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Ganguly R, Lee CS. A Poisson-Independent Approach to Precision Nucleic Acid Quantification in Microdroplets. ACS APPLIED BIO MATERIALS 2024; 7:3441-3451. [PMID: 38658190 DOI: 10.1021/acsabm.4c00350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Digital PCR (dPCR) has become indispensable in nucleic acid (NA) detection across various fields, including viral diagnostics and mutant detection. However, misclassification of partitions in dPCR can significantly impact accuracy. Despite existing methods to minimize misclassification bias, accurate classification remains elusive, especially for nonamplified target partitions. To address these challenges, this study introduces an innovative microdroplet-based competitive PCR platform for nucleic acid quantification in microfluidic devices independent of Poisson statistics. In this approach, the target concentration (T) is determined from the concentration of competitor DNA (C) at the equivalence point (E.P.), where C/T is 1. Competitive PCR ensures that the ratio of target to competitor DNA remains constant during amplification, reflected in the resultant fluorescence intensity, allowing the quantification of target DNA concentration at the equivalence point. The unique amplification technique eliminates Poisson distribution, addressing misclassification challenges. Additionally, our approach reduces the need for post-PCR procedures and shortens analytical time. We envision this platform as versatile, reproducible, and easily adaptable for driving significant progress in molecular biology and diagnostics.
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Affiliation(s)
- Reya Ganguly
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Chang-Soo Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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2
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Kumawat R, Tomar RS. Dissecting the role of mitogen-activated protein kinase Hog1 in yeast flocculation. FEBS J 2024. [PMID: 38648231 DOI: 10.1111/febs.17137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/25/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
Living organisms are frequently exposed to multiple biotic and abiotic stress forms during their lifetime. Organisms cope with stress conditions by regulating their gene expression programs. In response to different environmental stress conditions, yeast cells activate different tolerance mechanisms, many of which share common signaling pathways. Flocculation is one of the key mechanisms underlying yeast survival under unfavorable environmental conditions, and the Tup1-Cyc8 corepressor complex is a major regulator of this process. Additionally, yeast cells can utilize different mitogen-activated protein kinase (MAPK) pathways to modulate gene expression during stress conditions. Here, we show that the high osmolarity glycerol (HOG) MAPK pathway is involved in the regulation of yeast flocculation. We observed that the HOG MAPK pathway was constitutively activated in flocculating cells, and found that the interaction between phosphorylated Hog1 and the FLO genes promoter region increased significantly upon sodium chloride exposure. We found that treatment of cells with cantharidin decreased Hog1 phosphorylation, causing a sharp reduction in the expression of FLO genes and the flocculation phenotype. Similarly, deletion of HOG1 in yeast cells reduced flocculation. Altogether, our results suggest a role for HOG MAPK signaling in the regulation of FLO genes and yeast flocculation.
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Affiliation(s)
- Ramesh Kumawat
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India
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3
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A focus on yeast mating: From pheromone signaling to cell-cell fusion. Semin Cell Dev Biol 2023; 133:83-95. [PMID: 35148940 DOI: 10.1016/j.semcdb.2022.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 12/14/2022]
Abstract
Cells live in a chemical environment and are able to orient towards chemical cues. Unicellular haploid fungal cells communicate by secreting pheromones to reproduce sexually. In the yeast models Saccharomyces cerevisiae and Schizosaccharomyces pombe, pheromonal communication activates similar pathways composed of cognate G-protein-coupled receptors and downstream small GTPase Cdc42 and MAP kinase cascades. Local pheromone release and sensing, at a mobile surface polarity patch, underlie spatial gradient interpretation to form pairs between two cells of distinct mating types. Concentration of secretion at the point of cell-cell contact then leads to local cell wall digestion for cell fusion, forming a diploid zygote that prevents further fusion attempts. A number of asymmetries between mating types may promote efficiency of the system. In this review, we present our current knowledge of pheromone signaling in the two model yeasts, with an emphasis on how cells decode the pheromone signal spatially and ultimately fuse together. Though overall pathway architectures are similar in the two species, their large evolutionary distance allows to explore how conceptually similar solutions to a general biological problem can arise from divergent molecular components.
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4
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An Evolutionary Paradigm Favoring Cross Talk between Bacterial Two-Component Signaling Systems. mSystems 2022; 7:e0029822. [PMID: 36264076 PMCID: PMC9765234 DOI: 10.1128/msystems.00298-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The prevalent paradigm governing bacterial two-component signaling systems (TCSs) is specificity, wherein the histidine kinase (HK) of a TCS exclusively activates its cognate response regulator (RR). Cross talk, where HKs activate noncognate RRs, is considered evolutionarily disadvantageous because it can compromise adaptive responses by leaking signals. Yet cross talk is observed in several bacteria. Here, to resolve this paradox, we propose an alternative paradigm where cross talk can be advantageous. We envisioned programmed environments, wherein signals appear in predefined sequences. In such environments, cross talk that primes bacteria to upcoming signals may improve adaptive responses and confer evolutionary benefits. To test this hypothesis, we employed mathematical modeling of TCS signaling networks and stochastic evolutionary dynamics simulations. We considered the comprehensive set of bacterial phenotypes, comprising thousands of distinct cross talk patterns competing in varied signaling environments. Our simulations predicted that in programmed environments phenotypes with cross talk facilitating priming would outcompete phenotypes without cross talk. In environments where signals appear randomly, bacteria without cross talk would dominate, explaining the specificity widely seen. Additionally, a testable prediction was that the phenotypes selected in programmed environments would display one-way cross talk, ensuring priming to future signals. Interestingly, the cross talk networks we deduced from available data on TCSs of Mycobacterium tuberculosis all displayed one-way cross talk, which was consistent with our predictions. Our study thus identifies potential evolutionary underpinnings of cross talk in bacterial TCSs, suggests a reconciliation of specificity and cross talk, makes testable predictions of the nature of cross talk patterns selected, and has implications for understanding bacterial adaptation and the response to interventions. IMPORTANCE Bacteria use two-component signaling systems (TCSs) to sense and respond to environmental changes. The prevalent paradigm governing TCSs is specificity, where signal flow through TCSs is insulated; leakage to other TCSs is considered evolutionarily disadvantageous. Yet cross talk between TCSs is observed in many bacteria. Here, we present a potential resolution of this paradox. We envision programmed environments, wherein stimuli appear in predefined sequences. Cross talk that primes bacteria to upcoming stimuli could then confer evolutionary benefits. We demonstrate this benefit using mathematical modeling and evolutionary simulations. Interestingly, we found signatures of predicted cross talk patterns in Mycobacterium tuberculosis. Furthermore, specificity was selected in environments where stimuli occurred randomly, thus reconciling specificity and cross talk. Implications follow for understanding bacterial evolution and for interventions.
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5
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de Oya IG, Jiménez-Gutiérrez E, Gaillard H, Molina M, Martín H, Wellinger RE. Manganese Stress Tolerance Depends on Yap1 and Stress-Activated MAP Kinases. Int J Mol Sci 2022; 23:ijms232415706. [PMID: 36555348 PMCID: PMC9779322 DOI: 10.3390/ijms232415706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Understanding which intracellular signaling pathways are activated by manganese stress is crucial to decipher how metal overload compromise cellular integrity. Here, we unveil a role for oxidative and cell wall stress signaling in the response to manganese stress in yeast. We find that the oxidative stress transcription factor Yap1 protects cells against manganese toxicity. Conversely, extracellular manganese addition causes a rapid decay in Yap1 protein levels. In addition, manganese stress activates the MAPKs Hog1 and Slt2 (Mpk1) and leads to an up-regulation of the Slt2 downstream transcription factor target Rlm1. Importantly, Yap1 and Slt2 are both required to protect cells from oxidative stress in mutants impaired in manganese detoxification. Under such circumstances, Slt2 activation is enhanced upon Yap1 depletion suggesting an interplay between different stress signaling nodes to optimize cellular stress responses and manganese tolerance.
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Affiliation(s)
- Inés G. de Oya
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla, Avda. Américo Vespucio s/n, 41092 Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012 Sevilla, Spain
| | - Elena Jiménez-Gutiérrez
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28034 Madrid, Spain
| | - Hélène Gaillard
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla, Avda. Américo Vespucio s/n, 41092 Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012 Sevilla, Spain
| | - María Molina
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28034 Madrid, Spain
| | - Humberto Martín
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28034 Madrid, Spain
| | - Ralf Erik Wellinger
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla, Avda. Américo Vespucio s/n, 41092 Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012 Sevilla, Spain
- Correspondence:
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6
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Recent advances of integrated microfluidic systems for fungal and bacterial analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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7
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Richter F, Bindschedler S, Calonne-Salmon M, Declerck S, Junier P, Stanley CE. Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi. FEMS Microbiol Rev 2022; 46:6674677. [PMID: 36001464 PMCID: PMC9779915 DOI: 10.1093/femsre/fuac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 01/07/2023] Open
Abstract
This review highlights new advances in the emerging field of 'Fungi-on-a-Chip' microfluidics for single-cell studies on fungi and discusses several future frontiers, where we envisage microfluidic technology development to be instrumental in aiding our understanding of fungal biology. Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognized as key components of the microbiome in other eukaryotes, such as humans, where they play a fundamental role not only in human pathogenesis, but also likely as commensals. In the food sector, fungi are used either directly or as fermenting agents and are often key players in the biotechnological industry, where they are responsible for the production of both bulk chemicals and antibiotics. Although the macroscopic fruiting bodies are immediately recognizable by most observers, the structure, function, and interactions of fungi with other microbes at the microscopic scale still remain largely hidden. Herein, we shed light on new advances in the emerging field of Fungi-on-a-Chip microfluidic technologies for single-cell studies on fungi. We discuss the development and application of microfluidic tools in the fields of medicine and biotechnology, as well as in-depth biological studies having significance for ecology and general natural processes. Finally, a future perspective is provided, highlighting new frontiers in which microfluidic technology can benefit this field.
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Affiliation(s)
- Felix Richter
- Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Maryline Calonne-Salmon
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Claire E Stanley
- Corresponding author: Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, United Kingdom. E-mail:
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8
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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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9
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Tan YS, Zhang RK, Liu ZH, Li BZ, Yuan YJ. Microbial Adaptation to Enhance Stress Tolerance. Front Microbiol 2022; 13:888746. [PMID: 35572687 PMCID: PMC9093737 DOI: 10.3389/fmicb.2022.888746] [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: 03/03/2022] [Accepted: 03/18/2022] [Indexed: 01/28/2023] Open
Abstract
Microbial cell factories have been widely used in the production of various chemicals. Although synthetic biology is useful in improving the cell factories, adaptation is still widely applied to enhance its complex properties. Adaptation is an important strategy for enhancing stress tolerance in microbial cell factories. Adaptation involves gradual modifications of microorganisms in a stressful environment to enhance their tolerance. During adaptation, microorganisms use different mechanisms to enhance non-preferred substrate utilization and stress tolerance, thereby improving their ability to adapt for growth and survival. In this paper, the progress on the effects of adaptation on microbial substrate utilization capacity and environmental stress tolerance are reviewed, and the mechanisms involved in enhancing microbial adaptive capacity are discussed.
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Affiliation(s)
- Yong-Shui Tan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Ren-Kuan Zhang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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10
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Cells under pressure: how yeast cells respond to mechanical forces. Trends Microbiol 2022; 30:495-510. [PMID: 35000797 DOI: 10.1016/j.tim.2021.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/31/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022]
Abstract
In their natural habitats, unicellular fungal microbes are exposed to a myriad of mechanical cues such as shear forces from fluid flow, osmotic changes, and contact forces arising from microbial expansion in confined niches. While the rigidity of the cell wall is critical to withstand such external forces and balance high internal turgor pressure, it poses mechanical challenges during physiological processes such as cell growth, division, and mating that require cell wall remodeling. Thus, even organisms as simple as yeast have evolved complex signaling networks to sense and respond to intrinsic and extrinsic mechanical forces. In this review, we summarize the type and origin of mechanical forces experienced by unicellular yeast and discuss how these forces reorganize cell polarity and how pathogenic fungi exploit polarized assemblies to track weak spots in host tissues for successful penetration. We then describe mechanisms of force-sensing by conserved sets of mechanosensors. Finally, we elaborate downstream mechanotransduction mechanisms that orchestrate appropriate cellular responses, leading to improved mechanical fitness.
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11
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Yaakoub H, Sanchez NS, Ongay-Larios L, Courdavault V, Calenda A, Bouchara JP, Coria R, Papon N. The high osmolarity glycerol (HOG) pathway in fungi †. Crit Rev Microbiol 2021; 48:657-695. [PMID: 34893006 DOI: 10.1080/1040841x.2021.2011834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
While fungi are widely occupying nature, many species are responsible for devastating mycosis in humans. Such niche diversity explains how quick fungal adaptation is necessary to endow the capacity of withstanding fluctuating environments and to cope with host-imposed conditions. Among all the molecular mechanisms evolved by fungi, the most studied one is the activation of the phosphorelay signalling pathways, of which the high osmolarity glycerol (HOG) pathway constitutes one of the key molecular apparatus underpinning fungal adaptation and virulence. In this review, we summarize the seminal knowledge of the HOG pathway with its more recent developments. We specifically described the HOG-mediated stress adaptation, with a particular focus on osmotic and oxidative stress, and point out some lags in our understanding of its involvement in the virulence of pathogenic species including, the medically important fungi Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus, compared to the model yeast Saccharomyces cerevisiae. Finally, we also highlighted some possible applications of the HOG pathway modifications to improve the fungal-based production of natural products in the industry.
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Affiliation(s)
- Hajar Yaakoub
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
| | - Norma Silvia Sanchez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Vincent Courdavault
- EA2106 "Biomolécules et Biotechnologies Végétales", Université de Tours, Tours, France
| | | | | | - Roberto Coria
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Nicolas Papon
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
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12
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Bedekovic T, Brand AC. Microfabrication and its use in investigating fungal biology. Mol Microbiol 2021; 117:569-577. [PMID: 34592794 DOI: 10.1111/mmi.14816] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 11/29/2022]
Abstract
Advances in microfabrication technology, and its increasing accessibility, allow us to explore fungal biology as never before. By coupling molecular genetics with fluorescence live-cell imaging in custom-designed chambers, we can now probe single yeast cell responses to changing conditions over a lifetime, characterise population heterogeneity and investigate its underlying causes. By growing filamentous fungi in complex physical environments, we can identify cross-species commonalities, reveal species-specific growth responses and examine physiological differences relevant to diverse fungal lifestyles. As affordability and expertise broadens, microfluidic platforms will become a standard technique for examining the role of fungi in cross-kingdom interactions, ranging from rhizosphere to microbiome to interconnected human organ systems. This review brings together the perspectives already gained from studying fungal biology in microfabricated systems and outlines their potential in understanding the role of fungi in the environment, health and disease.
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Affiliation(s)
- Tina Bedekovic
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Alexandra C Brand
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
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13
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RTG Signaling Sustains Mitochondrial Respiratory Capacity in HOG1-Dependent Osmoadaptation. Microorganisms 2021; 9:microorganisms9091894. [PMID: 34576788 PMCID: PMC8466848 DOI: 10.3390/microorganisms9091894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 08/28/2021] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial RTG-dependent retrograde signaling, whose regulators have been characterized in Saccharomyces cerevisiae, plays a recognized role under various environmental stresses. Of special significance, the activity of the transcriptional complex Rtg1/3 has been shown to be modulated by Hog1, the master regulator of the high osmolarity glycerol pathway, in response to osmotic stress. The present work focuses on the role of RTG signaling in salt-induced osmotic stress and its interaction with HOG1. Wild-type and mutant cells, lacking HOG1 and/or RTG genes, are compared with respect to cell growth features, retrograde signaling activation and mitochondrial function in the presence and in the absence of high osmostress. We show that RTG2, the main upstream regulator of the RTG pathway, contributes to osmoadaptation in an HOG1-dependent manner and that, with RTG3, it is notably involved in a late phase of growth. Our data demonstrate that impairment of RTG signaling causes a decrease in mitochondrial respiratory capacity exclusively under osmostress. Overall, these results suggest that HOG1 and the RTG pathway may interact sequentially in the stress signaling cascade and that the RTG pathway may play a role in inter-organellar metabolic communication for osmoadaptation.
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14
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Kim Y, Song J, Lee Y, Cho S, Kim S, Lee SR, Park S, Shin Y, Jeon NL. High-throughput injection molded microfluidic device for single-cell analysis of spatiotemporal dynamics. LAB ON A CHIP 2021; 21:3150-3158. [PMID: 34180916 DOI: 10.1039/d0lc01245a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Single-cell level analysis of various cellular behaviors has been aided by recent developments in microfluidic technology. Polydimethylsiloxane (PDMS)-based microfluidic devices have been widely used to elucidate cell differentiation and migration under spatiotemporal stimulation. However, microfluidic devices fabricated with PDMS have inherent limitations due to material issues and non-scalable fabrication process. In this study, we designed and fabricated an injection molded microfluidic device that enables real-time chemical profile control. This device is made of polystyrene (PS), engineered with channel dimensions optimized for injection molding to achieve functionality and compatibility with single cell observation. We demonstrated the spatiotemporal dynamics in the device with computational simulation and experiments. In temporal dynamics, we observed extracellular signal-regulated kinase (ERK) activation of PC12 cells by stimulating the cells with growth factors (GFs). Also, we confirmed yes-associated protein (YAP) phase separation of HEK293 cells under stimulation using sorbitol. In spatial dynamics, we observed the migration of NIH 3T3 cells (transfected with Lifeact-GFP) under different spatiotemporal stimulations of PDGF. Using the injection molded plastic devices, we obtained comprehensive data more easily than before while using less time compared to previous PDMS models. This easy-to-use plastic microfluidic device promises to open a new approach for investigating the mechanisms of cell behavior at the single-cell level.
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Affiliation(s)
- Youngtaek Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Jiyoung Song
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Younggyun Lee
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Sunghyun Cho
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Suryong Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Seung-Ryeol Lee
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Seonghyuk Park
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea. and Institute of BioEngineering, Seoul National University, Seoul, Republic of Korea
| | - Noo Li Jeon
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea. and Institute of BioEngineering, Seoul National University, Seoul, Republic of Korea and Institute of Advanced Machinery and Design, Seoul National University, Seoul, Republic of Korea
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15
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Eigenfeld M, Kerpes R, Becker T. Understanding the Impact of Industrial Stress Conditions on Replicative Aging in Saccharomyces cerevisiae. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:665490. [PMID: 37744109 PMCID: PMC10512339 DOI: 10.3389/ffunb.2021.665490] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/30/2021] [Indexed: 09/26/2023]
Abstract
In yeast, aging is widely understood as the decline of physiological function and the decreasing ability to adapt to environmental changes. Saccharomyces cerevisiae has become an important model organism for the investigation of these processes. Yeast is used in industrial processes (beer and wine production), and several stress conditions can influence its intracellular aging processes. The aim of this review is to summarize the current knowledge on applied stress conditions, such as osmotic pressure, primary metabolites (e.g., ethanol), low pH, oxidative stress, heat on aging indicators, age-related physiological changes, and yeast longevity. There is clear evidence that yeast cells are exposed to many stressors influencing viability and vitality, leading to an age-related shift in age distribution. Currently, there is a lack of rapid, non-invasive methods allowing the investigation of aspects of yeast aging in real time on a single-cell basis using the high-throughput approach. Methods such as micromanipulation, centrifugal elutriator, or biotinylation do not provide real-time information on age distributions in industrial processes. In contrast, innovative approaches, such as non-invasive fluorescence coupled flow cytometry intended for high-throughput measurements, could be promising for determining the replicative age of yeast cells in fermentation and its impact on industrial stress conditions.
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Affiliation(s)
| | - Roland Kerpes
- Research Group Beverage and Cereal Biotechnology, Institute of Brewing and Beverage Technology, Technical University of Munich, Freising, Germany
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Affiliation(s)
- Keke Hu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Tho D. K. Nguyen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Stefania Rabasco
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Pieter E. Oomen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
- ParaMedir B.V., 1e Energieweg 13, 9301 LK Roden, The Netherlands
| | - Andrew G. Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
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Pandey P, Zaman K, Prokai L, Shulaev V. Comparative Proteomics Analysis Reveals Unique Early Signaling Response of Saccharomyces cerevisiae to Oxidants with Different Mechanism of Action. Int J Mol Sci 2020; 22:ijms22010167. [PMID: 33375274 PMCID: PMC7795614 DOI: 10.3390/ijms22010167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 01/18/2023] Open
Abstract
The early signaling events involved in oxidant recognition and triggering of oxidant-specific defense mechanisms to counteract oxidative stress still remain largely elusive. Our discovery driven comparative proteomics analysis revealed unique early signaling response of the yeast Saccharomyces cerevisiae on the proteome level to oxidants with a different mechanism of action as early as 3 min after treatment with four oxidants, namely H2O2, cumene hydroperoxide (CHP), and menadione and diamide, when protein abundances were compared using label-free quantification relying on a high-resolution mass analyzer (Orbitrap). We identified significant regulation of 196 proteins in response to H2O2, 569 proteins in response to CHP, 369 proteins in response to menadione and 207 proteins in response to diamide. Only 17 proteins were common across all treatments, but several more proteins were shared between two or three oxidants. Pathway analyses revealed that each oxidant triggered a unique signaling mechanism associated with cell survival and repair. Signaling pathways mostly regulated by oxidants were Ran, TOR, Rho, and eIF2. Furthermore, each oxidant regulated these pathways in a unique way indicating specificity of response to oxidants having different modes of action. We hypothesize that interplay of these signaling pathways may be important in recognizing different oxidants to trigger different downstream MAPK signaling cascades and to induce specific responses.
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Affiliation(s)
- Prajita Pandey
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA;
- Advanced Environmental Research Institute (AERI), University of North Texas, Denton, TX 76203, USA
| | - Khadiza Zaman
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (K.Z.); (L.P.)
| | - Laszlo Prokai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (K.Z.); (L.P.)
| | - Vladimir Shulaev
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA;
- Advanced Environmental Research Institute (AERI), University of North Texas, Denton, TX 76203, USA
- Correspondence: ; Tel.: +1-940-369-5368
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Van Drogen F, Dard N, Pelet S, Lee SS, Mishra R, Srejić N, Peter M. Crosstalk and spatiotemporal regulation between stress-induced MAP kinase pathways and pheromone signaling in budding yeast. Cell Cycle 2020; 19:1707-1715. [PMID: 32552303 DOI: 10.1080/15384101.2020.1779469] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Budding yeast, Saccharomyces cerevisiae, has been widely used as a model system to study cellular signaling in response to internal and external cues. Yeast was among the first organisms in which the architecture, feedback mechanisms and physiological responses of various MAP kinase signaling cascades were studied in detail. Although these MAP kinase pathways are activated by different signals and elicit diverse cellular responses, such as adaptation to stress and mating, they function as an interconnected signaling network, as they influence each other and, in some cases, even share components. Indeed, various stress signaling pathways interfere with pheromone signaling that triggers a distinct cellular differentiation program. However, the molecular mechanisms responsible for this crosstalk are still poorly understood. Here, we review the general topology of the yeast MAP kinase signaling network and highlight recent and new data revealing how conflicting intrinsic and extrinsic signals are interpreted to orchestrate appropriate cellular responses.
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Affiliation(s)
| | - Nicolas Dard
- Ufr Smbh, University Sorbonne Paris Nord , Bobigny, France
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne , Lausanne, Switzerland
| | - Sung Sik Lee
- ETH Zürich, Institute for Biochemistry , Zürich, Switzerland.,ETH Zürich, Scientific Center for Optical and Electron Microscopy (ScopeM) , Zürich, Switzerland
| | - Ranjan Mishra
- ETH Zürich, Institute for Biochemistry , Zürich, Switzerland
| | - Nevena Srejić
- ETH Zürich, Institute for Biochemistry , Zürich, Switzerland
| | - Matthias Peter
- ETH Zürich, Institute for Biochemistry , Zürich, Switzerland
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