi (Hohe & Reski, 2005; Huang & Hull, 2017; Vesty et al., 2016). Unfortunately, information on the complex signaling involved in the regulation of germination, particularly in fungi remains lacking. This chapter will discuss germination of fungal spores covering our current understanding of the regulation, signaling, outcomes, and implications of germination of pathogenic fungal spores. Owing to the morphological similarities between the spore-hyphal and yeast-hyphal transition and their relevance for disease progression, relevant aspects of fungal dimorphism will be discussed alongside spore germination in this chapter.
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Affiliation(s)
- Poppy C S Sephton-Clark
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Kerstin Voelz
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom.
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27
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Rico-Munoz E. Heat resistant molds in foods and beverages: recent advances on assessment and prevention. Curr Opin Food Sci 2017. [DOI: 10.1016/j.cofs.2017.10.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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28
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Cuecas A, Cruces J, Galisteo-López JF, Peng X, Gonzalez JM. Cellular Viscosity in Prokaryotes and Thermal Stability of Low Molecular Weight Biomolecules. Biophys J 2017; 111:875-882. [PMID: 27558730 DOI: 10.1016/j.bpj.2016.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 07/18/2016] [Indexed: 11/19/2022] Open
Abstract
Some low molecular weight biomolecules, i.e., NAD(P)H, are unstable at high temperatures. The use of these biomolecules by thermophilic microorganisms has been scarcely analyzed. Herein, NADH stability has been studied at different temperatures and viscosities. NADH decay increased at increasing temperatures. At increasing viscosities, NADH decay rates decreased. Thus, maintaining relatively high cellular viscosity in cells could result in increased stability of low molecular weight biomolecules (i.e., NADH) at high temperatures, unlike what was previously deduced from studies in diluted water solutions. Cellular viscosity was determined using a fluorescent molecular rotor in various prokaryotes covering the range from 10 to 100°C. Some mesophiles showed the capability of changing cellular viscosity depending on growth temperature. Thermophiles and extreme thermophiles presented a relatively high cellular viscosity, suggesting this strategy as a reasonable mechanism to thrive under these high temperatures. Results substantiate the capability of thermophiles and extreme thermophiles (growth range 50-80°C) to stabilize and use generally considered unstable, universal low molecular weight biomolecules. In addition, this study represents a first report, to our knowledge, on cellular viscosity measurements in prokaryotes and it shows the dependency of prokaryotic cellular viscosity on species and growth temperature.
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Affiliation(s)
- Alba Cuecas
- Institute of Natural Resources and Agrobiology, Institute of Materials Science of Seville, Spanish National Research Council (CSIC), Seville, Spain
| | - Jorge Cruces
- Institute of Natural Resources and Agrobiology, Institute of Materials Science of Seville, Spanish National Research Council (CSIC), Seville, Spain
| | - Juan F Galisteo-López
- Multifunctional Optical Material Group, Institute of Materials Science of Seville, Spanish National Research Council (CSIC), Seville, Spain
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, P.R. China
| | - Juan M Gonzalez
- Institute of Natural Resources and Agrobiology, Institute of Materials Science of Seville, Spanish National Research Council (CSIC), Seville, Spain.
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29
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Rabouille C, Alberti S. Cell adaptation upon stress: the emerging role of membrane-less compartments. Curr Opin Cell Biol 2017; 47:34-42. [PMID: 28342303 DOI: 10.1016/j.ceb.2017.02.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/06/2017] [Accepted: 02/09/2017] [Indexed: 11/26/2022]
Abstract
Cells under stress transition from a growth to a quiescent state. The conventional thinking is that this is achieved through transcriptional programs, translational regulation, protein degradation, and post-translational modifications. However, there is an increasing realization that stress adaptation also goes along with dramatic changes in the architecture and organization of cells. In particular, it seems to involve the formation of membrane-less compartments and macromolecular assemblies. We propose that cells make widespread use of this ability to change macromolecular organization to adapt to stress conditions and protect themselves. Here, we address what triggers the formation of these assemblies under stress conditions. We present examples illustrating that in some cases, sophisticated signaling pathways transmit environmental fluctuations from the outside to the inside and in others, that external fluctuations directly affect the internal conditions in cells. We further argue that changes in the organization of the cytoplasm and the formation of membrane-less compartments have many advantages over other ways of altering protein function, such as protein degradation, translation or transcription. Furthermore, membrane-less compartments may act as protective devices for key cellular components.
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Affiliation(s)
- Catherine Rabouille
- Hubrecht Institute of the KNAW & UMC Utrecht, 3584 CT Utrecht, The Netherlands; Department of Cell Biology, UMC Groningen, The Netherlands.
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
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30
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Nguyen Van Long N, Vasseur V, Coroller L, Dantigny P, Le Panse S, Weill A, Mounier J, Rigalma K. Temperature, water activity and pH during conidia production affect the physiological state and germination time of Penicillium species. Int J Food Microbiol 2016; 241:151-160. [PMID: 27780083 DOI: 10.1016/j.ijfoodmicro.2016.10.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 09/28/2016] [Accepted: 10/17/2016] [Indexed: 11/25/2022]
Abstract
Conidial germination and mycelial growth are generally studied with conidia produced under optimal conditions to increase conidial yield. Nonetheless, the physiological state of such conidia most likely differs from those involved in spoilage of naturally contaminated food. The present study aimed at investigating the impact of temperature, pH and water activity (aw) during production of conidia on the germination parameters and compatible solutes of conidia of Penicillium roqueforti and Penicillium expansum. Low temperature (5°C) and reduced aw (0.900 aw) during sporulation significantly reduced conidial germination times whereas the pH of the sporulation medium only had a slight effect at the tested values (2.5, 8.0). Conidia of P. roqueforti produced at 5°C germinated up to 45h earlier than those produced at 20°C. Conidia of P. roqueforti and P. expansum produced at 0.900 aw germinated respectively up to 8h and 3h earlier than conidia produced at 0.980 aw. Furthermore, trehalose and mannitol assessments suggested that earlier germination might be related to delayed conidial maturation even though no ultra-structural modifications were observed by transmission electron microscopy. Taken together, these results highlight the importance of considering environmental conditions during sporulation in mycological studies. The physiological state of fungal conidia should be taken into account to design challenge tests or predictive mycology studies. This knowledge may also be of interest to improve the germination capacity of fungal cultures commonly used in fermented foods.
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Affiliation(s)
- Nicolas Nguyen Van Long
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Valérie Vasseur
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Louis Coroller
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, UMT Spore Risk, IUT Quimper, 6 rue de l'Université, 29334 Quimper, France
| | - Philippe Dantigny
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Sophie Le Panse
- Plateforme Merimage, Station Biologique de Roscoff, CNRS-UPMC, Place Georges Teissier, CS90074, 29688 Roscoff, Cedex, France
| | - Amélie Weill
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Jérôme Mounier
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Karim Rigalma
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
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31
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Wyatt TT, Wösten HAB, Dijksterhuis J. Fungal spores for dispersion in space and time. ADVANCES IN APPLIED MICROBIOLOGY 2016; 85:43-91. [PMID: 23942148 DOI: 10.1016/b978-0-12-407672-3.00002-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Spores are an integral part of the life cycle of the gross majority of fungi. Their morphology and the mode of formation are both highly variable among the fungi, as is their resistance to stressors. The main aim for spores is to be dispersed, both in space, by various mechanisms or in time, by an extended period of dormancy. Some fungal ascospores belong to the most stress-resistant eukaryotic cells described to date. Stabilization is a process in which biomolecules and complexes thereof are protected by different types of molecules against heat, drought, or other molecules. This review discusses the most important compounds that are known to protect fungal spores and also addresses the biophysics of cell protection. It further covers the phenomena of dormancy, breaking of dormancy, and early germination. Germination is the transition from a dormant cell toward a vegetative cell and includes a number of specific changes. Finally, the applied aspects of spore biology are discussed.
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Affiliation(s)
- Timon T Wyatt
- Department of Applied and Industrial Mycology, CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, The Netherlands
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32
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Munder MC, Midtvedt D, Franzmann T, Nüske E, Otto O, Herbig M, Ulbricht E, Müller P, Taubenberger A, Maharana S, Malinovska L, Richter D, Guck J, Zaburdaev V, Alberti S. A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy. eLife 2016; 5. [PMID: 27003292 PMCID: PMC4850707 DOI: 10.7554/elife.09347] [Citation(s) in RCA: 277] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 02/13/2016] [Indexed: 01/19/2023] Open
Abstract
Cells can enter into a dormant state when faced with unfavorable conditions. However, how cells enter into and recover from this state is still poorly understood. Here, we study dormancy in different eukaryotic organisms and find it to be associated with a significant decrease in the mobility of organelles and foreign tracer particles. We show that this reduced mobility is caused by an influx of protons and a marked acidification of the cytoplasm, which leads to widespread macromolecular assembly of proteins and triggers a transition of the cytoplasm to a solid-like state with increased mechanical stability. We further demonstrate that this transition is required for cellular survival under conditions of starvation. Our findings have broad implications for understanding alternative physiological states, such as quiescence and dormancy, and create a new view of the cytoplasm as an adaptable fluid that can reversibly transition into a protective solid-like state.
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Affiliation(s)
| | - Daniel Midtvedt
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Titus Franzmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Oliver Otto
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Maik Herbig
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Elke Ulbricht
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Paul Müller
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Anna Taubenberger
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Shovamayee Maharana
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Liliana Malinovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jochen Guck
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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33
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Wyatt TT, Gerwig GJ, Kamerling JP, Wösten HA, Dijksterhuis J. Structural analysis of novel trehalose-based oligosaccharides from extremely stress-tolerant ascospores of Neosartorya fischeri (Aspergillus fischeri). Carbohydr Res 2015; 411:49-55. [DOI: 10.1016/j.carres.2015.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/08/2015] [Accepted: 04/10/2015] [Indexed: 11/29/2022]
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34
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Wyatt TT, van Leeuwen MR, Golovina EA, Hoekstra FA, Kuenstner EJ, Palumbo EA, Snyder NL, Visagie C, Verkennis A, Hallsworth JE, Wösten HAB, Dijksterhuis J. Functionality and prevalence of trehalose-based oligosaccharides as novel compatible solutes in ascospores of Neosartorya fischeri (Aspergillus fischeri) and other fungi. Environ Microbiol 2015; 17:395-411. [PMID: 25040129 PMCID: PMC4371660 DOI: 10.1111/1462-2920.12558] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/25/2014] [Accepted: 07/02/2014] [Indexed: 12/03/2022]
Abstract
Ascospores of Neosartorya, Byssochlamys and Talaromyces can be regarded as the most stress-resistant eukaryotic cells. They can survive exposure at temperatures as high as 85°C for 100 min or more. Neosartorya fischeri ascospores are more viscous and more resistant to the combined stress of heat and desiccation than the ascospores of Talaromyces macrosporus which contain predominantly trehalose. These ascospores contain trehalose-based oligosaccharides (TOS) that are novel compatible solutes, which are accumulated to high levels. These compounds are also found in other members of the genus Neosartorya and in some other genera within the order Eurotiales that also include Byssochlamys and Talaromyces. The presence of oligosaccharides was observed in species that had a relatively high growth temperature. TOS glasses have a higher glass transition temperature (Tg ) than trehalose, and they form a stable glass with crystallizing molecules, such as mannitol. Our data indicate that TOS are important for prolonged stabilization of cells against stress. The possible unique role of these solutes in protection against dry heat conditions is discussed.
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Affiliation(s)
- Timon T Wyatt
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, 3584CT, The Netherlands
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35
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Wyatt TT, Golovina EA, van Leeuwen R, Hallsworth JE, Wösten HAB, Dijksterhuis J. A decrease in bulk water and mannitol and accumulation of trehalose and trehalose-based oligosaccharides define a two-stage maturation process towards extreme stress resistance in ascospores of Neosartorya fischeri (Aspergillus fischeri). Environ Microbiol 2014; 17:383-94. [PMID: 25040022 DOI: 10.1111/1462-2920.12557] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/27/2014] [Accepted: 07/02/2014] [Indexed: 12/01/2022]
Abstract
Fungal propagules survive stresses better than vegetative cells. Neosartorya fischeri, an Aspergillus teleomorph, forms ascospores that survive high temperatures or drying followed by heat. Not much is known about maturation and development of extreme stress resistance in fungal cells. This study provides a novel two-step model for the acquisition of extreme stress resistance and entry into dormancy. Ascospores of 11- and 15-day-old cultures exhibited heat resistance, physiological activity, accumulation of compatible solutes and a steep increase in cytoplasmic viscosity. Electron spin resonance spectroscopy indicated that this stage is associated with the removal of bulk water and an increase of chemical stability. Older ascospores from 15- to 50-day-old cultures showed no changes in compatible solute content and cytoplasmic viscosity, but did exhibit a further increase of heat resistance and redox stability with age. This stage was also characterized by changes in the composition of the mixture of compatible solutes. Mannitol levels decreased and the relative quantities of trehalose and trehalose-based oligosaccharides increased. Dormant ascospores of N. fischeri survive in low-water habitats. After activation of the germination process, the stress resistance decreases, compatible solutes are degraded and the cellular viscosity drops. After 5 h, the hydrated cells enter the vegetative stage and redox stability has decreased notably.
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Affiliation(s)
- Timon T Wyatt
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, 3584CT, The Netherlands
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36
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Puchkov EO. Intracellular viscosity: Methods of measurement and role in metabolism. BIOCHEMISTRY MOSCOW SUPPLEMENT SERIES A-MEMBRANE AND CELL BIOLOGY 2013. [DOI: 10.1134/s1990747813050140] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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37
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van Leeuwen M, Krijgsheld P, Bleichrodt R, Menke H, Stam H, Stark J, Wösten H, Dijksterhuis J. Germination of conidia of Aspergillus niger is accompanied by major changes in RNA profiles. Stud Mycol 2013; 74:59-70. [PMID: 23449598 PMCID: PMC3563291 DOI: 10.3114/sim0009] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The transcriptome of conidia of Aspergillus niger was analysed during the first 8 h of germination. Dormant conidia started to grow isotropically two h after inoculation in liquid medium. Isotropic growth changed to polarised growth after 6 h, which coincided with one round of mitosis. Dormant conidia contained transcripts from 4 626 genes. The number of genes with transcripts decreased to 3 557 after 2 h of germination, after which an increase was observed with 4 780 expressed genes 8 h after inoculation. The RNA composition of dormant conidia was substantially different than all the subsequent stages of germination. The correlation coefficient between the RNA profiles of 0 h and 8 h was 0.46. They were between 0.76-0.93 when profiles of 2, 4 and 6 h were compared with that of 8 h. Dormant conidia were characterised by high levels of transcripts of genes involved in the formation of protecting components such as trehalose, mannitol, protective proteins (e.g. heat shock proteins and catalase). Transcripts belonging to the Functional Gene Categories (FunCat) protein synthesis, cell cycle and DNA processing and respiration were over-represented in the up-regulated genes at 2 h, whereas metabolism and cell cycle and DNA processing were over-represented in the up-regulated genes at 4 h. At 6 h and 8 h no functional gene classes were over- or under-represented in the differentially expressed genes. Taken together, it is concluded that the transcriptome of conidia changes dramatically during the first two h and that initiation of protein synthesis and respiration are important during early stages of germination.
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Affiliation(s)
- M.R. van Leeuwen
- Applied and Industrial Mycology, CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - P. Krijgsheld
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Molecular Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - R. Bleichrodt
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Molecular Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - H. Menke
- DSM Food Specialties, PO Box 1, 2600 MA Delft, The Netherlands
| | - H. Stam
- DSM Food Specialties, PO Box 1, 2600 MA Delft, The Netherlands
| | - J. Stark
- DSM Food Specialties, PO Box 1, 2600 MA Delft, The Netherlands
| | - H.A.B. Wösten
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Molecular Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - J. Dijksterhuis
- Applied and Industrial Mycology, CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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38
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Krijgsheld P, Bleichrodt R, van Veluw G, Wang F, Müller W, Dijksterhuis J, Wösten H. Development in Aspergillus. Stud Mycol 2013; 74:1-29. [PMID: 23450714 PMCID: PMC3563288 DOI: 10.3114/sim0006] [Citation(s) in RCA: 232] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The genus Aspergillus represents a diverse group of fungi that are among the most abundant fungi in the world. Germination of a spore can lead to a vegetative mycelium that colonizes a substrate. The hyphae within the mycelium are highly heterogeneous with respect to gene expression, growth, and secretion. Aspergilli can reproduce both asexually and sexually. To this end, conidiophores and ascocarps are produced that form conidia and ascospores, respectively. This review describes the molecular mechanisms underlying growth and development of Aspergillus.
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Affiliation(s)
- P. Krijgsheld
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - R. Bleichrodt
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - G.J. van Veluw
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - F. Wang
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - W.H. Müller
- Biomolecular Imaging, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - J. Dijksterhuis
- Applied and Industrial Mycology, CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - H.A.B. Wösten
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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39
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van Leeuwen MR, Krijgsheld P, Wyatt TT, Golovina EA, Menke H, Dekker A, Stark J, Stam H, Bleichrodt R, Wösten HAB, Dijksterhuis J. The effect of natamycin on the transcriptome of conidia of Aspergillus niger. Stud Mycol 2012; 74:71-85. [PMID: 23449730 PMCID: PMC3563292 DOI: 10.3114/sim0013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The impact of natamycin on Aspergillus niger was analysed during the first 8 h of germination of conidia. Polarisation, germ tube formation, and mitosis were inhibited in the presence of 3 and 10 μM of the anti-fungal compound, while at 10 μM also isotropic growth was affected. Natamycin did not have an effect on the decrease of microviscosity during germination and the concomitant reduction in mannitol and trehalose levels. However, it did abolish the increase of intracellular levels of glycerol and glucose during the 8 h period of germination. Natamycin hardly affected the changes that occur in the RNA profile during the first 2 h of germination. During this time period, genes related to transcription, protein synthesis, energy and cell cycle and DNA processing were particularly up-regulated. Differential expression of 280 and 2586 genes was observed when 8 h old germlings were compared with conidia that had been exposed to 3 μM and 10 μM natamycin, respectively. For instance, genes involved in ergosterol biosynthesis were down-regulated. On the other hand, genes involved in endocytosis and the metabolism of compatible solutes, and genes encoding protective proteins were up-regulated in natamycin treated conidia.
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Affiliation(s)
- M R van Leeuwen
- Applied and Industrial Mycology, CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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40
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Puchkov EO. Single yeast cell vacuolar milieu viscosity assessment by fluorescence polarization microscopy with computer image analysis. Yeast 2012; 29:185-90. [PMID: 22532478 DOI: 10.1002/yea.2899] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 04/03/2012] [Indexed: 11/06/2022] Open
Abstract
This study was undertaken to evaluate the apparent viscosity within the vacuoles of single Saccharomyces cerevisiae cells by steady-state fluorescence anisotropy measurements of quinacrine, using wide-field fluorescence polarization microscopy combined with computer image analysis. Quinacrine was shown to be rather specifically accumulated within the vacuoles of the cells. This accumulation was effectively reversed by ATP depletion of the cells, with no detectable binding of the dye within the vacuoles. Quinacrine fluorescence anisotropy in the sucrose solutions of various viscosities obeyed the Perrin equation. The fluorescence anisotropy of quinacrine was measured in the vacuoles of 39 cells. From cell to cell, this parameter changed in the range 0.032-0.086. Using the Perrin plot as a calibration curve, apparent viscosity values of the vacuolar milieu were calculated for each cell. The population of the cells studied was heterogeneous with regard to vacuolar viscosity, which was in the range 3.5 ± 0.4-14.06 ± 0.64 cP. There was a characteristic distribution of the frequencies of cells with apparent viscosities within certain limits, and cells with viscosity values in the range 5-6 cP were the most frequent. No relationship was found between the sizes of the vacuoles and their apparent viscosities.
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Affiliation(s)
- Evgeny O Puchkov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Pushchino, Russia.
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41
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Feofilova EP, Ivashechkin AA, Alekhin AI, Sergeeva YE. Fungal spores: Dormancy, germination, chemical composition, and role in biotechnology (review). APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683812010048] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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42
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Water- and air-distributed conidia differ in sterol content and cytoplasmic microviscosity. Appl Environ Microbiol 2009; 76:366-9. [PMID: 19897752 DOI: 10.1128/aem.01632-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Airborne and waterborne fungal spores were compared with respect to cytoplasmic viscosity and the presence of ergosterol. These parameters differed markedly between the two spore types and correlated with spore survival. This suggests that the mode of spore dispersal has a bearing on cellular composition, which is relevant for the eradication of industrially relevant fungal propagules.
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43
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Van Leeuwen MR, Golovina EA, Dijksterhuis J. The polyene antimycotics nystatin and filipin disrupt the plasma membrane, whereas natamycin inhibits endocytosis in germinating conidia of Penicillium discolor. J Appl Microbiol 2009; 106:1908-18. [PMID: 19228256 DOI: 10.1111/j.1365-2672.2009.04165.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AIMS To investigate the differences in membrane permeability and the effect on endocytosis of the polyene antimycotics nystatin, filipin and natamycin on germinating fungal conidia. METHODS AND RESULTS The model system was Penicillium discolor, a food spoilage fungus. Filipin resulted in permeabilization of germinating conidia for the fluorescent probes TOTO-1 and FM4-64, but not for ferricyanide ions. Nystatin caused influx of all these compounds while natamycin did not. Untreated germinating conidia internalize the endocytic marker FM4-64. Pretreatment of germinating conidia with natamycin showed a dose and time dependent inhibition of endocytosis as judged by the lack of formation of early endosomal compartments. CONCLUSIONS The results obtained from this study indicated that, unlike nystatin and filipin, natamycin is unable to permeabilize germinating conidia, but interferes with endocytosis in a dose and time dependent manner. SIGNIFICANCE AND IMPACT OF THE STUDY Natamycin acts via a different mode of action than other polyene antimycotics. These results offer useful information for new strategies to prevent fungal spoilage on food products and infection on agricultural crops. For laboratory use, natamycin can be used as a specific inhibitor of early endocytosis in fungal cells.
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Affiliation(s)
- M R Van Leeuwen
- Applied and Industrial Mycology, CBS/Fungal Biodiversity Centre, Utrecht, The Netherlands
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McCully ME, Canny MJ, Huang CX. Invited Review: Cryo-scanning electron microscopy (CSEM) in the advancement of functional plant biology. Morphological and anatomical applications. FUNCTIONAL PLANT BIOLOGY : FPB 2009; 36:97-124. [PMID: 32688631 DOI: 10.1071/fp08304] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 12/15/2008] [Indexed: 06/11/2023]
Abstract
Cryo-scanning electron microscopy (CSEM) is reviewed by exploring how the images obtained have changed paradigms of plant functions and interactions with their environment. Its power to arrest and stabilise plant parts in milliseconds, and to preserve them at full hydration for examination at micrometre resolution has changed many views of plant function. For example, it provides the only feasible way of accurately measuring stomatal aperture during active transpiration, and volume and shape changes in guard cells, or examining the contents of laticifers. It has revealed that many xylem conduits contain gas, not liquid, during the day, and that they can be refilled with sap and resume water transport. It has elucidated the management of ice to prevent cell damage in frost tolerant plants and has revealed for the first time inherent biological and physical features of root/soil interactions in the field. CSEM is increasingly used to reveal complementary structural information in studies of metabolism, fungal infection and symbiosis, molecular and genetic analysis.
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Affiliation(s)
| | - Martin J Canny
- Functional Ecology Group, Research School of Biological Sciences, Australian National University, Canberra, ACT 0200, Australia
| | - Cheng X Huang
- Electron Microscopy Unit, Research School of Biological Sciences, Australian National University, Canberra, ACT 0200, Australia
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High spatial resolution surface imaging and analysis of fungal cells using SEM and AFM. Micron 2008; 39:349-61. [DOI: 10.1016/j.micron.2007.10.023] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 10/17/2007] [Accepted: 10/18/2007] [Indexed: 11/22/2022]
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