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Jonak K, Suppanz I, Bender J, Chacinska A, Warscheid B, Topf U. Ageing-dependent thiol oxidation reveals early oxidation of proteins with core proteostasis functions. Life Sci Alliance 2024; 7:e202302300. [PMID: 38383455 PMCID: PMC10881836 DOI: 10.26508/lsa.202302300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024] Open
Abstract
Oxidative post-translational modifications of protein thiols are well recognized as a readily occurring alteration of proteins, which can modify their function and thus control cellular processes. The development of techniques enabling the site-specific assessment of protein thiol oxidation on a proteome-wide scale significantly expanded the number of known oxidation-sensitive protein thiols. However, lacking behind are large-scale data on the redox state of proteins during ageing, a physiological process accompanied by increased levels of endogenous oxidants. Here, we present the landscape of protein thiol oxidation in chronologically aged wild-type Saccharomyces cerevisiae in a time-dependent manner. Our data determine early-oxidation targets in key biological processes governing the de novo production of proteins, protein folding, and degradation, and indicate a hierarchy of cellular responses affected by a reversible redox modification. Comparison with existing datasets in yeast, nematode, fruit fly, and mouse reveals the evolutionary conservation of these oxidation targets. To facilitate accessibility, we integrated the cross-species comparison into the newly developed OxiAge Database.
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Affiliation(s)
- Katarzyna Jonak
- https://ror.org/034tvp782 Laboratory of Molecular Basis of Aging and Rejuvenation, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ida Suppanz
- CIBSS Centre for Integrative Biological Signalling Research, University of Freiburg, Freiburg, Germany
| | - Julian Bender
- https://ror.org/00fbnyb24 Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Bettina Warscheid
- CIBSS Centre for Integrative Biological Signalling Research, University of Freiburg, Freiburg, Germany
- https://ror.org/00fbnyb24 Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ulrike Topf
- https://ror.org/034tvp782 Laboratory of Molecular Basis of Aging and Rejuvenation, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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2
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Solari CA, Ortolá Martínez MC, Fernandez JM, Bates C, Cueto G, Valacco MP, Morales-Polanco F, Moreno S, Rossi S, Ashe MP, Portela P. Riboproteome remodeling during quiescence exit in Saccharomyces cerevisiae. iScience 2024; 27:108727. [PMID: 38235324 PMCID: PMC10792236 DOI: 10.1016/j.isci.2023.108727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/15/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
The quiescent state is the prevalent mode of cellular life in most cells. Saccharomyces cerevisiae is a useful model for studying the molecular basis of the cell cycle, quiescence, and aging. Previous studies indicate that heterogeneous ribosomes show a specialized translation function to adjust the cellular proteome upon a specific stimulus. Using nano LC-MS/MS, we identified 69 of the 79 ribosomal proteins (RPs) that constitute the eukaryotic 80S ribosome during quiescence. Our study shows that the riboproteome is composed of 444 accessory proteins comprising cellular functions such as translation, protein folding, amino acid and glucose metabolism, cellular responses to oxidative stress, and protein degradation. Furthermore, the stoichiometry of both RPs and accessory proteins on ribosome particles is different depending on growth conditions and among monosome and polysome fractions. Deficiency of different RPs resulted in defects of translational capacity, suggesting that ribosome composition can result in changes in translational activity during quiescence.
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Affiliation(s)
- Clara A. Solari
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - María Clara Ortolá Martínez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Juan M. Fernandez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Christian Bates
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Gerardo Cueto
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Instituto IEGEBA (CONICET-UBA), Buenos Aires, Argentina
| | - María Pía Valacco
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Fabián Morales-Polanco
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Silvia Moreno
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Mark P. Ashe
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
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3
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Kohler V, Kohler A, Berglund LL, Hao X, Gersing S, Imhof A, Nyström T, Höög JL, Ott M, Andréasson C, Büttner S. Nuclear Hsp104 safeguards the dormant translation machinery during quiescence. Nat Commun 2024; 15:315. [PMID: 38182580 PMCID: PMC10770042 DOI: 10.1038/s41467-023-44538-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/15/2023] [Indexed: 01/07/2024] Open
Abstract
The resilience of cellular proteostasis declines with age, which drives protein aggregation and compromises viability. The nucleus has emerged as a key quality control compartment that handles misfolded proteins produced by the cytosolic protein biosynthesis system. Here, we find that age-associated metabolic cues target the yeast protein disaggregase Hsp104 to the nucleus to maintain a functional nuclear proteome during quiescence. The switch to respiratory metabolism and the accompanying decrease in translation rates direct cytosolic Hsp104 to the nucleus to interact with latent translation initiation factor eIF2 and to suppress protein aggregation. Hindering Hsp104 from entering the nucleus in quiescent cells results in delayed re-entry into the cell cycle due to compromised resumption of protein synthesis. In sum, we report that cytosolic-nuclear partitioning of the Hsp104 disaggregase is a critical mechanism to protect the latent protein synthesis machinery during quiescence in yeast, ensuring the rapid restart of translation once nutrients are replenished.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
- Department of Molecular Biology, Umeå University, 90187, Umeå, Sweden
| | - Andreas Kohler
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187, Umeå, Sweden
| | - Lisa Larsson Berglund
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Xinxin Hao
- Department of Microbiology and Immunology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Sarah Gersing
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 1165, Copenhagen, Denmark
| | - Axel Imhof
- Biomedical Center Munich, Faculty of Medicine, Ludwig Maximilian University of Munich, 82152, Planegg-Martinsried, Germany
| | - Thomas Nyström
- Department of Microbiology and Immunology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
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4
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D'Alessio Y, D'Alfonso A, Camilloni G. Chromatin conformations of HSP12 during transcriptional activation in the Saccharomyces cerevisiae stationary phase. Adv Biol Regul 2023; 90:100986. [PMID: 37741159 DOI: 10.1016/j.jbior.2023.100986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/17/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023]
Abstract
During evolution, living cells have developed sophisticated molecular and physiological processes to cope with a variety of stressors. These mechanisms, which collectively constitute the Environmental Stress Response, involve the activation/repression of hundreds of genes that are regulated to respond rapidly and effectively to protect the cell. The main stressors include sudden increases in environmental temperature and osmolarity, exposure to heavy metals, nutrient limitation, ROS accumulation, and protein-damaging events. The growth stages of the yeast S. cerevisiae proceed from the exponential to the diauxic phase, finally reaching the stationary phase. It is in this latter phase that the main stressor events are more active. In the present work, we aim to understand whether the responses evoked by the sudden onset of a stressor, like what happens to cells going through the stationary phase, would be different or similar to those induced by a gradual increase in the same stimulus. To this aim, we studied the expression of the HSP12 gene of the HSP family of proteins, typically induced by stress conditions, with a focus on the role of chromatin in this regulation. Analyses of nucleosome occupancy and three-dimensional chromatin conformation suggest the activation of a different response pathway upon a sudden vs a gradual onset of a stress stimulus. Here we show that it is the three-dimensional chromatin structure of HSP12, rather than nucleosome remodeling, that becomes altered in HSP12 transcription during the stationary phase.
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Affiliation(s)
- Yuri D'Alessio
- Dipartimento di Biologia e Biotecnologie, University of Rome, Sapienza Piazzale A. Moro 5, 00185, Rome, Italy.
| | - Anna D'Alfonso
- Dipartimento di Biologia e Biotecnologie, University of Rome, Sapienza Piazzale A. Moro 5, 00185, Rome, Italy.
| | - Giorgio Camilloni
- Dipartimento di Biologia e Biotecnologie, University of Rome, Sapienza Piazzale A. Moro 5, 00185, Rome, Italy.
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5
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Rizzo J, Trottier A, Moyrand F, Coppée JY, Maufrais C, Zimbres ACG, Dang TTV, Alanio A, Desnos-Ollivier M, Mouyna I, Péhau-Arnaude G, Commere PH, Novault S, Ene IV, Nimrichter L, Rodrigues ML, Janbon G. Coregulation of extracellular vesicle production and fluconazole susceptibility in Cryptococcus neoformans. mBio 2023; 14:e0087023. [PMID: 37310732 PMCID: PMC10470540 DOI: 10.1128/mbio.00870-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 06/14/2023] Open
Abstract
Resistance to fluconazole (FLC), the most widely used antifungal drug, is typically achieved by altering the azole drug target and/or drug efflux pumps. Recent reports have suggested a link between vesicular trafficking and antifungal resistance. Here, we identified novel Cryptococcus neoformans regulators of extracellular vesicle (EV) biogenesis that impact FLC resistance. In particular, the transcription factor Hap2 does not affect the expression of the drug target or efflux pumps, yet it impacts the cellular sterol profile. Subinhibitory FLC concentrations also downregulate EV production. Moreover, in vitro spontaneous FLC-resistant colonies showed altered EV production, and the acquisition of FLC resistance was associated with decreased EV production in clinical isolates. Finally, the reversion of FLC resistance was associated with increased EV production. These data suggest a model in which fungal cells can regulate EV production in place of regulating the drug target gene expression as a first line of defense against antifungal assault in this fungal pathogen. IMPORTANCE Extracellular vesicles (EVs) are membrane-enveloped particles that are released by cells into the extracellular space. Fungal EVs can mediate community interactions and biofilm formation, but their functions remain poorly understood. Here, we report the identification of the first regulators of EV production in the major fungal pathogen Cryptococcus neoformans. Surprisingly, we uncover a novel role of EVs in modulating antifungal drug resistance. Disruption of EV production was associated with altered lipid composition and changes in fluconazole susceptibility. Spontaneous azole-resistant mutants were deficient in EV production, while loss of resistance restored initial EV production levels. These findings were recapitulated in C. neoformans clinical isolates, indicating that azole resistance and EV production are coregulated in diverse strains. Our study reveals a new mechanism of drug resistance in which cells adapt to azole stress by modulating EV production.
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Affiliation(s)
- Juliana Rizzo
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adèle Trottier
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Frédérique Moyrand
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
- Institut Pasteur, Université Paris Cité, USR 3756 IP CNRS, HUB Bioinformatique et Biostatistique, Paris, France
| | - Ana Claudia G. Zimbres
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thi Tuong Vi Dang
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, Université Paris Cité, Centre National de Référence Mycoses Invasives et Antifongiques, Groupe de recherche Mycologie Translationnelle, Département de Mycologie, Paris, France
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Marie Desnos-Ollivier
- Institut Pasteur, Université Paris Cité, Centre National de Référence Mycoses Invasives et Antifongiques, Groupe de recherche Mycologie Translationnelle, Département de Mycologie, Paris, France
| | - Isabelle Mouyna
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Gérard Péhau-Arnaude
- Institut Pasteur, Université Paris Cité, Plateforme de Bio-Imagerie Ultrastructurale, Paris, France
| | - Pierre-Henri Commere
- Institut Pasteur, Université Paris Cité, Cytometry and Biomarkers, Paris, France
| | - Sophie Novault
- Institut Pasteur, Université Paris Cité, Cytometry and Biomarkers, Paris, France
| | - Iuliana V. Ene
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Group, Paris, France
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcio L. Rodrigues
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Curitiba, Brazil
| | - Guilhem Janbon
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
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6
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Ridder MD, van den Brandeler W, Altiner M, Daran-Lapujade P, Pabst M. Proteome dynamics during transition from exponential to stationary phase under aerobic and anaerobic conditions in yeast. Mol Cell Proteomics 2023; 22:100552. [PMID: 37076048 DOI: 10.1016/j.mcpro.2023.100552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/23/2023] [Accepted: 04/13/2023] [Indexed: 04/21/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is a widely used eukaryotic model organism and a promising cell factory for industry. However, despite decades of research, the regulation of its metabolism is not yet fully understood, and its complexity represents a major challenge for engineering and optimising biosynthetic routes. Recent studies have demonstrated the potential of resource and proteomic allocation data in enhancing models for metabolic processes. However, comprehensive and accurate proteome dynamics data that can be used for such approaches are still very limited. Therefore, we performed a quantitative proteome dynamics study to comprehensively cover the transition from exponential to stationary phase for both aerobically and anaerobically grown yeast cells. The combination of highly controlled reactor experiments, biological replicates and standardised sample preparation procedures ensured reproducibility and accuracy. Additionally, we selected the CEN.PK lineage for our experiments because of its relevance for both fundamental and applied research. Together with the prototrophic, standard haploid strain CEN.PK113-7D, we also investigated an engineered strain with genetic minimisation of the glycolytic pathway, resulting in the quantitative assessment of 54 proteomes. The anaerobic cultures showed remarkably less proteome-level changes compared to the aerobic cultures, during transition from the exponential to the stationary phase as a consequence of the lack of the diauxic shift in the absence of oxygen. These results support the notion that anaerobically growing cells lack resources to adequately adapt to starvation. This proteome dynamics study constitutes an important step towards better understanding of the impact of glucose exhaustion and oxygen on the complex proteome allocation process in yeast. Finally, the established proteome dynamics data provide a valuable resource for the development of resource allocation models as well as for metabolic engineering efforts.
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Affiliation(s)
- Maxime den Ridder
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wiebeke van den Brandeler
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Meryem Altiner
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Martin Pabst
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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Moallem M, Akhter A, Burke GL, Babu J, Bergey BG, McNeil JB, Baig MS, Rosonina E. Sumoylation is Largely Dispensable for Normal Growth but Facilitates Heat Tolerance in Yeast. Mol Cell Biol 2023; 43:64-84. [PMID: 36720466 PMCID: PMC9936996 DOI: 10.1080/10985549.2023.2166320] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Numerous proteins are sumoylated in normally growing yeast and SUMO conjugation levels rise upon exposure to several stress conditions. We observe high levels of sumoylation also during early exponential growth and when nutrient-rich medium is used. However, we find that reduced sumoylation (∼75% less than normal) is remarkably well-tolerated, with no apparent growth defects under nonstress conditions or under osmotic, oxidative, or ethanol stresses. In contrast, strains with reduced activity of Ubc9, the sole SUMO conjugase, are temperature-sensitive, implicating sumoylation in the heat stress response, specifically. Aligned with this, a mild heat shock triggers increased sumoylation which requires functional levels of Ubc9, but likely also depends on decreased desumoylation, since heat shock reduces protein levels of Ulp1, the major SUMO protease. Furthermore, we find that a ubc9 mutant strain with only ∼5% of normal sumoylation levels shows a modest growth defect, has abnormal genomic distribution of RNA polymerase II (RNAPII), and displays a greatly expanded redistribution of RNAPII after heat shock. Together, our data implies that SUMO conjugations are largely dispensable under normal conditions, but a threshold level of Ubc9 activity is needed to maintain transcriptional control and to modulate the redistribution of RNAPII and promote survival when temperatures rise.
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Affiliation(s)
- Marjan Moallem
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Akhi Akhter
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Giovanni L Burke
- Department of Biology, York University, Toronto, Ontario, Canada
| | - John Babu
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | - J Bryan McNeil
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Mohammad S Baig
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Emanuel Rosonina
- Department of Biology, York University, Toronto, Ontario, Canada
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8
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Abstract
Most cells live in environments that are permissive for proliferation only a small fraction of the time. Entering quiescence enables cells to survive long periods of nondivision and reenter the cell cycle when signaled to do so. Here, we describe what is known about the molecular basis for quiescence in Saccharomyces cerevisiae, with emphasis on the progress made in the last decade. Quiescence is triggered by depletion of an essential nutrient. It begins well before nutrient exhaustion, and there is extensive crosstalk between signaling pathways to ensure that all proliferation-specific activities are stopped when any one essential nutrient is limiting. Every aspect of gene expression is modified to redirect and conserve resources. Chromatin structure and composition change on a global scale, from histone modifications to three-dimensional chromatin structure. Thousands of proteins and RNAs aggregate, forming unique structures with unique fates, and the cytoplasm transitions to a glass-like state.
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Affiliation(s)
- Linda L Breeden
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
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9
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Liu G, Yang Y, Yang G, Duan S, Yuan P, Zhang S, Li F, Gao XD, Nakanishi H. Triosephosphate Isomerase and Its Product Glyceraldehyde-3-Phosphate Are Involved in the Regulatory Mechanism That Suppresses Exit from the Quiescent State in Yeast Cells. Microbiol Spectr 2022; 10:e0089722. [PMID: 35924934 PMCID: PMC9430402 DOI: 10.1128/spectrum.00897-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/17/2022] [Indexed: 11/27/2022] Open
Abstract
Cells of the budding yeast Saccharomyces cerevisiae form spores or stationary cells upon nutrient starvation. These quiescent cells are known to resume mitotic growth in response to nutrient signals, but the mechanism remains elusive. Here, we report that quiescent yeast cells are equipped with a negative regulatory mechanism which suppresses the commencement of mitotic growth. The regulatory process involves a glycolytic enzyme, triosephosphate isomerase (Tpi1), and its product, glyceraldehyde-3-phosphate (GAP). GAP serves as an inhibitory signaling molecule; indeed, the return to growth of spores or stationary cells is suppressed by the addition of GAP even in nutrient-rich growth media, though mitotic cells are not affected. Reciprocally, dormancy is abolished by heat treatment because of the heat sensitivity of Tpi1. For example, spores commence germination merely upon heat treatment, which indicates that the negative regulatory mechanism is actively required for spores to prevent premature germination. Stationary cells of Candida glabrata are also manipulated by heat and GAP, suggesting that the regulatory process is conserved in the pathogenic yeast. IMPORTANCE Our results suggest that, in quiescent cells, nutrient signals do not merely provoke a positive regulatory process to commence mitotic growth. Exit from the quiescent state in yeast cells is regulated by balancing between the positive and negative signaling pathways. Identifying the negative regulatory pathway would provide new insight into the regulation of the transition from the quiescent to the mitotic state. Clinically, quiescent cells are problematic because they are resistant to environmental stresses and antibiotics. Given that the quiescent state is modulated by manipulation of the negative regulatory mechanism, understanding this process is important not only for its biological interest but also as a potential target for antifungal treatment.
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Affiliation(s)
- Guoyu Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Beijing Key Laboratory of the Innovative Development of Functional Staple and Nutritional Intervention for Chronic Diseases, China National Research Institute of Food and Fermentation Industries Co., Ltd., Beijing, China
| | - Yan Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Ganglong Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shenglin Duan
- Beijing Key Laboratory of the Innovative Development of Functional Staple and Nutritional Intervention for Chronic Diseases, China National Research Institute of Food and Fermentation Industries Co., Ltd., Beijing, China
| | - Peng Yuan
- Beijing Key Laboratory of the Innovative Development of Functional Staple and Nutritional Intervention for Chronic Diseases, China National Research Institute of Food and Fermentation Industries Co., Ltd., Beijing, China
| | - Shuang Zhang
- The State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Feng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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10
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Lee PH, Osley MA. Who gets a license: DNA synthesis in quiescent cells re-entering the cell cycle. Curr Genet 2021; 67:539-543. [PMID: 33682029 DOI: 10.1007/s00294-021-01170-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/23/2022]
Abstract
The precise regulation of the entry into S phase is critical for preventing genome instability. The first step in the initiation of eukaryotic DNA synthesis occurs in G1 phase cells and involves the loading of the conserved MCM helicase onto multiple origins of replication in a process known as origin licensing. In proliferating metazoan cells, an origin-licensing checkpoint delays initiation until high levels of MCM loading occur, with excess origins being licensed. One function of this checkpoint is to ensure that S phase can be completed in the face of replication stress by activation of dormant MCM bound origins. However, when both metazoan and yeast cells enter S phase from quiescence or G0 phase, a non-growing but reversible cell cycle state, origins are significantly under-licensed. In metazoan cells, under-licensing is the result of a compromised origin-licensing checkpoint. In budding yeast, our study has revealed that under-licensing can be attributed to the chromatin structure at a class of origins that is inhibitory to the binding of MCM. Thus, defects in multiple pathways may contribute to the failure to fully license origins in quiescent cells re-entering the cell cycle, thereby promoting a higher risk of genome instability.
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Affiliation(s)
- Po-Hsuen Lee
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Mary Ann Osley
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
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11
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Lee PH, Osley M. Chromatin structure restricts origin utilization when quiescent cells re-enter the cell cycle. Nucleic Acids Res 2021; 49:864-878. [PMID: 33367871 PMCID: PMC7826286 DOI: 10.1093/nar/gkaa1148] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/04/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Quiescent cells reside in G0 phase, which is characterized by the absence of cell growth and proliferation. These cells remain viable and re-enter the cell cycle when prompted by appropriate signals. Using a budding yeast model of cellular quiescence, we investigated the program that initiated DNA replication when these G0 cells resumed growth. Quiescent cells contained very low levels of replication initiation factors, and their entry into S phase was delayed until these factors were re-synthesized. A longer S phase in these cells correlated with the activation of fewer origins of replication compared to G1 cells. The chromatin structure around inactive origins in G0 cells showed increased H3 occupancy and decreased nucleosome positioning compared to the same origins in G1 cells, inhibiting the origin binding of the Mcm4 subunit of the MCM licensing factor. Thus, quiescent yeast cells are under-licensed during their re-entry into S phase.
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Affiliation(s)
- Po-Hsuen Lee
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Mary Ann Osley
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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12
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Sun S, Gresham D. Cellular quiescence in budding yeast. Yeast 2021; 38:12-29. [PMID: 33350503 DOI: 10.1002/yea.3545] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/20/2022] Open
Abstract
Cellular quiescence, the temporary and reversible exit from proliferative growth, is the predominant state of all cells. However, our understanding of the biological processes and molecular mechanisms that underlie cell quiescence remains incomplete. As with the mitotic cell cycle, budding and fission yeast are preeminent model systems for studying cellular quiescence owing to their rich experimental toolboxes and the evolutionary conservation across eukaryotes of pathways and processes that control quiescence. Here, we review current knowledge of cell quiescence in budding yeast and how it pertains to cellular quiescence in other organisms, including multicellular animals. Quiescence entails large-scale remodeling of virtually every cellular process, organelle, gene expression, and metabolic state that is executed dynamically as cells undergo the initiation, maintenance, and exit from quiescence. We review these major transitions, our current understanding of their molecular bases, and highlight unresolved questions. We summarize the primary methods employed for quiescence studies in yeast and discuss their relative merits. Understanding cell quiescence has important consequences for human disease as quiescent single-celled microbes are notoriously difficult to kill and quiescent human cells play important roles in diseases such as cancer. We argue that research on cellular quiescence will be accelerated through the adoption of common criteria, and methods, for defining cell quiescence. An integrated approach to studying cell quiescence, and a focus on the behavior of individual cells, will yield new insights into the pathways and processes that underlie cell quiescence leading to a more complete understanding of the life cycle of cells. TAKE AWAY: Quiescent cells are viable cells that have reversibly exited the cell cycle Quiescence is induced in response to a variety of nutrient starvation signals Quiescence is executed dynamically through three phases: initiation, maintenance, and exit Quiescence entails large-scale remodeling of gene expression, organelles, and metabolism Single-cell approaches are required to address heterogeneity among quiescent cells.
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Affiliation(s)
- Siyu Sun
- Center for Genomics and Systems Biology, New York University, New York, New York, 10003, USA.,Department of Biology, New York University, New York, New York, 10003, USA
| | - David Gresham
- Center for Genomics and Systems Biology, New York University, New York, New York, 10003, USA.,Department of Biology, New York University, New York, New York, 10003, USA
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13
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Measuring Endocytosis During Proliferative Cell Quiescence. Methods Mol Biol 2020; 2233:19-42. [PMID: 33222125 DOI: 10.1007/978-1-0716-1044-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
Abstract
Quiescence (also called "G0") is the state in which cells have exited the cell cycle but are capable to reenter as required. Though poorly understood, it represents one of the most prevalent cell states across all life. Many biologically important cell types reside in quiescence including mature hepatocytes, endothelial cells, and dormant adult stem cells. Furthermore, the quiescence program occurs in both short- and long-term varieties, depending on the physiological environments. A barrier slowing our understanding of quiescence has been a scarcity of available in vitro model systems to allow for the exploration of key regulatory pathways, such as endocytosis. Endocytosis, the internalization of extracellular material into the cell, is a fundamental and highly regulated process that impacts many cell biological functions. Accordingly, we have developed an in vitro model of deep quiescence in hTERT-immortalized RPE1 cells, combining both long-term contact inhibition and mitogen removal, to measure endocytosis. In addition, we present an analytical approach employing automated high-throughput microscopy and image analysis that yields high-content data allowing for meaningful and statistically robust interpretation. Importantly, the methods presented herein provide a suitable platform that can be easily adapted to investigate other regulatory processes across the cell cycle.
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14
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Gordhan BG, Peters J, Kana BD. Application of model systems to study adaptive responses of Mycobacterium tuberculosis during infection and disease. ADVANCES IN APPLIED MICROBIOLOGY 2019; 108:115-161. [PMID: 31495404 DOI: 10.1016/bs.aambs.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) claims more human lives than any other infectious organism. The lethal synergy between TB-HIV infection and the rapid emergence of drug resistant strains has created a global public health threat that requires urgent attention. Mycobacterium tuberculosis, the causative agent of TB is an exquisitely well-adapted human pathogen, displaying the ability to promptly remodel metabolism when encountering stressful environments during pathogenesis. A careful study of the mechanisms that enable this adaptation will enhance the understanding of key aspects related to the microbiology of TB disease. However, these efforts require microbiological model systems that mimic host conditions in the laboratory. Herein, we describe several in vitro model systems that generate non-replicating and differentially culturable mycobacteria. The changes that occur in the metabolism of M. tuberculosis in some of these models and how these relate to those reported for human TB disease are discussed. We describe mechanisms that tubercle bacteria use to resuscitate from these non-replicating conditions, together with phenotypic heterogeneity in terms of culturabiliy of M. tuberculosis in sputum. Transcriptional changes in M. tuberculosis that allow for adaptation of the organism to the lung environment are also summarized. Finally, given the emerging importance of the microbiome in various infectious diseases, we provide a description of how the lung and gut microbiome affect susceptibility to TB infection and response to treatment. Consideration of these collective aspects will enhance the understanding of basic metabolism, physiology, drug tolerance and persistence in M. tuberculosis to enable development of new therapeutic interventions.
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Affiliation(s)
- Bhavna Gowan Gordhan
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Julian Peters
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Bavesh Davandra Kana
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa.
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15
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Gulli J, Cook E, Kroll E, Rosebrock A, Caudy A, Rosenzweig F. Diverse conditions support near-zero growth in yeast: Implications for the study of cell lifespan. MICROBIAL CELL 2019; 6:397-413. [PMID: 31528631 PMCID: PMC6717879 DOI: 10.15698/mic2019.09.690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Baker's yeast has a finite lifespan and ages in two ways: a mother cell can only divide so many times (its replicative lifespan), and a non-dividing cell can only live so long (its chronological lifespan). Wild and laboratory yeast strains exhibit natural variation for each type of lifespan, and the genetic basis for this variation has been generalized to other eukaryotes, including metazoans. To date, yeast chronological lifespan has chiefly been studied in relation to the rate and mode of functional decline among non-dividing cells in nutrient-depleted batch culture. However, this culture method does not accurately capture two major classes of long-lived metazoan cells: cells that are terminally differentiated and metabolically active for periods that approximate animal lifespan (e.g. cardiac myocytes), and cells that are pluripotent and metabolically quiescent (e.g. stem cells). Here, we consider alternative ways of cultivating Saccharomyces cerevisiae so that these different metabolic states can be explored in non-dividing cells: (i) yeast cultured as giant colonies on semi-solid agar, (ii) yeast cultured in retentostats and provided sufficient nutrients to meet minimal energy requirements, and (iii) yeast encapsulated in a semisolid matrix and fed ad libitum in bioreactors. We review the physiology of yeast cultured under each of these conditions, and explore their potential to provide unique insights into determinants of chronological lifespan in the cells of higher eukaryotes.
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Affiliation(s)
- Jordan Gulli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Emily Cook
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Eugene Kroll
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Adam Rosebrock
- Donnelly Centre for Cellular and Biological Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Present address: Stony Brook School of Medicine, Stony Brook University, Stony Brook, NY 11794
| | - Amy Caudy
- Donnelly Centre for Cellular and Biological Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Frank Rosenzweig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
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16
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Hommel B, Sturny-Leclère A, Volant S, Veluppillai N, Duchateau M, Yu CH, Hourdel V, Varet H, Matondo M, Perfect JR, Casadevall A, Dromer F, Alanio A. Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype. PLoS Pathog 2019; 15:e1007945. [PMID: 31356623 PMCID: PMC6687208 DOI: 10.1371/journal.ppat.1007945] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/08/2019] [Accepted: 06/27/2019] [Indexed: 01/22/2023] Open
Abstract
Metabolically quiescent pathogens can persist in a viable non-replicating state for months or even years. For certain infectious diseases, such as tuberculosis, cryptococcosis, histoplasmosis, latent infection is a corollary of this dormant state, which has the risk for reactivation and clinical disease. During murine cryptococcosis and macrophage uptake, stress and host immunity induce Cryptococcus neoformans heterogeneity with the generation of a sub-population of yeasts that manifests a phenotype compatible with dormancy (low stress response, latency of growth). In this subpopulation, mitochondrial transcriptional activity is regulated and this phenotype has been considered as a hallmark of quiescence in stem cells. Based on these findings, we worked to reproduce this phenotype in vitro and then standardize the experimental conditions to consistently generate this dormancy in C. neoformans. We found that incubation of stationary phase yeasts (STAT) in nutriment limited conditions and hypoxia for 8 days (8D-HYPOx) was able to produced cells that mimic the phenotype obtained in vivo. In these conditions, mortality and/or apoptosis occurred in less than 5% of the yeasts compared to 30-40% of apoptotic or dead yeasts upon incubation in normoxia (8D-NORMOx). Yeasts in 8D-HYPOx harbored a lower stress response, delayed growth and less that 1% of culturability on agar plates, suggesting that these yeasts are viable but non culturable cells (VBNC). These VBNC were able to reactivate in the presence of pantothenic acid, a vitamin that is known to be involved in quorum sensing and a precursor of acetyl-CoA. Global metabolism of 8D-HYPOx cells showed some specific requirements and was globally shut down compared to 8D-NORMOx and STAT conditions. Mitochondrial analyses showed that the mitochondrial mass increased with mitochondria mostly depolarized in 8D-HYPOx compared to 8D-NORMox, with increased expression of mitochondrial genes. Proteomic and transcriptomic analyses of 8D-HYPOx revealed that the number of secreted proteins and transcripts detected also decreased compared to 8D-NORMOx and STAT, and the proteome, secretome and transcriptome harbored specific profiles that are engaged as soon as four days of incubation. Importantly, acetyl-CoA and the fatty acid pathway involving mitochondria are required for the generation and viability maintenance of VBNC. Altogether, these data show that we were able to generate for the first time VBNC phenotype in C. neoformans. This VBNC state is associated with a specific metabolism that should be further studied to understand dormancy/quiescence in this yeast.
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Affiliation(s)
- Benjamin Hommel
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Stevenn Volant
- Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | | | - Magalie Duchateau
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - Chen-Hsin Yu
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Véronique Hourdel
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - Hugo Varet
- Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
- Institut Pasteur - Transcriptome and Epigenome Platform - Biomics Pole - C2RT, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - John R. Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Françoise Dromer
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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17
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Abstract
Stem cells can reside in a state of reversible growth arrest, or quiescence, for prolonged periods of time. Although quiescence has long been viewed as a dormant, low-activity state, increasing evidence suggests that quiescence represents states of poised potential and active restraint, as stem cells "idle" in anticipation of activation, proliferation, and differentiation. Improved understanding of quiescent stem cell dynamics is leading to novel approaches to enhance maintenance and repair of aged or diseased tissues. In this Review, we discuss recent advances in our understanding of stem cell quiescence and techniques enabling more refined analyses of quiescence in vivo.
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Affiliation(s)
- Cindy T J van Velthoven
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Center for Tissue Regeneration, Repair and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
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18
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Bowling HL, Nayak S, Deinhardt K. Proteomic Approaches to Dissect Neuronal Signalling Pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:469-475. [PMID: 31347065 DOI: 10.1007/978-3-030-15950-4_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
With an increasing awareness of mental health issues and neurological disorders, "understanding the brain" is one of the biggest current challenges in biological research. This has been recognised by both governments and funding agencies, and it includes the need to understand connectivity of brain regions and coordinated network activity, as well as cellular and molecular mechanisms at play. In this chapter, we will describe how we have taken advantage of different proteomic techniques to unravel molecular mechanisms underlying two modulators of neuronal function: Neurotrophins and antipsychotics.
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Affiliation(s)
| | - Shruti Nayak
- Proteomics Laboratory, Alexandria Center for Life Science, NYU Langone, New York, NY, USA
| | - Katrin Deinhardt
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK.
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19
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Lee HY, Chao JC, Cheng KY, Leu JY. Misfolding-prone proteins are reversibly sequestered to an Hsp42-associated granule upon chronological aging. J Cell Sci 2018; 131:jcs.220202. [PMID: 30054385 DOI: 10.1242/jcs.220202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/20/2018] [Indexed: 12/19/2022] Open
Abstract
Alteration of protein localization is an important strategy for cells to regulate protein homeostasis upon environmental stresses. In the budding yeast Saccharomyces cerevisiae, many proteins relocalize and form cytosolic granules during chronological aging. However, the functions and exact components of these protein granules remain uncharacterized in most cases. In this study, we performed a genome-wide analysis of protein localization in stationary phase cells, leading to the discovery of 307 granule-forming proteins and the identification of new components in the Hsp42-stationary phase granule (Hsp42-SPG), P-bodies, Ret2 granules and actin bodies. We further characterized the Hsp42-SPG, which contains the largest number of protein components, including many molecular chaperones, metabolic enzymes and regulatory proteins. Formation of the Hsp42-SPG efficiently downregulates the activities of sequestered components, which can be differentially released from the granule based on environmental cues. We found a similar structure in the pre-whole genome duplication yeast species, Lachancea kluyveri, suggesting that the Hsp42-SPG is a common machinery allowing chronologically aged cells to contend with changing environments when available energy is limited. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Hsin-Yi Lee
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei 114, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Jung-Chi Chao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Kuo-Yu Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan.,Department of Life Sciences, Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Jun-Yi Leu
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei 114, Taiwan .,Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
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20
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Dubinski AF, Camasta R, Soule TGB, Reed BH, Glerum DM. Consequences of cytochrome c oxidase assembly defects for the yeast stationary phase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:445-458. [PMID: 29567354 DOI: 10.1016/j.bbabio.2018.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 12/24/2022]
Abstract
The assembly of cytochrome c oxidase (COX) is essential for a functional mitochondrial respiratory chain, although the consequences of a loss of assembled COX at yeast stationary phase, an excellent model for terminally differentiated cells in humans, remain largely unexamined. In this study, we show that a wild-type respiratory competent yeast strain at stationary phase is characterized by a decreased oxidative capacity, as seen by a reduction in the amount of assembled COX and by a decrease in protein levels of several COX assembly factors. In contrast, loss of assembled COX results in the decreased abundance of many mitochondrial proteins at stationary phase, which is likely due to decreased membrane potential and changes in mitophagy. In addition to an altered mitochondrial proteome, COX assembly mutants display unexpected changes in markers of cellular oxidative stress at stationary phase. Our results suggest that mitochondria may not be a major source of reactive oxygen species at stationary phase in cells lacking an intact respiratory chain.
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Affiliation(s)
- Alicia F Dubinski
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Raffaele Camasta
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Tyler G B Soule
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Bruce H Reed
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - D Moira Glerum
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada; Waterloo Institute of Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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21
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Abstract
In dividing cells, long-lived proteins are continuously diluted by being partitioned into newly formed daughter cells. Conversely, short-lived proteins are cleared from a cell primarily by proteolysis rather than cell division. Thus, when a cell stops dividing, there is a natural tendency for long-lived proteins to accumulate relative to short-lived proteins. This effect is disruptive to cells and leads to the accumulation of aged and damaged proteins over time. Here, we analyzed the degradation of thousands of proteins in dividing and nondividing (quiescent) skin cells. Our results demonstrate that quiescent cells avoid the accumulation of long-lived proteins by enhancing their degradation through pathways involving the lysosome. This mechanism may be important for promotion of protein homeostasis in aged organisms. In dividing cells, cytoplasmic dilution is the dominant route of clearance for long-lived proteins whose inherent degradation is slower than the cellular growth rate. Thus, as cells transition from a dividing to a nondividing state, there is a propensity for long-lived proteins to become stabilized relative to short-lived proteins, leading to alterations in the abundance distribution of the proteome. However, it is not known if cells mount a compensatory response to counter this potentially deleterious proteostatic disruption. We used a proteomic approach to demonstrate that fibroblasts selectively increase degradation rates of long-lived proteins as they transition from a proliferating to a quiescent state. The selective degradation of long-lived proteins occurs by the concurrent activation of lysosomal biogenesis and up-regulation of macroautophagy. Through this mechanism, quiescent cells avoid the accumulation of aged long-lived proteins that would otherwise result from the absence of cytoplasmic dilution by cell division.
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22
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Large-scale bioprocess competitiveness: the potential of dynamic metabolic control in two-stage fermentations. Curr Opin Chem Eng 2016. [DOI: 10.1016/j.coche.2016.09.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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23
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Welle KA, Zhang T, Hryhorenko JR, Shen S, Qu J, Ghaemmaghami S. Time-resolved Analysis of Proteome Dynamics by Tandem Mass Tags and Stable Isotope Labeling in Cell Culture (TMT-SILAC) Hyperplexing. Mol Cell Proteomics 2016; 15:3551-3563. [PMID: 27765818 DOI: 10.1074/mcp.m116.063230] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/03/2016] [Indexed: 12/20/2022] Open
Abstract
Recent advances in mass spectrometry have enabled system-wide analyses of protein turnover. By globally quantifying the kinetics of protein clearance and synthesis, these methodologies can provide important insights into the regulation of the proteome under varying cellular and environmental conditions. To facilitate such analyses, we have employed a methodology that combines metabolic isotopic labeling (Stable Isotope Labeling in Cell Culture - SILAC) with isobaric tagging (Tandem Mass Tags - TMT) for analysis of multiplexed samples. The fractional labeling of multiple time-points can be measured in a single mass spectrometry run, providing temporally resolved measurements of protein turnover kinetics. To demonstrate the feasibility of the approach, we simultaneously measured the kinetics of protein clearance and accumulation for more than 3000 proteins in dividing and quiescent human fibroblasts and verified the accuracy of the measurements by comparison to established non-multiplexed approaches. The results indicate that upon reaching quiescence, fibroblasts compensate for lack of cellular growth by globally downregulating protein synthesis and upregulating protein degradation. The described methodology significantly reduces the cost and complexity of temporally-resolved dynamic proteomic experiments and improves the precision of proteome-wide turnover data.
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Affiliation(s)
- Kevin A Welle
- From the ‡University of Rochester Mass Spectrometry Resource Laboratory, Rochester, NY
| | - Tian Zhang
- §Department of Biology, University of Rochester, Rochester, NY
| | - Jennifer R Hryhorenko
- From the ‡University of Rochester Mass Spectrometry Resource Laboratory, Rochester, NY
| | - Shichen Shen
- ¶Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY
| | - Jun Qu
- ¶Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY
| | - Sina Ghaemmaghami
- From the ‡University of Rochester Mass Spectrometry Resource Laboratory, Rochester, NY; .,§Department of Biology, University of Rochester, Rochester, NY
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24
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Kumar R, Srivastava S. Quantitative proteomic comparison of stationary/G0 phase cells and tetrads in budding yeast. Sci Rep 2016; 6:32031. [PMID: 27558777 PMCID: PMC4997312 DOI: 10.1038/srep32031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/02/2016] [Indexed: 02/08/2023] Open
Abstract
Most of the microbial cells on earth under natural conditions exist in a dormant condition, commonly known as quiescent state. Quiescent cells exhibit low rates of transcription and translation suggesting that cellular abundance of proteins may be similar in quiescent cells. Therefore, this study aim to compare the proteome of budding yeast cells from two quiescent states viz. stationary phase/G0 and tetrads. Using iTRAQ (isobaric tag for relative and absolute quantitation) based quantitative proteomics we identified 289 proteins, among which around 40 proteins exhibited ±1.5 fold change consistently from the four biological replicates. Proteomics data was validated by western blot and denstiometric analysis of Hsp12 and Spg4. Level of budding yeast 14-3-3 proteins was found to be similar in both the quiescent states, whereas Hsp12 and Spg4 expressed only during stress. FACS (fluorescence-activated cell sorting) analysis showed that budding yeast cells were arrested at G1 stages both in tetrads as well as in stationary phase. We also observed that quiescent states did not express Ime1 (inducer of meiosis). Taken together, our present study demonstrates that the cells in quiescent state may have similar proteome, and accumulation of proteins like Hsp12, Hsp26, and Spg4 may play an important role in retaining viability of the cells during dormancy.
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Affiliation(s)
- Ravinder Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, Maharashtra, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, Maharashtra, India
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25
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Puig-Castellví F, Alfonso I, Piña B, Tauler R. (1)H NMR metabolomic study of auxotrophic starvation in yeast using Multivariate Curve Resolution-Alternating Least Squares for Pathway Analysis. Sci Rep 2016; 6:30982. [PMID: 27485935 PMCID: PMC4971537 DOI: 10.1038/srep30982] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/12/2016] [Indexed: 11/15/2022] Open
Abstract
Disruption of specific metabolic pathways constitutes the mode of action of many known toxicants and it is responsible for the adverse phenotypes associated to human genetic defects. Conversely, many industrial applications rely on metabolic alterations of diverse microorganisms, whereas many therapeutic drugs aim to selectively disrupt pathogens’ metabolism. In this work we analyzed metabolic changes induced by auxotrophic starvation conditions in yeast in a non-targeted approach, using one-dimensional proton Nuclear Magnetic Resonance spectroscopy (1H NMR) and chemometric analyses. Analysis of the raw spectral datasets showed specific changes linked to the different stages during unrestricted yeast growth, as well as specific changes linked to each of the four tested starvation conditions (L-methionine, L-histidine, L-leucine and uracil). Analysis of changes in concentrations of more than 40 metabolites by Multivariate Curve Resolution – Alternating Least Squares (MCR-ALS) showed the normal progression of key metabolites during lag, exponential and stationary unrestricted growth phases, while reflecting the metabolic blockage induced by the starvation conditions. In this case, different metabolic intermediates accumulated over time, allowing identification of the different metabolic pathways specifically affected by each gene disruption. This synergy between NMR metabolomics and molecular biology may have clear implications for both genetic diagnostics and drug development.
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Affiliation(s)
- Francesc Puig-Castellví
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modelling, Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain
| | - Benjamin Piña
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain
| | - Romà Tauler
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain
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26
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The Proteome and Lipidome of Thermococcus kodakarensis across the Stationary Phase. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:5938289. [PMID: 27274708 PMCID: PMC4870337 DOI: 10.1155/2016/5938289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/07/2016] [Indexed: 12/25/2022]
Abstract
The majority of cells in nature probably exist in a stationary-phase-like state, due to nutrient limitation in most environments. Studies on bacteria and yeast reveal morphological and physiological changes throughout the stationary phase, which lead to an increased ability to survive prolonged nutrient limitation. However, there is little information on archaeal stationary phase responses. We investigated protein- and lipid-level changes in Thermococcus kodakarensis with extended time in the stationary phase. Adaptations to time in stationary phase included increased proportion of membrane lipids with a tetraether backbone, synthesis of proteins that ensure translational fidelity, specific regulation of ABC transporters (upregulation of some, downregulation of others), and upregulation of proteins involved in coenzyme production. Given that the biological mechanism of tetraether synthesis is unknown, we also considered whether any of the protein-level changes in T. kodakarensis might shed light on the production of tetraether lipids across the same period. A putative carbon-nitrogen hydrolase, a TldE (a protease in Escherichia coli) homologue, and a membrane bound hydrogenase complex subunit were candidates for possible involvement in tetraether-related reactions, while upregulation of adenosylcobalamin synthesis proteins might lend support to a possible radical mechanism as a trigger for tetraether synthesis.
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27
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Lee HY, Cheng KY, Chao JC, Leu JY. Differentiated cytoplasmic granule formation in quiescent and non-quiescent cells upon chronological aging. MICROBIAL CELL 2016; 3:109-119. [PMID: 28357341 PMCID: PMC5349021 DOI: 10.15698/mic2016.03.484] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Stationary phase cultures represent a complicated cell population comprising at
least two different cell types, quiescent (Q) and non-quiescent (NQ) cells. Q
and NQ cells have different lifespans and cell physiologies. However, less is
known about the organization of cytosolic protein structures in these two cell
types. In this study, we examined Q and NQ cells for the formation of several
stationary phase-prevalent granule structures including actin bodies, proteasome
storage granules, stress granules, P-bodies, the compartment for unconventional
protein secretion (CUPS), and Hsp42-associated stationary phase granules
(Hsp42-SPGs). Most of these structures preferentially form in NQ cells, except
for Hsp42-SPGs, which are enriched in Q cells. When nutrients are provided, NQ
cells enter mitosis less efficiently than Q cells, likely due to the time
requirement for reorganizing some granule structures. We observed that heat
shock-induced misfolded proteins often colocalize to Hsp42-SPGs, and Q cells
clear these protein aggregates more efficiently, suggesting that Hsp42-SPGs may
play an important role in the stress resistance of Q cells. Finally, we show
that the cell fate of NQ cells is largely irreversible even if they are allowed
to reenter mitosis. Our results reveal that the formation of different granule
structures may represent the early stage of cell type differentiation in yeast
stationary phase cultures.
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Affiliation(s)
- Hsin-Yi Lee
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan. ; Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Kuo-Yu Cheng
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan. ; Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jung-Chi Chao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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28
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Amor AJ, Castanzo DT, Delany SP, Selechnik DM, van Ooy A, Cameron DM. The ribosome-associated complex antagonizes prion formation in yeast. Prion 2016; 9:144-64. [PMID: 25739058 PMCID: PMC4601405 DOI: 10.1080/19336896.2015.1022022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The number of known fungal proteins capable of switching between alternative stable conformations is steadily increasing, suggesting that a prion-like mechanism may be broadly utilized as a means to propagate altered cellular states. To gain insight into the mechanisms by which cells regulate prion formation and toxicity we examined the role of the yeast ribosome-associated complex (RAC) in modulating both the formation of the [PSI(+)] prion - an alternative conformer of Sup35 protein - and the toxicity of aggregation-prone polypeptides. The Hsp40 RAC chaperone Zuo1 anchors the RAC to ribosomes and stimulates the ATPase activity of the Hsp70 chaperone Ssb. We found that cells lacking Zuo1 are sensitive to over-expression of some aggregation-prone proteins, including the Sup35 prion domain, suggesting that co-translational protein misfolding increases in Δzuo1 strains. Consistent with this finding, Δzuo1 cells exhibit higher frequencies of spontaneous and induced prion formation. Cells expressing mutant forms of Zuo1 lacking either a C-terminal charged region required for ribosome association, or the J-domain responsible for Ssb ATPase stimulation, exhibit similarly high frequencies of prion formation. Our findings are consistent with a role for the RAC in chaperoning nascent Sup35 to regulate folding of the N-terminal prion domain as it emerges from the ribosome.
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Affiliation(s)
- Alvaro J Amor
- a Biology Department ; Ursinus College ; Collegeville , PA USA
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29
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Replenishment and mobilization of intracellular nitrogen pools decouples wine yeast nitrogen uptake from growth. Appl Microbiol Biotechnol 2016; 100:3255-65. [DOI: 10.1007/s00253-015-7273-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/14/2015] [Accepted: 12/19/2015] [Indexed: 11/30/2022]
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30
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Guidi M, Ruault M, Marbouty M, Loïodice I, Cournac A, Billaudeau C, Hocher A, Mozziconacci J, Koszul R, Taddei A. Spatial reorganization of telomeres in long-lived quiescent cells. Genome Biol 2015; 16:206. [PMID: 26399229 PMCID: PMC4581094 DOI: 10.1186/s13059-015-0766-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/01/2015] [Indexed: 12/13/2022] Open
Abstract
Background The spatiotemporal behavior of chromatin is an important control mechanism of genomic function. Studies in Saccharomyces cerevisiae have broadly contributed to demonstrate the functional importance of nuclear organization. Although in the wild yeast survival depends on their ability to withstand adverse conditions, most of these studies were conducted on cells undergoing exponential growth. In these conditions, as in most eukaryotic cells, silent chromatin that is mainly found at the 32 telomeres accumulates at the nuclear envelope, forming three to five foci. Results Here, combining live microscopy, DNA FISH and chromosome conformation capture (HiC) techniques, we report that chromosomes adopt distinct organizations according to the metabolic status of the cell. In particular, following carbon source exhaustion the genome of long-lived quiescent cells undergoes a major spatial re-organization driven by the grouping of telomeres into a unique focus or hypercluster localized in the center of the nucleus. This change in genome conformation is specific to quiescent cells able to sustain long-term viability. We further show that reactive oxygen species produced by mitochondrial activity during respiration commit the cell to form a hypercluster upon starvation. Importantly, deleting the gene encoding telomere associated silencing factor SIR3 abolishes telomere grouping and decreases longevity, a defect that is rescued by expressing a silencing defective SIR3 allele competent for hypercluster formation. Conclusions Our data show that mitochondrial activity primes cells to group their telomeres into a hypercluster upon starvation, reshaping the genome architecture into a conformation that may contribute to maintain longevity of quiescent cells. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0766-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Micol Guidi
- Institut Curie, PSL Research University, Paris, F-75248, France.,CNRS, UMR 3664, Paris, F-75248, France.,Sorbonne Universités, UPMC Univ, Paris 06, France
| | - Myriam Ruault
- Institut Curie, PSL Research University, Paris, F-75248, France.,CNRS, UMR 3664, Paris, F-75248, France.,Sorbonne Universités, UPMC Univ, Paris 06, France
| | - Martial Marbouty
- Institut Pasteur, Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015, Paris, France.,CNRS, UMR 3525, 75015, Paris, France
| | - Isabelle Loïodice
- Institut Curie, PSL Research University, Paris, F-75248, France.,CNRS, UMR 3664, Paris, F-75248, France.,Sorbonne Universités, UPMC Univ, Paris 06, France
| | - Axel Cournac
- Institut Pasteur, Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015, Paris, France.,CNRS, UMR 3525, 75015, Paris, France
| | - Cyrille Billaudeau
- Institut Curie, PSL Research University, Paris, F-75248, France.,CNRS, UMR 3664, Paris, F-75248, France.,Sorbonne Universités, UPMC Univ, Paris 06, France
| | - Antoine Hocher
- Institut Curie, PSL Research University, Paris, F-75248, France.,CNRS, UMR 3664, Paris, F-75248, France.,Sorbonne Universités, UPMC Univ, Paris 06, France
| | - Julien Mozziconacci
- LPTMC, Université Pierre et Marie Curie, UMR 7600, Sorbonne Universités, 4 Place Jussieu, 75005, Paris, France
| | - Romain Koszul
- Institut Pasteur, Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015, Paris, France.,CNRS, UMR 3525, 75015, Paris, France
| | - Angela Taddei
- Institut Curie, PSL Research University, Paris, F-75248, France. .,CNRS, UMR 3664, Paris, F-75248, France. .,Sorbonne Universités, UPMC Univ, Paris 06, France.
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31
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Han J, Kim K, Lee S. Screening Molecular Chaperones Similar to Small Heat Shock Proteins in Schizosaccharomyces pombe. MYCOBIOLOGY 2015; 43:272-279. [PMID: 26539043 PMCID: PMC4630433 DOI: 10.5941/myco.2015.43.3.272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 08/23/2015] [Accepted: 09/21/2015] [Indexed: 06/05/2023]
Abstract
To screen molecular chaperones similar to small heat shock proteins (sHsps), but without α-crystalline domain, heat-stable proteins from Schizosaccharomyces pombe were analyzed by 2-dimensional electrophoresis and matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Sixteen proteins were identified, and four recombinant proteins, including cofilin, NTF2, pyridoxin biosynthesis protein (Snz1) and Wos2 that has an α-crystalline domain, were purified. Among these proteins, only Snz1 showed the anti-aggregation activity against thermal denaturation of citrate synthase. However, pre-heating of NTF2 and Wos2 at 70℃ for 30 min, efficiently prevented thermal aggregation of citrate synthase. These results indicate that Snz1 and NTF2 possess molecular chaperone activity similar to sHsps, even though there is no α-crystalline domain in their sequences.
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Affiliation(s)
- Jiyoung Han
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea
| | - Kanghwa Kim
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea
| | - Songmi Lee
- Department of Food and Nutrition, Dongshin University, Naju 58245, Korea
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32
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Tsvetkov P, Mendillo ML, Zhao J, Carette JE, Merrill PH, Cikes D, Varadarajan M, van Diemen FR, Penninger JM, Goldberg AL, Brummelkamp TR, Santagata S, Lindquist S. Compromising the 19S proteasome complex protects cells from reduced flux through the proteasome. eLife 2015; 4. [PMID: 26327695 PMCID: PMC4551903 DOI: 10.7554/elife.08467] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/29/2015] [Indexed: 12/11/2022] Open
Abstract
Proteasomes are central regulators of protein homeostasis in eukaryotes. Proteasome function is vulnerable to environmental insults, cellular protein imbalance and targeted pharmaceuticals. Yet, mechanisms that cells deploy to counteract inhibition of this central regulator are little understood. To find such mechanisms, we reduced flux through the proteasome to the point of toxicity with specific inhibitors and performed genome-wide screens for mutations that allowed cells to survive. Counter to expectation, reducing expression of individual subunits of the proteasome's 19S regulatory complex increased survival. Strong 19S reduction was cytotoxic but modest reduction protected cells from inhibitors. Protection was accompanied by an increased ratio of 20S to 26S proteasomes, preservation of protein degradation capacity and reduced proteotoxic stress. While compromise of 19S function can have a fitness cost under basal conditions, it provided a powerful survival advantage when proteasome function was impaired. This means of rebalancing proteostasis is conserved from yeast to humans.
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Affiliation(s)
- Peter Tsvetkov
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Marc L Mendillo
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Jinghui Zhao
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Parker H Merrill
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Domagoj Cikes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Ferdy R van Diemen
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Alfred L Goldberg
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Thijn R Brummelkamp
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sandro Santagata
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, United States
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33
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Werner-Washburne M, Roy S, Davidson GS. Aging and the survival of quiescent and non-quiescent cells in yeast stationary-phase cultures. Subcell Biochem 2015; 57:123-43. [PMID: 22094420 DOI: 10.1007/978-94-007-2561-4_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In this chapter, we argue that with careful attention to cell types in stationary-phase cultures of the yeast, S. cerevisiae provide an excellent model system for aging studies and hold much promise in pinpointing the set of causal genes and mechanisms driving aging. Importantly, a more detailed understanding of aging in this single celled organism will also shed light on aging in tissue-complex model organisms such as C. elegans and D. melanogaster. We feel strongly that the relationship between aging in yeast and tissue-complex organisms has been obscured by failure to notice the heterogeneity of stationary-phase cultures and the processes by which distinct cell types arise in these cultures. Although several studies have used yeast stationary-phase cultures for chronological aging, the majority of these studies have assumed that cultures in stationary phase are homogeneously composed of a single cell type. However, genome-scale analyses of yeast stationary-phase cultures have identified two major cell fractions: quiescent and non-quiescent, which we discuss in detail in this chapter. We review evidence that cell populations isolated from these cultures exhibit population-specific phenotypes spanning a range of metabolic and physiological processes including reproductive capacity, apoptosis, differences in metabolic activities, genetic hyper-mutability, and stress responses. The identification, in S. cerevisiae, of multiple sub-populations having differentiated physiological attributes relevant to aging offers an unprecedented opportunity. This opportunity to deeply understand yeast cellular (and population) aging programs will, also, give insight into genomic and metabolic processes in tissue-complex organism, as well as stem cell biology and the origins of differentiation.
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Affiliation(s)
- M Werner-Washburne
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA,
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34
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Bavli-Kertselli I, Melamed D, Bar-Ziv L, Volf H, Arava Y. Overexpression of eukaryotic initiation factor 5 rescues the translational defect of tpk1w in a manner that necessitates a novel phosphorylation site. FEBS J 2014; 282:504-20. [PMID: 25417541 DOI: 10.1111/febs.13158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 11/11/2014] [Accepted: 11/20/2014] [Indexed: 02/04/2023]
Abstract
Cells respond to changes in their environment through mechanisms that often necessitate reprogramming of the translation machinery. The fastest and strongest of all tested responses is the translation inhibition observed following abrupt depletion of glucose from the media of yeast cells. The speed of the response suggests a post-translational modification of a key component of the translation machinery. This translation factor is as yet unknown. A cAMP-dependent protein kinase mutant yeast strain (tpk1(w)) that does not respond properly to glucose depletion and maintains translation was described previously. We hypothesized that the inability of tpk1(w) to arrest translation results from abnormal expression of key translation mediators. Genome-wide analysis of steady-state mRNA levels in tpk1(w) revealed underexpression of several candidates. Elevating the cellular levels of eukaryotic initiation factor (eIF) 5 by overexpression rescued the translational defect of tpk1(w). Restoring ribosomal dissociation by eIF5 necessitated an active GAP domain and multiple regions throughout this protein. Phosphoproteomics analysis of wild-type cells overexpressing eIF5 revealed increased phosphorylation in a novel site (Thr191) upon glucose depletion. Mutating this residue and introducing it into tpk1(w) abolished the ability of eIF5 to rescue the translational defect. Intriguingly, introducing this mutation into the wild-type strain did not hamper its translational response. We further show that Thr191 is phosphorylated in vitro by Casein Kinase II (CKII), and yeast cells with a mutated CKII have a reduced response to glucose depletion. These results implicate phosphorylation of eIF5 at Thr191 by CKII as one of the pathways for regulating translation upon glucose depletion.
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Affiliation(s)
- Ira Bavli-Kertselli
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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35
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Iwakura T, Fujigaki Y, Fujikura T, Ohashi N, Kato A, Yasuda H. A high ratio of G1 to G0 phase cells and an accumulation of G1 phase cells before S phase progression after injurious stimuli in the proximal tubule. Physiol Rep 2014; 2:e12173. [PMID: 25293601 PMCID: PMC4254098 DOI: 10.14814/phy2.12173] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 09/09/2014] [Accepted: 09/10/2014] [Indexed: 12/25/2022] Open
Abstract
Proximal tubule (PT) cells can proliferate explosively after injurious stimuli. To investigate this proliferative capacity, we examined cell cycle status and the expression of cyclin-dependent kinase inhibitor p27, a G1 phase mediator, in PT cells after a proliferative or injurious stimulus. Rats were treated with lead acetate (proliferative stimulus) or uranyl acetate (UA; injurious stimulus). Isolated tubular cells were separated into PT and distal tubule (DT) cells by density-gradient centrifugation. Cell cycle status was analyzed with flow cytometry by using the Hoechst 33342/pyronin Y method. Most PT and DT cells from control rats were in G0/G1 phase, with a higher percentage of PT cells than DT cells in G1 phase. Lead acetate and UA administration promoted the G0-G1 transition and the accumulation of G1 phase cells before S phase progression. In PT cells from rats treated with lead acetate or a subnephrotoxic dose of UA, p27 levels increased or did not change, possibly reflecting G1 arrest. In contrast, p27 became undetectable before the appearance of apoptotic cells in rats treated with a nephrotoxic dose of UA. The decrease in p27 might facilitate rapid cell cycling. The decreased number of p27-positive cells was associated with PT cell proliferation in renal tissues after a proliferative or injurious stimulus. The findings suggest that a high ratio of G1 to G0 phase cells and a rapid accumulation of G1 phase cells before S phase progression in the PT is a biological strategy for safe, timely, and explosive cell proliferation in response to injurious stimuli.
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Affiliation(s)
- Takamasa Iwakura
- Internal Medicine I, Division of Nephrology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yoshihide Fujigaki
- Internal Medicine I, Division of Nephrology, Hamamatsu University School of Medicine, Hamamatsu, Japan
- Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Tomoyuki Fujikura
- Internal Medicine I, Division of Nephrology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Naro Ohashi
- Internal Medicine I, Division of Nephrology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Akihiko Kato
- Blood Purification Unit, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hideo Yasuda
- Internal Medicine I, Division of Nephrology, Hamamatsu University School of Medicine, Hamamatsu, Japan
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36
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Binai NA, Bisschops MMM, van Breukelen B, Mohammed S, Loeff L, Pronk JT, Heck AJR, Daran-Lapujade P, Slijper M. Proteome adaptation of Saccharomyces cerevisiae to severe calorie restriction in Retentostat cultures. J Proteome Res 2014; 13:3542-53. [PMID: 25000127 DOI: 10.1021/pr5003388] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Stationary-phase, carbon-starved shake-flask cultures of Saccharomyces cerevisiae are popular models for studying eukaryotic chronological aging. However, their nutrient-starved physiological status differs substantially from that of postmitotic metazoan cells. Retentostat cultures offer an attractive alternative model system in which yeast cells, maintained under continuous calorie restriction, hardly divide but retain high metabolic activity and viability for prolonged periods of time. Using TMT labeling and UHPLC-MS/MS, the present study explores the proteome of yeast cultures during transition from exponential growth to near-zero growth in severely calorie-restricted retentostats. This transition elicited protein level changes in 20% of the yeast proteome. Increased abundance of heat shock-related proteins correlated with increased transcript levels of the corresponding genes and was consistent with a strongly increased heat shock tolerance of retentostat-grown cells. A sizable fraction (43%) of the proteins with increased abundance under calorie restriction was involved in oxidative phosphorylation and in various mitochondrial functions that, under the anaerobic, nongrowing conditions used, have a very limited role. Although it may seem surprising that yeast cells confronted with severe calorie restriction invest in the synthesis of proteins that, under those conditions, do not contribute to fitness, these responses may confer metabolic flexibility and thereby a selective advantage in fluctuating natural habitats.
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Affiliation(s)
- Nadine A Binai
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH, Utrecht, The Netherlands
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37
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Kwasiborski A, Bajji M, Renaut J, Delaplace P, Jijakli MH. Identification of metabolic pathways expressed by Pichia anomala Kh6 in the presence of the pathogen Botrytis cinerea on apple: new possible targets for biocontrol improvement. PLoS One 2014; 9:e91434. [PMID: 24614090 PMCID: PMC3948861 DOI: 10.1371/journal.pone.0091434] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/12/2014] [Indexed: 11/19/2022] Open
Abstract
Yeast Pichia anomala strain Kh6 Kurtzman (Saccharomycetales: Endomycetaceae) exhibits biological control properties that provide an alternative to the chemical fungicides currently used by fruit or vegetable producers against main post-harvest pathogens, such as Botrytis cinerea (Helotiales: Sclerotiniaceae). Using an in situ model that takes into account interactions between organisms and a proteomic approach, we aimed to identify P. anomala metabolic pathways influenced by the presence of B. cinerea. A total of 105 and 60 P. anomala proteins were differentially represented in the exponential and stationary growth phases, respectively. In the exponential phase and in the presence of B. cinerea, the pentose phosphate pathway seems to be enhanced and would provide P. anomala with the needed nucleic acids and energy for the wound colonisation. In the stationary phase, P. anomala would use alcoholic fermentation both in the absence and presence of the pathogen. These results would suggest that the competitive colonisation of apple wounds could be implicated in the mode of action of P. anomala against B. cinerea.
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Affiliation(s)
- Anthony Kwasiborski
- Plant Pathology Unit, Gembloux Agro-Bio Tech/University of Liège, Gembloux, Belgium
| | - Mohammed Bajji
- Plant Pathology Unit, Gembloux Agro-Bio Tech/University of Liège, Gembloux, Belgium
| | - Jenny Renaut
- Proteomics Platform, Department of Environment and Agrobiotechnologies/Centre de Recherche Public Gabriel Lippmann, Belvaux, Luxemburg
| | - Pierre Delaplace
- Plant Biology Unit, Gembloux Agro-Bio Tech/University of Liège, Gembloux, Belgium
| | - M. Haissam Jijakli
- Plant Pathology Unit, Gembloux Agro-Bio Tech/University of Liège, Gembloux, Belgium
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Chiocchetti AG, Haslinger D, Boesch M, Karl T, Wiemann S, Freitag CM, Poustka F, Scheibe B, Bauer JW, Hintner H, Breitenbach M, Kellermann J, Lottspeich F, Klauck SM, Breitenbach-Koller L. Protein signatures of oxidative stress response in a patient specific cell line model for autism. Mol Autism 2014; 5:10. [PMID: 24512814 PMCID: PMC3931328 DOI: 10.1186/2040-2392-5-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 01/23/2014] [Indexed: 12/26/2022] Open
Abstract
Background Known genetic variants can account for 10% to 20% of all cases with autism spectrum disorders (ASD). Overlapping cellular pathomechanisms common to neurons of the central nervous system (CNS) and in tissues of peripheral organs, such as immune dysregulation, oxidative stress and dysfunctions in mitochondrial and protein synthesis metabolism, were suggested to support the wide spectrum of ASD on unifying disease phenotype. Here, we studied in patient-derived lymphoblastoid cell lines (LCLs) how an ASD-specific mutation in ribosomal protein RPL10 (RPL10[H213Q]) generates a distinct protein signature. We compared the RPL10[H213Q] expression pattern to expression patterns derived from unrelated ASD patients without RPL10[H213Q] mutation. In addition, a yeast rpl10 deficiency model served in a proof-of-principle study to test for alterations in protein patterns in response to oxidative stress. Methods Protein extracts of LCLs from patients, relatives and controls, as well as diploid yeast cells hemizygous for rpl10, were subjected to two-dimensional gel electrophoresis and differentially regulated spots were identified by mass spectrometry. Subsequently, Gene Ontology database (GO)-term enrichment and network analysis was performed to map the identified proteins into cellular pathways. Results The protein signature generated by RPL10[H213Q] is a functionally related subset of the ASD-specific protein signature, sharing redox-sensitive elements in energy-, protein- and redox-metabolism. In yeast, rpl10 deficiency generates a specific protein signature, harboring components of pathways identified in both the RPL10[H213Q] subjects’ and the ASD patients’ set. Importantly, the rpl10 deficiency signature is a subset of the signature resulting from response of wild-type yeast to oxidative stress. Conclusions Redox-sensitive protein signatures mapping into cellular pathways with pathophysiology in ASD have been identified in both LCLs carrying the ASD-specific mutation RPL10[H213Q] and LCLs from ASD patients without this mutation. At pathway levels, this redox-sensitive protein signature has also been identified in a yeast rpl10 deficiency and an oxidative stress model. These observations point to a common molecular pathomechanism in ASD, characterized in our study by dysregulation of redox balance. Importantly, this can be triggered by the known ASD-RPL10[H213Q] mutation or by yet unknown mutations of the ASD cohort that act upstream of RPL10 in differential expression of redox-sensitive proteins.
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Affiliation(s)
- Andreas G Chiocchetti
- Division of Molecular Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.,Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria.,Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University, Deutschordenstr. 50, 60528 Frankfurt am Main, Germany
| | - Denise Haslinger
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria.,Division of Molecular Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.,Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University, Deutschordenstr. 50, 60528 Frankfurt am Main, Germany
| | - Maximilian Boesch
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
| | - Thomas Karl
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University, Deutschordenstr. 50, 60528 Frankfurt am Main, Germany
| | - Fritz Poustka
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University, Deutschordenstr. 50, 60528 Frankfurt am Main, Germany
| | - Burghardt Scheibe
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
| | - Johann W Bauer
- Department of Dermatology, General Hospital Salzburg/PMU, Müllner-Hauptstr. 48, 5020 Salzburg, Austria
| | - Helmut Hintner
- Department of Dermatology, General Hospital Salzburg/PMU, Müllner-Hauptstr. 48, 5020 Salzburg, Austria
| | - Michael Breitenbach
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
| | - Josef Kellermann
- Max-Planck-Institute of Biochemistry, Protein Analysis Group, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Friedrich Lottspeich
- Max-Planck-Institute of Biochemistry, Protein Analysis Group, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Sabine M Klauck
- Division of Molecular Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Lore Breitenbach-Koller
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
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Bowling HL, Deinhardt K. Proteomic approaches to dissect neuronal signaling pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:499-508. [PMID: 24952199 DOI: 10.1007/978-3-319-06068-2_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
With an increasing awareness of mental health issues and neurological disorders, "understanding the brain" is one of the biggest current challenges in biological research. This has been recognized by both governments and funding agencies, and includes the need to understand connectivity of brain regions and coordinated network activity, as well as cellular and molecular mechanisms at play. In this chapter, we will describe how we have taken advantage of different proteomic techniques to unravel molecular mechanisms underlying two modulators of neuronal function: Neurotrophins and antipsychotics.
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Affiliation(s)
- Heather L Bowling
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA,
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40
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Rittershaus ESC, Baek SH, Sassetti CM. The normalcy of dormancy: common themes in microbial quiescence. Cell Host Microbe 2013; 13:643-51. [PMID: 23768489 DOI: 10.1016/j.chom.2013.05.012] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
All microorganisms are exposed to periodic stresses that inhibit growth. Many bacteria and fungi weather these periods by entering a hardy, nonreplicating state, often termed quiescence or dormancy. When this occurs during an infection, the resulting slowly growing pathogen is able to tolerate both immune insults and prolonged antibiotic exposure. While the stresses encountered in a free-living environment may differ from those imposed by host immunity, these growth-limiting conditions impose common pressures, and many of the corresponding microbial responses appear to be universal. In this review, we discuss the common features of these growth-limited states, which suggest new approaches for treating chronic infections such as tuberculosis.
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Affiliation(s)
- Emily S C Rittershaus
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA
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41
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Laporte D, Courtout F, Salin B, Ceschin J, Sagot I. An array of nuclear microtubules reorganizes the budding yeast nucleus during quiescence. ACTA ACUST UNITED AC 2013; 203:585-94. [PMID: 24247429 PMCID: PMC3840927 DOI: 10.1083/jcb.201306075] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The microtubule cytoskeleton is a highly dynamic network. In dividing cells, its complex architecture not only influences cell shape and movement but is also crucial for chromosome segregation. Curiously, nothing is known about the behavior of this cellular machinery in quiescent cells. Here we show that, upon quiescence entry, the Saccharomyces cerevisiae microtubule cytoskeleton is drastically remodeled. Indeed, while cytoplasmic microtubules vanish, the spindle pole body (SPB) assembles a long and stable monopolar array of nuclear microtubules that spans the entire nucleus. Consequently, the nucleolus is displaced. Kinetochores remain attached to microtubule tips but lose SPB clustering and distribute along the microtubule array, leading to a large reorganization of the nucleus. When cells exit quiescence, the nuclear microtubule array slowly depolymerizes and, by pulling attached centromeres back to the SPB, allows the recovery of a typical Rabl-like configuration. Finally, mutants that do not assemble a nuclear array of microtubules are impaired for both quiescence survival and exit.
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Affiliation(s)
- Damien Laporte
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, F-33077 Bordeaux Cedex, France
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42
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Saunier R, Esposito M, Dassa EP, Delahodde A. Integrity of the Saccharomyces cerevisiae Rpn11 protein is critical for formation of proteasome storage granules (PSG) and survival in stationary phase. PLoS One 2013; 8:e70357. [PMID: 23936414 PMCID: PMC3735599 DOI: 10.1371/journal.pone.0070357] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 06/19/2013] [Indexed: 11/18/2022] Open
Abstract
Decline of proteasome activity has been reported in mammals, flies and yeasts during aging. In the yeast Saccharomyces cerevisiae, the reduction of proteolysis in stationary phase is correlated with disassembly of the 26S proteasomes into their 20S and 19S subcomplexes. However a recent report showed that upon entry into the stationary phase, proteasome subunits massively re-localize from the nucleus into mobile cytoplasmic structures called proteasome storage granules (PSGs). Whether proteasome subunits in PSG are assembled into active complexes remains an open question that we addressed in the present study. We showed that a particular mutant of the RPN11 gene (rpn11-m1), encoding a proteasome lid subunit already known to exhibit proteasome assembly/stability defect in vitro, is unable to form PSGs and displays a reduced viability in stationary phase. Full restoration of long-term survival and PSG formation in rpn11-m1 cells can be achieved by the expression in trans of the last 45 amino acids of the C-terminal domain of Rpn11, which was moreover found to co-localize with PSGs. In addition, another rpn11 mutant leading to seven amino acids change in the Rpn11 C-terminal domain, which exhibits assembled-26S proteasomes, is able to form PSGs but with a delay compared to the wild type situation. Altogether, our findings indicate that PSGs are formed of fully assembled 26S proteasomes and suggest a critical role for the Rpn11 protein in this process.
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Affiliation(s)
- Rémy Saunier
- Univ Paris-Sud, CNRS UMR 8621, Institut de Génétique et Microbiologie, Orsay, France
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Webb KJ, Xu T, Park SK, Yates JR. Modified MuDPIT separation identified 4488 proteins in a system-wide analysis of quiescence in yeast. J Proteome Res 2013; 12:2177-84. [PMID: 23540446 DOI: 10.1021/pr400027m] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A modified multidimensional protein identification technology (MudPIT) separation was coupled to an LTQ Orbitrap Velos mass spectrometer and used to rapidly identify the near-complete yeast proteome from a whole cell tryptic digest. This modified online two-dimensional liquid chromatography separation consists of 39 strong cation exchange steps followed by a short 18.5 min reversed-phase (RP) gradient. A total of 4269 protein identifications were made from 4189 distinguishable protein families from yeast during log phase growth. The "Micro" MudPIT separation performed as well as a standard MudPIT separation in 40% less gradient time. The majority of the yeast proteome can now be routinely covered in less than a days' time with high reproducibility and sensitivity. The newly devised separation method was used to detect changes in protein expression during cellular quiescence in yeast. An enrichment in the GO annotations "oxidation reduction", "catabolic processing" and "cellular response to oxidative stress" was seen in the quiescent cellular fraction, consistent with their long-lived stress resistant phenotypes. Heterogeneity was observed in the stationary phase fraction with a less dense cell population showing reductions in KEGG pathway categories of "Ribosome" and "Proteasome", further defining the complex nature of yeast populations present during stationary phase growth. In total, 4488 distinguishable protein families were identified in all cellular conditions tested.
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Affiliation(s)
- Kristofor J Webb
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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44
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O'Connell JD, Zhao A, Ellington AD, Marcotte EM. Dynamic reorganization of metabolic enzymes into intracellular bodies. Annu Rev Cell Dev Biol 2013; 28:89-111. [PMID: 23057741 DOI: 10.1146/annurev-cellbio-101011-155841] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Both focused and large-scale cell biological and biochemical studies have revealed that hundreds of metabolic enzymes across diverse organisms form large intracellular bodies. These proteinaceous bodies range in form from fibers and intracellular foci--such as those formed by enzymes of nitrogen and carbon utilization and of nucleotide biosynthesis--to high-density packings inside bacterial microcompartments and eukaryotic microbodies. Although many enzymes clearly form functional mega-assemblies, it is not yet clear for many recently discovered cases whether they represent functional entities, storage bodies, or aggregates. In this article, we survey intracellular protein bodies formed by metabolic enzymes, asking when and why such bodies form and what their formation implies for the functionality--and dysfunctionality--of the enzymes that comprise them. The panoply of intracellular protein bodies also raises interesting questions regarding their evolution and maintenance within cells. We speculate on models for how such structures form in the first place and why they may be inevitable.
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Affiliation(s)
- Jeremy D O'Connell
- Center for Systems and Synthetic Biology, University of Texas, Austin, Texas 78712, USA
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45
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Guerreiro JF, Mira NP, Sá-Correia I. Adaptive response to acetic acid in the highly resistant yeast species Zygosaccharomyces bailii revealed by quantitative proteomics. Proteomics 2013; 12:2303-18. [PMID: 22685079 DOI: 10.1002/pmic.201100457] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Zygosaccharomyces bailii is the most tolerant yeast species to acetic acid-induced toxicity, being able to grow in the presence of concentrations of this food preservative close to the legal limits. For this reason, Z. bailii is the most important microbial contaminant of acidic food products but the mechanisms behind this intrinsic resistance to acetic acid are very poorly characterized. To gain insights into the adaptive response and tolerance to acetic acid in Z. bailii, we explored an expression proteomics approach, based on quantitative 2DE, to identify alterations occurring in the protein content in response to sudden exposure or balanced growth in the presence of an inhibitory but nonlethal concentration of this weak acid. A coordinate increase in the content of proteins involved in cellular metabolism, in particular, in carbohydrate metabolism (Mdh1p, Aco1p, Cit1p, Idh2p, and Lpd1p) and energy generation (Atp1p and Atp2p), as well as in general and oxidative stress response (Sod2p, Dak2p, Omp2p) was registered. Results reinforce the concept that glucose and acetic acid are coconsumed in Z. bailii, with acetate being channeled into the tricarboxylic acid cycle. When acetic acid is the sole carbon source, results suggest the activation of gluconeogenic and pentose phosphate pathways, based on the increased content of several proteins of these pathways after glucose exhaustion.
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Affiliation(s)
- Joana F Guerreiro
- Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico, Technical University of Lisbon, Portugal
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Van Dyke N, Chanchorn E, Van Dyke MW. The Saccharomyces cerevisiae protein Stm1p facilitates ribosome preservation during quiescence. Biochem Biophys Res Commun 2013. [DOI: 10.1016/j.bbrc.2012.11.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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47
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Chen BR, Cheng HH, Lin WC, Wang KH, Liou JY, Chen PF, Wu KK. Quiescent fibroblasts are more active in mounting robust inflammatory responses than proliferative fibroblasts. PLoS One 2012; 7:e49232. [PMID: 23155470 PMCID: PMC3498339 DOI: 10.1371/journal.pone.0049232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 10/09/2012] [Indexed: 11/18/2022] Open
Abstract
Quiescent cells are considered to be dormant. However, recent studies suggest that quiescent fibroblasts possess active metabolic profile and certain functional characteristics. We previously observed that serum-starved quiescent fibroblasts respond to proinflammatory stimuli by robust expression of cyclooxygenase-2 (COX-2), which declines after the quiescent fibroblasts are driven to proliferation. In this study, we elucidated the underlying signaling and transcriptional mechanism and identified by microarray genes with similar differential expression. By using pharmacological inhibitors coupled with gene silencing, we uncovered the key role of protein kinase C δ (PKCδ) and extracellular signal regulated protein kinase 1/2 (ERK1/2) signaling in mediating COX-2 expression in quiescent cells. Surprisingly, COX-2 expression in proliferative cells was not blocked by PKCδ or ERK1/2 inhibitors due to intrinsic inhibition of PKCδ and ERK1/2 in proliferative cells. Restrained COX-2 transcription in proliferative cells was attributable to reduced NF-κB binding. Microarray analysis identified 35 genes whose expressions were more robust in quiescent than in proliferative cells. A majority of those genes belong to proinflammatory cytokines, chemokines, adhesive molecules and metalloproteinases, which require NF-κB for transcription. Quiescent fibroblasts had a higher migratory activity than proliferative fibroblasts as determined by the transwell assay. Selective COX-2 inhibition reduced migration which was restored by prostaglandin E(2). As COX-2 and inflammatory mediators induce DNA oxidation, we measured 8-hydroxydeoxyguanosine (8-OHdG) in quiescent vs. proliferative fibroblasts. PMA-induced 8-OHdG accumulation was significantly higher in quiescent than in proliferative fibroblasts. These findings indicate that quiescent fibroblasts (and probably other quiescent cells) are at the forefront in mounting inflammatory responses through expression of an array of proinflammatory genes via the PKCδ/ERK1/2 signaling pathway.
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Affiliation(s)
- Bo-Rui Chen
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsin-Chu, Taiwan
| | - Huei-Hsuan Cheng
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Wei-Chung Lin
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Kai-Hsuan Wang
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Jun-Yang Liou
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Pei-Feng Chen
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Kenneth K. Wu
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsin-Chu, Taiwan
- * E-mail:
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Ayer A, Fellermeier S, Fife C, Li SS, Smits G, Meyer AJ, Dawes IW, Perrone GG. A genome-wide screen in yeast identifies specific oxidative stress genes required for the maintenance of sub-cellular redox homeostasis. PLoS One 2012; 7:e44278. [PMID: 22970195 PMCID: PMC3435413 DOI: 10.1371/journal.pone.0044278] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 07/31/2012] [Indexed: 01/10/2023] Open
Abstract
Maintenance of an optimal redox environment is critical for appropriate functioning of cellular processes and cell survival. Despite the importance of maintaining redox homeostasis, it is not clear how the optimal redox potential is sensed and set, and the processes that impact redox on a cellular/organellar level are poorly understood. The genetic bases of cellular redox homeostasis were investigated using a green fluorescent protein (GFP) based redox probe, roGFP2 and a pH sensitive GFP-based probe, pHluorin. The use of roGFP2, in conjunction with pHluorin, enabled determination of pH-adjusted sub-cellular redox potential in a non-invasive and real-time manner. A genome-wide screen using both the non-essential and essential gene collections was carried out in Saccharomyces cerevisiae using cytosolic-roGFP2 to identify factors essential for maintenance of cytosolic redox state under steady-state conditions. 102 genes of diverse function were identified that are required for maintenance of cytosolic redox state. Mutations in these genes led to shifts in the half-cell glutathione redox potential by 75-10 mV. Interestingly, some specific oxidative stress-response processes were identified as over-represented in the data set. Further investigation of the role of oxidative stress-responsive systems in sub-cellular redox homeostasis was conducted using roGFP2 constructs targeted to the mitochondrial matrix and peroxisome and E(GSH) was measured in cells in exponential and stationary phase. Analyses allowed for the identification of key redox systems on a sub-cellular level and the identification of novel genes involved in the regulation of cellular redox homeostasis.
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Affiliation(s)
- Anita Ayer
- University of New South Wales, Sydney, Australia
| | | | | | - Simone S. Li
- University of New South Wales, Sydney, Australia
| | - Gertien Smits
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Ian W. Dawes
- University of New South Wales, Sydney, Australia
- * E-mail:
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Valcourt JR, Lemons JMS, Haley EM, Kojima M, Demuren OO, Coller HA. Staying alive: metabolic adaptations to quiescence. Cell Cycle 2012; 11:1680-96. [PMID: 22510571 DOI: 10.4161/cc.19879] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Quiescence is a state of reversible cell cycle arrest that can grant protection against many environmental insults. In some systems, cellular quiescence is associated with a low metabolic state characterized by a decrease in glucose uptake and glycolysis, reduced translation rates and activation of autophagy as a means to provide nutrients for survival. For cells in multiple different quiescence model systems, including Saccharomyces cerevisiae, mammalian lymphocytes and hematopoietic stem cells, the PI3Kinase/TOR signaling pathway helps to integrate information about nutrient availability with cell growth rates. Quiescence signals often inactivate the TOR kinase, resulting in reduced cell growth and biosynthesis. However, quiescence is not always associated with reduced metabolism; it is also possible to achieve a state of cellular quiescence in which glucose uptake, glycolysis and flux through central carbon metabolism are not reduced. In this review, we compare and contrast the metabolic changes that occur with quiescence in different model systems.
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Affiliation(s)
- James R Valcourt
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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