1
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Watanabe D, Kawashima M, Yoshioka N, Sugimoto Y, Takagi H. Rational design of alcoholic fermentation targeting extracellular carbon. NPJ Sci Food 2023; 7:37. [PMID: 37479699 PMCID: PMC10361962 DOI: 10.1038/s41538-023-00215-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Breeding yeast strains for industrial alcoholic fermentation requires laborious screening due to the lack of in vivo modification strategies. Here we show that quiescence-specific cell wall thickening via synthesis of a major component, 1,3-β-glucan, critically antagonizes cellular fermentation ability by sequestering the available cytoplasmic carbon sources. This study provides insights into glycolytic control and reports an effective and reliable rational fermentation design.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
| | - Mikiya Kawashima
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Naoya Yoshioka
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Yukiko Sugimoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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2
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Sweeney K, McClean MN. Transcription factor localization dynamics and DNA binding drive distinct promoter interpretations. Cell Rep 2023; 42:112426. [PMID: 37087734 DOI: 10.1016/j.celrep.2023.112426] [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: 08/30/2022] [Revised: 02/17/2023] [Accepted: 04/07/2023] [Indexed: 04/24/2023] Open
Abstract
Environmental information may be encoded in the temporal dynamics of transcription factor (TF) activation and subsequently decoded by gene promoters to enact stimulus-specific gene expression programs. Previous studies of this behavior focused on the encoding and decoding of information in TF nuclear localization dynamics, yet cells control the activity of TFs in myriad ways, including by regulating their ability to bind DNA. Here, we use light-controlled mutants of the yeast TF Msn2 as a model system to investigate how promoter decoding of TF localization dynamics is affected by changes in the ability of the TF to bind DNA. We find that yeast promoters directly decode the light-controlled localization dynamics of Msn2 and that the effects of changing Msn2 affinity on that decoding behavior are highly promoter dependent, illustrating how cells could regulate TF localization dynamics and DNA binding in concert for improved control of gene expression.
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Affiliation(s)
- Kieran Sweeney
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Megan N McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA; University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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3
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Blomberg A. Yeast osmoregulation - glycerol still in pole position. FEMS Yeast Res 2022; 22:6655991. [PMID: 35927716 PMCID: PMC9428294 DOI: 10.1093/femsyr/foac035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/29/2022] [Accepted: 08/02/2022] [Indexed: 11/14/2022] Open
Abstract
In response to osmotic dehydration cells sense, signal, alter gene expression, and metabolically counterbalance osmotic differences. The main compatible solute/osmolyte that accumulates in yeast cells is glycerol, which is produced from the glycolytic intermediate dihydroxyacetone phosphate. This review covers recent advancements in understanding mechanisms involved in sensing, signaling, cell-cycle delays, transcriptional responses as well as post-translational modifications on key proteins in osmoregulation. The protein kinase Hog1 is a key-player in many of these events, however, there is also a growing body of evidence for important Hog1-independent mechanisms playing vital roles. Several missing links in our understanding of osmoregulation will be discussed and future avenues for research proposed. The review highlights that this rather simple experimental system—salt/sorbitol and yeast—has developed into an enormously potent model system unravelling important fundamental aspects in biology.
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Affiliation(s)
- Anders Blomberg
- Dept. of Chemistry and Molecular Biology, University of Gothenburg, Sweden
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4
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Interaction of TOR and PKA Signaling in S. cerevisiae. Biomolecules 2022; 12:biom12020210. [PMID: 35204711 PMCID: PMC8961621 DOI: 10.3390/biom12020210] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 01/13/2023] Open
Abstract
TOR and PKA signaling are the major growth-regulatory nutrient-sensing pathways in S. cerevisiae. A number of experimental findings demonstrated a close relationship between these pathways: Both are responsive to glucose availability. Both regulate ribosome production on the transcriptional level and repress autophagy and the cellular stress response. Sch9, a major downstream effector of TORC1 presumably shares its kinase consensus motif with PKA, and genetic rescue and synthetic defects between PKA and Sch9 have been known for a long time. Further, studies in the first decade of this century have suggested direct regulation of PKA by TORC1. Nonetheless, the contribution of a potential direct cross-talk vs. potential sharing of targets between the pathways has still not been completely resolved. What is more, other findings have in contrast highlighted an antagonistic relationship between the two pathways. In this review, I explore the association between TOR and PKA signaling, mainly by focusing on proteins that are commonly referred to as shared TOR and PKA targets. Most of these proteins are transcription factors which to a large part explain the major transcriptional responses elicited by TOR and PKA upon nutrient shifts. I examine the evidence that these proteins are indeed direct targets of both pathways and which aspects of their regulation are targeted by TOR and PKA. I further explore if they are phosphorylated on shared sites by PKA and Sch9 or when experimental findings point towards regulation via the PP2ASit4/PP2A branch downstream of TORC1. Finally, I critically review data suggesting direct cross-talk between the pathways and its potential mechanism.
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5
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Hollenstein DM, Gérecová G, Romanov N, Ferrari J, Veis J, Janschitz M, Beyer R, Schüller C, Ogris E, Hartl M, Ammerer G, Reiter W. A phosphatase-centric mechanism drives stress signaling response. EMBO Rep 2021; 22:e52476. [PMID: 34558777 PMCID: PMC8567219 DOI: 10.15252/embr.202152476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 12/14/2022] Open
Abstract
Changing environmental cues lead to the adjustment of cellular physiology by phosphorylation signaling networks that typically center around kinases as active effectors and phosphatases as antagonistic elements. Here, we report a signaling mechanism that reverses this principle. Using the hyperosmotic stress response in Saccharomyces cerevisiae as a model system, we find that a phosphatase-driven mechanism causes induction of phosphorylation. The key activating step that triggers this phospho-proteomic response is the Endosulfine-mediated inhibition of protein phosphatase 2A-Cdc55 (PP2ACdc55 ), while we do not observe concurrent kinase activation. In fact, many of the stress-induced phosphorylation sites appear to be direct substrates of the phosphatase, rendering PP2ACdc55 the main downstream effector of a signaling response that operates in parallel and independent of the well-established kinase-centric stress signaling pathways. This response affects multiple cellular processes and is required for stress survival. Our results demonstrate how a phosphatase can assume the role of active downstream effectors during signaling and allow re-evaluating the impact of phosphatases on shaping the phosphorylome.
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Affiliation(s)
- David Maria Hollenstein
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | - Gabriela Gérecová
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | | | - Jessica Ferrari
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | - Jiri Veis
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
- Center for Medical BiochemistryMax Perutz Labs, Vienna BioCenterMedical University of ViennaViennaAustria
| | - Marion Janschitz
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | - Reinhard Beyer
- Department of Applied Genetics and Cell Biology (DAGZ)University of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln a.d. DonauAustria
| | - Christoph Schüller
- Department of Applied Genetics and Cell Biology (DAGZ)University of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln a.d. DonauAustria
| | - Egon Ogris
- Center for Medical BiochemistryMax Perutz Labs, Vienna BioCenterMedical University of ViennaViennaAustria
| | - Markus Hartl
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
- Mass Spectrometry FacilityMax Perutz Labs, Vienna BioCenterUniversity of ViennaViennaAustria
| | - Gustav Ammerer
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | - Wolfgang Reiter
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
- Mass Spectrometry FacilityMax Perutz Labs, Vienna BioCenterUniversity of ViennaViennaAustria
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6
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Mat Nanyan NSB, Takagi H. Proline Homeostasis in Saccharomyces cerevisiae: How Does the Stress-Responsive Transcription Factor Msn2 Play a Role? Front Genet 2020; 11:438. [PMID: 32411186 PMCID: PMC7198862 DOI: 10.3389/fgene.2020.00438] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
Overexpression of MSN2, which is the transcription factor gene in response to stress, is well-known to increase the tolerance of the yeast Saccharomyces cerevisiae cells to a wide variety of environmental stresses. Recent studies have found that the Msn2 is a feasible potential mediator of proline homeostasis in yeast. This result is based on the finding that overexpression of the MSN2 gene exacerbates the cytotoxicity of yeast to various amino acid analogs whose uptake is increased by the active amino acid permeases localized on the plasma membrane as a result of a dysfunctional deubiquitination process. Increased understanding of the cellular responses induced by the Msn2-mediated proline incorporation will provide better comprehension of how cells respond to and counteract to different kinds of stimuli and will also contribute to the breeding of industrial yeast strains with increased productivity.
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Affiliation(s)
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
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7
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Andréasson C, Ott M, Büttner S. Mitochondria orchestrate proteostatic and metabolic stress responses. EMBO Rep 2019; 20:e47865. [PMID: 31531937 PMCID: PMC6776902 DOI: 10.15252/embr.201947865] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/13/2019] [Accepted: 08/27/2019] [Indexed: 01/06/2023] Open
Abstract
The eukaryotic cell is morphologically and functionally organized as an interconnected network of organelles that responds to stress and aging. Organelles communicate via dedicated signal transduction pathways and the transfer of information in form of metabolites and energy levels. Recent data suggest that the communication between organellar proteostasis systems is a cornerstone of cellular stress responses in eukaryotic cells. Here, we discuss the integration of proteostasis and energy fluxes in the regulation of cellular stress and aging. We emphasize the molecular architecture of the regulatory transcriptional pathways that both sense and control metabolism and proteostasis. A special focus is placed on mechanistic insights gained from the model organism budding yeast in signaling from mitochondria to the nucleus and how this shapes cellular fitness.
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Affiliation(s)
- Claes Andréasson
- Department of Molecular BiosciencesThe Wenner‐Gren InstituteStockholm UniversityStockholmSweden
| | - Martin Ott
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Sabrina Büttner
- Department of Molecular BiosciencesThe Wenner‐Gren InstituteStockholm UniversityStockholmSweden
- Institute of Molecular BiosciencesUniversity of GrazGrazAustria
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8
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van Drogen F, Mishra R, Rudolf F, Walczak MJ, Lee SS, Reiter W, Hegemann B, Pelet S, Dohnal I, Binolfi A, Yudina Z, Selenko P, Wider G, Ammerer G, Peter M. Mechanical stress impairs pheromone signaling via Pkc1-mediated regulation of the MAPK scaffold Ste5. J Cell Biol 2019; 218:3117-3133. [PMID: 31315942 PMCID: PMC6719448 DOI: 10.1083/jcb.201808161] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 04/23/2019] [Accepted: 06/19/2019] [Indexed: 01/10/2023] Open
Abstract
This study shows that Pkc1 inhibits yeast pheromone signaling upon intrinsic and extrinsic mechanical stress. Pkc1 phosphorylates the RING-H2 domains of the scaffolds Ste5 and Far1, thereby preventing their interaction with Gβγ at the plasma membrane. This crosstalk mechanism regulates polarized growth and cell–cell fusion during mating. Cells continuously adapt cellular processes by integrating external and internal signals. In yeast, multiple stress signals regulate pheromone signaling to prevent mating under unfavorable conditions. However, the underlying crosstalk mechanisms remain poorly understood. Here, we show that mechanical stress activates Pkc1, which prevents lysis of pheromone-treated cells by inhibiting polarized growth. In vitro Pkc1 phosphorylates conserved residues within the RING-H2 domains of the scaffold proteins Far1 and Ste5, which are also phosphorylated in vivo. Interestingly, Pkc1 triggers dispersal of Ste5 from mating projections upon mechanically induced stress and during cell–cell fusion, leading to inhibition of the MAPK Fus3. Indeed, RING phosphorylation interferes with Ste5 membrane association by preventing binding to the receptor-linked Gβγ protein. Cells expressing nonphosphorylatable Ste5 undergo increased lysis upon mechanical stress and exhibit defects in cell–cell fusion during mating, which is exacerbated by simultaneous expression of nonphosphorylatable Far1. These results uncover a mechanical stress–triggered crosstalk mechanism modulating pheromone signaling, polarized growth, and cell–cell fusion during mating.
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Affiliation(s)
| | - Ranjan Mishra
- Institute for Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Fabian Rudolf
- Institute for Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Michal J Walczak
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Sung Sik Lee
- Institute for Biochemistry, ETH Zürich, Zürich, Switzerland.,Scientific Center for Optical and Electron Microscopy, ETH Zürich, Zürich, Switzerland
| | - Wolfgang Reiter
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Björn Hegemann
- Institute for Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Ilse Dohnal
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Andres Binolfi
- Department of Nuclear Magnetic Resonance-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology, Berlin, Germany
| | - Zinaida Yudina
- Institute for Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Philipp Selenko
- Department of Nuclear Magnetic Resonance-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology, Berlin, Germany
| | - Gerhard Wider
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Gustav Ammerer
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Matthias Peter
- Institute for Biochemistry, ETH Zürich, Zürich, Switzerland
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9
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Ariño J, Velázquez D, Casamayor A. Ser/Thr protein phosphatases in fungi: structure, regulation and function. MICROBIAL CELL 2019; 6:217-256. [PMID: 31114794 PMCID: PMC6506691 DOI: 10.15698/mic2019.05.677] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reversible phospho-dephosphorylation of proteins is a major mechanism for the control of cellular functions. By large, Ser and Thr are the most frequently residues phosphorylated in eukar-yotes. Removal of phosphate from these amino acids is catalyzed by a large family of well-conserved enzymes, collectively called Ser/Thr protein phosphatases. The activity of these enzymes has an enormous impact on cellular functioning. In this work we pre-sent the members of this family in S. cerevisiae and other fungal species, and review the most recent findings concerning their regu-lation and the roles they play in the most diverse aspects of cell biology.
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Affiliation(s)
- Joaquín Ariño
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Diego Velázquez
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Antonio Casamayor
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
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10
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Pfanzagl V, Görner W, Radolf M, Parich A, Schuhmacher R, Strauss J, Reiter W, Schüller C. A constitutive active allele of the transcription factor Msn2 mimicking low PKA activity dictates metabolic remodeling in yeast. Mol Biol Cell 2018; 29:2848-2862. [PMID: 30256697 PMCID: PMC6249869 DOI: 10.1091/mbc.e18-06-0389] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In yeast, protein kinase A (PKA) adjusts transcriptional profiles, metabolic rates, and cell growth in accord with carbon source availability. PKA affects gene expression mostly via the transcription factors Msn2 and Msn4, two key regulators of the environmental stress response. Here we analyze the role of the PKA-Msn2 signaling module using an Msn2 allele that harbors serine-to-alanine substitutions at six functionally important PKA motifs (Msn2A6) . Expression of Msn2A6 mimics low PKA activity, entails a transcription profile similar to that of respiring cells, and prevents formation of colonies on glucose-containing medium. Furthermore, Msn2A6 leads to high oxygen consumption and hence high respiratory activity. Substantially increased intracellular concentrations of several carbon metabolites, such as trehalose, point to a metabolic adjustment similar to diauxic shift. This partial metabolic switch is the likely cause for the slow-growth phenotype in the presence of glucose. Consistently, Msn2A6 expression does not interfere with growth on ethanol and tolerated is to a limited degree in deletion mutant strains with a gene expression signature corresponding to nonfermentative growth. We propose that the lethality observed in mutants with hampered PKA activity resides in metabolic reprogramming that is initiated by Msn2 hyperactivity.
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Affiliation(s)
- Vera Pfanzagl
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria
| | - Wolfram Görner
- Department for Biochemistry, Max. F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Martin Radolf
- Management Scientific Service/EHS, Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
| | - Alexandra Parich
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences, 3430 Tulln, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences, 3430 Tulln, Austria
| | - Joseph Strauss
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria
| | - Wolfgang Reiter
- Department for Biochemistry, Max. F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Christoph Schüller
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, 3430 Tulln, Austria
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11
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Klopf E, Moes M, Amman F, Zimmermann B, von Pelchrzim F, Wagner C, Schroeder R. Nascent RNA signaling to yeast RNA Pol II during transcription elongation. PLoS One 2018; 13:e0194438. [PMID: 29570714 PMCID: PMC5865726 DOI: 10.1371/journal.pone.0194438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/02/2018] [Indexed: 11/18/2022] Open
Abstract
Transcription as the key step in gene expression is a highly regulated process. The speed of transcription elongation depends on the underlying gene sequence and varies on a gene by gene basis. The reason for this sequence dependence is not known in detail. Recently, our group studied the cross talk between the nascent RNA and the transcribing RNA polymerase by screening the Escherichia coli genome for RNA sequences with high affinity to RNA Pol by performing genomic SELEX. This approach led to the identification of RNA polymerase-binding APtamers termed "RAPs". RAPs can have positive and negative effects on gene expression. A subgroup is able to downregulate transcription via the activity of the termination factor Rho. In this study, we used a similar SELEX setup using yeast genomic DNA as source of RNA sequences and highly purified yeast RNA Pol II as bait and obtained almost 1300 yeast-derived RAPs. Yeast RAPs are found throughout the genome within genes and antisense to genes, they are overrepresented in the non-transcribed strand of yeast telomeres and underrepresented in intergenic regions. Genes harbouring a RAP are more likely to show lower mRNA levels. By determining the endogenous expression levels as well as using a reporter system, we show that RAPs located within coding regions can reduce the transcript level downstream of the RAP. Here we demonstrate that RAPs represent a novel type of regulatory RNA signal in Saccharomyces cerevisiae that act in cis and interfere with the elongating transcription machinery to reduce the transcriptional output.
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Affiliation(s)
- Eva Klopf
- Max F. Perutz Laboratories (MFPL); University of Vienna; Vienna, Austria
| | - Murielle Moes
- Max F. Perutz Laboratories (MFPL); University of Vienna; Vienna, Austria
| | - Fabian Amman
- Max F. Perutz Laboratories (MFPL); University of Vienna; Vienna, Austria
- Institute for Theoretical Chemistry; University of Vienna; Vienna, Austria
| | - Bob Zimmermann
- Department of Molecular Evolution and Development; University of Vienna; Vienna, Austria
| | | | - Christina Wagner
- Institute for Theoretical Chemistry; University of Vienna; Vienna, Austria
| | - Renée Schroeder
- Max F. Perutz Laboratories (MFPL); University of Vienna; Vienna, Austria
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12
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Klopf E, Schmidt HA, Clauder-Münster S, Steinmetz LM, Schüller C. INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes. Nucleic Acids Res 2017; 45:3752-3766. [PMID: 28025392 PMCID: PMC5397147 DOI: 10.1093/nar/gkw1292] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 12/13/2016] [Indexed: 12/19/2022] Open
Abstract
The conserved INO80 chromatin remodeling complex is involved in regulation of DNA damage repair, replication and transcription. It is commonly recruited to the transcription start region and contributes to the establishment of promoter-proximal nucleosomes. We find a substantial influence of INO80 on nucleosome dynamics and gene expression during stress induced transcription. Transcription induced by osmotic stress leads to genome-wide remodeling of promoter proximal nucleosomes. INO80 function is required for timely return of evicted nucleosomes to the 5΄ end of induced genes. Reduced INO80 function in Arp8-deficient cells leads to correlated prolonged transcription and nucleosome eviction. INO80 and the related complex SWR1 regulate incorporation of the H2A.Z isoform at promoter proximal nucleosomes. However, H2A.Z seems not to influence osmotic stress induced gene regulation. Furthermore, we show that high rates of transcription promote INO80 recruitment to promoter regions, suggesting a connection between active transcription and promoter proximal nucleosome remodeling. In addition, we find that absence of INO80 enhances bidirectional promoter activity at highly induced genes and expression of a number of stress induced transcripts. We suggest that INO80 has a direct repressive role via promoter proximal nucleosome remodeling to limit high levels of transcription in yeast.
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Affiliation(s)
- Eva Klopf
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), UFT-Campus Tulln, Konrad Lorenz Strasse 24, 3430 Tulln, Austria
| | - Heiko A Schmidt
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, Campus Vienna Biocenter 5 (VBC5), 1030 Vienna, Austria
| | - Sandra Clauder-Münster
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christoph Schüller
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), UFT-Campus Tulln, Konrad Lorenz Strasse 24, 3430 Tulln, Austria
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13
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Bodvard K, Peeters K, Roger F, Romanov N, Igbaria A, Welkenhuysen N, Palais G, Reiter W, Toledano MB, Käll M, Molin M. Light-sensing via hydrogen peroxide and a peroxiredoxin. Nat Commun 2017; 8:14791. [PMID: 28337980 PMCID: PMC5376668 DOI: 10.1038/ncomms14791] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 01/27/2017] [Indexed: 02/08/2023] Open
Abstract
Yeast lacks dedicated photoreceptors; however, blue light still causes pronounced oscillations of the transcription factor Msn2 into and out of the nucleus. Here we show that this poorly understood phenomenon is initiated by a peroxisomal oxidase, which converts light into a hydrogen peroxide (H2O2) signal that is sensed by the peroxiredoxin Tsa1 and transduced to thioredoxin, to counteract PKA-dependent Msn2 phosphorylation. Upon H2O2, the nuclear retention of PKA catalytic subunits, which contributes to delayed Msn2 nuclear concentration, is antagonized in a Tsa1-dependent manner. Conversely, peroxiredoxin hyperoxidation interrupts the H2O2 signal and drives Msn2 oscillations by superimposing on PKA feedback regulation. Our data identify a mechanism by which light could be sensed in all cells lacking dedicated photoreceptors. In particular, the use of H2O2 as a second messenger in signalling is common to Msn2 oscillations and to light-induced entrainment of circadian rhythms and suggests conserved roles for peroxiredoxins in endogenous rhythms. While yeasts lack dedicated photoreceptors, they nonetheless possess metabolic rhythms responsive to light. Here the authors find that light signalling in budding yeast involves the production of H2O2, which in turn regulates protein kinase A through a peroxiredoxin-thioredoxin redox relay.
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Affiliation(s)
- Kristofer Bodvard
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-413 90 Göteborg, Sweden.,Department of Physics, Chalmers University of Technology, S-412 96 Göteborg, Sweden
| | - Ken Peeters
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-413 90 Göteborg, Sweden
| | - Friederike Roger
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-413 90 Göteborg, Sweden
| | - Natalie Romanov
- Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Dr Bohrgasse 9, A-1030 Vienna, Austria
| | - Aeid Igbaria
- Oxidative Stress and Cancer, SBIGEM, iBiTec-S, FRE3377 CEA-CNRS-Université Paris-Sud, CEA-Saclay, bat 142 F-91191 Gif Sur Yvette, France
| | - Niek Welkenhuysen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-413 90 Göteborg, Sweden.,Hohmann Lab, Department of Biology and Biological Engineering, Chalmers University of Technology, S-412 96 Göteborg, Sweden
| | - Gaël Palais
- Oxidative Stress and Cancer, SBIGEM, iBiTec-S, FRE3377 CEA-CNRS-Université Paris-Sud, CEA-Saclay, bat 142 F-91191 Gif Sur Yvette, France
| | - Wolfgang Reiter
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr Bohrgasse 9, A-1030 Vienna, Austria
| | - Michel B Toledano
- Oxidative Stress and Cancer, SBIGEM, iBiTec-S, FRE3377 CEA-CNRS-Université Paris-Sud, CEA-Saclay, bat 142 F-91191 Gif Sur Yvette, France
| | - Mikael Käll
- Department of Physics, Chalmers University of Technology, S-412 96 Göteborg, Sweden
| | - Mikael Molin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-413 90 Göteborg, Sweden
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14
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Cho BR, Hahn JS. CK2-dependent phosphorylation positively regulates stress-induced activation of Msn2 in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:695-704. [PMID: 28330760 DOI: 10.1016/j.bbagrm.2017.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 03/07/2017] [Accepted: 03/14/2017] [Indexed: 01/28/2023]
Abstract
CK2 is a highly conserved Ser/Thr protein kinase involved in a large number of cellular processes. Here, we demonstrate that CK2-dependent phosphorylation positively regulates Msn2/4, the general stress response transcriptional activators in Saccharomyces cerevisiae, in response to various types of environmental stress conditions. CK2 overexpression elicits hyperactivation of Msn2/4, whereas deletion of one of the CK2 catalytic subunits, especially CKA2, leads to reduced transcriptional activity of Msn2/4 in response to glucose starvation, H2O2, and lactic acid. The CKA2 deletion mutant also shows increased stress sensitivity. CK2 phosphorylates Ser194 and Ser638 in Msn2 and replacement of Ser638 with alanine leads to reduced Msn2 activity upon stress and reduced tolerance to H2O2 and lactic acid. CKA2 deletion mutant shows shorter nuclear retention time of Msn2 upon lactic acid stress, suggesting that CK2 might regulate nuclear localization of Msn2. However, Msn2S194A, S638A mutant shows normal nuclear import and export patterns upon stress, suggesting that CK2 might positively regulate the general stress response not only by direct phosphorylation of Msn2/4, but also by regulating cellular translocation machinery.
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Affiliation(s)
- Bo-Ram Cho
- Interdisciplinary Program for Bioengineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Ji-Sook Hahn
- Interdisciplinary Program for Bioengineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
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15
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Romanov N, Hollenstein DM, Janschitz M, Ammerer G, Anrather D, Reiter W. Identifying protein kinase-specific effectors of the osmostress response in yeast. Sci Signal 2017; 10:10/469/eaag2435. [PMID: 28270554 DOI: 10.1126/scisignal.aag2435] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The budding yeast Saccharomyces cerevisiae reacts to increased external osmolarity by modifying many cellular processes. Adaptive signaling relies primarily on the high-osmolarity glycerol (HOG) pathway, which is closely related to the mammalian p38 mitogen-activated protein kinase (MAPK) pathway in core architecture. To identify target proteins of the MAPK Hog1, we designed a mass spectrometry-based high-throughput experiment to measure the impact of Hog1 activation or inhibition on the Scerevisiae phosphoproteome. In addition, we analyzed how deletion of RCK2, which encodes a known effector protein kinase target of Hog1, modulated osmotic stress-induced phosphorylation. Our results not only provide an overview of the diversity of cellular functions that are directly and indirectly affected by the activity of the HOG pathway but also enabled an assessment of the Hog1-independent events that occur under osmotic stress conditions. We extended the number of putative Hog1 direct targets by analyzing the modulation of motifs consisting of serine or threonine followed by a proline (S/T-P motif) and subsequently validated these with an in vivo interaction assay. Rck2 appears to act as a central hub for many Hog1-mediated secondary phosphorylation events. This study clarifies many of the direct and indirect effects of HOG signaling and its stress-adaptive functions.
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Affiliation(s)
- Natalie Romanov
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - David Maria Hollenstein
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Marion Janschitz
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Gustav Ammerer
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Dorothea Anrather
- Mass Spectrometry Facility, Max F. Perutz Laboratories, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Wolfgang Reiter
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.
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16
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Oma1 Links Mitochondrial Protein Quality Control and TOR Signaling To Modulate Physiological Plasticity and Cellular Stress Responses. Mol Cell Biol 2016; 36:2300-12. [PMID: 27325672 DOI: 10.1128/mcb.00156-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/09/2016] [Indexed: 12/17/2022] Open
Abstract
A network of conserved proteases known as the intramitochondrial quality control (IMQC) system is central to mitochondrial protein homeostasis and cellular health. IMQC proteases also appear to participate in establishment of signaling cues for mitochondrion-to-nucleus communication. However, little is known about this process. Here, we show that in Saccharomyces cerevisiae, inactivation of the membrane-bound IMQC protease Oma1 interferes with oxidative-stress responses through enhanced production of reactive oxygen species (ROS) during logarithmic growth and reduced stress signaling via the TORC1-Rim15-Msn2/Msn4 axis. Pharmacological or genetic prevention of ROS accumulation in Oma1-deficient cells restores this defective TOR signaling. Additionally, inactivation of the Oma1 ortholog in the human fungal pathogen Candida albicans also alters TOR signaling and, unexpectedly, leads to increased resistance to neutrophil killing and virulence in the invertebrate animal model Galleria mellonella Our findings reveal a novel and evolutionarily conserved link between IMQC and TOR-mediated signaling that regulates physiological plasticity and pancellular oxidative-stress responses.
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17
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Kondo K, Kubo T, Kunieda T. Suggested Involvement of PP1/PP2A Activity and De Novo Gene Expression in Anhydrobiotic Survival in a Tardigrade, Hypsibius dujardini, by Chemical Genetic Approach. PLoS One 2015; 10:e0144803. [PMID: 26690982 PMCID: PMC4686906 DOI: 10.1371/journal.pone.0144803] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/24/2015] [Indexed: 12/19/2022] Open
Abstract
Upon desiccation, some tardigrades enter an ametabolic dehydrated state called anhydrobiosis and can survive a desiccated environment in this state. For successful transition to anhydrobiosis, some anhydrobiotic tardigrades require pre-incubation under high humidity conditions, a process called preconditioning, prior to exposure to severe desiccation. Although tardigrades are thought to prepare for transition to anhydrobiosis during preconditioning, the molecular mechanisms governing such processes remain unknown. In this study, we used chemical genetic approaches to elucidate the regulatory mechanisms of anhydrobiosis in the anhydrobiotic tardigrade, Hypsibius dujardini. We first demonstrated that inhibition of transcription or translation drastically impaired anhydrobiotic survival, suggesting that de novo gene expression is required for successful transition to anhydrobiosis in this tardigrade. We then screened 81 chemicals and identified 5 chemicals that significantly impaired anhydrobiotic survival after severe desiccation, in contrast to little or no effect on survival after high humidity exposure only. In particular, cantharidic acid, a selective inhibitor of protein phosphatase (PP) 1 and PP2A, exhibited the most profound inhibitory effects. Another PP1/PP2A inhibitor, okadaic acid, also significantly and specifically impaired anhydrobiotic survival, suggesting that PP1/PP2A activity plays an important role for anhydrobiosis in this species. This is, to our knowledge, the first report of the required activities of signaling molecules for desiccation tolerance in tardigrades. The identified inhibitory chemicals could provide novel clues to elucidate the regulatory mechanisms underlying anhydrobiosis in tardigrades.
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Affiliation(s)
- Koyuki Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113–0033, Japan
| | - Takeo Kubo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113–0033, Japan
| | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113–0033, Japan
- * E-mail:
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18
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Sacristán-Reviriego A, Martín H, Molina M. Identification of putative negative regulators of yeast signaling through a screening for protein phosphatases acting on cell wall integrity and mating MAPK pathways. Fungal Genet Biol 2015; 77:1-11. [DOI: 10.1016/j.fgb.2015.02.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 12/24/2022]
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19
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Kanshin E, Bergeron-Sandoval LP, Isik S, Thibault P, Michnick S. A Cell-Signaling Network Temporally Resolves Specific versus Promiscuous Phosphorylation. Cell Rep 2015; 10:1202-14. [DOI: 10.1016/j.celrep.2015.01.052] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 12/22/2014] [Accepted: 01/20/2015] [Indexed: 01/13/2023] Open
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20
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Luo Z, Li Y, Mousa J, Bruner S, Zhang Y, Pei Y, Keyhani NO. Bbmsn2 acts as a pH-dependent negative regulator of secondary metabolite production in the entomopathogenic fungus Beauveria bassiana. Environ Microbiol 2014; 17:1189-202. [PMID: 24965521 DOI: 10.1111/1462-2920.12542] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 06/15/2014] [Indexed: 02/01/2023]
Abstract
Fungal secondary metabolites are chemical compounds important for development, environmental adaptation and for potential biotechnological and pharmaceutical applications. Oosporein, a red-pigmented benzoquinone, produced by many fungal insect pathogenic Beauveria spp., shows remarkable functional diversity, displaying antimicrobial, antiviral and even anti-proliferative activities. A homologue of the msn2/seb1 transcription factor was identified in a Beauveria bassiana random T-DNA insertion library. Targeted gene-knockout of Bbmsn2 resulted in reduced growth and increased sensitivity to Calcofluor White, H2 O2 and Congo Red. However, when normalized to growth at 26°C, the ΔBbmsn2 mutant was more tolerant to high temperature (32°C) than the wild type parent. The ΔBbmsn2 mutant also displayed a pH-dependent growth phenotype, with little growth seen at pH < 5.0 but, better growth at alkaline conditions (pH > 8.0). Unexpectedly, a pH-dependent deregulation of a red pigment, identified as oosporein, was seen in the ΔBbmsn2 mutant. The ΔBbmsn2 strain was impaired in virulence in both topical and intrahaemocoel injection bioassays against Galleria mellonella. ΔBbmsn2 proliferation in the host haemolymph and conidiation on the host cadaver was reduced. These data indicate that Bbmsn2 acts as a negative regulator of oosporein production and contributes to virulence and growth in response to external pH in B. bassiana.
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Affiliation(s)
- Zhibing Luo
- Biotechnology Research Center, Southwest University, Chongqing, 400716, China; Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
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21
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Cloning and characterization of TaPP2AbB"-α, a member of the PP2A regulatory subunit in wheat. PLoS One 2014; 9:e94430. [PMID: 24709994 PMCID: PMC3978047 DOI: 10.1371/journal.pone.0094430] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 03/17/2014] [Indexed: 11/19/2022] Open
Abstract
Protein phosphatase 2A (PP2A), a major Serine/Threonine protein phosphatase, consists of three subunits; a highly conserved structural subunit A, a catalytic subunit C, and a highly variable regulatory subunit B which determines the substrate specificity. Although the functional mechanism of PP2A in signaling transduction in Arabidopsis is known, their physiological roles in wheat remain to be characterized. In this study, we identified a novel regulatory subunit B, TaPP2AbB"-α, in wheat (Triticum aestivum L.). Subcellular localization indicated that TaPP2AbB"-α is located in the cell membrane, cytoplasm and nucleus. It interacts with both TaPP2Aa and TaPP2Ac. Expression pattern analyses revealed that TaPP2AbB"-α is strongly expressed in roots, and responds to NaCl, polyethylene glycol (PEG), cold and abscisic acid (ABA) stresses at the transcription level. Transgenic Arabidopsis plants overexpressing TaPP2AbB"-α developed more lateral roots, especially when treated with mannitol or NaCl. These results suggest that TaPP2AbB"-α, in conjunction with the other two PP2A subunits, is involved in multi-stress response, and positively regulates lateral root development under osmotic stress.
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22
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Pautasso C, Rossi S. Transcriptional regulation of the protein kinase A subunits in Saccharomyces cerevisiae: Autoregulatory role of the kinase A activity. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:275-87. [DOI: 10.1016/j.bbagrm.2014.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 02/06/2014] [Accepted: 02/07/2014] [Indexed: 11/27/2022]
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23
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Marinho HS, Real C, Cyrne L, Soares H, Antunes F. Hydrogen peroxide sensing, signaling and regulation of transcription factors. Redox Biol 2014; 2:535-62. [PMID: 24634836 PMCID: PMC3953959 DOI: 10.1016/j.redox.2014.02.006] [Citation(s) in RCA: 571] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 02/19/2014] [Accepted: 02/21/2014] [Indexed: 12/12/2022] Open
Abstract
The regulatory mechanisms by which hydrogen peroxide (H2O2) modulates the activity of transcription factors in bacteria (OxyR and PerR), lower eukaryotes (Yap1, Maf1, Hsf1 and Msn2/4) and mammalian cells (AP-1, NRF2, CREB, HSF1, HIF-1, TP53, NF-κB, NOTCH, SP1 and SCREB-1) are reviewed. The complexity of regulatory networks increases throughout the phylogenetic tree, reaching a high level of complexity in mammalians. Multiple H2O2 sensors and pathways are triggered converging in the regulation of transcription factors at several levels: (1) synthesis of the transcription factor by upregulating transcription or increasing both mRNA stability and translation; (ii) stability of the transcription factor by decreasing its association with the ubiquitin E3 ligase complex or by inhibiting this complex; (iii) cytoplasm–nuclear traffic by exposing/masking nuclear localization signals, or by releasing the transcription factor from partners or from membrane anchors; and (iv) DNA binding and nuclear transactivation by modulating transcription factor affinity towards DNA, co-activators or repressors, and by targeting specific regions of chromatin to activate individual genes. We also discuss how H2O2 biological specificity results from diverse thiol protein sensors, with different reactivity of their sulfhydryl groups towards H2O2, being activated by different concentrations and times of exposure to H2O2. The specific regulation of local H2O2 concentrations is also crucial and results from H2O2 localized production and removal controlled by signals. Finally, we formulate equations to extract from typical experiments quantitative data concerning H2O2 reactivity with sensor molecules. Rate constants of 140 M−1 s−1 and ≥1.3 × 103 M−1 s−1 were estimated, respectively, for the reaction of H2O2 with KEAP1 and with an unknown target that mediates NRF2 protein synthesis. In conclusion, the multitude of H2O2 targets and mechanisms provides an opportunity for highly specific effects on gene regulation that depend on the cell type and on signals received from the cellular microenvironment. Complexity of redox regulation increases along the phylogenetic tree. Complex regulatory networks allow for a high degree of H2O2 biological plasticity. H2O2 modulates gene expression at all steps from transcription to protein synthesis. Fast response (s) is mediated by sensors with high H2O2 reactivity. Low reactivity H2O2 sensors may mediate slow (h) or localized H2O2 responses.
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Affiliation(s)
- H. Susana Marinho
- Departamento de Química e Bioquímica, Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Carla Real
- Departamento de Química e Bioquímica, Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Luísa Cyrne
- Departamento de Química e Bioquímica, Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Helena Soares
- Departamento de Química e Bioquímica, Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Escola Superior de Tecnologia da Saúde de Lisboa, IPL, Lisboa, Portugal
| | - Fernando Antunes
- Departamento de Química e Bioquímica, Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Corresponding author.
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