1
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Jashnsaz H, Neuert G. Phenotypic consequences of logarithmic signaling in MAPK stress response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570188. [PMID: 38106069 PMCID: PMC10723343 DOI: 10.1101/2023.12.05.570188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
How cells respond to dynamic environmental changes is crucial for understanding fundamental biological processes and cell physiology. In this study, we developed an experimental and quantitative analytical framework to explore how dynamic stress gradients that change over time regulate cellular volume, signaling activation, and growth phenotypes. Our findings reveal that gradual stress conditions substantially enhance cell growth compared to conventional acute stress. This growth advantage correlates with a minimal reduction in cell volume dependent on the dynamic of stress. We explain the growth phenotype with our finding of a logarithmic signal transduction mechanism in the yeast Mitogen-Activated Protein Kinase (MAPK) osmotic stress response pathway. These insights into the interplay between gradual environments, cell volume change, dynamic cell signaling, and growth, advance our understanding of fundamental cellular processes in gradual stress environments.
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Affiliation(s)
- Hossein Jashnsaz
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232 USA
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232 USA
- Lead Contact
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2
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Liang J, Tang H, Snyder LF, Youngstrom CE, He BZ. Divergence of TORC1-mediated stress response leads to novel acquired stress resistance in a pathogenic yeast. PLoS Pathog 2023; 19:e1011748. [PMID: 37871123 PMCID: PMC10621968 DOI: 10.1371/journal.ppat.1011748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/02/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
Acquired stress resistance (ASR) enables organisms to prepare for environmental changes that occur after an initial stressor. However, the genetic basis for ASR and how the underlying network evolved remain poorly understood. In this study, we discovered that a short phosphate starvation induces oxidative stress response (OSR) genes in the pathogenic yeast C. glabrata and protects it against a severe H2O2 stress; the same treatment, however, provides little benefit in the low pathogenic-potential relative, S. cerevisiae. This ASR involves the same transcription factors (TFs) as the OSR, but with different combinatorial logics. We show that Target-of-Rapamycin Complex 1 (TORC1) is differentially inhibited by phosphate starvation in the two species and contributes to the ASR via its proximal effector, Sch9. Therefore, evolution of the phosphate starvation-induced ASR involves the rewiring of TORC1's response to phosphate limitation and the repurposing of TF-target gene networks for the OSR using new regulatory logics.
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Affiliation(s)
- Jinye Liang
- Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Hanxi Tang
- Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Lindsey F. Snyder
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, Iowa, United States of America
| | | | - Bin Z. He
- Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, Iowa, United States of America
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3
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Liang J, Tang H, Snyder LF, Youngstrom CE, He BZ. Divergence of TORC1-mediated Stress Response Leads to Novel Acquired Stress Resistance in a Pathogenic Yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.20.545716. [PMID: 37781605 PMCID: PMC10541095 DOI: 10.1101/2023.06.20.545716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Acquired stress resistance (ASR) enables organisms to prepare for environmental changes that occur after an initial stressor. However, the genetic basis for ASR and how the underlying network evolved remain poorly understood. In this study, we discovered that a short phosphate starvation induces oxidative stress response (OSR) genes in the pathogenic yeast C. glabrata and protects it against a severe H2O2 stress; the same treatment, however, provides little benefit in the low pathogenic-potential relative, S. cerevisiae. This ASR involves the same transcription factors (TFs) as the OSR, but with different combinatorial logics. We show that Target-of-Rapamycin Complex 1 (TORC1) is differentially inhibited by phosphate starvation in the two species and contributes to the ASR via its proximal effector, Sch9. Therefore, evolution of the phosphate starvation-induced ASR involves the rewiring of TORC1's response to phosphate limitation and the repurposing of TF-target gene networks for the OSR using new regulatory logics.
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Affiliation(s)
- Jinye Liang
- Biology Department, The University of Iowa, Iowa City, IA 52242
| | - Hanxi Tang
- Biology Department, The University of Iowa, Iowa City, IA 52242
| | - Lindsey F. Snyder
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242
| | | | - Bin Z. He
- Biology Department, The University of Iowa, Iowa City, IA 52242
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4
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Thiemicke A, Neuert G. Rate thresholds in cell signaling have functional and phenotypic consequences in non-linear time-dependent environments. Front Cell Dev Biol 2023; 11:1124874. [PMID: 37025183 PMCID: PMC10072286 DOI: 10.3389/fcell.2023.1124874] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
All cells employ signal transduction pathways to respond to physiologically relevant extracellular cytokines, stressors, nutrient levels, hormones, morphogens, and other stimuli that vary in concentration and rate in healthy and diseased states. A central unsolved fundamental question in cell signaling is whether and how cells sense and integrate information conveyed by changes in the rate of extracellular stimuli concentrations, in addition to the absolute difference in concentration. We propose that different environmental changes over time influence cell behavior in addition to different signaling molecules or different genetic backgrounds. However, most current biomedical research focuses on acute environmental changes and does not consider how cells respond to environments that change slowly over time. As an example of such environmental change, we review cell sensitivity to environmental rate changes, including the novel mechanism of rate threshold. A rate threshold is defined as a threshold in the rate of change in the environment in which a rate value below the threshold does not activate signaling and a rate value above the threshold leads to signal activation. We reviewed p38/Hog1 osmotic stress signaling in yeast, chemotaxis and stress response in bacteria, cyclic adenosine monophosphate signaling in Amoebae, growth factors signaling in mammalian cells, morphogen dynamics during development, temporal dynamics of glucose and insulin signaling, and spatio-temproral stressors in the kidney. These reviewed examples from the literature indicate that rate thresholds are widespread and an underappreciated fundamental property of cell signaling. Finally, by studying cells in non-linear environments, we outline future directions to understand cell physiology better in normal and pathophysiological conditions.
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Affiliation(s)
- Alexander Thiemicke
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, United States
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, United States
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, United States
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, United States
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, United States
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, United States
- *Correspondence: Gregor Neuert,
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5
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Kukhtevich IV, Rivero-Romano M, Rakesh N, Bheda P, Chadha Y, Rosales-Becerra P, Hamperl S, Bureik D, Dornauer S, Dargemont C, Kirmizis A, Schmoller KM, Schneider R. Quantitative RNA imaging in single live cells reveals age-dependent asymmetric inheritance. Cell Rep 2022; 41:111656. [DOI: 10.1016/j.celrep.2022.111656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 08/31/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022] Open
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6
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Altered expression response upon repeated gene repression in single yeast cells. PLoS Comput Biol 2022; 18:e1010640. [PMID: 36256678 PMCID: PMC9633002 DOI: 10.1371/journal.pcbi.1010640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/03/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
Cells must continuously adjust to changing environments and, thus, have evolved mechanisms allowing them to respond to repeated stimuli. While faster gene induction upon a repeated stimulus is known as reinduction memory, responses to repeated repression have been less studied so far. Here, we studied gene repression across repeated carbon source shifts in over 1,500 single Saccharomyces cerevisiae cells. By monitoring the expression of a carbon source-responsive gene, galactokinase 1 (Gal1), and fitting a mathematical model to the single-cell data, we observed a faster response upon repeated repressions at the population level. Exploiting our single-cell data and quantitative modeling approach, we discovered that the faster response is mediated by a shortened repression response delay, the estimated time between carbon source shift and Gal1 protein production termination. Interestingly, we can exclude two alternative hypotheses, i) stronger dilution because of e.g., increased proliferation, and ii) a larger fraction of repressing cells upon repeated repressions. Collectively, our study provides a quantitative description of repression kinetics in single cells and allows us to pinpoint potential mechanisms underlying a faster response upon repeated repression. The computational results of our study can serve as the starting point for experimental follow-up studies. Cells have to continuously adjust to their environment and cope with changing temperature, stress conditions, or metabolic resources. Yeast cells exposed to repeated carbon source shifts have shown to be “primed” by their first exposure, exhibiting enhanced gene expression of specific genes later on. However, how cells respond to a repeated repressive stimulus, e.g., withdrawal of metabolic resources, has been so far much less studied. For this, we investigated the expression kinetics of a carbon source-responsive gene across repeated repressions. We measured single-cell expression and used mathematical modeling to evaluate potential causes underlying an observed faster repression response upon a repeated stimulus. Specifically, we investigated whether i) an increased dilution due to e.g., proliferation, ii) an increased fraction of repressing cells, or iii) different kinetic parameters in the repeated repression cause the observed faster response in the second repression. Leveraging quantitative mathematical model comparison, we discovered that the faster response is mediated by a shortened estimated time between carbon source shift and protein production termination at the single-cell level. Our study provides a quantitative description of repression kinetics in single cells and allows us to pinpoint potential mechanisms underlying a faster response upon repeated repression.
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7
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Aspert T, Hentsch D, Charvin G. DetecDiv, a generalist deep-learning platform for automated cell division tracking and survival analysis. eLife 2022; 11:79519. [PMID: 35976090 PMCID: PMC9444243 DOI: 10.7554/elife.79519] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Automating the extraction of meaningful temporal information from sequences of microscopy images represents a major challenge to characterize dynamical biological processes. So far, strong limitations in the ability to quantitatively analyze single-cell trajectories have prevented large-scale investigations to assess the dynamics of entry into replicative senescence in yeast. Here, we have developed DetecDiv, a microfluidic-based image acquisition platform combined with deep learning-based software for high-throughput single-cell division tracking. We show that DetecDiv can automatically reconstruct cellular replicative lifespans with high accuracy and performs similarly with various imaging platforms and geometries of microfluidic traps. In addition, this methodology provides comprehensive temporal cellular metrics using time-series classification and image semantic segmentation. Last, we show that this method can be further applied to automatically quantify the dynamics of cellular adaptation and real-time cell survival upon exposure to environmental stress. Hence, this methodology provides an all-in-one toolbox for high-throughput phenotyping for cell cycle, stress response, and replicative lifespan assays.
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Affiliation(s)
- Théo Aspert
- Department of Developmental Biology and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
| | - Didier Hentsch
- Department of Developmental Biology and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
| | - Gilles Charvin
- Department of Developmental Biology and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
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8
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Padovani F, Mairhörmann B, Falter-Braun P, Lengefeld J, Schmoller KM. Segmentation, tracking and cell cycle analysis of live-cell imaging data with Cell-ACDC. BMC Biol 2022; 20:174. [PMID: 35932043 PMCID: PMC9356409 DOI: 10.1186/s12915-022-01372-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/08/2022] [Indexed: 12/12/2022] Open
Abstract
Background High-throughput live-cell imaging is a powerful tool to study dynamic cellular processes in single cells but creates a bottleneck at the stage of data analysis, due to the large amount of data generated and limitations of analytical pipelines. Recent progress on deep learning dramatically improved cell segmentation and tracking. Nevertheless, manual data validation and correction is typically still required and tools spanning the complete range of image analysis are still needed. Results We present Cell-ACDC, an open-source user-friendly GUI-based framework written in Python, for segmentation, tracking and cell cycle annotations. We included state-of-the-art deep learning models for single-cell segmentation of mammalian and yeast cells alongside cell tracking methods and an intuitive, semi-automated workflow for cell cycle annotation of single cells. Using Cell-ACDC, we found that mTOR activity in hematopoietic stem cells is largely independent of cell volume. By contrast, smaller cells exhibit higher p38 activity, consistent with a role of p38 in regulation of cell size. Additionally, we show that, in S. cerevisiae, histone Htb1 concentrations decrease with replicative age. Conclusions Cell-ACDC provides a framework for the application of state-of-the-art deep learning models to the analysis of live cell imaging data without programming knowledge. Furthermore, it allows for visualization and correction of segmentation and tracking errors as well as annotation of cell cycle stages. We embedded several smart algorithms that make the correction and annotation process fast and intuitive. Finally, the open-source and modularized nature of Cell-ACDC will enable simple and fast integration of new deep learning-based and traditional methods for cell segmentation, tracking, and downstream image analysis. Source code: https://github.com/SchmollerLab/Cell_ACDC Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01372-6.
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Affiliation(s)
- Francesco Padovani
- Institute of Functional Epigenetics (IFE), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Center Munich, 85764, Munich-Neuherberg, Germany.
| | - Benedikt Mairhörmann
- Institute of Functional Epigenetics (IFE), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Center Munich, 85764, Munich-Neuherberg, Germany.,Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Center Munich, 85764, Munich-Neuherberg, Germany
| | - Pascal Falter-Braun
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Center Munich, 85764, Munich-Neuherberg, Germany.,Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-University (LMU) München, 82152, Planegg-, Martinsried, Germany
| | - Jette Lengefeld
- Institute of Biotechnology, HiLIFE, University of Helsinki, Biocenter 2, P.O.Box 56 (Viikinkaari 5 D), 00014, Helsinki, Finland.,Department of Biosciences and Nutrition (BioNut), Karolinska Institutet, Huddinge, Sweden
| | - Kurt M Schmoller
- Institute of Functional Epigenetics (IFE), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Center Munich, 85764, Munich-Neuherberg, Germany. .,German Center for Diabetes Research (DZD), 85764, Munich-Neuherberg, Germany.
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9
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Aspert T, Jacquel B, Charvin G. A Microfluidic Platform for Tracking Individual Cell Dynamics during an Unperturbed Nutrients Exhaustion. Bio Protoc 2022; 12:e4470. [PMID: 35978570 PMCID: PMC9350916 DOI: 10.21769/bioprotoc.4470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 12/29/2022] Open
Abstract
Microorganisms have evolved adaptive strategies to respond to the autonomous degradation of their environment. Indeed, a growing culture progressively exhausts nutrients from its media and modifies its composition. Yet, how single cells react to these modifications remains difficult to study since it requires population-scale growth experiments to allow cell proliferation to have a collective impact on the environment, while monitoring the same individuals exposed to this environment for days. For this purpose, we have previously described an integrated microfluidic pipeline, based on continuous separation of the cells from the media and subsequent perfusion of the filtered media in an observation chamber containing isolated single cells. Here, we provide a detailed protocol to implement this methodology, including the setting up of the microfluidic system and the processing of timelapse images.
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Affiliation(s)
- Théo Aspert
- Department of Developmental Biology and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
,
Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
,
Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
,
Université de Strasbourg, Illkirch, France
,
*For correspondence:
;
| | - Basile Jacquel
- Department of Developmental Biology and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
,
Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
,
Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
,
Université de Strasbourg, Illkirch, France
,
*For correspondence:
;
| | - Gilles Charvin
- Department of Developmental Biology and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
,
Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
,
Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
,
Université de Strasbourg, Illkirch, France
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10
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Gomar-Alba M, Pozharskaia V, Cichocki B, Schaal C, Kumar A, Jacquel B, Charvin G, Igual JC, Mendoza M. Nuclear pore complex acetylation regulates mRNA export and cell cycle commitment in budding yeast. EMBO J 2022; 41:e110271. [PMID: 35735140 PMCID: PMC9340480 DOI: 10.15252/embj.2021110271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
Nuclear pore complexes (NPCs) mediate communication between the nucleus and the cytoplasm, and regulate gene expression by interacting with transcription and mRNA export factors. Lysine acetyltransferases (KATs) promote transcription through acetylation of chromatin‐associated proteins. We find that Esa1, the KAT subunit of the yeast NuA4 complex, also acetylates the nuclear pore basket component Nup60 to promote mRNA export. Acetylation of Nup60 recruits the mRNA export factor Sac3, the scaffolding subunit of the Transcription and Export 2 (TREX‐2) complex, to the nuclear basket. The Esa1‐mediated nuclear export of mRNAs in turn promotes entry into S phase, which is inhibited by the Hos3 deacetylase in G1 daughter cells to restrain their premature commitment to a new cell division cycle. This mechanism is not only limited to G1/S‐expressed genes but also inhibits the expression of the nutrient‐regulated GAL1 gene specifically in daughter cells. Overall, these results reveal how acetylation can contribute to the functional plasticity of NPCs in mother and daughter yeast cells. In addition, our work demonstrates dual gene expression regulation by the evolutionarily conserved NuA4 complex, at the level of transcription and at the stage of mRNA export by modifying the nucleoplasmic entrance to nuclear pores.
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Affiliation(s)
- Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Spain
| | - Vasilisa Pozharskaia
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Bogdan Cichocki
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Celia Schaal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Arun Kumar
- Department of Cell Biology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Basile Jacquel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Gilles Charvin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - J Carlos Igual
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Spain
| | - Manuel Mendoza
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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11
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Cuny AP, Schlottmann FP, Ewald JC, Pelet S, Schmoller KM. Live cell microscopy: From image to insight. BIOPHYSICS REVIEWS 2022; 3:021302. [PMID: 38505412 PMCID: PMC10903399 DOI: 10.1063/5.0082799] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/18/2022] [Indexed: 03/21/2024]
Abstract
Live-cell microscopy is a powerful tool that can reveal cellular behavior as well as the underlying molecular processes. A key advantage of microscopy is that by visualizing biological processes, it can provide direct insights. Nevertheless, live-cell imaging can be technically challenging and prone to artifacts. For a successful experiment, many careful decisions are required at all steps from hardware selection to downstream image analysis. Facing these questions can be particularly intimidating due to the requirement for expertise in multiple disciplines, ranging from optics, biophysics, and programming to cell biology. In this review, we aim to summarize the key points that need to be considered when setting up and analyzing a live-cell imaging experiment. While we put a particular focus on yeast, many of the concepts discussed are applicable also to other organisms. In addition, we discuss reporting and data sharing strategies that we think are critical to improve reproducibility in the field.
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Affiliation(s)
| | - Fabian P. Schlottmann
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Jennifer C. Ewald
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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12
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Schmoller KM, Lanz MC, Kim J, Koivomagi M, Qu Y, Tang C, Kukhtevich IV, Schneider R, Rudolf F, Moreno DF, Aldea M, Lucena R, Skotheim JM. Whi5 is diluted and protein synthesis does not dramatically increase in pre- Start G1. Mol Biol Cell 2022; 33:lt1. [PMID: 35482510 PMCID: PMC9282012 DOI: 10.1091/mbc.e21-01-0029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kurt M Schmoller
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Germany
| | - Michael C Lanz
- Department of Biology, Stanford University, Stanford CA 94305
| | - Jacob Kim
- Department of Biology, Stanford University, Stanford CA 94305
| | - Mardo Koivomagi
- Department of Biology, Stanford University, Stanford CA 94305
| | - Yimiao Qu
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chao Tang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Igor V Kukhtevich
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Germany
| | - Fabian Rudolf
- D-BSSE, ETH Zurich and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - David F Moreno
- Molecular Biology Institute of Barcelona, CSIC, Catalonia, Spain
| | - Martí Aldea
- Molecular Biology Institute of Barcelona, CSIC, Catalonia, Spain
| | - Rafael Lucena
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford CA 94305
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13
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Santiago E, Moreno DF, Acar M. Modeling aging and its impact on cellular function and organismal behavior. Exp Gerontol 2021; 155:111577. [PMID: 34582969 PMCID: PMC8560568 DOI: 10.1016/j.exger.2021.111577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 01/22/2023]
Abstract
Aging is a complex phenomenon of functional decay in a biological organism. Although the effects of aging are readily recognizable in a wide range of organisms, the cause(s) of aging are ill defined and poorly understood. Experimental methods on model organisms have driven significant insight into aging as a process, but have not provided a complete model of aging. Computational biology offers a unique opportunity to resolve this gap in our knowledge by generating extensive and testable models that can help us understand the fundamental nature of aging, identify the presence and characteristics of unaccounted aging factor(s), demonstrate the mechanics of particular factor(s) in driving aging, and understand the secondary effects of aging on biological function. In this review, we will address each of the above roles for computational biology in aging research. Concurrently, we will explore the different applications of computational biology to aging in single-celled versus multicellular organisms. Given the long history of computational biogerontological research on lower eukaryotes, we emphasize the key future goals of gradually integrating prior models into a holistic map of aging and translating successful models to higher-complexity organisms.
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Affiliation(s)
- Emerson Santiago
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA
| | - David F Moreno
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Murat Acar
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA.
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14
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Jacquel B, Aspert T, Laporte D, Sagot I, Charvin G. Monitoring single-cell dynamics of entry into quiescence during an unperturbed life cycle. eLife 2021; 10:73186. [PMID: 34723791 PMCID: PMC8594939 DOI: 10.7554/elife.73186] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022] Open
Abstract
The life cycle of microorganisms is associated with dynamic metabolic transitions and complex cellular responses. In yeast, how metabolic signals control the progressive choreography of structural reorganizations observed in quiescent cells during a natural life cycle remains unclear. We have developed an integrated microfluidic device to address this question, enabling continuous single-cell tracking in a batch culture experiencing unperturbed nutrient exhaustion to unravel the coordination between metabolic and structural transitions within cells. Our technique reveals an abrupt fate divergence in the population, whereby a fraction of cells is unable to transition to respiratory metabolism and undergoes a reversible entry into a quiescence-like state leading to premature cell death. Further observations reveal that nonmonotonous internal pH fluctuations in respiration-competent cells orchestrate the successive waves of protein superassemblies formation that accompany the entry into a bona fide quiescent state. This ultimately leads to an abrupt cytosolic glass transition that occurs stochastically long after proliferation cessation. This new experimental framework provides a unique way to track single-cell fate dynamics over a long timescale in a population of cells that continuously modify their ecological niche.
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Affiliation(s)
- Basile Jacquel
- Department of Developmental Biology and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Théo Aspert
- Department of Developmental Biology and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Damien Laporte
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France, Bordeaux, France
| | - Isabelle Sagot
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France, Bordeaux, France
| | - Gilles Charvin
- Department of Developmental Biology and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
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15
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Schlagowski AM, Knöringer K, Morlot S, Sánchez Vicente A, Flohr T, Krämer L, Boos F, Khalid N, Ahmed S, Schramm J, Murschall LM, Haberkant P, Stein F, Riemer J, Westermann B, Braun RJ, Winklhofer KF, Charvin G, Herrmann JM. Increased levels of mitochondrial import factor Mia40 prevent the aggregation of polyQ proteins in the cytosol. EMBO J 2021; 40:e107913. [PMID: 34191328 PMCID: PMC8365258 DOI: 10.15252/embj.2021107913] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
The formation of protein aggregates is a hallmark of neurodegenerative diseases. Observations on patient samples and model systems demonstrated links between aggregate formation and declining mitochondrial functionality, but causalities remain unclear. We used Saccharomyces cerevisiae to analyze how mitochondrial processes regulate the behavior of aggregation‐prone polyQ protein derived from human huntingtin. Expression of Q97‐GFP rapidly led to insoluble cytosolic aggregates and cell death. Although aggregation impaired mitochondrial respiration only slightly, it considerably interfered with the import of mitochondrial precursor proteins. Mutants in the import component Mia40 were hypersensitive to Q97‐GFP, whereas Mia40 overexpression strongly suppressed the formation of toxic Q97‐GFP aggregates both in yeast and in human cells. Based on these observations, we propose that the post‐translational import of mitochondrial precursor proteins into mitochondria competes with aggregation‐prone cytosolic proteins for chaperones and proteasome capacity. Mia40 regulates this competition as it has a rate‐limiting role in mitochondrial protein import. Therefore, Mia40 is a dynamic regulator in mitochondrial biogenesis that can be exploited to stabilize cytosolic proteostasis.
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Affiliation(s)
| | | | - Sandrine Morlot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Ana Sánchez Vicente
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Tamara Flohr
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Lena Krämer
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Felix Boos
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Nabeel Khalid
- German Research Center for Artificial Intelligence DFKI, Kaiserslautern, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence DFKI, Kaiserslautern, Germany
| | - Jana Schramm
- Cell Biology, University of Bayreuth, Bayreuth, Germany
| | | | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Jan Riemer
- Biochemistry, University of Cologne, Cologne, Germany
| | | | - Ralf J Braun
- Cell Biology, University of Bayreuth, Bayreuth, Germany.,Neurodegeneration, Danube Private University, Krems/Donau, Austria
| | - Konstanze F Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Gilles Charvin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
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16
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Impact of Hydrogen Peroxide on Protein Synthesis in Yeast. Antioxidants (Basel) 2021; 10:antiox10060952. [PMID: 34204720 PMCID: PMC8231629 DOI: 10.3390/antiox10060952] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 01/03/2023] Open
Abstract
Cells must be able to respond and adapt to different stress conditions to maintain normal function. A common response to stress is the global inhibition of protein synthesis. Protein synthesis is an expensive process consuming much of the cell's energy. Consequently, it must be tightly regulated to conserve resources. One of these stress conditions is oxidative stress, resulting from the accumulation of reactive oxygen species (ROS) mainly produced by the mitochondria but also by other intracellular sources. Cells utilize a variety of antioxidant systems to protect against ROS, directing signaling and adaptation responses at lower levels and/or detoxification as levels increase to preclude the accumulation of damage. In this review, we focus on the role of hydrogen peroxide, H2O2, as a signaling molecule regulating protein synthesis at different levels, including transcription and various parts of the translation process, e.g., initiation, elongation, termination and ribosome recycling.
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17
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A rate threshold mechanism regulates MAPK stress signaling and survival. Proc Natl Acad Sci U S A 2021; 118:2004998118. [PMID: 33443180 DOI: 10.1073/pnas.2004998118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cells are exposed to changes in extracellular stimulus concentration that vary as a function of rate. However, how cells integrate information conveyed from stimulation rate along with concentration remains poorly understood. Here, we examined how varying the rate of stress application alters budding yeast mitogen-activated protein kinase (MAPK) signaling and cell behavior at the single-cell level. We show that signaling depends on a rate threshold that operates in conjunction with stimulus concentration to determine the timing of MAPK signaling during rate-varying stimulus treatments. We also discovered that the stimulation rate threshold and stimulation rate-dependent cell survival are sensitive to changes in the expression levels of the Ptp2 phosphatase, but not of another phosphatase that similarly regulates osmostress signaling during switch-like treatments. Our results demonstrate that stimulation rate is a regulated determinant of cell behavior and provide a paradigm to guide the dissection of major stimulation rate dependent mechanisms in other systems.
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18
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Haggerty RA, Purvis JE. Inferring the structures of signaling motifs from paired dynamic traces of single cells. PLoS Comput Biol 2021; 17:e1008657. [PMID: 33539338 PMCID: PMC7889133 DOI: 10.1371/journal.pcbi.1008657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/17/2021] [Accepted: 12/26/2020] [Indexed: 11/18/2022] Open
Abstract
Individual cells show variability in their signaling dynamics that often correlates with phenotypic responses, indicating that cell-to-cell variability is not merely noise but can have functional consequences. Based on this observation, we reasoned that cell-to-cell variability under the same treatment condition could be explained in part by a single signaling motif that maps different upstream signals into a corresponding set of downstream responses. If this assumption holds, then repeated measurements of upstream and downstream signaling dynamics in a population of cells could provide information about the underlying signaling motif for a given pathway, even when no prior knowledge of that motif exists. To test these two hypotheses, we developed a computer algorithm called MISC (Motif Inference from Single Cells) that infers the underlying signaling motif from paired time-series measurements from individual cells. When applied to measurements of transcription factor and reporter gene expression in the yeast stress response, MISC predicted signaling motifs that were consistent with previous mechanistic models of transcription. The ability to detect the underlying mechanism became less certain when a cell's upstream signal was randomly paired with another cell's downstream response, demonstrating how averaging time-series measurements across a population obscures information about the underlying signaling mechanism. In some cases, motif predictions improved as more cells were added to the analysis. These results provide evidence that mechanistic information about cellular signaling networks can be systematically extracted from the dynamical patterns of single cells.
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Affiliation(s)
- Raymond A. Haggerty
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Computational Medicine Program, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeremy E. Purvis
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Computational Medicine Program, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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19
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Bistability in oxidative stress response determines the migration behavior of phytoplankton in turbulence. Proc Natl Acad Sci U S A 2021; 118:2005944118. [PMID: 33495340 PMCID: PMC7865155 DOI: 10.1073/pnas.2005944118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Turbulence has long been known to drive phytoplankton fitness and species succession: motile species dominate in calmer environments and non-motile species in turbulent conditions. Yet a mechanistic understanding of the effect of turbulence on phytoplankton migratory behavior and physiology is lacking. By combining a method to generate turbulent cues, quantification of stress accumulation and physiology, and a mathematical model of stress dynamics, we show that motile phytoplankton use their mechanical stability to sense the intensity of turbulent cues and integrate these cues in time via stress signaling to trigger switches in migratory behavior. The stress-mediated warning strategy we discovered provides a paradigm for how phytoplankton cope with turbulence, thereby potentially governing which species will be successful in a changing ocean. Turbulence is an important determinant of phytoplankton physiology, often leading to cell stress and damage. Turbulence affects phytoplankton migration both by transporting cells and by triggering switches in migratory behavior, whereby vertically migrating cells can actively invert their direction of migration upon exposure to turbulent cues. However, a mechanistic link between single-cell physiology and vertical migration of phytoplankton in turbulence is currently missing. Here, by combining physiological and behavioral experiments with a mathematical model of stress accumulation and dissipation, we show that the mechanism responsible for the switch in the direction of migration in the marine raphidophyte Heterosigma akashiwo is the integration of reactive oxygen species (ROS) signaling generated by turbulent cues. Within timescales as short as tens of seconds, the emergent downward-migrating subpopulation exhibited a twofold increase in ROS, an indicator of stress, 15% lower photosynthetic efficiency, and 35% lower growth rate over multiple generations compared to the upward-migrating subpopulation. The origin of the behavioral split as a result of a bistable oxidative stress response is corroborated by the observation that exposure of cells to exogenous stressors (H2O2, UV-A radiation, or high irradiance), in lieu of turbulence, caused comparable ROS accumulation and an equivalent split into the two subpopulations. By providing a mechanistic link between the single-cell mechanics of swimming and physiology on the one side and the emergent population-scale migratory response and impact on fitness on the other, the ROS-mediated early warning response we discovered contributes to our understanding of phytoplankton community composition in future ocean conditions.
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20
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Bheda P, Aguilar-Gómez D, Kukhtevich I, Becker J, Charvin G, Kirmizis A, Schneider R. Microfluidics for single-cell lineage tracking over time to characterize transmission of phenotypes in Saccharomyces cerevisiae. STAR Protoc 2020; 1:100228. [PMID: 33377118 PMCID: PMC7757727 DOI: 10.1016/j.xpro.2020.100228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae is an excellent model organism to dissect the maintenance and inheritance of phenotypes due to its asymmetric division. This requires following individual cells over time as they go through divisions to define pedigrees. Here, we provide a detailed protocol for collecting and analyzing time-lapse imaging data of yeast cells. The microfluidics protocol can achieve improved time resolution for single-cell tracking to enable characterization of maintenance and inheritance of phenotypes. For complete details on the use and execution of this protocol, please refer to Bheda et al. (2020a).
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Affiliation(s)
- Poonam Bheda
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | | | - Igor Kukhtevich
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Johannes Becker
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Gilles Charvin
- Development and Stem Cells, IGBMC, 67400 Illkirch, France
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, 2109 Nicosia, Cyprus
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Faculty of Biology, Ludwig-Maximilians Universität München, 80333 Munich, Germany
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21
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Ro SH, Fay J, Cyuzuzo CI, Jang Y, Lee N, Song HS, Harris EN. SESTRINs: Emerging Dynamic Stress-Sensors in Metabolic and Environmental Health. Front Cell Dev Biol 2020; 8:603421. [PMID: 33425907 PMCID: PMC7794007 DOI: 10.3389/fcell.2020.603421] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022] Open
Abstract
Proper timely management of various external and internal stresses is critical for metabolic and redox homeostasis in mammals. In particular, dysregulation of mechanistic target of rapamycin complex (mTORC) triggered from metabolic stress and accumulation of reactive oxygen species (ROS) generated from environmental and genotoxic stress are well-known culprits leading to chronic metabolic disease conditions in humans. Sestrins are one of the metabolic and environmental stress-responsive groups of proteins, which solely have the ability to regulate both mTORC activity and ROS levels in cells, tissues and organs. While Sestrins are originally reported as one of several p53 target genes, recent studies have further delineated the roles of this group of stress-sensing proteins in the regulation of insulin sensitivity, glucose and fat metabolism, and redox-function in metabolic disease and aging. In this review, we discuss recent studies that investigated and manipulated Sestrins-mediated stress signaling pathways in metabolic and environmental health. Sestrins as an emerging dynamic group of stress-sensor proteins are drawing a spotlight as a preventive or therapeutic mechanism in both metabolic stress-associated pathologies and aging processes at the same time.
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Affiliation(s)
- Seung-Hyun Ro
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Julianne Fay
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Cesar I Cyuzuzo
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Yura Jang
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.,Department of Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Naeun Lee
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Hyun-Seob Song
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States.,Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Edward N Harris
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
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22
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N Kolodkin A, Sharma RP, Colangelo AM, Ignatenko A, Martorana F, Jennen D, Briedé JJ, Brady N, Barberis M, Mondeel TDGA, Papa M, Kumar V, Peters B, Skupin A, Alberghina L, Balling R, Westerhoff HV. ROS networks: designs, aging, Parkinson's disease and precision therapies. NPJ Syst Biol Appl 2020; 6:34. [PMID: 33106503 PMCID: PMC7589522 DOI: 10.1038/s41540-020-00150-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
How the network around ROS protects against oxidative stress and Parkinson's disease (PD), and how processes at the minutes timescale cause disease and aging after decades, remains enigmatic. Challenging whether the ROS network is as complex as it seems, we built a fairly comprehensive version thereof which we disentangled into a hierarchy of only five simpler subnetworks each delivering one type of robustness. The comprehensive dynamic model described in vitro data sets from two independent laboratories. Notwithstanding its five-fold robustness, it exhibited a relatively sudden breakdown, after some 80 years of virtually steady performance: it predicted aging. PD-related conditions such as lack of DJ-1 protein or increased α-synuclein accelerated the collapse, while antioxidants or caffeine retarded it. Introducing a new concept (aging-time-control coefficient), we found that as many as 25 out of 57 molecular processes controlled aging. We identified new targets for "life-extending interventions": mitochondrial synthesis, KEAP1 degradation, and p62 metabolism.
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Affiliation(s)
- Alexey N Kolodkin
- Infrastructure for Systems Biology Europe (ISBE.NL), Amsterdam, The Netherlands.
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands.
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
| | - Raju Prasad Sharma
- Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands
- Environmental Engineering Laboratory, Departament d'Enginyeria Quimica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Anna Maria Colangelo
- Infrastructure for Systems Biology Europe (ISBE.IT), Milan, Italy
- SysBio Centre of Systems Biology (ISBE.IT), University of Milano-Bicocca, Milan, Italy
- Laboratory of Neuroscience "R Levi-Montalcini" Dept of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Andrew Ignatenko
- Luxembourg Institute of Science and Technology (LIST), Esch-sur-Alzette, Luxembourg
| | - Francesca Martorana
- Infrastructure for Systems Biology Europe (ISBE.IT), Milan, Italy
- SysBio Centre of Systems Biology (ISBE.IT), University of Milano-Bicocca, Milan, Italy
- Laboratory of Neuroscience "R Levi-Montalcini" Dept of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Danyel Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Jacco J Briedé
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Nathan Brady
- Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Matteo Barberis
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK
- Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Surrey, UK
| | - Thierry D G A Mondeel
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK
- Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Surrey, UK
| | - Michele Papa
- SysBio Centre of Systems Biology (ISBE.IT), University of Milano-Bicocca, Milan, Italy
- Infrastructure for Systems Biology Europe (ISBE.IT), Naples, Italy
- Department of Mental and Physical Health, University of Campania-L. Vanvitelli, Napoli, Italia
| | - Vikas Kumar
- Environmental Engineering Laboratory, Departament d'Enginyeria Quimica, Universitat Rovira i Virgili, Tarragona, Spain
- IISPV, Hospital Universitari Sant Joan de Reus, Universitat Rovira I Virgili, Reus, Spain
| | - Bernhard Peters
- Faculty of Science, Technology and Communication, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Lilia Alberghina
- Infrastructure for Systems Biology Europe (ISBE.IT), Milan, Italy
- SysBio Centre of Systems Biology (ISBE.IT), University of Milano-Bicocca, Milan, Italy
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Hans V Westerhoff
- Infrastructure for Systems Biology Europe (ISBE.NL), Amsterdam, The Netherlands.
- Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands.
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
- Manchester Centre for Integrative Systems Biology, School for Chemical Engineering and Analytical Science, The University of Manchester, Manchester, UK.
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23
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Theoretical study of the impact of adaptation on cell-fate heterogeneity and fractional killing. Sci Rep 2020; 10:17429. [PMID: 33060729 PMCID: PMC7562916 DOI: 10.1038/s41598-020-74238-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
Fractional killing illustrates the cell propensity to display a heterogeneous fate response over a wide range of stimuli. The interplay between the nonlinear and stochastic dynamics of biochemical networks plays a fundamental role in shaping this probabilistic response and in reconciling requirements for heterogeneity and controllability of cell-fate decisions. The stress-induced fate choice between life and death depends on an early adaptation response which may contribute to fractional killing by amplifying small differences between cells. To test this hypothesis, we consider a stochastic modeling framework suited for comprehensive sensitivity analysis of dose response curve through the computation of a fractionality index. Combining bifurcation analysis and Langevin simulation, we show that adaptation dynamics enhances noise-induced cell-fate heterogeneity by shifting from a saddle-node to a saddle-collision transition scenario. The generality of this result is further assessed by a computational analysis of a detailed regulatory network model of apoptosis initiation and by a theoretical analysis of stochastic bifurcation mechanisms. Overall, the present study identifies a cooperative interplay between stochastic, adaptation and decision intracellular processes that could promote cell-fate heterogeneity in many contexts.
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24
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Excessive rDNA Transcription Drives the Disruption in Nuclear Homeostasis during Entry into Senescence in Budding Yeast. Cell Rep 2020; 28:408-422.e4. [PMID: 31291577 DOI: 10.1016/j.celrep.2019.06.032] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/09/2019] [Accepted: 06/07/2019] [Indexed: 01/11/2023] Open
Abstract
Budding yeast cells undergo a limited number of divisions before they enter senescence and die. Despite recent mechanistic advances, whether and how molecular events are temporally and causally linked during the transition to senescence remain elusive. Here, using real-time observation of the accumulation of extrachromosomal rDNA circles (ERCs) in single cells, we provide evidence that ERCs build up rapidly with exponential kinetics well before any physiological decline. We then show that ERCs fuel a massive increase in ribosomal RNA (rRNA) levels in the nucleolus, which do not mature into functional ribosomes. This breakdown in nucleolar coordination is followed by a loss of nuclear homeostasis, thus defining a chronology of causally related events leading to cell death. A computational analysis supports a model in which a series of age-independent processes lead to an age-dependent increase in cell mortality, hence explaining the emergence of aging in budding yeast.
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25
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Jashnsaz H, Fox ZR, Hughes JJ, Li G, Munsky B, Neuert G. Diverse Cell Stimulation Kinetics Identify Predictive Signal Transduction Models. iScience 2020; 23:101565. [PMID: 33083733 PMCID: PMC7549069 DOI: 10.1016/j.isci.2020.101565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 08/18/2020] [Accepted: 09/11/2020] [Indexed: 11/28/2022] Open
Abstract
Computationally understanding the molecular mechanisms that give rise to cell signaling responses upon different environmental, chemical, and genetic perturbations is a long-standing challenge that requires models that fit and predict quantitative responses for new biological conditions. Overcoming this challenge depends not only on good models and detailed experimental data but also on the rigorous integration of both. We propose a quantitative framework to perturb and model generic signaling networks using multiple and diverse changing environments (hereafter "kinetic stimulations") resulting in distinct pathway activation dynamics. We demonstrate that utilizing multiple diverse kinetic stimulations better constrains model parameters and enables predictions of signaling dynamics that would be impossible using traditional dose-response or individual kinetic stimulations. To demonstrate our approach, we use experimentally identified models to predict signaling dynamics in normal, mutated, and drug-treated conditions upon multitudes of kinetic stimulations and quantify which proteins and reaction rates are most sensitive to which extracellular stimulations.
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Affiliation(s)
- Hossein Jashnsaz
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Zachary R Fox
- Inria Saclay Ile-de-France, Palaiseau 91120, France.,Institut Pasteur, USR 3756 IP CNRS, Paris 75015, France.,Keck Scholars, School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Jason J Hughes
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Guoliang Li
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Brian Munsky
- Keck Scholars, School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA.,Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA.,Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN 37232, USA.,Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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26
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Roger F, Picazo C, Reiter W, Libiad M, Asami C, Hanzén S, Gao C, Lagniel G, Welkenhuysen N, Labarre J, Nyström T, Grøtli M, Hartl M, Toledano MB, Molin M. Peroxiredoxin promotes longevity and H 2O 2-resistance in yeast through redox-modulation of protein kinase A. eLife 2020; 9:e60346. [PMID: 32662770 PMCID: PMC7392609 DOI: 10.7554/elife.60346] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/08/2020] [Indexed: 12/16/2022] Open
Abstract
Peroxiredoxins are H2O2 scavenging enzymes that also carry out H2O2 signaling and chaperone functions. In yeast, the major cytosolic peroxiredoxin, Tsa1 is required for both promoting resistance to H2O2 and extending lifespan upon caloric restriction. We show here that Tsa1 effects both these functions not by scavenging H2O2, but by repressing the nutrient signaling Ras-cAMP-PKA pathway at the level of the protein kinase A (PKA) enzyme. Tsa1 stimulates sulfenylation of cysteines in the PKA catalytic subunit by H2O2 and a significant proportion of the catalytic subunits are glutathionylated on two cysteine residues. Redox modification of the conserved Cys243 inhibits the phosphorylation of a conserved Thr241 in the kinase activation loop and enzyme activity, and preventing Thr241 phosphorylation can overcome the H2O2 sensitivity of Tsa1-deficient cells. Results support a model of aging where nutrient signaling pathways constitute hubs integrating information from multiple aging-related conduits, including a peroxiredoxin-dependent response to H2O2.
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Affiliation(s)
- Friederike Roger
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Cecilia Picazo
- Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburgSweden
| | - Wolfgang Reiter
- Mass Spectrometry Facility, Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenterViennaAustria
| | - Marouane Libiad
- Oxidative Stress and Cancer Laboratory, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Gif sur YvetteFrance
| | - Chikako Asami
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Sarah Hanzén
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Chunxia Gao
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Gilles Lagniel
- Oxidative Stress and Cancer Laboratory, Integrative Biology and Molecular Genetics Unit (SBIGEM)CEA SaclayFrance
| | - Niek Welkenhuysen
- Department of Mathematical Sciences, Chalmers University of Technology and University of GothenburgGothenburgSweden
| | - Jean Labarre
- Oxidative Stress and Cancer Laboratory, Integrative Biology and Molecular Genetics Unit (SBIGEM)CEA SaclayFrance
| | - Thomas Nyström
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Markus Hartl
- Mass Spectrometry Facility, Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenterViennaAustria
| | - Michel B Toledano
- Oxidative Stress and Cancer Laboratory, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Gif sur YvetteFrance
| | - Mikael Molin
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
- Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburgSweden
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27
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Cell size sets the diameter of the budding yeast contractile ring. Nat Commun 2020; 11:2952. [PMID: 32528053 PMCID: PMC7289848 DOI: 10.1038/s41467-020-16764-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/21/2020] [Indexed: 01/02/2023] Open
Abstract
The formation and maintenance of subcellular structures and organelles with a well-defined size is a key requirement for cell function, yet our understanding of the underlying size control mechanisms is limited. While budding yeast cell polarization and subsequent assembly of a septin ring at the site of bud formation has been successfully used as a model for biological self-assembly processes, the mechanisms that set the size of the septin ring at the bud neck are unknown. Here, we use live-cell imaging and genetic manipulation of cell volume to show that the septin ring diameter increases with cell volume. This cell-volume-dependence largely accounts for modulations of ring size due to changes in ploidy and genetic manipulation of cell polarization. Our findings suggest that the ring diameter is set through the dynamic interplay of septin recruitment and Cdc42 polarization, establishing it as a model for size homeostasis of self-assembling organelles. Budding yeast cell polarization is known to self-assemble, but it is still not clear what controls the size of the resulting septin ring. Here the authors show that the septin ring diameter is set by cell volume, ensuring that larger cells have larger rings.
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28
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Bheda P, Aguilar-Gómez D, Becker NB, Becker J, Stavrou E, Kukhtevich I, Höfer T, Maerkl S, Charvin G, Marr C, Kirmizis A, Schneider R. Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory. Mol Cell 2020; 78:915-925.e7. [DOI: 10.1016/j.molcel.2020.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/15/2020] [Accepted: 04/15/2020] [Indexed: 10/24/2022]
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29
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Chang N, Yao S, Chen D, Zhang L, Huang J, Zhang L. The Hog1 positive regulated YCT1 gene expression under cadmium tolerance of budding yeast. FEMS Microbiol Lett 2019; 365:5049003. [PMID: 29982432 DOI: 10.1093/femsle/fny170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/30/2018] [Indexed: 12/24/2022] Open
Abstract
Cadmium (Cd) is a heavy metal that is the cause of irreversible hazards to living organisms. Cadmium ions can induce the phosphorylation of MAPKs pathway molecules such as Hog1 and Slt2, but downstream effectors and potential activation pathways are still unclear. In this study, the RNA-seq data analysis in Cd-stressed yeast was performed to predict and screen the signal transduction pathway and the potential effect molecules regulated by MAPKs. Based on differentially expressed genes and Venn diagrams, 31 genes regulated by Hog1p and two genes induced by Slt2p, which related to carbohydrate metabolism, oxidative damage, DNA replication stress and detoxification, were characterized under Cd exposure to yeast. A cysteine-specific transporter (Yct1) modulated by Hog1 was confirmed via RNA-seq results. Meanwhile, we tested the Cd-sensitivity, intracellular Cd concentrations and β-galactosidase assay, and results indicated that the hypersensitivity of the hog1 mutant to Cd was partly abrogated in YCT1 gene deletion, induction of YCT1 was dependent on Hog1 and its transcription factors, and Yct1p would be epistatic to the Hog1p in Cd-tolerance. The investigation of the transcriptome of MAPKs under Cd stress provided valuable information for future molecular studies of Cd-tolerance.
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Affiliation(s)
- Na Chang
- School of Life Sciences, Tianjin University, Tianjin, China, 300072
| | - Shunyu Yao
- School of Life Sciences, Tianjin University, Tianjin, China, 300072
| | - Deguang Chen
- School of Life Sciences, Tianjin University, Tianjin, China, 300072
| | - Lei Zhang
- School of Life Sciences, Tianjin University, Tianjin, China, 300072
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, Tianjin, China, 300072
| | - Lilin Zhang
- School of Life Sciences, Tianjin University, Tianjin, China, 300072
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30
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Moreno DF, Jenkins K, Morlot S, Charvin G, Csikasz-Nagy A, Aldea M. Proteostasis collapse, a hallmark of aging, hinders the chaperone-Start network and arrests cells in G1. eLife 2019; 8:48240. [PMID: 31518229 PMCID: PMC6744273 DOI: 10.7554/elife.48240] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/05/2019] [Indexed: 12/26/2022] Open
Abstract
Loss of proteostasis and cellular senescence are key hallmarks of aging, but direct cause-effect relationships are not well understood. We show that most yeast cells arrest in G1 before death with low nuclear levels of Cln3, a key G1 cyclin extremely sensitive to chaperone status. Chaperone availability is seriously compromised in aged cells, and the G1 arrest coincides with massive aggregation of a metastable chaperone-activity reporter. Moreover, G1-cyclin overexpression increases lifespan in a chaperone-dependent manner. As a key prediction of a model integrating autocatalytic protein aggregation and a minimal Start network, enforced protein aggregation causes a severe reduction in lifespan, an effect that is greatly alleviated by increased expression of specific chaperones or cyclin Cln3. Overall, our data show that proteostasis breakdown, by compromising chaperone activity and G1-cyclin function, causes an irreversible arrest in G1, configuring a molecular pathway postulating proteostasis decay as a key contributing effector of cell senescence.
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Affiliation(s)
- David F Moreno
- Molecular Biology Institute of Barcelona (IBMB), CSIC, Barcelona, Spain
| | - Kirsten Jenkins
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.,Institute of Mathematical and Molecular Biomedicine, King's College London, London, United Kingdom
| | - Sandrine Morlot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France.,Université de Strasbourg, Illkirch, France
| | - Gilles Charvin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France.,Université de Strasbourg, Illkirch, France
| | - Attila Csikasz-Nagy
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.,Institute of Mathematical and Molecular Biomedicine, King's College London, London, United Kingdom.,Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Martí Aldea
- Molecular Biology Institute of Barcelona (IBMB), CSIC, Barcelona, Spain.,Department of Basic Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain
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31
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Thiemicke A, Jashnsaz H, Li G, Neuert G. Generating kinetic environments to study dynamic cellular processes in single cells. Sci Rep 2019; 9:10129. [PMID: 31300695 PMCID: PMC6625993 DOI: 10.1038/s41598-019-46438-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/27/2019] [Indexed: 01/28/2023] Open
Abstract
Cells of any organism are consistently exposed to changes over time in their environment. The kinetics by which these changes occur are critical for the cellular response and fate decision. It is therefore important to control the temporal changes of extracellular stimuli precisely to understand biological mechanisms in a quantitative manner. Most current cell culture and biochemical studies focus on instant changes in the environment and therefore neglect the importance of kinetic environments. To address these shortcomings, we developed two experimental methodologies to precisely control the environment of single cells. These methodologies are compatible with standard biochemistry, molecular, cell and quantitative biology assays. We demonstrate applicability by obtaining time series and time point measurements in both live and fixed cells. We demonstrate the feasibility of the methodology in yeast and mammalian cell culture in combination with widely used assays such as flow cytometry, time-lapse microscopy and single-molecule RNA Fluorescent in-situ Hybridization (smFISH). Our experimental methodologies are easy to implement in most laboratory settings and allows the study of kinetic environments in a wide range of assays and different cell culture conditions.
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Affiliation(s)
- Alexander Thiemicke
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - Hossein Jashnsaz
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - Guoliang Li
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA. .,Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, 37232, USA. .,Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA.
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32
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Labavić D, Ladjimi MT, Thommen Q, Pfeuty B. Scaling laws of cell-fate responses to transient stress. J Theor Biol 2019; 478:14-25. [PMID: 31202789 DOI: 10.1016/j.jtbi.2019.06.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 06/05/2019] [Accepted: 06/13/2019] [Indexed: 10/26/2022]
Abstract
Analysis and modelling of dose-survival curves of cells and tissues are often used to assess therapeutic efficacy or environmental risks, much less to infer the intracellular regulatory mechanisms of cellular stress response. However, systematic measurements of how cell survival depends on the time profile of stress, such as exposure duration, provide practical means to decipher the homeostatic dynamics of stress-response regulatory networks. In this paper, we propose a dynamical framework to theoretically address the relationship between cell fate response to a transient stress and the underlying regulatory feedback mechanisms. A simple network topology that couples a homeostatic negative feedback and a death-triggering positive feedback is shown to display four response regimes for which the iso-effect relationships between duration and intensity are captured by specific power laws. These distinct response regimes define several windows of stress duration for which lethality is not merely proportional to the product of intensity and duration, and, thus, for which cells are either more tolerant or more vulnerable to a given dose. Overall, this study highlights the differential roles of feedback strength, timescale and nonlinearity in promoting survivability to particular stress profiles, providing a valuable framework for a comparative analysis of diverse stress-specific regulatory networks.
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Affiliation(s)
- Darka Labavić
- Univ. Lille CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France.
| | - Mohamed Tahar Ladjimi
- Univ. Lille CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Quentin Thommen
- Univ. Lille CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Benjamin Pfeuty
- Univ. Lille CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France.
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33
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Del Giudice M, Buck CL, Chaby LE, Gormally BM, Taff CC, Thawley CJ, Vitousek MN, Wada H. What Is Stress? A Systems Perspective. Integr Comp Biol 2019; 58:1019-1032. [PMID: 30204874 DOI: 10.1093/icb/icy114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The term "stress" is used to describe important phenomena at multiple levels of biological organization, but finding a general and rigorous definition of the concept has proven challenging. Current models in the behavioral literature emphasize the cognitive aspects of stress, which is said to occur when threats to the organism are perceived as uncontrollable and/or unpredictable. Here we adopt the perspective of systems biology and take a step toward a general definition of stress by unpacking the concept in light of control theory. Our goal is to clarify the concept so as to facilitate integrative research and formal analysis. We argue that stress occurs when a biological control system detects a failure to control a fitness-critical variable, which may be either internal or external to the organism. Biological control systems typically include both feedback (reactive, compensatory) and feedforward (predictive, anticipatory) components; their interplay accounts for the complex phenomenology of stress in living organisms. The simple and abstract definition we propose applies to animals, plants, and single cells, highlighting connections across levels of organization. In the final section of the paper we explore some extensions of our approach and suggest directions for future research. Specifically, we discuss the classic concepts of conditioning and hormesis and review relevant work on cellular stress responses; show how control theory suggests the existence of fundamental trade-offs in the design of stress responses; and point to potential insights into the effects of novel environmental conditions, including those resulting from anthropogenic change.
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Affiliation(s)
- Marco Del Giudice
- Department of Psychology, University of New Mexico, Logan Hall, 2001 Redondo Dr. NE, Albuquerque, NM 87131, USA
| | - C Loren Buck
- Northern Arizona University, Flagstaff, AZ 86011-0001, USA
| | - Lauren E Chaby
- Wayne State University, 42 W Warren Avenue, Detroit, MI 48202, USA
| | | | - Conor C Taff
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Maren N Vitousek
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Haruka Wada
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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34
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Haupt A, Ershov D, Minc N. A Positive Feedback between Growth and Polarity Provides Directional Persistency and Flexibility to the Process of Tip Growth. Curr Biol 2018; 28:3342-3351.e3. [DOI: 10.1016/j.cub.2018.09.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/24/2018] [Accepted: 09/11/2018] [Indexed: 12/12/2022]
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35
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Controllable stress patterns over multi-generation timescale in microfluidic devices. Methods Cell Biol 2018. [PMID: 30165960 DOI: 10.1016/bs.mcb.2018.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The generation of complex temporal stress patterns may be instrumental to investigate the adaptive properties of individual cells submitted to environmental stress on physiological timescale. However, it is difficult to accurately control stress concentration over time in bulk experiments. Here, we describe a microfluidics-based protocol to induce tightly controllable H2O2 stress in budding yeast while constantly monitoring cell growth with single cell resolution over multi-generation timescale. Moreover, we describe a simple methodology to produce ramping H2O2 stress to investigate the homeostatic properties of the H2O2 scavenging system.
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36
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Berlin R, Gruen R, Best J. Systems Medicine Disease: Disease Classification and Scalability Beyond Networks and Boundary Conditions. Front Bioeng Biotechnol 2018; 6:112. [PMID: 30131956 PMCID: PMC6090066 DOI: 10.3389/fbioe.2018.00112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/18/2018] [Indexed: 12/26/2022] Open
Abstract
In order to accommodate the forthcoming wealth of health and disease related information, from genome to body sensors to population and the environment, the approach to disease description and definition demands re-examination. Traditional classification methods remain trapped by history; to provide the descriptive features that are required for a comprehensive description of disease, systems science, which realizes dynamic processes, adaptive response, and asynchronous communication channels, must be applied (Wolkenhauer et al., 2013). When Disease is viewed beyond the thresholds of lines and threshold boundaries, disease definition is not only the result of reductionist, mechanistic categories which reluctantly face re-composition. Disease is process and synergy as the characteristics of Systems Biology and Systems Medicine are included. To capture the wealth of information and contribute meaningfully to medical practice and biology research, Disease classification goes beyond a single spatial biologic level or static time assignment to include the interface of Disease process and organism response (Bechtel, 2017a; Green et al., 2017).
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Affiliation(s)
- Richard Berlin
- Department of Computer Science, University of Illinois, Urbana, IL, United States
| | - Russell Gruen
- Department of Surgery, Nanyang Institute of Technology in Health and Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - James Best
- Lee Kong China School of Medicine, Nanyang Technological University, Singapore, Singapore
- Imperial College, London, United Kingdom
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37
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Garmendia-Torres C, Tassy O, Matifas A, Molina N, Charvin G. Multiple inputs ensure yeast cell size homeostasis during cell cycle progression. eLife 2018; 7:34025. [PMID: 29972352 PMCID: PMC6085122 DOI: 10.7554/elife.34025] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 07/01/2018] [Indexed: 12/27/2022] Open
Abstract
Coordination of cell growth with division is essential for proper cell function. In budding yeast, although some molecular mechanisms responsible for cell size control during G1 have been elucidated, the mechanism by which cell size homeostasis is established remains to be discovered. Here, we developed a new technique based on quantification of histone levels to monitor cell cycle progression in individual cells with unprecedented accuracy. Our analysis establishes the existence of a mechanism controlling bud size in G2/M that prevents premature onset of anaphase, and controls the overall size variability. While most G1 mutants do not display impaired size homeostasis, mutants in which cyclin B-Cdk regulation is altered display large size variability. Our study thus demonstrates that size homeostasis is not controlled by a G1-specific mechanism alone but is likely to be an emergent property resulting from the integration of several mechanisms that coordinate cell and bud growth with division.
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Affiliation(s)
- Cecilia Garmendia-Torres
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Olivier Tassy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Audrey Matifas
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Nacho Molina
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Gilles Charvin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
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38
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Distributed and dynamic intracellular organization of extracellular information. Proc Natl Acad Sci U S A 2018; 115:6088-6093. [PMID: 29784812 DOI: 10.1073/pnas.1716659115] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.
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