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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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2
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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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3
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Stephan OOH. Effects of environmental stress factors on the actin cytoskeleton of fungi and plants: Ionizing radiation and ROS. Cytoskeleton (Hoboken) 2023; 80:330-355. [PMID: 37066976 DOI: 10.1002/cm.21758] [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: 01/16/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 04/18/2023]
Abstract
Actin is an abundant and multifaceted protein in eukaryotic cells that has been detected in the cytoplasm as well as in the nucleus. In cooperation with numerous interacting accessory-proteins, monomeric actin (G-actin) polymerizes into microfilaments (F-actin) which constitute ubiquitous subcellular higher order structures. Considering the extensive spatial dimensions and multifunctionality of actin superarrays, the present study analyses the issue if and to what extent environmental stress factors, specifically ionizing radiation (IR) and reactive oxygen species (ROS), affect the cellular actin-entity. In that context, this review particularly surveys IR-response of fungi and plants. It examines in detail which actin-related cellular constituents and molecular pathways are influenced by IR and related ROS. This comprehensive survey concludes that the general integrity of the total cellular actin cytoskeleton is a requirement for IR-tolerance. Actin's functions in genome organization and nuclear events like chromatin remodeling, DNA-repair, and transcription play a key role. Beyond that, it is highly significant that the macromolecular cytoplasmic and cortical actin-frameworks are affected by IR as well. In response to IR, actin-filament bundling proteins (fimbrins) are required to stabilize cables or patches. In addition, the actin-associated factors mediating cellular polarity are essential for IR-survivability. Moreover, it is concluded that a cellular homeostasis system comprising ROS, ROS-scavengers, NADPH-oxidases, and the actin cytoskeleton plays an essential role here. Consequently, besides the actin-fraction which controls crucial genome-integrity, also the portion which facilitates orderly cellular transport and polarized growth has to be maintained in order to survive IR.
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Affiliation(s)
- Octavian O H Stephan
- Department of Biology, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Bavaria, 91058, Germany
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4
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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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5
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Mudoi KD, Gogoi B, Borah G, Hussain M, Tasfia T, Borah K, Lekhak H, Saikia SP. An assessment for in vitro propagation and genetic stability of Phoebe goalparensis Hutchinson, an endemic valuable timber tree of North East India. J Genet Eng Biotechnol 2023; 21:29. [PMID: 36897435 PMCID: PMC10006360 DOI: 10.1186/s43141-023-00487-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/01/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND Phoebe goalparensis is an endemic forest species of North East India that belongs to Lauraceae family. P. goalparensis is used as timbers yielding plants for commercial importance in the local furniture markets of North East India. A rapid in vitro micropropagation protocol was established by using apical and axillary shoot tips on Murashige and Skoog medium with varied concentrations of plant growth regulators. RESULTS In this study, 5.0 mg/l BAP augmented medium was chosen as the best for shoot multiplication of the plant. However, IBA (2.0 mg/l) was the most responsive for root induction. Moreover, 70% of root induction was recorded during rooting experiment and 80-85% survivability was observed during the acclimatization of this species. Clonal fidelity of P. goalparensis was determined with ISSR marker and it was observed that in vitro raised plantlets were polymonomorphic. CONCLUSION Hence, an efficient protocol with high proliferation and rooting was established for P. Goalparensis that could aid in massive propagation in future.
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Affiliation(s)
- Kalpataru Dutta Mudoi
- Agrotechnology and Rural Development Division (ARDD), CSIR-North East Institute of Science & Technology, Jorhat, Assam, 785006, India
| | - Barbi Gogoi
- Agrotechnology and Rural Development Division (ARDD), CSIR-North East Institute of Science & Technology, Jorhat, Assam, 785006, India
| | - Gitasree Borah
- Agrotechnology and Rural Development Division (ARDD), CSIR-North East Institute of Science & Technology, Jorhat, Assam, 785006, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Marine Hussain
- Agrotechnology and Rural Development Division (ARDD), CSIR-North East Institute of Science & Technology, Jorhat, Assam, 785006, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Tabassum Tasfia
- Agrotechnology and Rural Development Division (ARDD), CSIR-North East Institute of Science & Technology, Jorhat, Assam, 785006, India
| | - Krishnakhi Borah
- Agrotechnology and Rural Development Division (ARDD), CSIR-North East Institute of Science & Technology, Jorhat, Assam, 785006, India
| | - Himangshu Lekhak
- Agrotechnology and Rural Development Division (ARDD), CSIR-North East Institute of Science & Technology, Jorhat, Assam, 785006, India
| | - Siddhartha Proteem Saikia
- Agrotechnology and Rural Development Division (ARDD), CSIR-North East Institute of Science & Technology, Jorhat, Assam, 785006, India.
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6
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Actin dynamics in protein homeostasis. Biosci Rep 2022; 42:231720. [PMID: 36043949 PMCID: PMC9469105 DOI: 10.1042/bsr20210848] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Cell homeostasis is maintained in all organisms by the constant adjustment of cell constituents and organisation to account for environmental context. Fine-tuning of the optimal balance of proteins for the conditions, or protein homeostasis, is critical to maintaining cell homeostasis. Actin, a major constituent of the cytoskeleton, forms many different structures which are acutely sensitive to the cell environment. Furthermore, actin structures interact with and are critically important for the function and regulation of multiple factors involved with mRNA and protein production and degradation, and protein regulation. Altogether, actin is a key, if often overlooked, regulator of protein homeostasis across eukaryotes. In this review, we highlight these roles and how they are altered following cell stress, from mRNA transcription to protein degradation.
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7
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Dorweiler JE, Lyke DR, Lemoine NP, Guereca S, Buchholz HE, Legan ER, Radtke CM, Manogaran AL. Implications of the Actin Cytoskeleton on the Multi-Step Process of [PSI+] Prion Formation. Viruses 2022; 14:v14071581. [PMID: 35891561 PMCID: PMC9321047 DOI: 10.3390/v14071581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/27/2022] [Accepted: 07/02/2022] [Indexed: 11/23/2022] Open
Abstract
Yeast prions are self-perpetuating misfolded proteins that are infectious. In yeast, [PSI+] is the prion form of the Sup35 protein. While the study of [PSI+] has revealed important cellular mechanisms that contribute to prion propagation, the underlying cellular factors that influence prion formation are not well understood. Prion formation has been described as a multi-step process involving both the initial nucleation and growth of aggregates, followed by the subsequent transmission of prion particles to daughter cells. Prior evidence suggests that actin plays a role in this multi-step process, but actin’s precise role is unclear. Here, we investigate how actin influences the cell’s ability to manage newly formed visible aggregates and how actin influences the transmission of newly formed aggregates to future generations. At early steps, using 3D time-lapse microscopy, several actin mutants, and Markov modeling, we find that the movement of newly formed aggregates is random and actin independent. At later steps, our prion induction studies provide evidence that the transmission of newly formed prion particles to daughter cells is limited by the actin cytoskeletal network. We suspect that this limitation is because actin is used to possibly retain prion particles in the mother cell.
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Affiliation(s)
- Jane E. Dorweiler
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
| | - Douglas R. Lyke
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
| | - Nathan P. Lemoine
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI 53233, USA
| | - Samantha Guereca
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
| | - Hannah E. Buchholz
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
| | - Emily R. Legan
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
| | - Claire M. Radtke
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
| | - Anita L. Manogaran
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
- Correspondence:
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8
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Schnitzer B, Welkenhuysen N, Leake MC, Shashkova S, Cvijovic M. The effect of stress on biophysical characteristics of misfolded protein aggregates in living Saccharomyces cerevisiae cells. Exp Gerontol 2022; 162:111755. [PMID: 35240259 DOI: 10.1016/j.exger.2022.111755] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/11/2022] [Accepted: 02/24/2022] [Indexed: 11/28/2022]
Abstract
Aggregation of misfolded or damaged proteins is often attributed to numerous metabolic and neurodegenerative disorders. To reveal underlying mechanisms and cellular responses, it is crucial to investigate protein aggregate dynamics in cells. Here, we used super-resolution single-molecule microscopy to obtain biophysical characteristics of individual aggregates of a model misfolded protein ∆ssCPY* labelled with GFP. We demonstrated that oxidative and hyperosmotic stress lead to increased aggregate stoichiometries but not necessarily the total number of aggregates. Moreover, our data suggest the importance of the thioredoxin peroxidase Tsa1 for the controlled sequestering and clearance of aggregates upon both conditions. Our work provides novel insights into the understanding of the cellular response to stress via revealing the dynamical properties of stress-induced protein aggregates.
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Affiliation(s)
- Barbara Schnitzer
- Department of Mathematical Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden; Department of Mathematical Sciences, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Niek Welkenhuysen
- Department of Mathematical Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden; Department of Mathematical Sciences, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Mark C Leake
- Department of Physics, University of York, YO10 5DD York, UK; Department of Biology, University of York, YO10 5DD York, UK
| | - Sviatlana Shashkova
- Department of Mathematical Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden; Department of Mathematical Sciences, University of Gothenburg, 412 96 Gothenburg, Sweden; Department of Physics, University of York, YO10 5DD York, UK.
| | - Marija Cvijovic
- Department of Mathematical Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden; Department of Mathematical Sciences, University of Gothenburg, 412 96 Gothenburg, Sweden.
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9
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Do Transgenerational Epigenetic Inheritance and Immune System Development Share Common Epigenetic Processes? J Dev Biol 2021; 9:jdb9020020. [PMID: 34065783 PMCID: PMC8162332 DOI: 10.3390/jdb9020020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022] Open
Abstract
Epigenetic modifications regulate gene expression for development, immune response, disease, and other processes. A major role of epigenetics is to control the dynamics of chromatin structure, i.e., the condensed packaging of DNA around histone proteins in eukaryotic nuclei. Key epigenetic factors include enzymes for histone modifications and DNA methylation, non-coding RNAs, and prions. Epigenetic modifications are heritable but during embryonic development, most parental epigenetic marks are erased and reset. Interestingly, some epigenetic modifications, that may be resulting from immune response to stimuli, can escape remodeling and transmit to subsequent generations who are not exposed to those stimuli. This phenomenon is called transgenerational epigenetic inheritance if the epigenetic phenotype persists beyond the third generation in female germlines and second generation in male germlines. Although its primary function is likely immune response for survival, its role in the development and functioning of the immune system is not extensively explored, despite studies reporting transgenerational inheritance of stress-induced epigenetic modifications resulting in immune disorders. Hence, this review draws from studies on transgenerational epigenetic inheritance, immune system development and function, high-throughput epigenetics tools to study those phenomena, and relevant clinical trials, to focus on their significance and deeper understanding for future research, therapeutic developments, and various applications.
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10
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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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11
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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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12
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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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13
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Moravec CE, Pelegri F. The role of the cytoskeleton in germ plasm aggregation and compaction in the zebrafish embryo. Curr Top Dev Biol 2020; 140:145-179. [PMID: 32591073 DOI: 10.1016/bs.ctdb.2020.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The transmission of genetic information from one generation to another is crucial for survival of animal species. This is accomplished by the induction of primordial germ cells (PGCs) that will eventually establish the germline. In some animals the germline is induced by signals in gastrula, whereas in others it is specified by inheritance of maternal determinants, known as germ plasm. In zebrafish, aggregation and compaction of maternally derived germ plasm during the first several embryonic cell cycles is essential for generation of PGCs. These processes are controlled by cellular functions associated with the cellular division apparatus. Ribonucleoparticles containing germ plasm components are bound to both the ends of astral microtubules and a dynamic F-actin network through a mechanism integrated with that which drives the cell division program. In this chapter we discuss the role that modifications of the cell division apparatus, including the cytoskeleton and cytoskeleton-associated proteins, play in the regulation of zebrafish germ plasm assembly.
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Affiliation(s)
- Cara E Moravec
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Francisco Pelegri
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States.
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14
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Dorweiler JE, Oddo MJ, Lyke DR, Reilly JA, Wisniewski BT, Davis EE, Kuborn AM, Merrill SJ, Manogaran AL. The actin cytoskeletal network plays a role in yeast prion transmission and contributes to prion stability. Mol Microbiol 2020; 114:480-494. [PMID: 32426863 DOI: 10.1111/mmi.14528] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 04/21/2020] [Accepted: 05/09/2020] [Indexed: 01/22/2023]
Abstract
Chaperone networks are required for the shearing and generation of transmissible propagons from pre-existing prion aggregates. However, other cellular networks needed for maintaining yeast prions are largely uncharacterized. Here, we establish a novel role for actin networks in prion maintenance. The [PIN+ ] prion, also known as [RNQ+ ], exists as stable variants dependent upon the chaperone machinery for the transmission of propagons to daughter cells during cell division and cytoplasmic transfer. Loss of the Hsp104 molecular chaperone leads to the growth of prion particles until they are too large to be transmitted. Here, we isolated a unique [PIN+ ] variant, which is unstable in actin mutants. This prion loss is observed over many generations, and coincides with the detection of both high molecular weight species of Rnq1 and large visible aggregates that are asymmetrically retained during cell division. Our data suggest that the irregular actin networks found in these mutants may influence propagon number by slowly permitting aggregate growth over time, resulting in the generation of nontransmissible large aggregates. Thus, we show the potential contribution of cytoskeletal networks in the transmission of prion propagons, which parallels models that have been proposed for cell-to-cell transmission of small amyloids in neurodegenerative protein aggregation diseases.
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Affiliation(s)
- Jane E Dorweiler
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Mitchell J Oddo
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Douglas R Lyke
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Jacob A Reilly
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Brett T Wisniewski
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Emily E Davis
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Abigail M Kuborn
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Stephen J Merrill
- Department of Mathematical and Statistical Sciences, Marquette University, Milwaukee, WI, USA
| | - Anita L Manogaran
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
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15
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Ahmadpour D, Babazadeh R, Nystrom T. Hitchhiking on vesicles: a way to harness age-related proteopathies? FEBS J 2020; 287:5068-5079. [PMID: 32336030 DOI: 10.1111/febs.15345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/06/2020] [Accepted: 04/23/2020] [Indexed: 12/27/2022]
Abstract
Central to proteopathies and leading to most age-related neurodegenerative disorders is a failure in protein quality control (PQC). To harness the toxicity of misfolded and damaged disease proteins, such proteins are either refolded, degraded by temporal PQC, or sequestered by spatial PQC into specific, organelle-associated, compartments within the cell. Here, we discuss the impact of vesicle trafficking pathways in general, and syntaxin 5 in particular, as key players in spatial PQC directing misfolded proteins to the surface of vacuole and mitochondria, which facilitates their clearance and detoxification. Since boosting vesicle trafficking genetically can positively impact on spatial PQC and make cells less sensitive to misfolded disease proteins, we speculate that regulators of such trafficking might serve as therapeutic targets for age-related neurological disorders.
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Affiliation(s)
- Doryaneh Ahmadpour
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Sweden.,Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Sweden
| | - Roja Babazadeh
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Thomas Nystrom
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Sweden
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16
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Shorter J, Southworth DR. Spiraling in Control: Structures and Mechanisms of the Hsp104 Disaggregase. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a034033. [PMID: 30745294 DOI: 10.1101/cshperspect.a034033] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hsp104 is a hexameric AAA+ ATPase and protein disaggregase found in yeast, which couples ATP hydrolysis to the dissolution of diverse polypeptides trapped in toxic preamyloid oligomers, phase-transitioned gels, disordered aggregates, amyloids, and prions. Hsp104 shows plasticity in disaggregating diverse substrates, but how its hexameric architecture operates as a molecular machine has remained unclear. Here, we highlight structural advances made via cryoelectron microscopy (cryo-EM) that enhance our mechanistic understanding of Hsp104 and other related AAA+ translocases. Hsp104 hexamers are dynamic and adopt open "lock-washer" spiral states and closed ring structures that envelope polypeptide substrate inside the axial channel. ATP hydrolysis-driven conformational changes at the spiral seam ratchet substrate deeper into the channel. Remarkably, this mode of polypeptide translocation is reminiscent of models for how hexameric helicases unwind DNA and RNA duplexes. Thus, Hsp104 likely adapts elements of a deeply rooted, ring-translocase mechanism to the specialized task of protein disaggregation.
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Affiliation(s)
- James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics; and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California 94158
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17
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Ali Q, Dainese R, Cvijovic M. Adaptive damage retention mechanism enables healthier yeast population. J Theor Biol 2019; 473:52-66. [PMID: 30980870 DOI: 10.1016/j.jtbi.2019.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 03/04/2019] [Accepted: 04/08/2019] [Indexed: 11/29/2022]
Abstract
During cytokinesis in budding yeast (Saccharomyces cerevisiae) damaged proteins are distributed asymmetrically between the daughter and the mother cell. Retention of damaged proteins is a crucial mechanism ensuring a healthy daughter cell with full replicative potential and an ageing mother cell. However, the protein quality control (PQC) system is tuned for optimal reproduction success which suggests optimal health and size of the population, rather than long-term survival of the mother cell. Modelling retention of damage as an adaptable mechanism, we propose two damage retention strategies to find an optimal way of decreasing damage retention efficiency to maximize population size and minimize the damage in the individual yeast cell. A pedigree model is used to investigate the impact of small variations in the strategies over the whole population. These impacts are based on the altruistic effects of damage retention mechanism and are measured by a cost function whose minimum value provides the optimal health and size of the population. We showed that fluctuations in the cost function allow yeast cell to continuously vary its strategy, suggesting that optimal reproduction success is a local minimum of the cost function. Our results suggest that a rapid decrease in the efficiency of damage retention, at the time when the mother cell is almost exhausted, produces fewer daughters with high levels of damaged proteins. In addition, retaining more damage during the early divisions increases the number of healthy daughters in the population.
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Affiliation(s)
- Qasim Ali
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Chalmers tvärgata 3, SE-41296 Gothenburg, Sweden; Department of Mathematics, North Carolina State University, NC 27607, USA
| | - Riccardo Dainese
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Chalmers tvärgata 3, SE-41296 Gothenburg, Sweden; Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marija Cvijovic
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Chalmers tvärgata 3, SE-41296 Gothenburg, Sweden.
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18
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Howie RL, Jay-Garcia LM, Kiktev DA, Faber QL, Murphy M, Rees KA, Sachwani N, Chernoff YO. Role of the Cell Asymmetry Apparatus and Ribosome-Associated Chaperones in the Destabilization of a Saccharomyces cerevisiae Prion by Heat Shock. Genetics 2019; 212:757-771. [PMID: 31142614 PMCID: PMC6614889 DOI: 10.1534/genetics.119.302237] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/10/2019] [Indexed: 11/18/2022] Open
Abstract
Self-perpetuating transmissible protein aggregates, termed prions, are implicated in mammalian diseases and control phenotypically detectable traits in Saccharomyces cerevisiae Yeast stress-inducible chaperone proteins, including Hsp104 and Hsp70-Ssa that counteract cytotoxic protein aggregation, also control prion propagation. Stress-damaged proteins that are not disaggregated by chaperones are cleared from daughter cells via mother-specific asymmetric segregation in cell divisions following heat shock. Short-term mild heat stress destabilizes [PSI+ ], a prion isoform of the yeast translation termination factor Sup35 This destabilization is linked to the induction of the Hsp104 chaperone. Here, we show that the region of Hsp104 known to be required for curing by artificially overproduced Hsp104 is also required for heat-shock-mediated [PSI+ ] destabilization. Moreover, deletion of the SIR2 gene, coding for a deacetylase crucial for asymmetric segregation of heat-damaged proteins, also counteracts heat-shock-mediated destabilization of [PSI+ ], and Sup35 aggregates are colocalized with aggregates of heat-damaged proteins marked by Hsp104-GFP. These results support the role of asymmetric segregation in prion destabilization. Finally, we show that depletion of the heat-shock noninducible ribosome-associated chaperone Hsp70-Ssb decreases heat-shock-mediated destabilization of [PSI+ ], while disruption of a cochaperone complex mediating the binding of Hsp70-Ssb to the ribosome increases prion loss. Our data indicate that Hsp70-Ssb relocates from the ribosome to the cytosol during heat stress. Cytosolic Hsp70-Ssb has been shown to antagonize the function of Hsp70-Ssa in prion propagation, which explains the Hsp70-Ssb effect on prion destabilization by heat shock. This result uncovers the stress-related role of a stress noninducible chaperone.
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Affiliation(s)
- Rebecca L Howie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | | | - Denis A Kiktev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia 199034
| | - Quincy L Faber
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Margaret Murphy
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Katherine A Rees
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Numera Sachwani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia 199034
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19
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Asymmetric Inheritance of Cell Fate Determinants: Focus on RNA. Noncoding RNA 2019; 5:ncrna5020038. [PMID: 31075989 PMCID: PMC6630313 DOI: 10.3390/ncrna5020038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 12/20/2022] Open
Abstract
During the last decade, and mainly primed by major developments in high-throughput sequencing technologies, the catalogue of RNA molecules harbouring regulatory functions has increased at a steady pace. Current evidence indicates that hundreds of mammalian RNAs have regulatory roles at several levels, including transcription, translation/post-translation, chromatin structure, and nuclear architecture, thus suggesting that RNA molecules are indeed mighty controllers in the flow of biological information. Therefore, it is logical to suggest that there must exist a series of molecular systems that safeguard the faithful inheritance of RNA content throughout cell division and that those mechanisms must be tightly controlled to ensure the successful segregation of key molecules to the progeny. Interestingly, whilst a handful of integral components of mammalian cells seem to follow a general pattern of asymmetric inheritance throughout division, the fate of RNA molecules largely remains a mystery. Herein, we will discuss current concepts of asymmetric inheritance in a wide range of systems, including prions, proteins, and finally RNA molecules, to assess overall the biological impact of RNA inheritance in cellular plasticity and evolutionary fitness.
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20
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Senohrabkova L, Malcova I, Hasek J. An aggregation-prone mutant of eIF3a forms reversible assemblies escaping spatial control in exponentially growing yeast cells. Curr Genet 2019; 65:919-940. [PMID: 30715564 DOI: 10.1007/s00294-019-00940-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 10/27/2022]
Abstract
Cells have elaborated a complex strategy to maintain protein homeostasis under physiological as well as stress conditions with the aim to ensure the smooth functioning of vital processes and producing healthy offspring. Impairment of one of the most important processes in living cells, translation, might have serious consequences including various brain disorders in humans. Here, we describe a variant of the translation initiation factor eIF3a, Rpg1-3, mutated in its PCI domain that displays an attenuated translation efficiency and formation of reversible assemblies at physiological growth conditions. Rpg1-3-GFP assemblies are not sequestered within mother cells only as usual for misfolded-protein aggregates and are freely transmitted from the mother cell into the bud although they are of non-amyloid nature. Their bud-directed transmission and the active movement within the cell area depend on the intact actin cytoskeleton and the related molecular motor Myo2. Mutations in the Rpg1-3 protein render not only eIF3a but, more importantly, also the eIF3 core complex prone to aggregation that is potentiated by the limited availability of Hsp70 and Hsp40 chaperones. Our results open the way to understand mechanisms yeast cells employ to cope with malfunction and aggregation of essential proteins and their complexes.
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Affiliation(s)
- Lenka Senohrabkova
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, Videnska 1083, 14220, Prague 4, Czech Republic
- First Faculty of Medicine, Charles University, Katerinska 42, 12108, Prague 2, Czech Republic
| | - Ivana Malcova
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, Videnska 1083, 14220, Prague 4, Czech Republic.
| | - Jiri Hasek
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, Videnska 1083, 14220, Prague 4, Czech Republic.
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21
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Venkei ZG, Yamashita YM. Emerging mechanisms of asymmetric stem cell division. J Cell Biol 2018; 217:3785-3795. [PMID: 30232100 PMCID: PMC6219723 DOI: 10.1083/jcb.201807037] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/06/2018] [Accepted: 09/13/2018] [Indexed: 01/10/2023] Open
Abstract
Venkei and Yamashita summarize recent advances in our understanding of asymmetric stem cell division in tissue homeostasis. The asymmetric cell division of stem cells, which produces one stem cell and one differentiating cell, has emerged as a mechanism to balance stem cell self-renewal and differentiation. Elaborate cellular mechanisms that orchestrate the processes required for asymmetric cell divisions are often shared between stem cells and other asymmetrically dividing cells. During asymmetric cell division, cells must establish asymmetry/polarity, which is guided by varying degrees of intrinsic versus extrinsic cues, and use intracellular machineries to divide in a desired orientation in the context of the asymmetry/polarity. Recent studies have expanded our knowledge on the mechanisms of asymmetric cell divisions, revealing the previously unappreciated complexity in setting up the cellular and/or environmental asymmetry, ensuring binary outcomes of the fate determination. In this review, we summarize recent progress in understanding the mechanisms and regulations of asymmetric stem cell division.
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Affiliation(s)
- Zsolt G Venkei
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Yukiko M Yamashita
- Life Sciences Institute, University of Michigan, Ann Arbor, MI .,Department of Cell and Developmental Biology, Medical School, University of Michigan, Ann Arbor, MI.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI
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22
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Rothe S, Prakash A, Tyedmers J. The Insoluble Protein Deposit (IPOD) in Yeast. Front Mol Neurosci 2018; 11:237. [PMID: 30050408 PMCID: PMC6052365 DOI: 10.3389/fnmol.2018.00237] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
The appearance of protein aggregates is a hallmark of several pathologies including many neurodegenerative diseases. Mounting evidence suggests that the accumulation of misfolded proteins into inclusions is a secondary line of defense when the extent of protein misfolding exceeds the capacity of the Protein Quality Control System, which mediates refolding or degradation of misfolded species. Such exhaustion can occur during severe proteotoxic stress, the excessive occurrence of aggregation prone protein species, e.g., amyloids, or during ageing. However, the machinery that mediates recognition, recruitment and deposition of different types of misfolded proteins into specific deposition sites is only poorly understood. Since emerging principles of aggregate deposition appear evolutionarily conserved, yeast represents a powerful model to study basic mechanisms of recognition of different types of misfolded proteins, their recruitment to the respective deposition site and the molecular organization at the corresponding site. Yeast possesses at least three different aggregate deposition sites, one of which is a major deposition site for amyloid aggregates termed Insoluble PrOtein Deposit (IPOD). Due to the link between neurodegenerative disease and accumulation of amyloid aggregates, the IPOD is of particular interest when we aim to identify the molecular mechanisms that cells have evolved to counteract toxicity associated with the occurrence of amyloid aggregates. Here, we will review what is known about IPOD composition and the mechanisms of recognition and recruitment of amyloid aggregates to this site in yeast. Finally, we will briefly discuss the possible physiological role of aggregate deposition at the IPOD.
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Affiliation(s)
- Stephanie Rothe
- Department of Medicine I and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany
| | - Abaya Prakash
- Department of Medicine I and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany
| | - Jens Tyedmers
- Department of Medicine I and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany
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23
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Higuchi-Sanabria R, Frankino PA, Paul JW, Tronnes SU, Dillin A. A Futile Battle? Protein Quality Control and the Stress of Aging. Dev Cell 2018; 44:139-163. [PMID: 29401418 PMCID: PMC5896312 DOI: 10.1016/j.devcel.2017.12.020] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/30/2017] [Accepted: 12/20/2017] [Indexed: 12/15/2022]
Abstract
There exists a phenomenon in aging research whereby early life stress can have positive impacts on longevity. The mechanisms underlying these observations suggest a robust, long-lasting induction of cellular defense mechanisms. These include the various unfolded protein responses of the endoplasmic reticulum (ER), cytosol, and mitochondria. Indeed, ectopic induction of these pathways, in the absence of stress, is sufficient to increase lifespan in organisms as diverse as yeast, worms, and flies. Here, we provide an overview of the protein quality control mechanisms that operate in the cytosol, mitochondria, and ER and discuss how they affect cellular health and viability during stress and aging.
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Affiliation(s)
- Ryo Higuchi-Sanabria
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Phillip Andrew Frankino
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joseph West Paul
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sarah Uhlein Tronnes
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew Dillin
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720, USA.
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24
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Deprez MA, Eskes E, Wilms T, Ludovico P, Winderickx J. pH homeostasis links the nutrient sensing PKA/TORC1/Sch9 ménage-à-trois to stress tolerance and longevity. MICROBIAL CELL 2018; 5:119-136. [PMID: 29487859 PMCID: PMC5826700 DOI: 10.15698/mic2018.03.618] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The plasma membrane H+-ATPase Pma1 and the vacuolar V-ATPase act in close harmony to tightly control pH homeostasis, which is essential for a vast number of physiological processes. As these main two regulators of pH are responsive to the nutritional status of the cell, it seems evident that pH homeostasis acts in conjunction with nutrient-induced signalling pathways. Indeed, both PKA and the TORC1-Sch9 axis influence the proton pumping activity of the V-ATPase and possibly also of Pma1. In addition, it recently became clear that the proton acts as a second messenger to signal glucose availability via the V-ATPase to PKA and TORC1-Sch9. Given the prominent role of nutrient signalling in longevity, it is not surprising that pH homeostasis has been linked to ageing and longevity as well. A first indication is provided by acetic acid, whose uptake by the cell induces toxicity and affects longevity. Secondly, vacuolar acidity has been linked to autophagic processes, including mitophagy. In agreement with this, a decline in vacuolar acidity was shown to induce mitochondrial dysfunction and shorten lifespan. In addition, the asymmetric inheritance of Pma1 has been associated with replicative ageing and this again links to repercussions on vacuolar pH. Taken together, accumulating evidence indicates that pH homeostasis plays a prominent role in the determination of ageing and longevity, thereby providing new perspectives and avenues to explore the underlying molecular mechanisms.
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Affiliation(s)
| | - Elja Eskes
- Functional Biology, KU Leuven, Leuven, Belgium
| | | | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
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25
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Is Aggregate-Dependent Yeast Aging Fortuitous? A Model of Damage Segregation and Aggregate Dynamics. Biophys J 2017; 113:2464-2476. [PMID: 29212000 DOI: 10.1016/j.bpj.2017.09.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 09/26/2017] [Accepted: 09/28/2017] [Indexed: 10/18/2022] Open
Abstract
During cytokinesis in Saccharomyces cerevisiae, damaged proteins are distributed unequally between the daughter and mother cells. The retention of these proteins is correlated with yeast aging. Even though evidence suggests that aggregates are retained due to an underlying molecular mechanism, the debate on whether an active mechanism is necessary for this asymmetry remains unsolved. In particular, passive diffusion and a bud-specific dilution remain as possible explanations. Here, a computational and mathematical model is provided to test whether passive mechanisms alone are sufficient to account for the aggregate distribution patterns and the aggregate kinetics observed in living cells. To this author's knowledge, this is the most comprehensive model available on this subject and the only one combining key potentially essential passive-only mechanisms proposed in existing bibliography-namely, the geometrical effect of the dividing yeast cell on the diffusion of protein aggregates, and the possibility of aggregate binding and aggregate formation at different rates. Results suggest that although passive processes alone can reproduce certain averaged observables from experimental bibliography, they are insufficient to vindicate aggregate activity observed in living budding yeast cells. These results are complemented by showing that under basic forms of active quality control, discrepancies between the outputs of the model and experimental bibliography are reduced.
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26
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Asymmetric Inheritance of Aggregated Proteins and Age Reset in Yeast Are Regulated by Vac17-Dependent Vacuolar Functions. Cell Rep 2017; 16:826-38. [PMID: 27373154 PMCID: PMC4963537 DOI: 10.1016/j.celrep.2016.06.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/29/2016] [Accepted: 05/31/2016] [Indexed: 11/24/2022] Open
Abstract
Age can be reset during mitosis in both yeast and stem cells to generate a young daughter cell from an aged and deteriorated one. This phenomenon requires asymmetry-generating genes (AGGs) that govern the asymmetrical inheritance of aggregated proteins. Using a genome-wide imaging screen to identify AGGs in Saccharomyces cerevisiae, we discovered a previously unknown role for endocytosis, vacuole fusion, and the myosin-dependent adaptor protein Vac17 in asymmetrical inheritance of misfolded proteins. Overproduction of Vac17 increases deposition of aggregates into cytoprotective vacuole-associated sites, counteracts age-related breakdown of endocytosis and vacuole integrity, and extends replicative lifespan. The link between damage asymmetry and vesicle trafficking can be explained by a direct interaction between aggregates and vesicles. We also show that the protein disaggregase Hsp104 interacts physically with endocytic vesicle-associated proteins, such as the dynamin-like protein, Vps1, which was also shown to be required for Vac17-dependent sequestration of protein aggregates. These data demonstrate that two physiognomies of aging-reduced endocytosis and protein aggregation-are interconnected and regulated by Vac17.
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27
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Azbarova AV, Galkina KV, Sorokin MI, Severin FF, Knorre DA. The contribution of Saccharomyces cerevisiae replicative age to the variations in the levels of Trx2p, Pdr5p, Can1p and Idh isoforms. Sci Rep 2017; 7:13220. [PMID: 29038504 PMCID: PMC5643315 DOI: 10.1038/s41598-017-13576-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/25/2017] [Indexed: 01/09/2023] Open
Abstract
Asymmetrical division can be a reason for microbial populations heterogeneity. In particular, budding yeast daughter cells are more vulnerable to stresses than the mothers. It was suggested that yeast mother cells could also differ from each other depending on their replicative age. To test this, we measured the levels of Idh1-GFP, Idh2-GFP, Trx2-GFP, Pdr5-GFP and Can1-GFP proteins in cells of the few first, most represented, age cohorts. Pdr5p and Can1p were selected because of the pronounced mother-bud asymmetry for these proteins distributions, Trx2p as indicator of oxidative stress. Isocitrate dehydrogenase subunits Idh1p and Idh2p were assessed because their levels are regulated by mitochondria. We found a small negative correlation between yeast replicative age and Idh1-GFP or Idh2-GFP but not Trx2-GFP levels. Mitochondrial network fragmentation was also confirmed as an early event of replicative aging. No significant difference in the membrane proteins levels Pdr5p and Can1p was found. Moreover, the elder mother cells showed lower coefficient of variation for Pdr5p levels compared to the younger ones and the daughters. Our data suggest that the levels of stress-response proteins Pdr5p and Trx2p in the mother cells are stable during the first few cell cycles regardless of their mother-bud asymmetry.
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Affiliation(s)
- Aglaia V Azbarova
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Leninskiye Gory 1-73, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskiye Gory 1-40, Moscow, 119991, Russia
| | - Kseniia V Galkina
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Leninskiye Gory 1-73, Moscow, 119991, Russia
| | - Maxim I Sorokin
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskiye Gory 1-40, Moscow, 119991, Russia.,National Research Centre Kurchatov Institute, Centre for Convergence of Nano-, Bio-Information and Cognitive Sciences and Technologies, Moscow, 123182, Russia.,OmicsWay Corp., 340S Lemon Ave, Walnut, CA, 91789, USA
| | - Fedor F Severin
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskiye Gory 1-40, Moscow, 119991, Russia
| | - Dmitry A Knorre
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskiye Gory 1-40, Moscow, 119991, Russia.
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28
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Florea M. Aging and immortality in unicellular species. Mech Ageing Dev 2017; 167:5-15. [PMID: 28844968 DOI: 10.1016/j.mad.2017.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/21/2017] [Accepted: 08/13/2017] [Indexed: 12/22/2022]
Abstract
It has been historically thought that in conditions that permit growth, most unicellular species do not to age. This was particularly thought to be the case for symmetrically dividing species, as such species lack a clear distinction between the soma and the germline. Despite this, studies of the symmetrically dividing species Escherichia coli and Schizosaccharomyces pombe have recently started to challenge this notion. They indicate that E. coli and S. pombe do age, but only when subjected to environmental stress. If true, this suggests that aging may be widespread among microbial species in general, and that studying aging in microbes may inform other long-standing questions in aging. This review examines the recent evidence for and against replicative aging in symmetrically dividing unicellular organisms, the mechanisms that underlie aging, why aging evolved in these species, and how microbial aging fits into the context of other questions in aging.
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Affiliation(s)
- Michael Florea
- Graduate School of Arts and Sciences, Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA.
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29
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Cellular strategies to cope with protein aggregation. Essays Biochem 2017; 60:153-161. [PMID: 27744331 DOI: 10.1042/ebc20160002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/09/2016] [Indexed: 11/17/2022]
Abstract
Nature has evolved several mechanisms to detoxify intracellular protein aggregates that arise upon proteotoxic challenges. These include the controlled deposition of misfolded proteins at distinct cellular sites, the protein disaggregation and refolding by molecular chaperones and/or degradation of misfolded and aggregated protein species by cellular clearance pathways. In this article, we discuss cellular the strategies of prokaroytes and eukaryotes to control protein aggregation.
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30
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Gottschling DE, Nyström T. The Upsides and Downsides of Organelle Interconnectivity. Cell 2017; 169:24-34. [PMID: 28340346 DOI: 10.1016/j.cell.2017.02.030] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/13/2017] [Accepted: 02/21/2017] [Indexed: 12/31/2022]
Abstract
Interconnectivity and feedback control are hallmarks of biological systems. This includes communication between organelles, which allows them to function and adapt to changing cellular environments. While the specific mechanisms for all communications remain opaque, unraveling the wiring of organelle networks is critical to understand how biological systems are built and why they might collapse, as occurs in aging. A comprehensive understanding of all the routes involved in inter-organelle communication is still lacking, but important themes are beginning to emerge, primarily in budding yeast. These routes are reviewed here in the context of sub-system proteostasis and complex adaptive systems theory.
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Affiliation(s)
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden.
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31
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Böckler S, Chelius X, Hock N, Klecker T, Wolter M, Weiss M, Braun RJ, Westermann B. Fusion, fission, and transport control asymmetric inheritance of mitochondria and protein aggregates. J Cell Biol 2017; 216:2481-2498. [PMID: 28615194 PMCID: PMC5551707 DOI: 10.1083/jcb.201611197] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 04/13/2017] [Accepted: 05/12/2017] [Indexed: 12/18/2022] Open
Abstract
Asymmetric inheritance of cell organelles determines the fate of daughter cells. Böckler et al. use yeast as a model to demonstrate that the dynamics of mitochondrial fusion, fission, and transport determine partitioning of mitochondria and cytosolic protein aggregates, which is critical for rejuvenation of daughter cells. Partitioning of cell organelles and cytoplasmic components determines the fate of daughter cells upon asymmetric division. We studied the role of mitochondria in this process using budding yeast as a model. Anterograde mitochondrial transport is mediated by the myosin motor, Myo2. A genetic screen revealed an unexpected interaction of MYO2 and genes required for mitochondrial fusion. Genetic analyses, live-cell microscopy, and simulations in silico showed that fused mitochondria become critical for inheritance and transport across the bud neck in myo2 mutants. Similarly, fused mitochondria are essential for retention in the mother when bud-directed transport is enforced. Inheritance of a less than critical mitochondrial quantity causes a severe decline of replicative life span of daughter cells. Myo2-dependent mitochondrial distribution also is critical for the capture of heat stress–induced cytosolic protein aggregates and their retention in the mother cell. Together, these data suggest that coordination of mitochondrial transport, fusion, and fission is critical for asymmetric division and rejuvenation of daughter cells.
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Affiliation(s)
| | - Xenia Chelius
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | - Nadine Hock
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | - Till Klecker
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | - Madita Wolter
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | - Matthias Weiss
- Experimentalphysik I, Universität Bayreuth, Bayreuth, Germany
| | - Ralf J Braun
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
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32
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Abstract
Amyloids and amyloid-based prions are self-perpetuating protein aggregates which can spread by converting a normal protein of the same sequence into a prion form. They are associated with diseases in humans and mammals, and control heritable traits in yeast and other fungi. Some amyloids are implicated in biologically beneficial processes. As prion formation generates reproducible memory of a conformational change, prions can be considered as molecular memory devices. We have demonstrated that in yeast, stress-inducible cytoskeleton-associated protein Lsb2 forms a metastable prion in response to high temperature. This prion promotes conversion of other proteins into prions and can persist in a fraction of cells for a significant number of cell generations after stress, thus maintaining the memory of stress in a population of surviving cells. Acquisition of an amino acid substitution required for Lsb2 to form a prion coincides with acquisition of increased thermotolerance in the evolution of Saccharomyces yeast. Thus the ability to form an Lsb2 prion in response to stress coincides with yeast adaptation to growth at higher temperatures. These findings intimately connect prion formation to the cellular response to environmental stresses.
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Affiliation(s)
- Tatiana A Chernova
- a Department of Biochemistry , Emory University School of Medicine , Atlanta , GA , USA
| | - Yury O Chernoff
- b School of Biological Sciences , Georgia Institute of Technology , Atlanta , GA , USA.,c Laboratory of Amyloid Biology and Institute of Translational Biomedicine , St. Petersburg State University , St. Petersburg , Russia
| | - Keith D Wilkinson
- a Department of Biochemistry , Emory University School of Medicine , Atlanta , GA , USA
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33
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Saarikangas J, Caudron F. Spatial regulation of coalesced protein assemblies: Lessons from yeast to diseases. Prion 2017; 11:162-173. [PMID: 28574744 PMCID: PMC5480387 DOI: 10.1080/19336896.2017.1322239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Organisms rely on correctly folded proteins to carry out essential functions. Protein quality control factors guard proteostasis and prevent protein misfolding. When quality control fails and in response to diverse stresses, many proteins start to accumulate at specific deposit sites that maintain cellular organization and protect the functionality of coalescing proteins. These transitions involve dedicated proteins that promote coalescence and are facilitated by endo-membranes and cytoskeletal platforms. Moreover, several proteins make use of weak multivalent interactions or conformational templating to drive the formation of large-scale assemblies. Formation of such assemblies is often associated with a change in biochemical activity that can be used by cells to execute biochemical decisions in a localized manner during development and adaption. Since all assembly types impact cell physiology, their localization and dynamics need to be tightly regulated. Interestingly, at least some of the regulatory mechanisms are shared by functional membrane-less organelles and assemblies of terminally aggregated proteins. Furthermore, constituents of functional assemblies can aggregate and become non-functional during aging. Here we present the current knowledge as to how coalescing protein assemblies are spatially organized in cells and we postulate that failures in their spatial confinement might underscore certain aspects of aging and neurodegenerative diseases.
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Affiliation(s)
- Juha Saarikangas
- a ETH Zurich, Institute of Biochemistry , Zurich , Switzerland.,b Wissenschaftskolleg zu Berlin , Institute for Advanced Study , Berlin , Germany.,c Helsinki Institute of Life Science, University of Helsinki , Helsinki , Finland.,d Faculty of Biological and Environmental Sciences , University of Helsinki , Helsinki , Finland
| | - Fabrice Caudron
- e Randall Division of Cell and Molecular Biophysics , King's College London , London , UK
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34
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Kumar R, Neuser N, Tyedmers J. Hitchhiking vesicular transport routes to the vacuole: Amyloid recruitment to the Insoluble Protein Deposit (IPOD). Prion 2017; 11:71-81. [PMID: 28277942 PMCID: PMC5399893 DOI: 10.1080/19336896.2017.1293226] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sequestration of aggregates into specialized deposition sites occurs in many species across all kingdoms of life ranging from bacteria to mammals and is commonly believed to have a cytoprotective function. Yeast cells possess at least 3 different spatially separated deposition sites, one of which is termed “Insoluble Protein Deposit (IPOD)” and harbors amyloid aggregates. We have recently discovered that recruitment of amyloid aggregates to the IPOD uses an actin cable based recruitment machinery that also involves vesicular transport.1 Here we discuss how different proteins known to be involved in vesicular transport processes to the vacuole might act to guide amyloid aggregates to the IPOD. These factors include the Myosin V motor protein Myo2 involved in transporting vacuolar vesicles along actin cables, the transmembrane protein Atg9 involved in the recruitment of large precursor hydrolase complexes to the vacuole, the phosphatidylinositol/ phosphatidylcholine (PI/PC) transfer protein Sec 14 and the SNARE chaperone Sec 18. Furthermore, we present new data suggesting that the yeast dynamin homolog Vps1 is also crucial for faithful delivery of the amyloid model protein PrD-GFP to the IPOD. This is in agreement with a previously identified role for Vps1 in recruitment of heat-denatured aggregates to a perivacuolar deposition site.2
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Affiliation(s)
- Rajesh Kumar
- a Department of Medicine I and Clinical Chemistry , University Hospital Heidelberg , Heidelberg , Germany
| | - Nicole Neuser
- a Department of Medicine I and Clinical Chemistry , University Hospital Heidelberg , Heidelberg , Germany
| | - Jens Tyedmers
- a Department of Medicine I and Clinical Chemistry , University Hospital Heidelberg , Heidelberg , Germany
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35
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Hill SM, Hanzén S, Nyström T. Restricted access: spatial sequestration of damaged proteins during stress and aging. EMBO Rep 2017; 18:377-391. [PMID: 28193623 PMCID: PMC5331209 DOI: 10.15252/embr.201643458] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/19/2016] [Accepted: 01/24/2017] [Indexed: 01/08/2023] Open
Abstract
The accumulation of damaged and aggregated proteins is a hallmark of aging and increased proteotoxic stress. To limit the toxicity of damaged and aggregated proteins and to ensure that the damage is not inherited by succeeding cell generations, a system of spatial quality control operates to sequester damaged/aggregated proteins into inclusions at specific protective sites. Such spatial sequestration and asymmetric segregation of damaged proteins have emerged as key processes required for cellular rejuvenation. In this review, we summarize findings on the nature of the different quality control sites identified in yeast, on genetic determinants required for spatial quality control, and on how aggregates are recognized depending on the stress generating them. We also briefly compare the yeast system to spatial quality control in other organisms. The data accumulated demonstrate that spatial quality control involves factors beyond the canonical quality control factors, such as chaperones and proteases, and opens up new venues in approaching how proteotoxicity might be mitigated, or delayed, upon aging.
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Affiliation(s)
- Sandra Malmgren Hill
- Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Sarah Hanzén
- Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Thomas Nyström
- Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
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36
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Chernova TA, Wilkinson KD, Chernoff YO. Prions, Chaperones, and Proteostasis in Yeast. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a023663. [PMID: 27815300 DOI: 10.1101/cshperspect.a023663] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Prions are alternatively folded, self-perpetuating protein isoforms involved in a variety of biological and pathological processes. Yeast prions are protein-based heritable elements that serve as an excellent experimental system for studying prion biology. The propagation of yeast prions is controlled by the same Hsp104/70/40 chaperone machinery that is involved in the protection of yeast cells against proteotoxic stress. Ribosome-associated chaperones, proteolytic pathways, cellular quality-control compartments, and cytoskeletal networks influence prion formation, maintenance, and toxicity. Environmental stresses lead to asymmetric prion distribution in cell divisions. Chaperones and cytoskeletal proteins mediate this effect. Overall, this is an intimate relationship with the protein quality-control machinery of the cell, which enables prions to be maintained and reproduced. The presence of many of these same mechanisms in higher eukaryotes has implications for the diagnosis and treatment of mammalian amyloid diseases.
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Affiliation(s)
- Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Keith D Wilkinson
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332-2000.,Laboratory of Amyloid Biology and Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
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37
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Paoletti C, Quintin S, Matifas A, Charvin G. Kinetics of Formation and Asymmetrical Distribution of Hsp104-Bound Protein Aggregates in Yeast. Biophys J 2016; 110:1605-1614. [PMID: 27074685 DOI: 10.1016/j.bpj.2016.02.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 02/17/2016] [Accepted: 02/23/2016] [Indexed: 02/05/2023] Open
Abstract
Budding yeast cells have a finite replicative life span; that is, a mother cell produces only a limited number of daughter cells before it slows division and dies. Despite the gradual aging of the mother cell, all daughters are born rejuvenated and enjoy a full replicative lifespan. It has been proposed that entry of mother cells into senescence is driven by the progressive accumulation and retention of damaged material, including protein aggregates. This additionally allows the daughter cells to be born damage free. However, the mechanism underlying such asymmetrical segregation of protein aggregates by mother and daughter cells remains controversial, in part because of the difficulties inherent in tracking the dynamics and fate of protein aggregates in vivo. To overcome such limitations, we have developed single-cell real-time imaging methodology to track the formation of heat-induced protein aggregates in otherwise unperturbed dividing cells. By combining the imaging data with a simple computational model of protein aggregation, we show that the establishment of asymmetrical partitioning of protein aggregates upon division is driven by the large bud-specific dilution rate associated with polarized growth and the absence of significant mother/bud exchange of protein aggregates during the budded phase of the cell cycle. To our knowledge, this study sheds new light on the mechanism of establishment of a segregation bias, which can be accounted for by simple physical arguments.
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Affiliation(s)
- Camille Paoletti
- Development and Stem Cells Department, IGBMC, CNRS UMR 7104, INSERM U964, Université de Strasbourg, Illkirch, France
| | - Sophie Quintin
- Development and Stem Cells Department, IGBMC, CNRS UMR 7104, INSERM U964, Université de Strasbourg, Illkirch, France
| | - Audrey Matifas
- Development and Stem Cells Department, IGBMC, CNRS UMR 7104, INSERM U964, Université de Strasbourg, Illkirch, France
| | - Gilles Charvin
- Development and Stem Cells Department, IGBMC, CNRS UMR 7104, INSERM U964, Université de Strasbourg, Illkirch, France.
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38
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Prion Aggregates Are Recruited to the Insoluble Protein Deposit (IPOD) via Myosin 2-Based Vesicular Transport. PLoS Genet 2016; 12:e1006324. [PMID: 27689885 PMCID: PMC5045159 DOI: 10.1371/journal.pgen.1006324] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 08/25/2016] [Indexed: 12/31/2022] Open
Abstract
Aggregation of amyloidogenic proteins is associated with several neurodegenerative diseases. Sequestration of misfolded and aggregated proteins into specialized deposition sites may reduce their potentially detrimental properties. Yeast exhibits a distinct deposition site for amyloid aggregates termed "Insoluble PrOtein Deposit (IPOD)", but nothing is known about the mechanism of substrate recruitment to this site. The IPOD is located directly adjacent to the Phagophore Assembly Site (PAS) where the cell initiates autophagy and the Cytoplasm-to-Vacuole Targeting (CVT) pathway destined for delivery of precursor peptidases to the vacuole. Recruitment of CVT substrates to the PAS was proposed to occur via vesicular transport on Atg9 vesicles and requires an intact actin cytoskeleton and "SNAP (Soluble NSF Attachment Protein) Receptor Proteins (SNARE)" protein function. It is, however, unknown how this vesicular transport machinery is linked to the actin cytoskeleton. We demonstrate that recruitment of model amyloid PrD-GFP and the CVT substrate precursor-aminopeptidase 1 (preApe1) to the IPOD or PAS, respectively, is disturbed after genetic impairment of Myo2-based actin cable transport and SNARE protein function. Rather than accumulating at the respective deposition sites, both substrates reversibly accumulated often together in the same punctate structures. Components of the CVT vesicular transport machinery including Atg8 and Atg9 as well as Myo2 partially co-localized with the joint accumulations. Thus we propose a model where vesicles, loaded with preApe1 or PrD-GFP, are recruited to tropomyosin coated actin cables via the Myo2 motor protein for delivery to the PAS and IPOD, respectively. We discuss that deposition at the IPOD is not an integrated mandatory part of the degradation pathway for amyloid aggregates, but more likely stores excess aggregates until downstream degradation pathways have the capacity to turn them over after liberation by the Hsp104 disaggregation machinery.
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39
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Zhao L, Yang Q, Zheng J, Zhu X, Hao X, Song J, Lebacq T, Franssens V, Winderickx J, Nystrom T, Liu B. A genome-wide imaging-based screening to identify genes involved in synphilin-1 inclusion formation in Saccharomyces cerevisiae. Sci Rep 2016; 6:30134. [PMID: 27440388 PMCID: PMC4954962 DOI: 10.1038/srep30134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/27/2016] [Indexed: 11/09/2022] Open
Abstract
Synphilin-1 is a major component of Parkinson's disease (PD) inclusion bodies implicated in PD pathogenesis. However, the machinery controlling synphilin-1 inclusion formation remains unclear. Here, we investigated synphilin-1 inclusion formation using a systematic genome-wide, high-content imaging based screening approach (HCI) in the yeast Saccharomyces cerevisiae. By combining with a secondary screening for mutants showing significant changes on fluorescence signal intensity, we filtered out hits that significantly decreased the expression level of synphilin-1. We found 133 yeast genes that didn't affect synphilin-1 expression but that were required for the formation of synphilin-1 inclusions. Functional enrichment and physical interaction network analysis revealed these genes to encode for functions involved in cytoskeleton organization, histone modification, sister chromatid segregation, glycolipid biosynthetic process, DNA repair and replication. All hits were confirmed by conventional microscopy. Complementation assays were performed with a selected group of mutants, results indicated that the observed phenotypic changes in synphilin-1 inclusion formation were directly caused by the loss of corresponding genes of the deletion mutants. Further growth assays of these mutants showed a significant synthetic sick effect upon synphilin-1 expression, which supports the hypothesis that matured inclusions represent an end stage of several events meant to protect cells against the synphilin-1 cytotoxicity.
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Affiliation(s)
- Lei Zhao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Qian Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Ju Zheng
- Department of Biology, Functional Biology, KU Leuven, 3001 Heverlee, Belgium
| | - Xuefeng Zhu
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, S-405 30, Göteborg, Sweden
| | - Xinxin Hao
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden
| | - Jia Song
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Tom Lebacq
- Department of Biology, Functional Biology, KU Leuven, 3001 Heverlee, Belgium
| | - Vanessa Franssens
- Department of Biology, Functional Biology, KU Leuven, 3001 Heverlee, Belgium
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, 3001 Heverlee, Belgium
| | - Thomas Nystrom
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden
| | - Beidong Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China.,Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden
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40
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Vedel S, Nunns H, Košmrlj A, Semsey S, Trusina A. Asymmetric Damage Segregation Constitutes an Emergent Population-Level Stress Response. Cell Syst 2016; 3:187-198. [PMID: 27426983 DOI: 10.1016/j.cels.2016.06.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 04/05/2016] [Accepted: 06/16/2016] [Indexed: 01/15/2023]
Abstract
Asymmetric damage segregation (ADS) is a mechanism for increasing population fitness through non-random, asymmetric partitioning of damaged macromolecules at cell division. ADS has been reported across multiple organisms, though the measured effects on fitness of individuals are often small. Here, we introduce a cell-lineage-based framework that quantifies the population-wide effects of ADS and then verify our results experimentally in E. coli under heat and antibiotic stress. Using an experimentally validated mathematical model, we find that the beneficial effect of ADS increases with stress. In effect, low-damage subpopulations divide faster and amplify within the population acting like a positive feedback loop whose strength scales with stress. Analysis of protein aggregates shows that the degree of asymmetric inheritance is damage dependent in single cells. Together our results indicate that, despite small effects in single cell, ADS exerts a strong beneficial effect on the population level and arises from the redistribution of damage within a population, through both single-cell and population-level feedback.
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Affiliation(s)
- Søren Vedel
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark; Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark.
| | - Harry Nunns
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Andrej Košmrlj
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Szabolcs Semsey
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Ala Trusina
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark.
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41
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Nyström T. Interview with Professor Thomas Nyström, awardee of the Emil Christian Hansen Gold Medal 2015. FEMS Yeast Res 2015; 15:fov104. [PMID: 26658235 DOI: 10.1093/femsyr/fov104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thomas Nyström
- Institute of Biomedicine at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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42
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Mechanistic and Structural Insights into the Prion-Disaggregase Activity of Hsp104. J Mol Biol 2015; 428:1870-85. [PMID: 26608812 DOI: 10.1016/j.jmb.2015.11.016] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/11/2015] [Accepted: 11/12/2015] [Indexed: 11/23/2022]
Abstract
Hsp104 is a dynamic ring translocase and hexameric AAA+ protein found in yeast, which couples ATP hydrolysis to disassembly and reactivation of proteins trapped in soluble preamyloid oligomers, disordered protein aggregates, and stable amyloid or prion conformers. Here, we highlight advances in our structural understanding of Hsp104 and how Hsp104 deconstructs Sup35 prions. Although the atomic structure of Hsp104 hexamers remains uncertain, volumetric reconstruction of Hsp104 hexamers in ATPγS, ADP-AlFx (ATP hydrolysis transition-state mimic), and ADP via small-angle x-ray scattering has revealed a peristaltic pumping motion upon ATP hydrolysis. This pumping motion likely drives directional substrate translocation across the central Hsp104 channel. Hsp104 initially engages Sup35 prions immediately C-terminal to their cross-β structure. Directional pulling by Hsp104 then resolves N-terminal cross-β structure in a stepwise manner. First, Hsp104 fragments the prion. Second, Hsp104 unfolds cross-β structure. Third, Hsp104 releases soluble Sup35. Deletion of the Hsp104 N-terminal domain yields a hypomorphic disaggregase, Hsp104(∆N), with an altered pumping mechanism. Hsp104(∆N) fragments Sup35 prions without unfolding cross-β structure or releasing soluble Sup35. Moreover, Hsp104(∆N) activity cannot be enhanced by mutations in the middle domain that potentiate disaggregase activity. Thus, the N-terminal domain is critical for the full repertoire of Hsp104 activities.
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Garcia DM, Jarosz DF. Rebels with a cause: molecular features and physiological consequences of yeast prions. FEMS Yeast Res 2015; 14:136-47. [PMID: 25667942 DOI: 10.1111/1567-1364.12116] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Prions are proteins that convert between structurally and functionally distinct states, at least one of which is self-perpetuating. The prion fold templates the conversion of native protein, altering its structure and function, and thus serves as a protein-based element of inheritance. Molecular chaperones ensure that these prion aggregates are divided and faithfully passed from mother cells to their daughters. Prions were originally identified as the cause of several rare neurodegenerative diseases in mammals, but the last decade has brought great progress in understanding their broad importance in biology and evolution. Most prion proteins regulate information flow in signaling networks, or otherwise affect gene expression. Consequently, switching into and out of prion states creates diverse new traits – heritable changes based on protein structure rather than nucleic acid. Despite intense study of the molecular mechanisms of this paradigm-shifting, epigenetic mode of inheritance, many key questions remain. Recent studies in yeast that support the view that prions are common, often beneficial elements of inheritance that link environmental stress to the appearance of new traits.
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Arlia-Ciommo A, Piano A, Leonov A, Svistkova V, Titorenko VI. Quasi-programmed aging of budding yeast: a trade-off between programmed processes of cell proliferation, differentiation, stress response, survival and death defines yeast lifespan. Cell Cycle 2015; 13:3336-49. [PMID: 25485579 PMCID: PMC4614525 DOI: 10.4161/15384101.2014.965063] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recent findings suggest that evolutionarily distant organisms share the key features of the aging process and exhibit similar mechanisms of its modulation by certain genetic, dietary and pharmacological interventions. The scope of this review is to analyze mechanisms that in the yeast Saccharomyces cerevisiae underlie: (1) the replicative and chronological modes of aging; (2) the convergence of these 2 modes of aging into a single aging process; (3) a programmed differentiation of aging cell communities in liquid media and on solid surfaces; and (4) longevity-defining responses of cells to some chemical compounds released to an ecosystem by other organisms populating it. Based on such analysis, we conclude that all these mechanisms are programs for upholding the long-term survival of the entire yeast population inhabiting an ecological niche; however, none of these mechanisms is a ʺprogram of agingʺ - i.e., a program for progressing through consecutive steps of the aging process.
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Key Words
- D, diauxic growth phase
- ERCs, extrachromosomal rDNA circles
- IPOD, insoluble protein deposit
- JUNQ, juxtanuclear quality control compartment
- L, logarithmic growth phase
- MBS, the mitochondrial back-signaling pathway
- MTC, the mitochondrial translation control signaling pathway
- NPCs, nuclear pore complexes
- NQ, non-quiescent cells
- PD, post-diauxic growth phase
- Q, quiescent cells
- ROS, reactive oxygen species
- RTG, the mitochondrial retrograde signaling pathway
- Ras/cAMP/PKA, the Ras family GTPase/cAMP/protein kinase A signaling pathway
- ST, stationary growth phase
- TOR/Sch9, the target of rapamycin/serine-threonine protein kinase Sch9 signaling pathway
- UPRER, the unfolded protein response pathway in the endoplasmic reticulum
- UPRmt, the unfolded protein response pathway in mitochondria
- cell growth and proliferation
- cell survival
- cellular aging
- ecosystems
- evolution
- longevity
- programmed cell death
- yeast
- yeast colony
- yeast replicative and chronological aging
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Coelho M, Tolić IM. Asymmetric damage segregation at cell division via protein aggregate fusion and attachment to organelles. Bioessays 2015; 37:740-7. [PMID: 25966295 DOI: 10.1002/bies.201400224] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The segregation of damaged components at cell division determines the survival and aging of cells. In cells that divide asymmetrically, such as Saccharomyces cerevisiae, aggregated proteins are retained by the mother cell. Yet, where and how aggregation occurs is not known. Recent work by Zhou and collaborators shows that the birth of protein aggregates, under specific stress conditions, requires active translation, and occurs mainly at the endoplasmic reticulum. Later, aggregates move to the mitochondrial surface through fis1-dependent association. During replicative aging, aggregate association with the mother-cell mitochondria contributes to the asymmetric segregation of aggregates, because mitochondria in the daughter cell do not carry aggregates. With increasing age of mother cells, aggregates lose their connection to the mitochondria, and segregation is less asymmetric. Relating these findings to other mechanisms of aggregate segregation in different organisms, we postulate that fusion between aggregates and their tethering to organelles such as the vacuole, nucleus, ER, or mitochondria are common principles that establish asymmetric segregation during stress resistance and aging.
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Affiliation(s)
- Miguel Coelho
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Iva M Tolić
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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46
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Pattabiraman S, Kaganovich D. Imperfect asymmetry: The mechanism governing asymmetric partitioning of damaged cellular components during mitosis. BIOARCHITECTURE 2015; 4:203-9. [PMID: 25941938 DOI: 10.1080/19490992.2015.1014213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Aging is universally associated with organism-wide dysfunction and a decline in cellular fitness. From early development onwards, the efficiency of self-repair, energy production, and homeostasis all decrease. Due to the multiplicity of systems that undergo agingrelated decline, the mechanistic basis of organismal aging has been difficult to pinpoint. At the cellular level, however, recent work has provided important insight. Cellular aging is associated with the accumulation of several types of damage, in particular damage to the proteome and organelles. Groundbreaking studies have shown that replicative aging is the result of a rejuvenation mechanism that prevents the inheritance of damaged components during division, thereby confining the effects of aging to specific cells, while removing damage from others. Asymmetric inheritance of misfolded and aggregated proteins, as well as reduced mitochondria, has been shown in yeast. Until recently, however, it was not clear whether a similar mechanism operates in mammalian cells, which were thought to mostly divide symmetrically. Our group has recently shown that vimentin establishes mitotic polarity in immortalized mammalian cells, and mediates asymmetric partitioning of multiple factors through direct interaction. These findings prompt a provocative hypothesis: that intermediate filaments serve as asymmetric partitioning modules or "sponges" that, when expressed prior to mitosis, can "clean" emerging cells of the damage they have accumulated.
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Affiliation(s)
- Sundararaghavan Pattabiraman
- a Department of Cell and Developmental Biology ; Alexander Silberman Institute of Life Sciences; Hebrew University of Jerusalem ; Jerusalem , Israel
| | - Daniel Kaganovich
- a Department of Cell and Developmental Biology ; Alexander Silberman Institute of Life Sciences; Hebrew University of Jerusalem ; Jerusalem , Israel
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Amen T, Kaganovich D. Dynamic droplets: the role of cytoplasmic inclusions in stress, function, and disease. Cell Mol Life Sci 2015; 72:401-415. [PMID: 25283146 PMCID: PMC11113435 DOI: 10.1007/s00018-014-1740-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/16/2014] [Accepted: 09/22/2014] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases and other proteinopathies constitute a class of several dozen illnesses etiologically linked to pathological protein misfolding and aggregation. Because of this strong association with disease pathology, cell death, and aging, accumulation of proteins in aggregates or aggregation-associated structures (inclusions) has come to be regarded by many as a deleterious process, to be avoided if possible. Recent work has led us to see inclusion structures and disordered aggregate-like protein mixtures (which we call dynamic droplets) in a new light: not necessarily as a result of a pathological breakdown of cellular order, but as an elaborate cellular architecture regulating function and stress response. In this review, we discuss what is currently known about the role of inclusion structures in cellular homeostasis, stress response, toxicity, and disease. We will focus on possible mechanisms of aggregate toxicity, in contrast to the homeostatic function of several inclusion structures.
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Affiliation(s)
- Triana Amen
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Alexander Grass Center for Bioengineering, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Kaganovich
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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48
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Higuchi-Sanabria R, Pernice WMA, Vevea JD, Alessi Wolken DM, Boldogh IR, Pon LA. Role of asymmetric cell division in lifespan control in Saccharomyces cerevisiae. FEMS Yeast Res 2014; 14:1133-46. [PMID: 25263578 PMCID: PMC4270926 DOI: 10.1111/1567-1364.12216] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/22/2014] [Accepted: 09/22/2014] [Indexed: 11/29/2022] Open
Abstract
Aging determinants are asymmetrically distributed during cell division in S. cerevisiae, which leads to production of an immaculate, age-free daughter cell. During this process, damaged components are sequestered and retained in the mother cell, and higher functioning organelles and rejuvenating factors are transported to and/or enriched in the bud. Here, we will describe the key quality control mechanisms in budding yeast that contribute to asymmetric cell division of aging determinants including mitochondria, endoplasmic reticulum (ER), vacuoles, extrachromosomal rDNA circles (ERCs), and protein aggregates.
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Affiliation(s)
- Ryo Higuchi-Sanabria
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
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Ali M, Chernova TA, Newnam GP, Yin L, Shanks J, Karpova TS, Lee A, Laur O, Subramanian S, Kim D, McNally JG, Seyfried NT, Chernoff YO, Wilkinson KD. Stress-dependent proteolytic processing of the actin assembly protein Lsb1 modulates a yeast prion. J Biol Chem 2014; 289:27625-39. [PMID: 25143386 PMCID: PMC4183801 DOI: 10.1074/jbc.m114.582429] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/06/2014] [Indexed: 11/06/2022] Open
Abstract
Yeast prions are self-propagating amyloid-like aggregates of Q/N-rich protein that confer heritable traits and provide a model of mammalian amyloidoses. [PSI(+)] is a prion isoform of the translation termination factor Sup35. Propagation of [PSI(+)] during cell division under normal conditions and during the recovery from damaging environmental stress depends on cellular chaperones and is influenced by ubiquitin proteolysis and the actin cytoskeleton. The paralogous yeast proteins Lsb1 and Lsb2 bind the actin assembly protein Las17 (a yeast homolog of human Wiskott-Aldrich syndrome protein) and participate in the endocytic pathway. Lsb2 was shown to modulate maintenance of [PSI(+)] during and after heat shock. Here, we demonstrate that Lsb1 also regulates maintenance of the Sup35 prion during and after heat shock. These data point to the involvement of Lsb proteins in the partitioning of protein aggregates in stressed cells. Lsb1 abundance and cycling between actin patches, endoplasmic reticulum, and cytosol is regulated by the Guided Entry of Tail-anchored proteins pathway and Rsp5-dependent ubiquitination. Heat shock-induced proteolytic processing of Lsb1 is crucial for prion maintenance during stress. Our findings identify Lsb1 as another component of a tightly regulated pathway controlling protein aggregation in changing environments.
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Affiliation(s)
- Moiez Ali
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Tatiana A Chernova
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322,
| | - Gary P Newnam
- the School of Biology and Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Luming Yin
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - John Shanks
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Tatiana S Karpova
- the Center for Cancer Research Core Fluorescence Imaging Facility, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrew Lee
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Oskar Laur
- the Division of Microbiology, Yerkes Research Center, Emory University, Atlanta, Georgia 30329, and
| | - Sindhu Subramanian
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Dami Kim
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - James G McNally
- the Center for Cancer Research Core Fluorescence Imaging Facility, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Nicholas T Seyfried
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Yury O Chernoff
- the School of Biology and Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, the Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia 199034
| | - Keith D Wilkinson
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322,
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50
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Identification of long-lived proteins retained in cells undergoing repeated asymmetric divisions. Proc Natl Acad Sci U S A 2014; 111:14019-26. [PMID: 25228775 DOI: 10.1073/pnas.1416079111] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Long-lived proteins have been implicated in age-associated decline in metazoa, but they have only been identified in extracellular matrices or postmitotic cells. However, the aging process also occurs in dividing cells undergoing repeated asymmetric divisions. It was not clear whether long-lived proteins exist in asymmetrically dividing cells or whether they are involved in aging. Here we identify long-lived proteins in dividing cells during aging using the budding yeast, Saccharomyces cerevisiae. Yeast mother cells undergo a limited number of asymmetric divisions that define replicative lifespan. We used stable-isotope pulse-chase and total proteome mass-spectrometry to identify proteins that were both long-lived and retained in aging mother cells after ∼ 18 cells divisions. We identified ∼ 135 proteins that we designate as long-lived asymmetrically retained proteins (LARPS). Surprisingly, the majority of LARPs appeared to be stable fragments of their original full-length protein. However, 15% of LARPs were full-length proteins and we confirmed several candidates to be long-lived and retained in mother cells by time-lapse microscopy. Some LARPs localized to the plasma membrane and remained robustly in the mother cell upon cell division. Other full-length LARPs were assembled into large cytoplasmic structures that had a strong bias to remain in mother cells. We identified age-associated changes to LARPs that include an increase in their levels during aging because of their continued synthesis, which is not balanced by turnover. Additionally, several LARPs were posttranslationally modified during aging. We suggest that LARPs contribute to age-associated phenotypes and likely exist in other organisms.
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