1
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Rubio LS, Mohajan S, Gross DS. Heat Shock Factor 1 forms nuclear condensates and restructures the yeast genome before activating target genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.28.560064. [PMID: 37808805 PMCID: PMC10557744 DOI: 10.1101/2023.09.28.560064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
In insects and mammals, 3D genome topology has been linked to transcriptional states yet whether this link holds for other eukaryotes is unclear. Using both ligation proximity and fluorescence microscopy assays, we show that in Saccharomyces cerevisiae, Heat Shock Response (HSR) genes dispersed across multiple chromosomes and under the control of Heat Shock Factor (Hsf1) rapidly reposition in cells exposed to acute ethanol stress and engage in concerted, Hsf1-dependent intergenic interactions. Accompanying 3D genome reconfiguration is equally rapid formation of Hsf1-containing condensates. However, in contrast to the transience of Hsf1-driven intergenic interactions that peak within 10-20 min and dissipate within 1 h in the presence of 8.5% (v/v) ethanol, transcriptional condensates are stably maintained for hours. Moreover, under the same conditions, Pol II occupancy of HSR genes and RNA expression are detectable only later in the response and peak much later (>1 h). This contrasts with the coordinate response of HSR genes to thermal stress (39°C) where Pol II occupancy, transcription, intergenic interactions, and formation of Hsf1 condensates are all rapid yet transient (peak within 2.5-10 min and dissipate within 1 h). Therefore, Hsf1 forms condensates, restructures the genome and transcriptionally activates HSR genes in response to both forms of proteotoxic stress but does so with strikingly different kinetics. In cells subjected to ethanol stress, Hsf1 forms condensates and repositions target genes before transcriptionally activating them.
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2
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Hipp MS, Hartl FU. Interplay of Proteostasis Capacity and Protein Aggregation: Implications for Cellular Function and Disease. J Mol Biol 2024; 436:168615. [PMID: 38759929 DOI: 10.1016/j.jmb.2024.168615] [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: 02/08/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Eukaryotic cells are equipped with an intricate proteostasis network (PN), comprising nearly 3,000 components dedicated to preserving proteome integrity and sustaining protein homeostasis. This protective system is particularly important under conditions of external and intrinsic cell stress, where inherently dynamic proteins may unfold and lose functionality. A decline in proteostasis capacity is associated with the aging process, resulting in a reduced folding efficiency of newly synthesized proteins and a deficit in the cellular capacity to degrade misfolded proteins. A critical consequence of PN insufficiency is the accumulation of cytotoxic protein aggregates that underlie various age-related neurodegenerative conditions and other pathologies. By interfering with specific proteostasis components, toxic aggregates place an excessive burden on the PN's ability to maintain proteome integrity. This initiates a feed-forward loop, wherein the generation of misfolded and aggregated proteins ultimately leads to proteostasis collapse and cellular demise.
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Affiliation(s)
- Mark S Hipp
- Department of Biomedical Sciences, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan, 1, 9713 AV Groningen, the Netherlands; Research School of Behavioural and Cognitive Neurosciences, University of Groningen, Groningen, the Netherlands; School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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3
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Aranda-Anzaldo A, Dent MAR, Segura-Anaya E, Martínez-Gómez A. Protein folding, cellular stress and cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 191:40-57. [PMID: 38969306 DOI: 10.1016/j.pbiomolbio.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Proteins are acknowledged as the phenotypical manifestation of the genotype, because protein-coding genes carry the information for the strings of amino acids that constitute the proteins. It is widely accepted that protein function depends on the corresponding "native" structure or folding achieved within the cell, and that native protein folding corresponds to the lowest free energy minimum for a given protein. However, protein folding within the cell is a non-deterministic dissipative process that from the same input may produce different outcomes, thus conformational heterogeneity of folded proteins is the rule and not the exception. Local changes in the intracellular environment promote variation in protein folding. Hence protein folding requires "supervision" by a host of chaperones and co-chaperones that help their client proteins to achieve the folding that is most stable according to the local environment. Such environmental influence on protein folding is continuously transduced with the help of the cellular stress responses (CSRs) and this may lead to changes in the rules of engagement between proteins, so that the corresponding protein interactome could be modified by the environment leading to an alternative cellular phenotype. This allows for a phenotypic plasticity useful for adapting to sudden and/or transient environmental changes at the cellular level. Starting from this perspective, hereunder we develop the argument that the presence of sustained cellular stress coupled to efficient CSRs may lead to the selection of an aberrant phenotype as the resulting adaptation of the cellular proteome (and the corresponding interactome) to such stressful conditions, and this can be a common epigenetic pathway to cancer.
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Affiliation(s)
- Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, 50180, Edo. Méx., Mexico.
| | - Myrna A R Dent
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, 50180, Edo. Méx., Mexico
| | - Edith Segura-Anaya
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, 50180, Edo. Méx., Mexico
| | - Alejandro Martínez-Gómez
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, 50180, Edo. Méx., Mexico
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4
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Biba DA, Wolf YI, Koonin EV, Rochman ND. Balance between asymmetric allocation and repair of somatic damage in unicellular life forms as an ancient form of r/K selection. Proc Natl Acad Sci U S A 2024; 121:e2400008121. [PMID: 38787879 PMCID: PMC11145259 DOI: 10.1073/pnas.2400008121] [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: 01/01/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Over the course of multiple divisions, cells accumulate diverse nongenetic, somatic damage including misfolded and aggregated proteins and cell wall defects. If the rate of damage accumulation exceeds the rate of dilution through cell growth, a dedicated mitigation strategy is required to prevent eventual population collapse. Strategies for somatic damage control can be divided into two categories, asymmetric allocation and repair, which are not, in principle, mutually exclusive. We explore a mathematical model to identify the optimal strategy, maximizing the total cell number, over a wide range of environmental and physiological conditions. The optimal strategy is primarily determined by extrinsic, damage-independent mortality and the physiological model for damage accumulation that can be either independent (linear) or increasing (exponential) with respect to the prior accumulated damage. Under the linear regime, the optimal strategy is either exclusively repair or asymmetric allocation, whereas under the exponential regime, the optimal strategy is a combination of asymmetry and repair. Repair is preferred when extrinsic mortality is low, whereas at high extrinsic mortality, asymmetric damage allocation becomes the strategy of choice. We hypothesize that at an early stage of life evolution, optimization over repair and asymmetric allocation of somatic damage gave rise to r and K selection strategists.
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Affiliation(s)
- Dmitry A. Biba
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20894
- Oak Ridge Institute for Science and Education, Oak Ridge, TN37830
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20894
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20894
| | - Nash D. Rochman
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20894
- Institute for Implementation Science in Population Health, City University of New York, New York, NY10027
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy City, University of New York, New York, NY10027
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5
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Dhar A, Bagyashree VT, Biswas S, Kumari J, Sridhara A, Jeevan Subodh B, Shekhar S, Palani S. Functional redundancy and formin-independent localization of tropomyosin isoforms in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.587703. [PMID: 38617342 PMCID: PMC11014519 DOI: 10.1101/2024.04.04.587703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Tropomyosin is an actin binding protein which protects actin filaments from cofilin-mediated disassembly. Distinct tropomyosin isoforms have long been hypothesized to differentially sort to subcellular actin networks and impart distinct functionalities. Nevertheless, a mechanistic understanding of the interplay between Tpm isoforms and their functional contributions to actin dynamics has been lacking. In this study, we present acetylation-mimic engineered mNeonGreen-Tpm fusion proteins that exhibit complete functionality as a sole copy, surpassing limitations of existing probes and enabling real-time dynamic tracking of Tpm-actin filaments in vivo. Using these functional Tpm fusion proteins, we find that both Tpm1 and Tpm2 indiscriminately bind to actin filaments nucleated by either formin isoform- Bnr1 and Bni1 in vivo, in contrast to the long-held paradigm of Tpm-formin pairing. We also show that Tpm2 can protect and organize functional actin cables in absence of Tpm1. Overall, our work supports a concentration-dependent and formin-independent model of Tpm-actin binding and demonstrates for the first time, the functional redundancy of the paralog Tpm2 in actin cable maintenance in S. cerevisiae.
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Affiliation(s)
- Anubhav Dhar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
- equal contribution
| | - VT Bagyashree
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
- equal contribution
| | - Sudipta Biswas
- Departments of Physics, Cell Biology and Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Jayanti Kumari
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Amruta Sridhara
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - B Jeevan Subodh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Shashank Shekhar
- Departments of Physics, Cell Biology and Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Saravanan Palani
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
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6
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Schneider KL, Hao X, Keuenhof KS, Berglund LL, Fischbach A, Ahmadpour D, Chawla S, Gómez P, Höög JL, Widlund PO, Nyström T. Elimination of virus-like particles reduces protein aggregation and extends replicative lifespan in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2024; 121:e2313538121. [PMID: 38527193 PMCID: PMC10998562 DOI: 10.1073/pnas.2313538121] [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: 08/07/2023] [Accepted: 02/04/2024] [Indexed: 03/27/2024] Open
Abstract
A major consequence of aging and stress, in yeast to humans, is an increased accumulation of protein aggregates at distinct sites within the cells. Using genetic screens, immunoelectron microscopy, and three-dimensional modeling in our efforts to elucidate the importance of aggregate annexation, we found that most aggregates in yeast accumulate near the surface of mitochondria. Further, we show that virus-like particles (VLPs), which are part of the retrotransposition cycle of Ty elements, are markedly enriched in these sites of protein aggregation. RNA interference-mediated silencing of Ty expression perturbed aggregate sequestration to mitochondria, reduced overall protein aggregation, mitigated toxicity of a Huntington's disease model, and expanded the replicative lifespan of yeast in a partially Hsp104-dependent manner. The results are in line with recent data demonstrating that VLPs might act as aging factors in mammals, including humans, and extend these findings by linking VLPs to a toxic accumulation of protein aggregates and raising the possibility that they might negatively influence neurological disease progression.
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Affiliation(s)
- K. L. Schneider
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - X. Hao
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - K. S. Keuenhof
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg41390, Sweden
| | - L. L. Berglund
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg41390, Sweden
| | - A. Fischbach
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - D. Ahmadpour
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - S. Chawla
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - P. Gómez
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - J. L. Höög
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg41390, Sweden
| | - P. O. Widlund
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - T. Nyström
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
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7
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Chen M, Zhu Z, Wu S, Huang A, Xie Z, Cai J, Huang R, Yu S, Liu M, Zhang J, Tse Y, Wu Q, Wang J, Ding Y. SKN-1 is indispensable for protection against Aβ-induced proteotoxicity by a selenopeptide derived from Cordyceps militaris. Redox Biol 2024; 70:103065. [PMID: 38340636 PMCID: PMC10869277 DOI: 10.1016/j.redox.2024.103065] [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: 01/04/2024] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
Oxidative stress (OS) and disruption of proteostasis caused by aggregated proteins are the primary causes of cell death in various diseases. Selenopeptides have shown the potential to control OS and alleviate inflammatory damage, suggesting promising therapeutic applications. However, their potential function in inhibiting proteotoxicity is not yet fully understood. To address this gap in knowledge, this study aimed to investigate the effects and underlying mechanisms of the selenopeptide VPRKL(Se)M on amyloid β protein (Aβ) toxicity in transgenic Caenorhabditis elegans. The results revealed that supplementation with VPRKL(Se)M can alleviate Aβ-induced toxic effects in the transgenic C. elegans model. Moreover, the addition of VPRKL(Se)M inhibited the Aβ aggregates formation, reduced the reactive oxygen species (ROS) levels, and ameliorated the overall proteostasis. Importantly, we found that the inhibitory effects of VPRKL(Se)M on Aβ toxicity and activation of the unfolded protein are dependent on skinhead-1 (SKN-1). These findings suggested that VPRKL(Se)M is a potential bioactive agent for modulating SKN-1, which subsequently improves proteostasis and reduces OS. Collectively, the findings from the current study suggests VPRKL(Se)M may play a critical role in preventing protein disorder and related diseases.
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Affiliation(s)
- Mengfei Chen
- Department of Food Science and Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, 510070, China
| | - Zhenjun Zhu
- Department of Food Science and Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Shujian Wu
- Department of Food Science and Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Aohuan Huang
- Department of Food Science and Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, 510070, China
| | - Zhiqing Xie
- Department of Food Science and Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Jie Cai
- Department of Food Science and Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, 510070, China
| | - Rong Huang
- Department of Food Science and Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, 510070, China
| | - Shubo Yu
- Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, 510070, China
| | - Ming Liu
- Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, 510070, China
| | - Jumei Zhang
- Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, 510070, China
| | - Yuchung Tse
- Core Research Facilities, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qingping Wu
- Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, 510070, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yu Ding
- Department of Food Science and Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
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8
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Yang EJN, Liao PC, Pon L. Mitochondrial protein and organelle quality control-Lessons from budding yeast. IUBMB Life 2024; 76:72-87. [PMID: 37731280 PMCID: PMC10842221 DOI: 10.1002/iub.2783] [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: 06/30/2023] [Accepted: 08/11/2023] [Indexed: 09/22/2023]
Abstract
Mitochondria are essential for normal cellular function and have emerged as key aging determinants. Indeed, defects in mitochondrial function have been linked to cardiovascular, skeletal muscle and neurodegenerative diseases, premature aging, and age-linked diseases. Here, we describe mechanisms for mitochondrial protein and organelle quality control. These surveillance mechanisms mediate repair or degradation of damaged or mistargeted mitochondrial proteins, segregate mitochondria based on their functional state during asymmetric cell division, and modulate cellular fitness, the response to stress, and lifespan control in yeast and other eukaryotes.
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Affiliation(s)
- Emily Jie-Ning Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Pin-Chao Liao
- Institute of Molecular Medicine & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan 30013
| | - Liza Pon
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
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9
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Eisele-Bürger AM, Eisele F, Malmgren Hill S, Hao X, Schneider KL, Imamoglu R, Balchin D, Liu B, Hartl FU, Bozhkov PV, Nyström T. Calmodulin regulates protease versus co-chaperone activity of a metacaspase. Cell Rep 2023; 42:113372. [PMID: 37938971 DOI: 10.1016/j.celrep.2023.113372] [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: 03/24/2023] [Revised: 09/11/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023] Open
Abstract
Metacaspases are ancestral homologs of caspases that can either promote cell death or confer cytoprotection. Furthermore, yeast (Saccharomyces cerevisiae) metacaspase Mca1 possesses dual biochemical activity: proteolytic activity causing cell death and cytoprotective, co-chaperone-like activity retarding replicative aging. The molecular mechanism favoring one activity of Mca1 over another remains elusive. Here, we show that this mechanism involves calmodulin binding to the N-terminal pro-domain of Mca1, which prevents its proteolytic activation and promotes co-chaperone-like activity, thus switching from pro-cell death to anti-aging function. The longevity-promoting effect of Mca1 requires the Hsp40 co-chaperone Sis1, which is necessary for Mca1 recruitment to protein aggregates and their clearance. In contrast, proteolytically active Mca1 cleaves Sis1 both in vitro and in vivo, further clarifying molecular mechanism behind a dual role of Mca1 as a cell-death protease versus gerontogene.
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Affiliation(s)
- Anna Maria Eisele-Bürger
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden; Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, 75007 Uppsala, Sweden
| | - Frederik Eisele
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 413 90 Göteborg, Sweden
| | - Sandra Malmgren Hill
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Xinxin Hao
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Kara L Schneider
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Rahmi Imamoglu
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - David Balchin
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 413 90 Göteborg, Sweden
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, 75007 Uppsala, Sweden.
| | - Thomas Nyström
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden.
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10
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Biba DA, Wolf YI, Koonin EV, Rochman ND. Unicellular life balances asymmetric allocation and repair of somatic damage representing the origin of r/K selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568103. [PMID: 38076808 PMCID: PMC10705550 DOI: 10.1101/2023.11.21.568103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Over the course of multiple divisions, cells accumulate diverse non-genetic, somatic damage including misfolded and aggregated proteins and cell wall defects. If the rate of damage accumulation exceeds the rate of dilution through cell growth, a dedicated mitigation strategy is required to prevent eventual population collapse. Strategies for somatic damage control can be divided into two categories, asymmetric allocation and repair, which are not, in principle, mutually exclusive. Through mathematical modelling, we identify the optimal strategy, maximizing the total cell number, over a wide range of environmental and physiological conditions. The optimal strategy is primarily determined by extrinsic (damage-independent) mortality and the physiological model for damage accumulation that can be either independent (linear) or increasing (exponential) with respect to the prior accumulated damage. Under the linear regime, the optimal strategy is either exclusively repair or asymmetric allocation whereas under the exponential regime, the optimal strategy is mixed. Repair is preferred when extrinsic mortality is low, whereas at high extrinsic mortality, asymmetric damage allocation becomes the strategy of choice. We hypothesize that optimization over somatic damage repair and asymmetric allocation in early cellular life forms gave rise to the r and K selection strategies.
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Affiliation(s)
- Dmitry A. Biba
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Nash D. Rochman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
- Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY), New York, NY, USA
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York (CUNY), New York, NY, USA
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11
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Okada H, Chen X, Wang K, Marquardt J, Bi E. Bni5 tethers myosin-II to septins to enhance retrograde actin flow and the robustness of cytokinesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566094. [PMID: 37986946 PMCID: PMC10659389 DOI: 10.1101/2023.11.07.566094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The collaboration between septins and myosin-II in driving processes outside of cytokinesis remains largely uncharted. Here, we demonstrate that Bni5 in the budding yeast S. cerevisiae interacts with myosin-II, septin filaments, and the septin-associated kinase Elm1 via distinct domains at its N- and C-termini, thereby tethering the mobile myosin-II to the stable septin hourglass at the division site from bud emergence to the onset of cytokinesis. The septin and Elm1-binding domains, together with a central disordered region, of Bni5 control timely remodeling of the septin hourglass into a double ring, enabling the actomyosin ring constriction. The Bni5-tethered myosin-II enhances retrograde actin cable flow, which contributes to the asymmetric inheritance of mitochondria-associated protein aggregates during cell division, and also strengthens cytokinesis against various perturbations. Thus, we have established a biochemical pathway involving septin-Bni5-myosin-II interactions at the division site, which can inform mechanistic understanding of the role of myosin-II in other retrograde flow systems. Summary Okada et al. have determined the molecular mechanism underlying the Bni5 interactions with septins and myosin-II at the cell division site and uncovered its roles in promoting retrograde actin flow and the robustness of cytokinesis in budding yeast.
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12
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Farley FW, McCully RR, Maslo PB, Yu L, Sheff MA, Sadeghi H, Elion EA. Effects of HSP70 chaperones Ssa1 and Ssa2 on Ste5 scaffold and the mating mitogen-activated protein kinase (MAPK) pathway in Saccharomyces cerevisiae. PLoS One 2023; 18:e0289339. [PMID: 37851593 PMCID: PMC10584130 DOI: 10.1371/journal.pone.0289339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 07/17/2023] [Indexed: 10/20/2023] Open
Abstract
Ste5 is a prototype of scaffold proteins that regulate activation of mitogen-activated protein kinase (MAPK) cascades in all eukaryotes. Ste5 associates with many proteins including Gβγ (Ste4), Ste11 MAPKKK, Ste7 MAPKK, Fus3 and Kss1 MAPKs, Bem1, Cdc24. Here we show that Ste5 also associates with heat shock protein 70 chaperone (Hsp70) Ssa1 and that Ssa1 and its ortholog Ssa2 are together important for Ste5 function and efficient mating responses. The majority of purified overexpressed Ste5 associates with Ssa1. Loss of Ssa1 and Ssa2 has deleterious effects on Ste5 abundance, integrity, and localization particularly when Ste5 is expressed at native levels. The status of Ssa1 and Ssa2 influences Ste5 electrophoresis mobility and formation of high molecular weight species thought to be phosphorylated, ubiquitinylated and aggregated and lower molecular weight fragments. A Ste5 VWA domain mutant with greater propensity to form punctate foci has reduced predicted propensity to bind Ssa1 near the mutation sites and forms more punctate foci when Ssa1 Is overexpressed, supporting a dynamic protein quality control relationship between Ste5 and Ssa1. Loss of Ssa1 and Ssa2 reduces activation of Fus3 and Kss1 MAPKs and FUS1 gene expression and impairs mating shmoo morphogenesis. Surprisingly, ssa1, ssa2, ssa3 and ssa4 single, double and triple mutants can still mate, suggesting compensatory mechanisms exist for folding. Additional analysis suggests Ssa1 is the major Hsp70 chaperone for the mating and invasive growth pathways and reveals several Hsp70-Hsp90 chaperone-network proteins required for mating morphogenesis.
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Affiliation(s)
- Francis W. Farley
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Ryan R. McCully
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Paul B. Maslo
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Lu Yu
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Mark A. Sheff
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Homayoun Sadeghi
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Elaine A. Elion
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
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13
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Babazadeh R, Schneider KL, Fischbach A, Hao X, Liu B, Nystrom T. The yeast guanine nucleotide exchange factor Sec7 is a bottleneck in spatial protein quality control and detoxifies neurological disease proteins. Sci Rep 2023; 13:14068. [PMID: 37640758 PMCID: PMC10462735 DOI: 10.1038/s41598-023-41188-0] [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: 01/30/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023] Open
Abstract
ER-to-Golgi trafficking partakes in the sorting of misfolded cytoplasmic proteins to reduce their cytological toxicity. We show here that yeast Sec7, a protein involved in proliferation of the Golgi, is part of this pathway and participates in an Hsp70-dependent formation of insoluble protein deposits (IPOD). Sec7 associates with the disaggregase Hsp104 during a mild heat shock and increases the rate of Hsp104 diffusion in an Hsp70-dependent manner when overproduced. Sec7 overproduction increased formation of IPODs from smaller aggregates and mitigated the toxicity of Huntingtin exon-1 upon heat stress while Sec7 depletion increased sensitivity to aẞ42 of the Alzheimer's disease and α-synuclein of the Parkinson's disease, suggesting a role of Sec7 in mitigating proteotoxicity.
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Affiliation(s)
- Roja Babazadeh
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Kara L Schneider
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Arthur Fischbach
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Xinxin Hao
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9 C, 413 90, Gothenburg, Sweden
| | - Thomas Nystrom
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, 405 30, Gothenburg, Sweden.
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14
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Stanford KE, Zhao X, Kim N, Masison DC, Greene LE. Overexpression of Hsp104 by Causing Dissolution of the Prion Seeds Cures the Yeast [ PSI+] Prion. Int J Mol Sci 2023; 24:10833. [PMID: 37446010 DOI: 10.3390/ijms241310833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
The yeast Sup35 protein misfolds into the infectious [PSI+] prion, which is then propagated by the severing activity of the molecular chaperone, Hsp104. Unlike other yeast prions, this prion is unique in that it is efficiently cured by the overexpression as well as the inactivation of Hsp104. However, it is controversial whether curing by overexpression is due to the dissolution of the prion seeds by the trimming activity of Hsp104 or the asymmetric segregation of the prion seeds between mother and daughter cells which requires cell division. To answer this question, we conducted experiments and found no difference in the extent of curing between mother and daughter cells when half of the cells were cured by Hsp104 overexpression in one generation. Furthermore, curing was not affected by the lack of Sir2 expression, which was reported to be required for asymmetric segregation of the [PSI+] seeds. More importantly, when either hydroxyurea or ethanol were used to inhibit cell division, the extent of curing by Hsp104 overexpression was not significantly reduced. Therefore, the curing of [PSI+] by Hsp104 overexpression is not due to asymmetric segregation of the prion seeds, but rather their dissolution by Hsp104.
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Affiliation(s)
- Katherine E Stanford
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaohong Zhao
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nathan Kim
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Masison
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lois E Greene
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Josefson R, Kumar N, Hao X, Liu B, Nyström T. The GET pathway is a major bottleneck for maintaining proteostasis in Saccharomyces cerevisiae. Sci Rep 2023; 13:9285. [PMID: 37286562 DOI: 10.1038/s41598-023-35666-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/18/2023] [Indexed: 06/09/2023] Open
Abstract
A hallmark of aging in a variety of organisms is a breakdown of proteostasis and an ensuing accumulation of protein aggregates and inclusions. However, it is not clear if the proteostasis network suffers from a uniform breakdown during aging or if some distinct components act as bottlenecks especially sensitive to functional decline. Here, we report on a genome-wide, unbiased, screen for single genes in young cells of budding yeast required to keep the proteome aggregate-free under non-stress conditions as a means to identify potential proteostasis bottlenecks. We found that the GET pathway, required for the insertion of tail-anchored (TA) membrane proteins in the endoplasmic reticulum, is such a bottleneck as single mutations in either GET3, GET2 or GET1 caused accumulation of cytosolic Hsp104- and mitochondria-associated aggregates in nearly all cells when growing at 30 °C (non-stress condition). Further, results generated by a second screen identifying proteins aggregating in GET mutants and analyzing the behavior of cytosolic reporters of misfolding, suggest that there is a general collapse in proteostasis in GET mutants that affects other proteins than TA proteins.
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Affiliation(s)
- Rebecca Josefson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Navinder Kumar
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Xinxin Hao
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Nyström
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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16
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Fischbach A, Johns A, Schneider KL, Hao X, Tessarz P, Nyström T. Artificial Hsp104-mediated systems for re-localizing protein aggregates. Nat Commun 2023; 14:2663. [PMID: 37160881 PMCID: PMC10169802 DOI: 10.1038/s41467-023-37706-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
Spatial Protein Quality Control (sPQC) sequesters misfolded proteins into specific, organelle-associated inclusions within the cell to control their toxicity. To approach the role of sPQC in cellular fitness, neurodegenerative diseases and aging, we report on the construction of Hsp100-based systems in budding yeast cells, which can artificially target protein aggregates to non-canonical locations. We demonstrate that aggregates of mutant huntingtin (mHtt), the disease-causing agent of Huntington's disease can be artificially targeted to daughter cells as well as to eisosomes and endosomes with this approach. We find that the artificial removal of mHtt inclusions from mother cells protects them from cell death suggesting that even large mHtt inclusions may be cytotoxic, a trait that has been widely debated. In contrast, removing inclusions of endogenous age-associated misfolded proteins does not significantly affect the lifespan of mother cells. We demonstrate also that this approach is able to manipulate mHtt inclusion formation in human cells and has the potential to be useful as an alternative, complementary approach to study the role of sPQC, for example in aging and neurodegenerative disease.
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Affiliation(s)
- Arthur Fischbach
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden.
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany.
| | - Angela Johns
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Kara L Schneider
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Xinxin Hao
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Peter Tessarz
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), Cologne, Germany
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden.
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17
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Zhang L, Wu J, Zhu Z, He Y, Fang R. Mitochondrion: A bridge linking aging and degenerative diseases. Life Sci 2023; 322:121666. [PMID: 37030614 DOI: 10.1016/j.lfs.2023.121666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/10/2023]
Abstract
Aging is a natural process, characterized by progressive loss of physiological integrity, impaired function, and increased vulnerability to death. For centuries, people have been trying hard to understand the process of aging and find effective ways to delay it. However, limited breakthroughs have been made in anti-aging area. Since the hallmarks of aging were summarized in 2013, increasing studies focus on the role of mitochondrial dysfunction in aging and aging-related degenerative diseases, such as neurodegenerative diseases, osteoarthritis, metabolic diseases, and cardiovascular diseases. Accumulating evidence indicates that restoring mitochondrial function and biogenesis exerts beneficial effects in extending lifespan and promoting healthy aging. In this paper, we provide an overview of mitochondrial changes during aging and summarize the advanced studies in mitochondrial therapies for the treatment of degenerative diseases. Current challenges and future perspectives are proposed to provide novel and promising directions for future research.
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Affiliation(s)
- Lanlan Zhang
- Center for Plastic & Reconstructive Surgery, Department of Hand & Reconstructive Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jianlong Wu
- Center for Plastic & Reconstructive Surgery, Department of Hand & Reconstructive Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ziguan Zhu
- Center for Plastic & Reconstructive Surgery, Department of Hand & Reconstructive Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yuchen He
- Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Department of Orthopaedics, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Renpeng Fang
- Center for Plastic & Reconstructive Surgery, Department of Hand & Reconstructive Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
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18
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Staples MI, Frazer C, Fawzi NL, Bennett RJ. Phase separation in fungi. Nat Microbiol 2023; 8:375-386. [PMID: 36782025 PMCID: PMC10081517 DOI: 10.1038/s41564-022-01314-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/16/2022] [Indexed: 02/15/2023]
Abstract
Phase separation, in which macromolecules partition into a concentrated phase that is immiscible with a dilute phase, is involved with fundamental cellular processes across the tree of life. We review the principles of phase separation and highlight how it impacts diverse processes in the fungal kingdom. These include the regulation of autophagy, cell signalling pathways, transcriptional circuits and the establishment of asymmetry in fungal cells. We describe examples of stable, phase-separated assemblies including membraneless organelles such as the nucleolus as well as transient condensates that also arise through phase separation and enable cells to rapidly and reversibly respond to important environmental cues. We showcase how research into phase separation in model yeasts, such as Saccharomyces cerevisiae and Schizosaccharomyces pombe, in conjunction with that in plant and human fungal pathogens, such as Ashbya gossypii and Candida albicans, is continuing to enrich our understanding of fundamental molecular processes.
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Affiliation(s)
- Mae I Staples
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Corey Frazer
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
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19
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Wilkinson MD, Ferreira JL, Beeby M, Baum J, Willison KR. The malaria parasite chaperonin containing TCP-1 (CCT) complex: Data integration with other CCT proteomes. Front Mol Biosci 2022; 9:1057232. [PMID: 36567946 PMCID: PMC9772883 DOI: 10.3389/fmolb.2022.1057232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
The multi-subunit chaperonin containing TCP-1 (CCT) is an essential molecular chaperone that functions in the folding of key cellular proteins. This paper reviews the interactome of the eukaryotic chaperonin CCT and its primary clients, the ubiquitous cytoskeletal proteins, actin and tubulin. CCT interacts with other nascent proteins, especially the WD40 propeller proteins, and also assists in the assembly of several protein complexes. A new proteomic dataset is presented for CCT purified from the human malarial parasite, P. falciparum (PfCCT). The CCT8 subunit gene was C-terminally FLAG-tagged using Selection Linked Integration (SLI) and CCT complexes were extracted from infected human erythrocyte cultures synchronized for maximum expression levels of CCT at the trophozoite stage of the parasite's asexual life cycle. We analyze the new PfCCT proteome and incorporate it into our existing model of the CCT system, supported by accumulated data from biochemical and cell biological experiments in many eukaryotic species. Together with measurements of CCT mRNA, CCT protein subunit copy number and the post-translational and chemical modifications of the CCT subunits themselves, a cumulative picture is emerging of an essential molecular chaperone system sitting at the heart of eukaryotic cell growth control and cell cycle regulation.
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Affiliation(s)
- Mark D. Wilkinson
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Josie L. Ferreira
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Jake Baum
- Department of Life Sciences, Imperial College London, London, United Kingdom,School of Biomedical Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Keith R. Willison
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom,*Correspondence: Keith R. Willison,
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20
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Kukhtevich IV, Rivero-Romano M, Rakesh N, Bheda P, Chadha Y, Rosales-Becerra P, Hamperl S, Bureik D, Dornauer S, Dargemont C, Kirmizis A, Schmoller KM, Schneider R. Quantitative RNA imaging in single live cells reveals age-dependent asymmetric inheritance. Cell Rep 2022; 41:111656. [DOI: 10.1016/j.celrep.2022.111656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 08/31/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022] Open
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21
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Murley A, Wickham K, Dillin A. Life in lockdown: Orchestrating endoplasmic reticulum and lysosome homeostasis for quiescent cells. Mol Cell 2022; 82:3526-3537. [PMID: 36044901 DOI: 10.1016/j.molcel.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/06/2022] [Accepted: 08/04/2022] [Indexed: 11/25/2022]
Abstract
Cellular quiescence-reversible exit from the cell cycle-is an important feature of many cell types important for organismal health. Quiescent cells activate protective mechanisms that allow their persistence in the absence of growth and division for long periods of time. Aging and cellular dysfunction compromise the survival and re-activation of quiescent cells over time. Counteracting this decline are two interconnected organelles that lie at opposite ends of the secretory pathway: the endoplasmic reticulum and lysosomes. In this review, we highlight recent studies exploring the roles of these two organelles in quiescent cells from diverse contexts and speculate on potential other roles they may play, such as through organelle contact sites. Finally, we discuss emerging models of cellular quiescence, utilizing new cell culture systems and model organisms, that are suited to the mechanistic investigation of the functions of these organelles in quiescent cells.
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Affiliation(s)
- Andrew Murley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Kevin Wickham
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Andrew Dillin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
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22
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Swamy KBS, Lee HY, Ladra C, Liu CFJ, Chao JC, Chen YY, Leu JY. Proteotoxicity caused by perturbed protein complexes underlies hybrid incompatibility in yeast. Nat Commun 2022; 13:4394. [PMID: 35906261 PMCID: PMC9338014 DOI: 10.1038/s41467-022-32107-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 07/18/2022] [Indexed: 02/08/2023] Open
Abstract
Dobzhansky–Muller incompatibilities represent a major driver of reproductive isolation between species. They are caused when interacting components encoded by alleles from different species cannot function properly when mixed. At incipient stages of speciation, complex incompatibilities involving multiple genetic loci with weak effects are frequently observed, but the underlying mechanisms remain elusive. Here we show perturbed proteostasis leading to compromised mitosis and meiosis in Saccharomyces cerevisiae hybrid lines carrying one or two chromosomes from Saccharomyces bayanus var. uvarum. Levels of proteotoxicity are correlated with the number of protein complexes on replaced chromosomes. Proteomic approaches reveal that multi-protein complexes with subunits encoded by replaced chromosomes tend to be unstable. Furthermore, hybrid defects can be alleviated or aggravated, respectively, by up- or down-regulating the ubiquitin-proteasomal degradation machinery, suggesting that destabilized complex subunits overburden the proteostasis machinery and compromise hybrid fitness. Our findings reveal the general role of impaired protein complex assembly in complex incompatibilities. Hybrid incompatibility can be an important element of reproductive isolation and speciation. Using chromosome replacement lines of yeast, the authors show that perturbed proteostasis caused by destabilized hybrid protein complexes may represent a general mechanism of hybrid incompatibility.
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Affiliation(s)
- Krishna B S Swamy
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.,Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, 380009, India
| | - Hsin-Yi Lee
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Carmina Ladra
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chien-Fu Jeff Liu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jung-Chi Chao
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Yun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.
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23
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Lsm7 phase-separated condensates trigger stress granule formation. Nat Commun 2022; 13:3701. [PMID: 35764627 PMCID: PMC9240020 DOI: 10.1038/s41467-022-31282-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/02/2022] [Indexed: 11/09/2022] Open
Abstract
Stress granules (SGs) are non-membranous organelles facilitating stress responses and linking the pathology of age-related diseases. In a genome-wide imaging-based phenomic screen, we identify Pab1 co-localizing proteins under 2-deoxy-D-glucose (2-DG) induced stress in Saccharomyces cerevisiae. We find that deletion of one of the Pab1 co-localizing proteins, Lsm7, leads to a significant decrease in SG formation. Under 2-DG stress, Lsm7 rapidly forms foci that assist in SG formation. The Lsm7 foci form via liquid-liquid phase separation, and the intrinsically disordered region and the hydrophobic clusters within the Lsm7 sequence are the internal driving forces in promoting Lsm7 phase separation. The dynamic Lsm7 phase-separated condensates appear to work as seeding scaffolds, promoting Pab1 demixing and subsequent SG initiation, seemingly mediated by RNA interactions. The SG initiation mechanism, via Lsm7 phase separation, identified in this work provides valuable clues for understanding the mechanisms underlying SG formation and SG-associated human diseases.
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24
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Zhao G, Rusche LN. Sirtuins in Epigenetic Silencing and Control of Gene Expression in Model and Pathogenic Fungi. Annu Rev Microbiol 2022; 76:157-178. [PMID: 35609947 DOI: 10.1146/annurev-micro-041020-100926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fungi, including yeasts, molds, and mushrooms, proliferate on decaying matter and then adopt quiescent forms once nutrients are depleted. This review explores how fungi use sirtuin deacetylases to sense and respond appropriately to changing nutrients. Because sirtuins are NAD+-dependent deacetylases, their activity is sensitive to intracellular NAD+ availability. This allows them to transmit information about a cell's metabolic state on to the biological processes they influence. Fungal sirtuins are primarily known to deacetylate histones, repressing transcription and modulating genome stability. Their target genes include those involved in NAD+ homeostasis, metabolism, sporulation, secondary metabolite production, and virulence traits of pathogenic fungi. By targeting different genes over evolutionary time, sirtuins serve as rewiring points that allow organisms to evolve novel responses to low NAD+ stress by bringing relevant biological processes under the control of sirtuins. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Guolei Zhao
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, New York, USA; ,
| | - Laura N Rusche
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, New York, USA; ,
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25
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Identification of a modulator of the actin cytoskeleton, mitochondria, nutrient metabolism and lifespan in yeast. Nat Commun 2022; 13:2706. [PMID: 35577788 PMCID: PMC9110415 DOI: 10.1038/s41467-022-30045-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
In yeast, actin cables are F-actin bundles that are essential for cell division through their function as tracks for cargo movement from mother to daughter cell. Actin cables also affect yeast lifespan by promoting transport and inheritance of higher-functioning mitochondria to daughter cells. Here, we report that actin cable stability declines with age. Our genome-wide screen for genes that affect actin cable stability identified the open reading frame YKL075C. Deletion of YKL075C results in increases in actin cable stability and abundance, mitochondrial fitness, and replicative lifespan. Transcriptome analysis revealed a role for YKL075C in regulating branched-chain amino acid (BCAA) metabolism. Consistent with this, modulation of BCAA metabolism or decreasing leucine levels promotes actin cable stability and function in mitochondrial quality control. Our studies support a role for actin stability in yeast lifespan, and demonstrate that this process is controlled by BCAA and a previously uncharacterized ORF YKL075C, which we refer to as actin, aging and nutrient modulator protein 1 (AAN1). Actin cables affect lifespan by supporting movement and inheritance of fitter mitochondria to daughter cells in yeast. Here the authors show that branched-chain amino acid (BCAA) levels affect actin cable stability and a role for YKL075C/AAN1 in control of BCAA metabolism and actin cable stability and function.
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26
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Pallapati AR, Prasad S, Roy I. Glycerol 3-phosphate dehydrogenase regulates heat shock response in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119238. [PMID: 35150808 DOI: 10.1016/j.bbamcr.2022.119238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/19/2022] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
The aim of this work was to identify elements of adaptive regulatory mechanism for basal level of yeast histone deacetylase Sir2. Heat shock response (HSR) was altered in the absence of the NAD-dependent glycerol 3-phosphate dehydrogenase (Gpd1). Increase in HSR was lower in ΔGpd1 cells than wild-type cells. An inverse correlation existed between Gpd1 and Sir2; Sir2-deleted cells showed higher expression of Gpd1 while deletion of Gpd1 led to higher expression of Sir2. In the absence of Gpd1, basal activity of Sir2 promoter was higher and was increased further upon heat shock, suggesting higher Sir2 levels. No interaction between Gpd1 and Sir2 was detected without or with heat shock using immunoprecipitation. The results show that Gpd1 regulates HSR in yeast cells and likely blocks its uncontrolled activation. As uncontrolled stress adversely affects the cellular adaptive response, Gpd1 may be a component of the cell's catalogue to ensure a balanced response to unmitigated thermal stress.
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Affiliation(s)
- Anusha Rani Pallapati
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Shivcharan Prasad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160062, India.
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Zhouravleva GA, Bondarev SA, Zemlyanko OM, Moskalenko SE. Role of Proteins Interacting with the eRF1 and eRF3 Release Factors in the Regulation of Translation and Prionization. Mol Biol 2022. [DOI: 10.1134/s0026893322010101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Differential Interactions of Molecular Chaperones and Yeast Prions. J Fungi (Basel) 2022; 8:jof8020122. [PMID: 35205876 PMCID: PMC8877571 DOI: 10.3390/jof8020122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
Baker’s yeast Saccharomyces cerevisiae is an important model organism that is applied to study various aspects of eukaryotic cell biology. Prions in yeast are self-perpetuating heritable protein aggregates that can be leveraged to study the interaction between the protein quality control (PQC) machinery and misfolded proteins. More than ten prions have been identified in yeast, of which the most studied ones include [PSI+], [URE3], and [PIN+]. While all of the major molecular chaperones have been implicated in propagation of yeast prions, many of these chaperones differentially impact propagation of different prions and/or prion variants. In this review, we summarize the current understanding of the life cycle of yeast prions and systematically review the effects of different chaperone proteins on their propagation. Our analysis clearly shows that Hsp40 proteins play a central role in prion propagation by determining the fate of prion seeds and other amyloids. Moreover, direct prion-chaperone interaction seems to be critically important for proper recruitment of all PQC components to the aggregate. Recent results also suggest that the cell asymmetry apparatus, cytoskeleton, and cell signaling all contribute to the complex network of prion interaction with the yeast cell.
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Kang PJ, Mullner R, Li H, Hansford D, Shen HW, Park HO. Upregulation of the Cdc42 GTPase limits the replicative lifespan of budding yeast. Mol Biol Cell 2022; 33:br5. [PMID: 35044837 PMCID: PMC9250358 DOI: 10.1091/mbc.e21-04-0208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Cdc42, a conserved Rho GTPase, plays a central role in polarity establishment in yeast and animals. Cell polarity is critical for asymmetric cell division, and asymmetric cell division underlies replicative aging of budding yeast. Yet how Cdc42 and other polarity factors impact life span is largely unknown. Here we show by live-cell imaging that the active Cdc42 level is sporadically elevated in wild type during repeated cell divisions but rarely in the long-lived bud8 deletion cells. We find a novel Bud8 localization with cytokinesis remnants, which also recruit Rga1, a Cdc42 GTPase activating protein. Genetic analyses and live-cell imaging suggest that Rga1 and Bud8 oppositely impact life span likely by modulating active Cdc42 levels. An rga1 mutant, which has a shorter life span, dies at the unbudded state with a defect in polarity establishment. Remarkably, Cdc42 accumulates in old cells, and its mild overexpression accelerates aging with frequent symmetric cell divisions, despite no harmful effects on young cells. Our findings implicate that the interplay among these positive and negative polarity factors limits the life span of budding yeast.
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Affiliation(s)
- Pil Jung Kang
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Rachel Mullner
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Haoyu Li
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Derek Hansford
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Han-Wei Shen
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Hay-Oak Park
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
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Kovacs M, Geltinger F, Verwanger T, Weiss R, Richter K, Rinnerthaler M. Lipid Droplets Protect Aging Mitochondria and Thus Promote Lifespan in Yeast Cells. Front Cell Dev Biol 2021; 9:774985. [PMID: 34869375 PMCID: PMC8640092 DOI: 10.3389/fcell.2021.774985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/26/2021] [Indexed: 12/20/2022] Open
Abstract
Besides their role as a storage for neutral lipids and sterols, there is increasing evidence that lipid droplets (LDs) are involved in cellular detoxification. LDs are in close contact to a broad variety of organelles where protein- and lipid exchange is mediated. Mitochondria as a main driver of the aging process produce reactive oxygen species (ROS), which damage several cellular components. LDs as highly dynamic organelles mediate a potent detoxification mechanism by taking up toxic lipids and proteins. A stimulation of LDs induced by the simultaneously overexpression of Lro1p and Dga1p (both encoding acyltransferases) prolongs the chronological as well as the replicative lifespan of yeast cells. The increased number of LDs reduces mitochondrial fragmentation as well as mitochondrial ROS production, both phenotypes that are signs of aging. Strains with an altered LD content or morphology as in the sei1∆ or lro1∆ mutant lead to a reduced replicative lifespan. In a yeast strain defective for the LON protease Pim1p, which showed an enhanced ROS production, increased doubling time and an altered mitochondrial morphology, a LRO1 overexpression resulted in a partially reversion of this "premature aging" phenotype.
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Affiliation(s)
| | | | | | | | | | - Mark Rinnerthaler
- Department of Biosciences, Paris-Lodron University Salzburg, Salzburg, Austria
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Belyavsky A, Petinati N, Drize N. Hematopoiesis during Ontogenesis, Adult Life, and Aging. Int J Mol Sci 2021; 22:ijms22179231. [PMID: 34502137 PMCID: PMC8430730 DOI: 10.3390/ijms22179231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/13/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
In the bone marrow of vertebrates, two types of stem cells coexist-hematopoietic stem cells (HSCs) and mesenchymal stem cells (MSCs). Hematopoiesis only occurs when these two stem cell types and their descendants interact. The descendants of HSCs supply the body with all the mature blood cells, while MSCs give rise to stromal cells that form a niche for HSCs and regulate the process of hematopoiesis. The studies of hematopoiesis were initially based on morphological observations, later extended by the use of physiological methods, and were subsequently augmented by massive application of sophisticated molecular techniques. The combination of these methods produced a wealth of new data on the organization and functional features of hematopoiesis in the ontogenesis of mammals and humans. This review summarizes the current views on hematopoiesis in mice and humans, discusses the development of blood elements and hematopoiesis in the embryo, and describes how the hematopoietic system works in the adult organism and how it changes during aging.
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Affiliation(s)
- Alexander Belyavsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | | | - Nina Drize
- National Research Center for Hematology, 125167 Moscow, Russia;
- Correspondence:
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Abstract
The evolutionary theory of aging has set the foundations for a comprehensive understanding of aging. The biology of aging has listed and described the "hallmarks of aging," i.e., cellular and molecular mechanisms involved in human aging. The present paper is the first to infer the order of appearance of the hallmarks of bilaterian and thereby human aging throughout evolution from their presence in progressively narrower clades. Its first result is that all organisms, even non-senescent, have to deal with at least one mechanism of aging - the progressive accumulation of misfolded or unstable proteins. Due to their cumulation, these mechanisms are called "layers of aging." A difference should be made between the first four layers of unicellular aging, present in some unicellular organisms and in all multicellular opisthokonts, that stem and strike "from the inside" of individual cells and span from increasingly abnormal protein folding to deregulated nutrient sensing, and the last four layers of metacellular aging, progressively appearing in metazoans, that strike the cells of a multicellular organism "from the outside," i.e., because of other cells, and span from transcriptional alterations to the disruption of intercellular communication. The evolution of metazoans and eumetazoans probably solved the problem of aging along with the problem of unicellular aging. However, metacellular aging originates in the mechanisms by which the effects of unicellular aging are kept under control - e.g., the exhaustion of stem cells that contribute to replace damaged somatic cells. In bilaterians, additional functions have taken a toll on generally useless potentially limited lifespan to increase the fitness of organisms at the price of a progressively less efficient containment of the damage of unicellular aging. In the end, this picture suggests that geroscience should be more efficient in targeting conditions of metacellular aging rather than unicellular aging itself.
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Affiliation(s)
- Maël Lemoine
- CNRS, ImmunoConcEpT, UMR 5164, Univ. Bordeaux, Bordeaux, France
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Miranda VPN, Coimbra DR, Bastos RR, Miranda Júnior MV, Amorim PRDS. Use of latent class analysis as a method of assessing the physical activity level, sedentary behavior and nutritional habit in the adolescents' lifestyle: A scoping review. PLoS One 2021; 16:e0256069. [PMID: 34411143 PMCID: PMC8376087 DOI: 10.1371/journal.pone.0256069] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 07/29/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Currently, adolescents' lifestyle is commonly characterized by physical inactivity, sedentary behavior, and inappropriate eating habits in general. A person-oriented approach as Latent Class Analysis (LCA) can offer more insight than a variable-centered approach when investigating lifestyle practices, habits, and behaviors of adolescent population. OBJECTIVE The aim of the present study was to assess which variables are mostly used to represent the physical activity level, sedentary behavior SB) and nutritional habit in the adolescents' lifestyle in studies that used the LCA. DESIGN Scoping review. METHODS The study was a performed in accordance with the proposed criteria for systematic reviews and meta-analyses-Preferred Reporting Items for Systematic Reviews and Meta-Analyses and registered in PROSPERO (CRD42018108444). The original articles were searched in MEDLINE/PubMed, Scopus, ScienceDirect, Web of Science, PsycINFO, and SPORTdiscus. The Quality Assessment Tool analyzed the risk of bias of the included studies. RESULTS 30 original articles were selected. The physical activity level (28 studies), SB and nutritional habits (18 studies) were the most common variable used to evaluate the adolescent's lifestyle by LCA model. Specifically, physical inactivity and high SB were the manifest variables with higher frequency in the negative latent classes (LCs) in adolescent girls. On the other hand, physical exercises and sports were activities more commonly labeled as positive LCs. CONCLUSIONS The LCA models of the most of selected studies showed that physical inactivity, high SB were the most common in the LCs with negative characteristics of the adolescents' lifestyle. Better understanding the results of analyzes of clusters of multivariate behaviors such as the LCA can help to create more effective strategies that can make the lifestyle of adolescents healthier.
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Affiliation(s)
- Valter Paulo Neves Miranda
- Department of Physical Education, Federal University of Viçosa, Minas Gerais, Brazil
- Department of Sports Science and Clinic Hospital (EBSERH), Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Danilo Reis Coimbra
- Department of Physical Education, Federal University of Juiz de Fora / Campus Governador Valadares, Governador Valadares, Minas Gerais, Brazil
| | - Ronaldo Rocha Bastos
- Department of Statistics, Geo-Referenced Information Lab (LINGE), Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Márcio Vidigal Miranda Júnior
- School of Physical Education, Physiotherapy and Occupational Therapy, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Nakazawa N, Fukuda M, Ashizaki M, Shibata Y, Takahashi K. Hsp104 contributes to freeze-thaw tolerance by maintaining proteasomal activity in a spore clone isolated from Shirakami kodama yeast. J GEN APPL MICROBIOL 2021; 67:170-178. [PMID: 34148914 DOI: 10.2323/jgam.2020.11.002] [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] [Indexed: 11/03/2022]
Abstract
The supply of oven-fresh bakery products to consumers has been improved by frozen dough technology; however, freeze-thaw stress decreases the activity of yeast cells. To breed better baker's yeasts for frozen dough, it is important to understand the factors affecting freeze-thaw stress tolerance in baker's yeast. We analyzed the stress response in IB1411, a spore clone from Saccharomyces cerevisiae Shirakami kodama yeast, with an exceptionally high tolerance to freeze-thaw stress. Genes encoding trehalose-6-phosphate synthase (TPS1), catalase (CTT1), and disaggregase (HSP104) were highly expressed in IB1411 cells even under conditions of non-stress. The expression of Hsp104 protein was also higher in IB1411 cells even under non-stress conditions. Deletion of HSP104 (hsp104Δ) in IB1411 cells reduced the activity of the ubiquitin-proteasome system (UPS). By monitoring the accumulation of aggregated proteins using the ΔssCPY*-GFP fusion protein under freeze-thaw stress or treatment with proteasomal inhibitor, we found that IB1411 cells resolved aggregated proteins faster than the hsp104Δ strain. Thus, Hsp104 seems to contribute to freeze-thaw tolerance by maintaining UPS activity via the disaggregation of aggregated proteins. Lastly, we found that the IB1411 cells maintained high leavening ability in frozen dough as compared with the parental strain, Shirakami kodama yeast, and thus will be useful for making bread.
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Affiliation(s)
- Nobushige Nakazawa
- Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University
| | - Mami Fukuda
- Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University
| | - Mizuki Ashizaki
- Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University
| | - Yukari Shibata
- Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University
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Kim D, Kim S, Na AY, Sohn CH, Lee S, Lee HS. Identification of Decrease in TRiC Proteins as Novel Targets of Alpha-Amanitin-Derived Hepatotoxicity by Comparative Proteomic Analysis In Vitro. Toxins (Basel) 2021; 13:toxins13030197. [PMID: 33803263 PMCID: PMC7999322 DOI: 10.3390/toxins13030197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 11/30/2022] Open
Abstract
Alpha-amanitin (α-AMA) is a cyclic peptide and one of the most lethal mushroom amatoxins found in Amanita phalloides. α-AMA is known to cause hepatotoxicity through RNA polymerase II inhibition, which acts in RNA and DNA translocation. To investigate the toxic signature of α-AMA beyond known mechanisms, we used quantitative nanoflow liquid chromatography–tandem mass spectrometry analysis coupled with tandem mass tag labeling to examine proteome dynamics in Huh-7 human hepatoma cells treated with toxic concentrations of α-AMA. Among the 1828 proteins identified, we quantified 1563 proteins, which revealed that four subunits in the T-complex protein 1-ring complex protein decreased depending on the α-AMA concentration. We conducted bioinformatics analyses of the quantified proteins to characterize the toxic signature of α-AMA in hepatoma cells. This is the first report of global changes in proteome abundance with variations in α-AMA concentration, and our findings suggest a novel molecular regulation mechanism for hepatotoxicity.
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Affiliation(s)
- Doeun Kim
- BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (D.K.); (A.-Y.N.)
| | - Sunjoo Kim
- BK21 Four-Sponsored Advanced Program for SmartPharma Leaders, College of Pharmacy, The Catholic University of Korea, Bucheon 14662, Korea;
| | - Ann-Yae Na
- BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (D.K.); (A.-Y.N.)
| | - Chang Hwan Sohn
- Department of Emergency Medicine, Asan Medical Center, College of Medicine, University of Ulsan, Seoul 05505, Korea;
| | - Sangkyu Lee
- BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (D.K.); (A.-Y.N.)
- Correspondence: (S.L.); (H.S.L.); Tel.: +82-53-950-8571 (S.L.); +82-2-2164-4061 (H.S.L.)
| | - Hye Suk Lee
- BK21 Four-Sponsored Advanced Program for SmartPharma Leaders, College of Pharmacy, The Catholic University of Korea, Bucheon 14662, Korea;
- Correspondence: (S.L.); (H.S.L.); Tel.: +82-53-950-8571 (S.L.); +82-2-2164-4061 (H.S.L.)
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36
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Yeasts as Complementary Model Systems for the Study of the Pathological Repercussions of Enhanced Synphilin-1 Glycation and Oxidation. Int J Mol Sci 2021; 22:ijms22041677. [PMID: 33562355 PMCID: PMC7915245 DOI: 10.3390/ijms22041677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 01/22/2023] Open
Abstract
Synphilin-1 has previously been identified as an interaction partner of α-Synuclein (αSyn), a primary constituent of neurodegenerative disease-linked Lewy bodies. In this study, the repercussions of a disrupted glyoxalase system and aldose reductase function on Synphilin-1 inclusion formation characteristics and cell growth were investigated. To this end, either fluorescent dsRed-tagged or non-tagged human SNCAIP, which encodes the Synphilin-1 protein, was expressed in Saccharomyces cerevisiae and Schizosaccharomyces pombe yeast strains devoid of enzymes Glo1, Glo2, and Gre3. Presented data shows that lack of Glo2 and Gre3 activity in S. cerevisiae increases the formation of large Synphilin-1 inclusions. This correlates with enhanced oxidative stress levels and an inhibitory effect on exponential growth, which is most likely caused by deregulation of autophagic degradation capacity, due to excessive Synphilin-1 aggresome build-up. These findings illustrate the detrimental impact of increased oxidation and glycation on Synphilin-1 inclusion formation. Similarly, polar-localised inclusions were observed in wild-type S. pombe cells and strains deleted for either glo1+ or glo2+. Contrary to S. cerevisiae, however, no growth defects were observed upon expression of SNCAIP. Altogether, our findings show the relevance of yeasts, especially S. cerevisiae, as complementary models to unravel mechanisms contributing to Synphilin-1 pathology in the context of neurodegenerative diseases.
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37
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Extracellular Vesicles-Encapsulated Yeast Prions and What They Can Tell Us about the Physical Nature of Propagons. Int J Mol Sci 2020; 22:ijms22010090. [PMID: 33374854 PMCID: PMC7794690 DOI: 10.3390/ijms22010090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/14/2020] [Accepted: 12/20/2020] [Indexed: 12/25/2022] Open
Abstract
The yeast Saccharomyces cerevisiae hosts an ensemble of protein-based heritable traits, most of which result from the conversion of structurally and functionally diverse cytoplasmic proteins into prion forms. Among these, [PSI+], [URE3] and [PIN+] are the most well-documented prions and arise from the assembly of Sup35p, Ure2p and Rnq1p, respectively, into insoluble fibrillar assemblies. Yeast prions propagate by molecular chaperone-mediated fragmentation of these aggregates, which generates small self-templating seeds, or propagons. The exact molecular nature of propagons and how they are faithfully transmitted from mother to daughter cells despite spatial protein quality control are not fully understood. In [PSI+] cells, Sup35p forms detergent-resistant assemblies detectable on agarose gels under semi-denaturant conditions and cytosolic fluorescent puncta when the protein is fused to green fluorescent protein (GFP); yet, these macroscopic manifestations of [PSI+] do not fully correlate with the infectivity measured during growth by the mean of protein infection assays. We also discovered that significant amounts of infectious Sup35p particles are exported via extracellular (EV) and periplasmic (PV) vesicles in a growth phase and glucose-dependent manner. In the present review, I discuss how these vesicles may be a source of actual propagons and a suitable vehicle for their transmission to the bud.
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38
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Nuckolls NL, Mok AC, Lange JJ, Yi K, Kandola TS, Hunn AM, McCroskey S, Snyder JL, Bravo Núñez MA, McClain M, McKinney SA, Wood C, Halfmann R, Zanders SE. The wtf4 meiotic driver utilizes controlled protein aggregation to generate selective cell death. eLife 2020; 9:e55694. [PMID: 33108274 PMCID: PMC7591262 DOI: 10.7554/elife.55694] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 09/16/2020] [Indexed: 12/19/2022] Open
Abstract
Meiotic drivers are parasitic loci that force their own transmission into greater than half of the offspring of a heterozygote. Many drivers have been identified, but their molecular mechanisms are largely unknown. The wtf4 gene is a meiotic driver in Schizosaccharomyces pombe that uses a poison-antidote mechanism to selectively kill meiotic products (spores) that do not inherit wtf4. Here, we show that the Wtf4 proteins can function outside of gametogenesis and in a distantly related species, Saccharomyces cerevisiae. The Wtf4poison protein forms dispersed, toxic aggregates. The Wtf4antidote can co-assemble with the Wtf4poison and promote its trafficking to vacuoles. We show that neutralization of the Wtf4poison requires both co-assembly with the Wtf4antidote and aggregate trafficking, as mutations that disrupt either of these processes result in cell death in the presence of the Wtf4 proteins. This work reveals that wtf parasites can exploit protein aggregate management pathways to selectively destroy spores.
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Affiliation(s)
| | - Anthony C Mok
- Stowers Institute for Medical ResearchKansas CityUnited States
- University of Missouri-Kansas CityKansas CityUnited States
| | - Jeffrey J Lange
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Kexi Yi
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Tejbir S Kandola
- Stowers Institute for Medical ResearchKansas CityUnited States
- Open UniversityMilton KeynesUnited Kingdom
| | - Andrew M Hunn
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Scott McCroskey
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Julia L Snyder
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | | | - Sean A McKinney
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | - Randal Halfmann
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Molecular and Integrative Physiology, University of Kansas Medical CenterKansas CityUnited States
| | - Sarah E Zanders
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Molecular and Integrative Physiology, University of Kansas Medical CenterKansas CityUnited States
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Schnitzer B, Borgqvist J, Cvijovic M. The synergy of damage repair and retention promotes rejuvenation and prolongs healthy lifespans in cell lineages. PLoS Comput Biol 2020; 16:e1008314. [PMID: 33044956 PMCID: PMC7598927 DOI: 10.1371/journal.pcbi.1008314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/30/2020] [Accepted: 09/04/2020] [Indexed: 01/29/2023] Open
Abstract
Damaged proteins are inherited asymmetrically during cell division in the yeast Saccharomyces cerevisiae, such that most damage is retained within the mother cell. The consequence is an ageing mother and a rejuvenated daughter cell with full replicative potential. Daughters of old and damaged mothers are however born with increasing levels of damage resulting in lowered replicative lifespans. Remarkably, these prematurely old daughters can give rise to rejuvenated cells with low damage levels and recovered lifespans, called second-degree rejuvenation. We aimed to investigate how damage repair and retention together can promote rejuvenation and at the same time ensure low damage levels in mother cells, reflected in longer health spans. We developed a dynamic model for damage accumulation over successive divisions in individual cells as part of a dynamically growing cell lineage. With detailed knowledge about single-cell dynamics and relationships between all cells in the lineage, we can infer how individual damage repair and retention strategies affect the propagation of damage in the population. We show that damage retention lowers damage levels in the population by reducing the variability across the lineage, and results in larger population sizes. Repairing damage efficiently in early life, as opposed to investing in repair when damage has already accumulated, counteracts accelerated ageing caused by damage retention. It prolongs the health span of individual cells which are moreover less prone to stress. In combination, damage retention and early investment in repair are beneficial for healthy ageing in yeast cell populations.
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Affiliation(s)
- Barbara Schnitzer
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Johannes Borgqvist
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
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40
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Babazadeh R, Ahmadpour D, Jia S, Hao X, Widlund P, Schneider K, Eisele F, Edo LD, Smits GJ, Liu B, Nystrom T. Syntaxin 5 Is Required for the Formation and Clearance of Protein Inclusions during Proteostatic Stress. Cell Rep 2020; 28:2096-2110.e8. [PMID: 31433985 DOI: 10.1016/j.celrep.2019.07.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 06/14/2019] [Accepted: 07/17/2019] [Indexed: 12/12/2022] Open
Abstract
Spatial sorting to discrete quality control sites in the cell is a process harnessing the toxicity of aberrant proteins. We show that the yeast t-snare phosphoprotein syntaxin5 (Sed5) acts as a key factor in mitigating proteotoxicity and the spatial deposition and clearance of IPOD (insoluble protein deposit) inclusions associates with the disaggregase Hsp104. Sed5 phosphorylation promotes dynamic movement of COPII-associated Hsp104 and boosts disaggregation by favoring anterograde ER-to-Golgi trafficking. Hsp104-associated aggregates co-localize with Sed5 as well as components of the ER, trans Golgi network, and endocytic vesicles, transiently during proteostatic stress, explaining mechanistically how misfolded and aggregated proteins formed at the vicinity of the ER can hitchhike toward vacuolar IPOD sites. Many inclusions become associated with mitochondria in a HOPS/vCLAMP-dependent manner and co-localize with Vps39 (HOPS/vCLAMP) and Vps13, which are proteins providing contacts between vacuole and mitochondria. Both Vps39 and Vps13 are required also for efficient Sed5-dependent clearance of aggregates.
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Affiliation(s)
- Roja Babazadeh
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Doryaneh Ahmadpour
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Song Jia
- School of Life Science, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin 150030, China
| | - Xinxin Hao
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Per Widlund
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Kara Schneider
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Frederik Eisele
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Laura Dolz Edo
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1090, the Netherlands
| | - Gertien J Smits
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1090, the Netherlands
| | - Beidong Liu
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Thomas Nystrom
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden.
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Xie Y, Loh ZY, Xue J, Zhou F, Sun J, Qiao Z, Jin S, Deng Y, Li H, Wang Y, Lu L, Gao Y, Miao Y. Orchestrated actin nucleation by the Candida albicans polarisome complex enables filamentous growth. J Biol Chem 2020; 295:14840-14854. [PMID: 32848016 DOI: 10.1074/jbc.ra120.013890] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/09/2020] [Indexed: 12/29/2022] Open
Abstract
Candida albicans is a dimorphic fungus that converts from a yeast form to a hyphae form during infection. This switch requires the formation of actin cable to coordinate polarized cell growth. It's known that nucleation of this cable requires a multiprotein complex localized at the tip called the polarisome, but the mechanisms underpinning this process were unclear. Here, we found that C. albicans Aip5, a homolog of polarisome component ScAip5 in Saccharomyces cerevisiae that nucleates actin polymerization and synergizes with the formin ScBni1, regulates actin assembly and hyphae growth synergistically with other polarisome proteins Bni1, Bud6, and Spa2. The C terminus of Aip5 binds directly to G-actin, Bni1, and the C-terminal of Bud6, which form the core of the nucleation complex to polymerize F-actin. Based on insights from structural biology and molecular dynamic simulations, we propose a possible complex conformation of the actin nucleation core, which provides cooperative positioning and supports the synergistic actin nucleation activity of a tri-protein complex Bni1-Bud6-Aip5. Together with known interactions of Bni1 with Bud6 and Aip5 in S. cerevisiae, our findings unravel molecular mechanisms of C. albicans by which the tri-protein complex coordinates the actin nucleation in actin cable assembly and hyphal growth, which is likely a conserved mechanism in different filamentous fungi and yeast.
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Affiliation(s)
- Ying Xie
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Zhi Yang Loh
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jiao Xue
- School of Biological Sciences, Nanyang Technological University, Singapore; College of Life Science and Technology, Jinan University, Guangzhou, China; The College of Life Sciences, Northwest University, Xi'an, China
| | - Feng Zhou
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jialin Sun
- School of Biological Sciences, Nanyang Technological University, Singapore; Institute of Molecular and Cell Biology, A*STAR, Singapore
| | - Zhu Qiao
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Shengyang Jin
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Yinyue Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Hongye Li
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Yue Wang
- Institute of Molecular and Cell Biology, A*STAR, Singapore
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Yonggui Gao
- School of Biological Sciences, Nanyang Technological University, Singapore; Institute of Molecular and Cell Biology, A*STAR, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Nanyang Drive, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore.
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42
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Aggregation and Prion-Inducing Properties of the G-Protein Gamma Subunit Ste18 are Regulated by Membrane Association. Int J Mol Sci 2020; 21:ijms21145038. [PMID: 32708832 PMCID: PMC7403958 DOI: 10.3390/ijms21145038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/03/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
Yeast prions and mnemons are respectively transmissible and non-transmissible self-perpetuating protein assemblies, frequently based on cross-β ordered detergent-resistant aggregates (amyloids). Prions cause devastating diseases in mammals and control heritable traits in yeast. It was shown that the de novo formation of the prion form [PSI+] of yeast release factor Sup35 is facilitated by aggregates of other proteins. Here we explore the mechanism of the promotion of [PSI+] formation by Ste18, an evolutionarily conserved gamma subunit of a G-protein coupled receptor, a key player in responses to extracellular stimuli. Ste18 forms detergent-resistant aggregates, some of which are colocalized with de novo generated Sup35 aggregates. Membrane association of Ste18 is required for both Ste18 aggregation and [PSI+] induction, while functional interactions involved in signal transduction are not essential for these processes. This emphasizes the significance of a specific location for the nucleation of protein aggregation. In contrast to typical prions, Ste18 aggregates do not show a pattern of heritability. Our finding that Ste18 levels are regulated by the ubiquitin-proteasome system, in conjunction with the previously reported increase in Ste18 levels upon the exposure to mating pheromone, suggests that the concentration-dependent Ste18 aggregation may mediate a mnemon-like response to physiological stimuli.
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43
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Moreno DF, Aldea M. Proteostatic stress as a nodal hallmark of replicative aging. Exp Cell Res 2020; 394:112163. [PMID: 32640194 DOI: 10.1016/j.yexcr.2020.112163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 11/30/2022]
Abstract
Aging is characterized by the progressive decline of physiology at the cell, tissue and organism level, leading to an increased risk of mortality. Proteotoxic stress, mitochondrial dysfunction and genomic instability are considered major universal drivers of cell aging, and accumulating evidence establishes clear biunivocal relationships among these key hallmarks. In this regard, the finite lifespan of the budding yeast, together with the extensive armamentarium of available analytical tools, has made this single cell eukaryote a key model to study aging at molecular and cellular levels. Here we review the current data that link proteostasis to cell cycle progression in the budding yeast, focusing on senescence as an inherent phenotype displayed by aged cells. Recent advances in high-throughput systems to study yeast mother cells while they replicate are providing crucial information on aging-related processes and their temporal interdependencies at a systems level. In our view, the available data point to the existence of multiple feedback mechanisms among the major causal factors of aging, which would converge into the loss of proteostasis as a nodal driver of cell senescence and death.
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Affiliation(s)
- David F Moreno
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028, Barcelona, Catalonia, Spain
| | - Martí Aldea
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028, Barcelona, Catalonia, Spain.
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44
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Wickner RB, Edskes HK, Son M, Wu S, Niznikiewicz M. How Do Yeast Cells Contend with Prions? Int J Mol Sci 2020; 21:ijms21134742. [PMID: 32635197 PMCID: PMC7369894 DOI: 10.3390/ijms21134742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 06/26/2020] [Accepted: 06/30/2020] [Indexed: 12/11/2022] Open
Abstract
Infectious proteins (prions) include an array of human (mammalian) and yeast amyloid diseases in which a protein or peptide forms a linear β-sheet-rich filament, at least one functional amyloid prion, and two functional infectious proteins unrelated to amyloid. In Saccharomyces cerevisiae, at least eight anti-prion systems deal with pathogenic amyloid yeast prions by (1) blocking their generation (Ssb1,2, Ssz1, Zuo1), (2) curing most variants as they arise (Btn2, Cur1, Hsp104, Upf1,2,3, Siw14), and (3) limiting the pathogenicity of variants that do arise and propagate (Sis1, Lug1). Known mechanisms include facilitating proper folding of the prion protein (Ssb1,2, Ssz1, Zuo1), producing highly asymmetric segregation of prion filaments in mitosis (Btn2, Hsp104), competing with the amyloid filaments for prion protein monomers (Upf1,2,3), and regulation of levels of inositol polyphosphates (Siw14). It is hoped that the discovery of yeast anti-prion systems and elucidation of their mechanisms will facilitate finding analogous or homologous systems in humans, whose manipulation may be useful in treatment.
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Abstract
Exposure to arsenic in contaminated drinking water is a worldwide public health problem that affects more than 200 million people. Protein quality control constitutes an evolutionarily conserved mechanism for promoting proper folding of proteins, refolding of misfolded proteins, and removal of aggregated proteins, thereby maintaining homeostasis of the proteome (i.e., proteostasis). Accumulating lines of evidence from epidemiological and laboratory studies revealed that chronic exposure to inorganic arsenic species can elicit proteinopathies that contribute to neurodegenerative disorders, cancer, and type II diabetes. Here, we review the effects of arsenic exposure on perturbing various elements of the proteostasis network, including mitochondrial homeostasis, molecular chaperones, inflammatory response, ubiquitin-proteasome system, autophagy, as well as asymmetric segregation and axonal transport of misfolded proteins. We also discuss arsenic-induced disruptions of post-translational modifications of proteins, for example, ubiquitination, and their implications in proteostasis. Together, studies in the past few decades support that disruption of protein quality control may constitute an important mechanism underlying the arsenic-induced toxicity.
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46
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Liu Q, Zhu X, Lindström M, Shi Y, Zheng J, Hao X, Gustafsson CM, Liu B. Yeast mismatch repair components are required for stable inheritance of gene silencing. PLoS Genet 2020; 16:e1008798. [PMID: 32469861 PMCID: PMC7286534 DOI: 10.1371/journal.pgen.1008798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 06/10/2020] [Accepted: 04/26/2020] [Indexed: 11/19/2022] Open
Abstract
Alterations in epigenetic silencing have been associated with ageing and tumour formation. Although substantial efforts have been made towards understanding the mechanisms of gene silencing, novel regulators in this process remain to be identified. To systematically search for components governing epigenetic silencing, we developed a genome-wide silencing screen for yeast (Saccharomyces cerevisiae) silent mating type locus HMR. Unexpectedly, the screen identified the mismatch repair (MMR) components Pms1, Mlh1, and Msh2 as being required for silencing at this locus. We further found that the identified genes were also required for proper silencing in telomeres. More intriguingly, the MMR mutants caused a redistribution of Sir2 deacetylase, from silent mating type loci and telomeres to rDNA regions. As a consequence, acetylation levels at histone positions H3K14, H3K56, and H4K16 were increased at silent mating type loci and telomeres but were decreased in rDNA regions. Moreover, knockdown of MMR components in human HEK293T cells increased subtelomeric DUX4 gene expression. Our work reveals that MMR components are required for stable inheritance of gene silencing patterns and establishes a link between the MMR machinery and the control of epigenetic silencing.
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Affiliation(s)
- Qian Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan, Goteborg, Sweden
| | - Xuefeng Zhu
- Institute of Biomedicine, University of Gothenburg, Goteborg, Sweden
- * E-mail: (XZ); (BL)
| | - Michelle Lindström
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan, Goteborg, Sweden
| | - Yonghong Shi
- Institute of Biomedicine, University of Gothenburg, Goteborg, Sweden
| | - Ju Zheng
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan, Goteborg, Sweden
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Xinxin Hao
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan, Goteborg, Sweden
| | | | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan, Goteborg, Sweden
- Center for Large-scale cell-based screening, Faculty of Science, University of Gothenburg, Medicinaregatan, Goteborg, Sweden
- * E-mail: (XZ); (BL)
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Kabani M, Pilard M, Melki R. Glucose availability dictates the export of the soluble and prion forms of Sup35p via periplasmic or extracellular vesicles. Mol Microbiol 2020; 114:322-332. [PMID: 32339313 DOI: 10.1111/mmi.14515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/25/2020] [Accepted: 04/06/2020] [Indexed: 11/28/2022]
Abstract
The yeast [PSI+ ] prion originates from the self-perpetuating transmissible aggregates of the translation termination factor Sup35p. We previously showed that infectious Sup35p particles are exported outside the cells via extracellular vesicles (EV). This finding suggested a function for EV in the vertical and horizontal transmission of yeast prions. Here we report a significant export of Sup35p within periplasmic vesicles (PV) upon glucose starvation. We show that PV are up to three orders of magnitude more abundant than EV. However, PV and EV are different in terms of size and protein content, and their export is oppositely regulated by glucose availability in the growth medium. Overall, our work suggests that the export of prion particles to both the periplasm and the extracellular space needs to be considered to address the physiological consequences of vesicle-mediated yeast prions trafficking.
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Affiliation(s)
- Mehdi Kabani
- Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale (DRF), Laboratoire des Maladies Neurodégénératives, Centre National de la Recherche Scientifique (CNRS), Fontenay-aux-Roses, France
| | - Marion Pilard
- Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale (DRF), Laboratoire des Maladies Neurodégénératives, Centre National de la Recherche Scientifique (CNRS), Fontenay-aux-Roses, France
| | - Ronald Melki
- Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale (DRF), Laboratoire des Maladies Neurodégénératives, Centre National de la Recherche Scientifique (CNRS), Fontenay-aux-Roses, France
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48
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Morita A, Hamoh T, Perona Martinez FP, Chipaux M, Sigaeva A, Mignon C, van der Laan KJ, Hochstetter A, Schirhagl R. The Fate of Lipid-Coated and Uncoated Fluorescent Nanodiamonds during Cell Division in Yeast. NANOMATERIALS 2020; 10:nano10030516. [PMID: 32178407 PMCID: PMC7153471 DOI: 10.3390/nano10030516] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 11/18/2022]
Abstract
Fluorescent nanodiamonds are frequently used as biolabels. They have also recently been established for magnetic resonance and temperature sensing at the nanoscale level. To properly use them in cell biology, we first have to understand their intracellular fate. Here, we investigated, for the first time, what happens to diamond particles during and after cell division in yeast (Saccharomyces cerevisiae) cells. More concretely, our goal was to answer the question of whether nanodiamonds remain in the mother cells or end up in the daughter cells. Yeast cells are widely used as a model organism in aging and biotechnology research, and they are particularly interesting because their asymmetric cell division leads to morphologically different mother and daughter cells. Although yeast cells have a mechanism to prevent potentially harmful substances from entering the daughter cells, we found an increased number of diamond particles in daughter cells. Additionally, we found substantial excretion of particles, which has not been reported for mammalian cells. We also investigated what types of movement diamond particles undergo in the cells. Finally, we also compared bare nanodiamonds with lipid-coated diamonds, and there were no significant differences in respect to either movement or intracellular fate.
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Affiliation(s)
- Aryan Morita
- Department of Biomedical Engineering, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; (A.M.); (T.H.); (F.P.P.M.); (M.C.); (A.S.); (C.M.); (K.J.v.d.L.)
- Department of Dental Biomedical Sciences, Faculty of Dentistry, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Thamir Hamoh
- Department of Biomedical Engineering, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; (A.M.); (T.H.); (F.P.P.M.); (M.C.); (A.S.); (C.M.); (K.J.v.d.L.)
| | - Felipe P. Perona Martinez
- Department of Biomedical Engineering, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; (A.M.); (T.H.); (F.P.P.M.); (M.C.); (A.S.); (C.M.); (K.J.v.d.L.)
| | - Mayeul Chipaux
- Department of Biomedical Engineering, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; (A.M.); (T.H.); (F.P.P.M.); (M.C.); (A.S.); (C.M.); (K.J.v.d.L.)
| | - Alina Sigaeva
- Department of Biomedical Engineering, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; (A.M.); (T.H.); (F.P.P.M.); (M.C.); (A.S.); (C.M.); (K.J.v.d.L.)
| | - Charles Mignon
- Department of Biomedical Engineering, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; (A.M.); (T.H.); (F.P.P.M.); (M.C.); (A.S.); (C.M.); (K.J.v.d.L.)
| | - Kiran J. van der Laan
- Department of Biomedical Engineering, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; (A.M.); (T.H.); (F.P.P.M.); (M.C.); (A.S.); (C.M.); (K.J.v.d.L.)
| | - Axel Hochstetter
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, UK;
| | - Romana Schirhagl
- Department of Biomedical Engineering, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; (A.M.); (T.H.); (F.P.P.M.); (M.C.); (A.S.); (C.M.); (K.J.v.d.L.)
- Correspondence:
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Abstract
Ageing is a major risk factor for the development of many diseases, prominently including neurodegenerative disorders such as Alzheimer disease and Parkinson disease. A hallmark of many age-related diseases is the dysfunction in protein homeostasis (proteostasis), leading to the accumulation of protein aggregates. In healthy cells, a complex proteostasis network, comprising molecular chaperones and proteolytic machineries and their regulators, operates to ensure the maintenance of proteostasis. These factors coordinate protein synthesis with polypeptide folding, the conservation of protein conformation and protein degradation. However, sustaining proteome balance is a challenging task in the face of various external and endogenous stresses that accumulate during ageing. These stresses lead to the decline of proteostasis network capacity and proteome integrity. The resulting accumulation of misfolded and aggregated proteins affects, in particular, postmitotic cell types such as neurons, manifesting in disease. Recent analyses of proteome-wide changes that occur during ageing inform strategies to improve proteostasis. The possibilities of pharmacological augmentation of the capacity of proteostasis networks hold great promise for delaying the onset of age-related pathologies associated with proteome deterioration and for extending healthspan.
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50
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Habib N, Ali Q, Ali S, Javed MT, Zulqurnain Haider M, Perveen R, Shahid MR, Rizwan M, Abdel-Daim MM, Elkelish A, Bin-Jumah M. Use of Nitric Oxide and Hydrogen Peroxide for Better Yield of Wheat ( Triticum aestivum L.) under Water Deficit Conditions: Growth, Osmoregulation, and Antioxidative Defense Mechanism. PLANTS (BASEL, SWITZERLAND) 2020; 9:E285. [PMID: 32098385 PMCID: PMC7076392 DOI: 10.3390/plants9020285] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/15/2020] [Accepted: 02/15/2020] [Indexed: 12/12/2022]
Abstract
The present experiment was carried out to study the influences of exogenously-applied nitric oxide (NO) donor sodium nitroprusside (SNP) and hydrogen peroxide (H2O2) as seed primers on growth and yield in relation with different physio-biochemical parameters, antioxidant activities, and osmolyte accumulation in wheat plants grown under control (100% field capacity) and water stress (60% field capacity) conditions. During soaking, the seeds were covered and kept in completely dark. Drought stress markedly reduced the plant growth, grain yield, leaf photosynthetic pigments, total phenolic content (TPC), total soluble proteins (TSP), leaf water potential (Ψw), leaf turgor potential (Ψp), osmotic potential (Ψs), and leaf relative water content (LRWC), while it increased the activities of enzymatic antioxidants and the accumulation of leaf ascorbic acid (AsA), proline (Pro), glycine betaine (GB), malondialdehyde (MDA), and H2O2. However, seed priming with SNP and H2O2 alone and in combination mitigated the deleterious effects of water stress on growth and yield by improving the Ψw, Ψs, Ψp, photosynthetic pigments, osmolytes accumulation (GB and Pro), TSP, and the antioxidative defense mechanism. Furthermore, the application of NO and H2O2 as seed primers also reduced the accumulation of H2O2 and MDA contents. The effectiveness was treatment-specific and the combined application was also found to be effective. The results revealed that exogenous application of NO and H2O2 was effective in increasing the tolerance of wheat plants under drought stress in terms of growth and grain yield by regulating plant-water relations, the antioxidative defense mechanism, and accumulation of osmolytes, and by reducing the membrane lipid peroxidation.
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Affiliation(s)
- Noman Habib
- Department of Botany, Government College University, Faisalabad 38000, Pakistan
| | - Qasim Ali
- Department of Botany, Government College University, Faisalabad 38000, Pakistan
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University, Faisalabad 38000, Pakistan
- Department of Biological Sciences and Technology, China Medical University, Taichung 40402, Taiwan
| | | | | | - Rashida Perveen
- Department of Physics, University of Agriculture, Faisalabad 38040, Pakistan
| | - Muhammad Rizwan Shahid
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Muhammad Rizwan
- Department of Environmental Sciences and Engineering, Government College University, Faisalabad 38000, Pakistan
| | - Mohamed M. Abdel-Daim
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Amr Elkelish
- Botany Department, Faculty of Science, Suez Canal University Ismailia, Ismailia 41522, Egypt;
| | - May Bin-Jumah
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11474, Saudi Arabia;
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