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Naeimzadeh Y, Tajbakhsh A, Fallahi J. Understanding the prion-like behavior of mutant p53 proteins in triple-negative breast cancer pathogenesis: The current therapeutic strategies and future directions. Heliyon 2024; 10:e26260. [PMID: 38390040 PMCID: PMC10881377 DOI: 10.1016/j.heliyon.2024.e26260] [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: 10/23/2023] [Revised: 01/20/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Breast cancer (BC) is viewed as a significant public health issue and is the primary cause of cancer-related deaths among women worldwide. Triple-negative breast cancer (TNBC) is a particularly aggressive subtype that predominantly affects young premenopausal women. The tumor suppressor p53 playsa vital role in the cellular response to DNA damage, and its loss or mutations are commonly present in many cancers, including BC. Recent evidence suggests that mutant p53 proteins can aggregate and form prion-like structures, which may contribute to the pathogenesis of different types of malignancies, such as BC. This review provides an overview of BC molecular subtypes, the epidemiology of TNBC, and the role of p53 in BC development. We also discuss the potential implications of prion-like aggregation in BC and highlight future research directions. Moreover, a comprehensive analysis of the current therapeutic approaches targeting p53 aggregates in BC treatment is presented. Strategies including small molecules, chaperone inhibitors, immunotherapy, CRISPR-Cas9, and siRNA are discussed, along with their potential benefits and drawbacks. The use of these approaches to inhibit p53 aggregation and degradation represents a promising target for cancer therapy. Future investigations into the efficacy of these approaches against various p53 mutations or binding to non-p53 proteins should be conducted to develop more effective and personalized therapies for BC treatment.
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Affiliation(s)
- Yasaman Naeimzadeh
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran
| | - Amir Tajbakhsh
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jafar Fallahi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran
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2
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George JT. Optimal phenotypic adaptation in fluctuating environments. Biophys J 2023; 122:4414-4424. [PMID: 37876159 PMCID: PMC10698328 DOI: 10.1016/j.bpj.2023.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/28/2023] [Accepted: 10/18/2023] [Indexed: 10/26/2023] Open
Abstract
Phenotypic adaptation is a universal feature of biological systems navigating highly variable environments. Recent empirical data support the role of memory-driven decision making in cellular systems navigating uncertain future nutrient landscapes, wherein a distinct growth phenotype emerges in fluctuating conditions. We develop a simple stochastic mathematical model to describe memory-driven cellular adaptation required for systems to optimally navigate such uncertainty. In this framework, adaptive populations traverse dynamic environments by inferring future variation from a memory of prior states, and memory capacity imposes a fundamental trade-off between the speed and accuracy of adaptation to new fluctuating environments. Our results suggest that the observed growth reductions that occur in fluctuating environments are a direct consequence of optimal decision making and result from bet hedging and occasional phenotypic-environmental mismatch. We anticipate that this modeling framework will be useful for studying the role of memory in phenotypic adaptation, including in the design of temporally varying therapies against adaptive systems.
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Affiliation(s)
- Jason T George
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas; Engineering Medicine Program, Texas A&M University, Houston, Texas; Center for Theoretical Biological Physics, Rice University, Houston, Texas.
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3
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Son M, Han S, Lee S. Prions in Microbes: The Least in the Most. J Microbiol 2023; 61:881-889. [PMID: 37668956 DOI: 10.1007/s12275-023-00070-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 09/06/2023]
Abstract
Prions are infectious proteins that mostly replicate in self-propagating amyloid conformations (filamentous protein polymers) and consist of structurally altered normal soluble proteins. Prions can arise spontaneously in the cell without any clear reason and are generally considered fatal disease-causing agents that are only present in mammals. However, after the seminal discovery of two prions, [PSI+] and [URE3], in the eukaryotic model microorganism Saccharomyces cerevisiae, at least ten more prions have been discovered, and their biological and pathological effects on the host, molecular structure, and the relationship between prions and cellular components have been studied. In a filamentous fungus model, Podospora anserina, a vegetative incomparability-related [Het-s] prion that directly triggers cell death during anastomosis (hyphal fusion) was discovered. These prions in eukaryotic microbes have extended our understanding to overcome most fatal human prion/amyloid diseases. A prokaryotic microorganism (Clostridium botulinum) was reported to have a prion analog. The transcriptional regulators of C. botulinum-Rho can be converted into the self-replicating prion form ([RHO-X-C+]), which may affect global transcription. Here, we outline the major issues with prions in microbes and the lessons learned from the relatively uncovered microbial prion world.
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Affiliation(s)
- Moonil Son
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea.
- Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
| | - Sia Han
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Seyeon Lee
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
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4
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Jager K, Orozco-Hidalgo MT, Springstein BL, Joly-Smith E, Papazotos F, McDonough E, Fleming E, McCallum G, Yuan AH, Hilfinger A, Hochschild A, Potvin-Trottier L. Measuring prion propagation in single bacteria elucidates a mechanism of loss. Proc Natl Acad Sci U S A 2023; 120:e2221539120. [PMID: 37738299 PMCID: PMC10523482 DOI: 10.1073/pnas.2221539120] [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: 01/13/2023] [Accepted: 07/26/2023] [Indexed: 09/24/2023] Open
Abstract
Prions are self-propagating protein aggregates formed by specific proteins that can adopt alternative folds. Prions were discovered as the cause of the fatal transmissible spongiform encephalopathies in mammals, but prions can also constitute nontoxic protein-based elements of inheritance in fungi and other species. Prion propagation has recently been shown to occur in bacteria for more than a hundred cell divisions, yet a fraction of cells in these lineages lost the prion through an unknown mechanism. Here, we investigate prion propagation in single bacterial cells as they divide using microfluidics and fluorescence microscopy. We show that the propagation occurs in two distinct modes. In a fraction of the population, cells had multiple small visible aggregates and lost the prion through random partitioning of aggregates to one of the two daughter cells at division. In the other subpopulation, cells had a stable large aggregate localized to the pole; upon division the mother cell retained this polar aggregate and a daughter cell was generated that contained small aggregates. Extending our findings to prion domains from two orthologous proteins, we observe similar propagation and loss properties. Our findings also provide support for the suggestion that bacterial prions can form more than one self-propagating state. We implement a stochastic version of the molecular model of prion propagation from yeast and mammals that recapitulates all the observed single-cell properties. This model highlights challenges for prion propagation that are unique to prokaryotes and illustrates the conservation of fundamental characteristics of prion propagation.
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Affiliation(s)
- Krista Jager
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
| | | | | | - Euan Joly-Smith
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
| | - Fotini Papazotos
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
| | | | - Eleanor Fleming
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Giselle McCallum
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
| | - Andy H. Yuan
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Andreas Hilfinger
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
- Department of Mathematics, University of Toronto, Toronto, ONM5S 2E4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ONM5S 3G5, Canada
| | - Ann Hochschild
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Laurent Potvin-Trottier
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
- Department of Physics, Concordia University, Montréal, QCH4B 1R6, Canada
- Center for Applied Synthetic Biology, Concordia University, Montréal, QCH4B 1R6, Canada
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5
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Zajkowski T, Lee MD, Sharma S, Vallota-Eastman A, Kuska M, Malczewska M, Rothschild LJ. Conserved functions of prion candidates suggest a primeval role of protein self-templating. Proteins 2023; 91:1298-1315. [PMID: 37519023 DOI: 10.1002/prot.26558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
Amyloid-based prions have simple structures, a wide phylogenetic distribution, and a plethora of functions in contemporary organisms, suggesting they may be an ancient phenomenon. However, this hypothesis has yet to be addressed with a systematic, computational, and experimental approach. Here we present a framework to help guide future experimental verification of candidate prions with conserved functions to understand their role in the early stages of evolution and potentially in the origins of life. We identified candidate prions in all high-quality proteomes available in UniProt computationally, assessed their phylogenomic distributions, and analyzed candidate-prion functional annotations. Of the 27 980 560 proteins scanned, 228 561 were identified as candidate prions (~0.82%). Among these candidates, there were 84 Gene Ontology (GO) terms conserved across the three domains of life. We found that candidate prions with a possible role in adaptation were particularly well-represented within this group. We discuss unifying features of candidate prions to elucidate the primeval roles of prions and their associated functions. Candidate prions annotated as transcription factors, DNA binding, and kinases are particularly well suited to generating diverse responses to changes in their environment and could allow for adaptation and population expansion into more diverse environments. We hypothesized that a relationship between these functions and candidate prions could be evolutionarily ancient, even if individual prion domains themselves are not evolutionarily conserved. Candidate prions annotated with these universally occurring functions potentially represent the oldest extant prions on Earth and are therefore excellent experimental targets.
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Affiliation(s)
- Tomasz Zajkowski
- Universities Space Research Association at NASA Ames Research Center, Mountain View, California, USA
- Polish Astrobiology Society, Warsaw, Poland
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- KBR, NASA Ames Research Center, Mountain View, California, USA
| | - Siddhant Sharma
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Alec Vallota-Eastman
- Department of Earth Science, University of California, Santa Barbara, California, USA
| | - Mikołaj Kuska
- Polish Astrobiology Society, Warsaw, Poland
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Małgorzata Malczewska
- Polish Astrobiology Society, Warsaw, Poland
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Lynn J Rothschild
- Space Science and Astrobiology Division, NASA Ames Research Center, Mountain View, California, USA
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6
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Zhouravleva GA, Bondarev SA, Trubitsina NP. How Big Is the Yeast Prion Universe? Int J Mol Sci 2023; 24:11651. [PMID: 37511408 PMCID: PMC10380529 DOI: 10.3390/ijms241411651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The number of yeast prions and prion-like proteins described since 1994 has grown from two to nearly twenty. If in the early years most scientists working with the classic mammalian prion, PrPSc, were skeptical about the possibility of using the term prion to refer to yeast cytoplasmic elements with unusual properties, it is now clear that prion-like phenomena are widespread and that yeast can serve as a convenient model for studying them. Here we give a brief overview of the yeast prions discovered so far and focus our attention to the various approaches used to identify them. The prospects for the discovery of new yeast prions are also discussed.
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Affiliation(s)
- Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Nina P Trubitsina
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
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7
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Segal D, Maier S, Mastromarco GJ, Qian WW, Nabeel-Shah S, Lee H, Moore G, Lacoste J, Larsen B, Lin ZY, Selvabaskaran A, Liu K, Smibert C, Zhang Z, Greenblatt J, Peng J, Lee HO, Gingras AC, Taipale M. A central chaperone-like role for 14-3-3 proteins in human cells. Mol Cell 2023; 83:974-993.e15. [PMID: 36931259 DOI: 10.1016/j.molcel.2023.02.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 11/30/2022] [Accepted: 02/15/2023] [Indexed: 03/18/2023]
Abstract
14-3-3 proteins are highly conserved regulatory proteins that interact with hundreds of structurally diverse clients and act as central hubs of signaling networks. However, how 14-3-3 paralogs differ in specificity and how they regulate client protein function are not known for most clients. Here, we map the interactomes of all human 14-3-3 paralogs and systematically characterize the effect of disrupting these interactions on client localization. The loss of 14-3-3 binding leads to the coalescence of a large fraction of clients into discrete foci in a client-specific manner, suggesting a central chaperone-like function for 14-3-3 proteins. Congruently, the engraftment of 14-3-3 binding motifs to nonclients can suppress their aggregation or phase separation. Finally, we show that 14-3-3s negatively regulate the localization of the RNA-binding protein SAMD4A to cytoplasmic granules and inhibit its activity as a translational repressor. Our work suggests that 14-3-3s have a more prominent role as chaperone-like molecules than previously thought.
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Affiliation(s)
- Dmitri Segal
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Stefan Maier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | | | - Wesley Wei Qian
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Syed Nabeel-Shah
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hyunmin Lee
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Gaelen Moore
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jessica Lacoste
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Abeeshan Selvabaskaran
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Karen Liu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Craig Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada.
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
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8
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Howell-Bray T, Byrne L. The effect of prions on cellular metabolism: The metabolic impact of the [RNQ +] prion and potential role of native Rnq1p. RESEARCH SQUARE 2023:rs.3.rs-2511186. [PMID: 36909567 PMCID: PMC10002837 DOI: 10.21203/rs.3.rs-2511186/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Within the field of amyloid and prion disease there is a need for a more comprehensive understanding of the fundamentals of disease biology. In order to facilitate the progression treatment and underpin comprehension of toxicity, fundamental understanding of the disruption to normal cellular biochemistry and trafficking is needed. Here, by removing the complex biochemistry of the brain, we have utilised known prion forming strains of Saccharomyces cerevisiae carrying different conformational variants of the Rnq1p to obtain Liquid Chromatography-Mass Spectrometry (LC-MS) metabolic profiles and identify key perturbations of prion presence. These studies reveal that prion containing [RNQ+] cells display a significant reduction in amino acid biosynthesis and distinct perturbations in sphingolipid metabolism, with significant downregulation in metabolites within these pathways. Moreover, that native Rnq1p appears to downregulate ubiquinone biosynthesis pathways within cells, suggesting that Rnq1p may play a lipid/mevalonate-based cytoprotective role as a regulator of ubiquinone production. These findings contribute to the understanding of how prion proteins interact in vivo in both their prion and non-prion confirmations and indicate potential targets for the mitigation of these effects. We demonstrate specific sphingolipid centred metabolic disruptions due to prion presence and give insight into a potential cytoprotective role of the native Rnq1 protein. This provides evidence of metabolic similarities between yeast and mammalian cells as a consequence of prion presence and establishes the application of metabolomics as a tool to investigate prion/amyloid-based phenomena.
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Abstract
Most cells live in environments that are permissive for proliferation only a small fraction of the time. Entering quiescence enables cells to survive long periods of nondivision and reenter the cell cycle when signaled to do so. Here, we describe what is known about the molecular basis for quiescence in Saccharomyces cerevisiae, with emphasis on the progress made in the last decade. Quiescence is triggered by depletion of an essential nutrient. It begins well before nutrient exhaustion, and there is extensive crosstalk between signaling pathways to ensure that all proliferation-specific activities are stopped when any one essential nutrient is limiting. Every aspect of gene expression is modified to redirect and conserve resources. Chromatin structure and composition change on a global scale, from histone modifications to three-dimensional chromatin structure. Thousands of proteins and RNAs aggregate, forming unique structures with unique fates, and the cytoplasm transitions to a glass-like state.
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Affiliation(s)
- Linda L Breeden
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
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10
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Chakravarty AK, McGrail DJ, Lozanoski TM, Dunn BS, Shih DJ, Cirillo KM, Cetinkaya SH, Zheng WJ, Mills GB, Yi SS, Jarosz DF, Sahni N. Biomolecular Condensation: A New Phase in Cancer Research. Cancer Discov 2022; 12:2031-2043. [PMID: 35852417 PMCID: PMC9437557 DOI: 10.1158/2159-8290.cd-21-1605] [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: 12/07/2021] [Revised: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 01/09/2023]
Abstract
Multicellularity was a watershed development in evolution. However, it also meant that individual cells could escape regulatory mechanisms that restrict proliferation at a severe cost to the organism: cancer. From the standpoint of cellular organization, evolutionary complexity scales to organize different molecules within the intracellular milieu. The recent realization that many biomolecules can "phase-separate" into membraneless organelles, reorganizing cellular biochemistry in space and time, has led to an explosion of research activity in this area. In this review, we explore mechanistic connections between phase separation and cancer-associated processes and emerging examples of how these become deranged in malignancy. SIGNIFICANCE One of the fundamental functions of phase separation is to rapidly and dynamically respond to environmental perturbations. Importantly, these changes often lead to alterations in cancer-relevant pathways and processes. This review covers recent advances in the field, including emerging principles and mechanisms of phase separation in cancer.
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Affiliation(s)
- Anupam K. Chakravarty
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Daniel J. McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, Ohio
| | | | - Brandon S. Dunn
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David J.H. Shih
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas
| | - Kara M. Cirillo
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sueda H. Cetinkaya
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wenjin Jim Zheng
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas
| | - Gordon B. Mills
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon
| | - S. Stephen Yi
- Department of Oncology, Livestrong Cancer Institutes, The University of Texas at Austin, Austin, Texas
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
- Interdisciplinary Life Sciences Graduate Programs (ILSGP) and Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, Texas
| | - Daniel F. Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, Texas
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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11
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Anti-Prion Systems in Saccharomyces cerevisiae Turn an Avalanche of Prions into a Flurry. Viruses 2022; 14:v14091945. [PMID: 36146752 PMCID: PMC9503967 DOI: 10.3390/v14091945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/01/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022] Open
Abstract
Prions are infectious proteins, mostly having a self-propagating amyloid (filamentous protein polymer) structure consisting of an abnormal form of a normally soluble protein. These prions arise spontaneously in the cell without known reason, and their effects were generally considered to be fatal based on prion diseases in humans or mammals. However, the wide array of prion studies in yeast including filamentous fungi revealed that their effects can range widely, from lethal to very mild (even cryptic) or functional, depending on the nature of the prion protein and the specific prion variant (or strain) made by the same prion protein but with a different conformation. This prion biology is affected by an array of molecular chaperone systems, such as Hsp40, Hsp70, Hsp104, and combinations of them. In parallel with the systems required for prion propagation, yeast has multiple anti-prion systems, constantly working in the normal cell without overproduction of or a deficiency in any protein, which have negative effects on prions by blocking their formation, curing many prions after they arise, preventing prion infections, and reducing the cytotoxicity produced by prions. From the protectors of nascent polypeptides (Ssb1/2p, Zuo1p, and Ssz1p) to the protein sequesterase (Btn2p), the disaggregator (Hsp104), and the mysterious Cur1p, normal levels of each can cure the prion variants arising in its absence. The controllers of mRNA quality, nonsense-mediated mRNA decay proteins (Upf1, 2, 3), can cure newly formed prion variants by association with a prion-forming protein. The regulator of the inositol pyrophosphate metabolic pathway (Siw14p) cures certain prion variants by lowering the levels of certain organic compounds. Some of these proteins have other cellular functions (e.g., Btn2), while others produce an anti-prion effect through their primary role in the normal cell (e.g., ribosomal chaperones). Thus, these anti-prion actions are the innate defense strategy against prions. Here, we outline the anti-prion systems in yeast that produce innate immunity to prions by a multi-layered operation targeting each step of prion development.
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12
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Seuma M, Bolognesi B. Understanding and evolving prions by yeast multiplexed assays. Curr Opin Genet Dev 2022; 75:101941. [PMID: 35777350 DOI: 10.1016/j.gde.2022.101941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 11/15/2022]
Abstract
Yeast genetics made it possible to derive the first fundamental insights into prion composition, conformation, and propagation. Fast-forward 30 years and the same model organism is now proving an extremely powerful tool to comprehensively explore the impact of mutations in prion sequences on their function, toxicity, and physical properties. Here, we provide an overview of novel multiplexed strategies where deep mutagenesis is combined to a range of tailored selection assays in yeast, which are particularly amenable for investigating prions and prion-like sequences. By mimicking evolution in a flask, these multiplexed approaches are revealing mechanistic insights on the consequences of prion self-assembly, while also reporting on the structure prion sequences adopt in vivo.
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Affiliation(s)
- Mireia Seuma
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain. https://twitter.com/@mseumaar
| | - Benedetta Bolognesi
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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13
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Lau Y, Oamen HP, Grogg M, Parfenova I, Saarikangas J, Hannay R, Nichols RA, Hilvert D, Barral Y, Caudron F. Whi3 mnemon association with endoplasmic reticulum membranes confines the memory of deceptive courtship to the yeast mother cell. Curr Biol 2022; 32:963-974.e7. [PMID: 35085498 PMCID: PMC8938615 DOI: 10.1016/j.cub.2022.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 12/17/2022]
Abstract
Prion-like proteins are involved in many aspects of cellular physiology, including cellular memory. In response to deceptive courtship, budding yeast escapes pheromone-induced cell-cycle arrest through the coalescence of the G1/S inhibitor Whi3 into a dominant, inactive super-assembly. Whi3 is a mnemon (Whi3mnem), a protein that conformational change maintains as a trait in the mother cell but is not inherited by the daughter cells. How the maintenance and asymmetric inheritance of Whi3mnem are achieved is unknown. Here, we report that Whi3mnem is closely associated with endoplasmic reticulum (ER) membranes and is retained in the mother cell by the lateral diffusion barriers present at the bud neck. Strikingly, barrier defects made Whi3mnem propagate in a mitotically stable, prion-like manner. The amyloid-forming glutamine-rich domain of Whi3 was required for both mnemon and prion-like behaviors. Thus, we propose that Whi3mnem is in a self-templating state, lending temporal maintenance of memory, whereas its association with the compartmentalized membranes of the ER prevents infectious propagation to the daughter cells. These results suggest that confined self-templating super-assembly is a powerful mechanism for the long-term encoding of information in a spatially defined manner. Yeast courtship may provide insights on how individual synapses become potentiated in neuronal memory.
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Affiliation(s)
- Yasmin Lau
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Henry Patrick Oamen
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Marcel Grogg
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg, 8093 Zürich, Switzerland
| | - Iuliia Parfenova
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg, 8093 Zürich, Switzerland
| | - Juha Saarikangas
- Helsinki Institute of Life Science HiLIFE, Viikinkaari 5, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, Viikinkaari 5, 00790 Helsinki, Finland; Neuroscience Center, University of Helsinki, Viikinkaari 5, 00790 Helsinki, Finland
| | - Robin Hannay
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Richard Alan Nichols
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg, 8093 Zürich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg, 8093 Zürich, Switzerland
| | - Fabrice Caudron
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; IGMM, Univ Montpellier, CNRS, Route de Mende, 34293 Montpellier, France.
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14
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Garcia DM, Campbell EA, Jakobson CM, Tsuchiya M, Shaw EA, DiNardo AL, Kaeberlein M, Jarosz DF. A prion accelerates proliferation at the expense of lifespan. eLife 2021; 10:e60917. [PMID: 34545808 PMCID: PMC8455135 DOI: 10.7554/elife.60917] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/12/2021] [Indexed: 12/23/2022] Open
Abstract
In fluctuating environments, switching between different growth strategies, such as those affecting cell size and proliferation, can be advantageous to an organism. Trade-offs arise, however. Mechanisms that aberrantly increase cell size or proliferation-such as mutations or chemicals that interfere with growth regulatory pathways-can also shorten lifespan. Here we report a natural example of how the interplay between growth and lifespan can be epigenetically controlled. We find that a highly conserved RNA-modifying enzyme, the pseudouridine synthase Pus4/TruB, can act as a prion, endowing yeast with greater proliferation rates at the cost of a shortened lifespan. Cells harboring the prion grow larger and exhibit altered protein synthesis. This epigenetic state, [BIG+] (better in growth), allows cells to heritably yet reversibly alter their translational program, leading to the differential synthesis of dozens of proteins, including many that regulate proliferation and aging. Our data reveal a new role for prion-based control of an RNA-modifying enzyme in driving heritable epigenetic states that transform cell growth and survival.
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Affiliation(s)
- David M Garcia
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Edgar A Campbell
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Christopher M Jakobson
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Mitsuhiro Tsuchiya
- Department of Pathology, University of Washington, Seattle, United States
| | - Ethan A Shaw
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Acadia L DiNardo
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, United States
| | - Daniel F Jarosz
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
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15
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Zajkowski T, Lee MD, Mondal SS, Carbajal A, Dec R, Brennock PD, Piast RW, Snyder JE, Bense NB, Dzwolak W, Jarosz DF, Rothschild LJ. The Hunt for Ancient Prions: Archaeal Prion-Like Domains Form Amyloid-Based Epigenetic Elements. Mol Biol Evol 2021; 38:2088-2103. [PMID: 33480998 DOI: 10.1093/molbev/msab010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Prions, proteins that can convert between structurally and functionally distinct states and serve as non-Mendelian mechanisms of inheritance, were initially discovered and only known in eukaryotes, and consequently considered to likely be a relatively late evolutionary acquisition. However, the recent discovery of prions in bacteria and viruses has intimated a potentially more ancient evolutionary origin. Here, we provide evidence that prion-forming domains exist in the domain archaea, the last domain of life left unexplored with regard to prions. We searched for archaeal candidate prion-forming protein sequences computationally, described their taxonomic distribution and phylogeny, and analyzed their associated functional annotations. Using biophysical in vitro assays, cell-based and microscopic approaches, and dye-binding analyses, we tested select candidate prion-forming domains for prionogenic characteristics. Out of the 16 tested, eight formed amyloids, and six acted as protein-based elements of information transfer driving non-Mendelian patterns of inheritance. We also identified short peptides from our archaeal prion candidates that can form amyloid fibrils independently. Lastly, candidates that tested positively in our assays had significantly higher tyrosine and phenylalanine content than candidates that tested negatively, an observation that may help future archaeal prion predictions. Taken together, our discovery of functional prion-forming domains in archaea provides evidence that multiple archaeal proteins are capable of acting as prions-thus expanding our knowledge of this epigenetic phenomenon to the third and final domain of life and bolstering the possibility that they were present at the time of the last universal common ancestor.
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Affiliation(s)
- Tomasz Zajkowski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,University Space Research Association, Mountain View, CA, USA.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Shamba S Mondal
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Amanda Carbajal
- University Space Research Association, Mountain View, CA, USA.,University of California Santa Cruz, Santa Cruz, CA, USA
| | - Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | | | - Radoslaw W Piast
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | | | | | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynn J Rothschild
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA, USA
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16
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Generic nature of the condensed states of proteins. Nat Cell Biol 2021; 23:587-594. [PMID: 34108660 DOI: 10.1038/s41556-021-00697-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/07/2021] [Indexed: 02/05/2023]
Abstract
Proteins undergoing liquid-liquid phase separation are being discovered at an increasing rate. Since at the high concentrations present in the cell most proteins would be expected to form a liquid condensed state, this state should be considered to be a fundamental state of proteins along with the native state and the amyloid state. Here we discuss the generic nature of the liquid-like and solid-like condensed states, and describe a wide variety of biological functions conferred by these condensed states.
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17
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Defining the role of the polyasparagine repeat domain of the S. cerevisiae transcription factor Azf1p. PLoS One 2021; 16:e0247285. [PMID: 34019539 PMCID: PMC8139511 DOI: 10.1371/journal.pone.0247285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/26/2021] [Indexed: 11/23/2022] Open
Abstract
Across eukaryotes, homopolymeric repeats of amino acids are enriched in regulatory proteins such as transcription factors and chromatin remodelers. These domains play important roles in signaling, binding, prion formation, and functional phase separation. Azf1p is a prion-forming yeast transcription factor that contains two homorepeat domains, a polyglutamine and a polyasparagine domain. In this work, we report a new phenotype for Azf1p and identify a large set of genes that are regulated by Azf1p during growth in glucose. We show that the polyasparagine (polyN) domain plays a subtle role in transcription but is dispensable for Azf1p localization and prion formation. Genes upregulated upon deletion of the polyN domain are enriched in functions related to carbon metabolism and storage. This domain may therefore be a useful target for engineering yeast strains for fermentation applications and small molecule production. We also report that both the polyasparagine and polyglutamine domains vary in length across strains of S. cerevisiae and propose a model for how this variation may impact protein function.
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18
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Chen YR, Ziv I, Swaminathan K, Elias JE, Jarosz DF. Protein aggregation and the evolution of stress resistance in clinical yeast. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200127. [PMID: 33866806 DOI: 10.1098/rstb.2020.0127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Protein aggregation, particularly in its prion-like form, has long been thought to be detrimental. However, recent studies have identified multiple instances where protein aggregation is important for normal physiological functions. Combining mass spectrometry and cell biological approaches, we developed a strategy for the identification of protein aggregates in cell lysates. We used this approach to characterize prion-based traits in pathogenic strains of the yeast Saccharomyces cerevisiae isolated from immunocompromised human patients. The proteins that we found, including the metabolic enzyme Cdc19, the translation elongation factor Yef3 and the fibrillarin homologue Nop1, are known to assemble under certain physiological conditions. Yet, such assemblies have not been reported to be stable or heritable. Our data suggest that some proteins which aggregate in response to stress have the capacity to acquire diverse assembled states, certain ones of which can be propagated across generations in a form of protein-based epigenetics. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Yiwen R Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Inbal Ziv
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Kavya Swaminathan
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.,Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
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19
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Saad S, Jarosz DF. Protein self-assembly: A new frontier in cell signaling. Curr Opin Cell Biol 2021; 69:62-69. [PMID: 33493989 PMCID: PMC8058241 DOI: 10.1016/j.ceb.2020.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022]
Abstract
Long viewed as paradigm-shifting, but rare, prions have recently been discovered in all domains of life. Protein sequences that can drive this form of self-assembly are strikingly common in eukaryotic proteomes, where they are enriched in proteins involved in information flow and signal transduction. Although prions were thought to be a consequence of random errors in protein folding, recent studies suggest that prion formation can be a controlled process initiated by defined cellular signals. Many are present in normal biological contexts, yet are invisible to most technologies used to interrogate the proteome. Here, we review mechanisms by which protein self-assembly can create a stable record of past stimuli, altering adaptive responses, and how prion behavior is controlled by signaling processes. We touch on the diverse implications that this has for normal biological function and regulation, ranging from drug resistance in fungi to the innate immune response in humans. Finally, we discuss the potential for prion domains in transcription factors and RNA-binding proteins to orchestrate heritable gene expression changes in response to transient signals, such as during development.
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Affiliation(s)
- Shady Saad
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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20
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Reichert P, Caudron F. Mnemons and the memorization of past signaling events. Curr Opin Cell Biol 2021; 69:127-135. [PMID: 33618243 DOI: 10.1016/j.ceb.2021.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/28/2022]
Abstract
Current advances are raising our awareness of the diverse roles that protein condensation plays in the biology of cells. Particularly, findings in organisms as diverse as yeast and Drosophila suggest that cells may utilize protein condensation to establish long-lasting changes in cellular activities and thereby encode a memory of past signaling events. Proteins that oligomerize to confer such cellular memory have been termed 'mnemons'. In the forming of super-assemblies, mnemons change their function and modulate the influence that the affected protein originally had on cellular processes. Because mnemon assemblies are self-templating, they allow cells to retain the memory of past decisions over larger timescales. Here, we review the mechanisms behind the formation of cellular memory with an emphasis on mnemon-mediated memorization of past signaling events.
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Affiliation(s)
- Polina Reichert
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Fabrice Caudron
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
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21
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Jiang Y, Hao N. Memorizing environmental signals through feedback and feedforward loops. Curr Opin Cell Biol 2021; 69:96-102. [PMID: 33549848 DOI: 10.1016/j.ceb.2020.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022]
Abstract
Cells in diverse organisms can store the information of previous environmental conditions for long periods of time. This form of cellular memory adjusts the cell's responses to future challenges, providing fitness advantages in fluctuating environments. Many biological functions, including cellular memory, are mediated by specific recurring patterns of interactions among proteins and genes, known as 'network motifs.' In this review, we focus on three well-characterized network motifs - negative feedback loops, positive feedback loops, and feedforward loops, which underlie different types of cellular memories. We describe the latest studies identifying these motifs in various molecular processes and discuss how the topologies and dynamics of these motifs can enable memory encoding and storage.
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Affiliation(s)
- Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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22
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Levkovich SA, Rencus-Lazar S, Gazit E, Laor Bar-Yosef D. Microbial Prions: Dawn of a New Era. Trends Biochem Sci 2021; 46:391-405. [PMID: 33423939 DOI: 10.1016/j.tibs.2020.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/22/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022]
Abstract
Protein misfolding and aggregation are associated with human diseases and aging. However, microorganisms widely exploit the self-propagating properties of misfolded infectious protein particles, prions, as epigenetic information carriers that drive various phenotypic adaptations and encode molecular information. Microbial prion research has faced a paradigm shift in recent years, with breakthroughs that demonstrate the great functional and structural diversity of these agents. Here, we outline unorthodox examples of microbial prions in yeast and other microorganisms, focusing on their noncanonical functions. We discuss novel molecular mechanisms for the inheritance of conformationally-encoded epigenetic information and the evolutionary advantages they confer. Lastly, in light of recent advancements in the field of molecular self-assembly, we present a hypothesis regarding the existence of non-proteinaceous prion-like entities.
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Affiliation(s)
- Shon A Levkovich
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sigal Rencus-Lazar
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ehud Gazit
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel; Sagol Interdisciplinary School of Neurosciences, Tel Aviv University, Tel Aviv, Israel.
| | - Dana Laor Bar-Yosef
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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23
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Ishikawa T. Saccharomyces cerevisiae in neuroscience: how unicellular organism helps to better understand prion protein? Neural Regen Res 2021; 16:489-495. [PMID: 32985470 PMCID: PMC7996030 DOI: 10.4103/1673-5374.293137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The baker’s yeast Saccharomyces (S.) cerevisiae is a single-celled eukaryotic model organism widely used in research on life sciences. Being a unicellular organism, S. cerevisiae has some evident limitations in application to neuroscience. However, yeast prions are extensively studied and they are known to share some hallmarks with mammalian prion protein or other amyloidogenic proteins found in the pathogenesis of Alzheimer’s, Parkinson’s, or Huntington’s diseases. Therefore, the yeast S. cerevisiae has been widely used for basic research on aggregation properties of proteins in cellulo and on their propagation. Recently, a yeast-based study revealed that some regions of mammalian prion protein and amyloid β1–42 are capable of induction and propagation of yeast prions. It is one of the examples showing that evolutionarily distant organisms share common mechanisms underlying the structural conversion of prion proteins making yeast cells a useful system for studying mammalian prion protein. S. cerevisiae has also been used to design novel screening systems for anti-prion compounds from chemical libraries. Yeast-based assays are cheap in maintenance and safe for the researcher, making them a very good choice to perform preliminary screening before further characterization in systems engaging mammalian cells infected with prions. In this review, not only classical red/white colony assay but also yeast-based screening assays developed during last year are discussed. Computational analysis and research carried out using yeast prions force us to expect that prions are widely present in nature. Indeed, the last few years brought us several examples indicating that the mammalian prion protein is no more peculiar protein – it seems that a better understanding of prion proteins nature-wide may aid us with the treatment of prion diseases and other amyloid-related medical conditions.
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Affiliation(s)
- Takao Ishikawa
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
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24
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Simpson-Lavy K, Kupiec M. Noise buffering by biomolecular condensates in glucose sensing. Curr Opin Cell Biol 2020; 69:1-6. [PMID: 33388622 DOI: 10.1016/j.ceb.2020.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 02/05/2023]
Abstract
Many cellular processes involve buffering mechanisms against noise to enhance state stability. Such processes include the cell cycle and the switch between respiration and fermentation. In recent years, protein aggregation/condensation has emerged as an important regulatory mechanism. In this article, we examine the regulation of Std1, an activator of the Snf1/AMPK kinase, by sequestration into foci of liquid drops, and how foci of metabolic signaling and enzymatic proteins are regulated by chaperones, anti-aggregases and by phosphorylation.
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Affiliation(s)
- Kobi Simpson-Lavy
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, 69978, Israel.
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25
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Park SK, Park S, Pentek C, Liebman SW. Tumor suppressor protein p53 expressed in yeast can remain diffuse, form a prion, or form unstable liquid-like droplets. iScience 2020; 24:102000. [PMID: 33490908 PMCID: PMC7811139 DOI: 10.1016/j.isci.2020.102000] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/20/2020] [Accepted: 12/23/2020] [Indexed: 01/08/2023] Open
Abstract
Mutations in the p53 tumor suppressor are frequent causes of cancer. Because p53 aggregates appear in some tumor cells, it has been suggested that p53 could also cause cancer by forming self-replicating protein aggregates (prions). Here, using yeast, we show that transient p53 overexpression induced the formation of p53 prion aggregates that were transmitted for >100 generations, found in lysate pellets, stained with Thioflavin T, and transmitted by cytoplasmic transfer, or transfection with lysates of cells carrying the prion or with p53 amyloid peptide. As predicted for a prion, transient interruption of p53 expression caused permanent p53 prion loss. Importantly, p53 transcription factor activity was reduced by prion formation suggesting that prion aggregation could cause cancer. p53 has also been found in liquid-like nuclear droplets in animal cell culture. In yeast, we found that liquid-like p53 foci appear in response to stress and disappear with stress removal. A published yeast model of functional nuclear human p53 tumor suppressor was used Upon transient overexpression p53 loses its transcription function and aggregates These p53 aggregates are cytoplasmic and behave like stable heritable prions Stress induces p53 to form liquid-like droplets that are unstable and not prion-like
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Affiliation(s)
- Sei-Kyoung Park
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
| | - Sangeun Park
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
| | - Christine Pentek
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
| | - Susan W Liebman
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
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26
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Klim J, Zielenkiewicz U, Kurlandzka A, Kaczanowski S, Skoneczny M. Slow Adaptive Response of Budding Yeast Cells to Stable Conditions of Continuous Culture Can Occur without Genome Modifications. Genes (Basel) 2020; 11:genes11121419. [PMID: 33261040 PMCID: PMC7759791 DOI: 10.3390/genes11121419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 11/20/2022] Open
Abstract
Continuous cultures assure the invariability of environmental conditions and the metabolic state of cultured microorganisms, whereas batch-cultured cells undergo constant changes in nutrients availability. For that reason, continuous culture is sometimes employed in the whole transcriptome, whole proteome, or whole metabolome studies. However, the typical method for establishing uniform growth of a cell population, i.e., by limited chemostat, results in the enrichment of the cell population gene pool with mutations adaptive for starvation conditions. These adaptive changes can skew the results of large-scale studies. It is commonly assumed that these adaptations reflect changes in the genome, and this assumption has been confirmed experimentally in rare cases. Here we show that in a population of budding yeast cells grown for over 200 generations in continuous culture in non-limiting minimal medium and therefore not subject to selection pressure, remodeling of transcriptome occurs, but not as a result of the accumulation of adaptive mutations. The observed changes indicate a shift in the metabolic balance towards catabolism, a decrease in ribosome biogenesis, a decrease in general stress alertness, reorganization of the cell wall, and transactions occurring at the cell periphery. These adaptive changes signify the acquisition of a new lifestyle in a stable nonstressful environment. The absence of underlying adaptive mutations suggests these changes may be regulated by another mechanism.
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Affiliation(s)
- Joanna Klim
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (J.K.); (U.Z.)
| | - Urszula Zielenkiewicz
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (J.K.); (U.Z.)
| | - Anna Kurlandzka
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland;
| | - Szymon Kaczanowski
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland;
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland;
- Correspondence: ; Tel.: +48-22-5921217
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27
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A framework for understanding the functions of biomolecular condensates across scales. Nat Rev Mol Cell Biol 2020; 22:215-235. [PMID: 33169001 DOI: 10.1038/s41580-020-00303-z] [Citation(s) in RCA: 362] [Impact Index Per Article: 90.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
Biomolecular condensates are found throughout eukaryotic cells, including in the nucleus, in the cytoplasm and on membranes. They are also implicated in a wide range of cellular functions, organizing molecules that act in processes ranging from RNA metabolism to signalling to gene regulation. Early work in the field focused on identifying condensates and understanding how their physical properties and regulation arise from molecular constituents. Recent years have brought a focus on understanding condensate functions. Studies have revealed functions that span different length scales: from molecular (modulating the rates of chemical reactions) to mesoscale (organizing large structures within cells) to cellular (facilitating localization of cellular materials and homeostatic responses). In this Roadmap, we discuss representative examples of biochemical and cellular functions of biomolecular condensates from the recent literature and organize these functions into a series of non-exclusive classes across the different length scales. We conclude with a discussion of areas of current interest and challenges in the field, and thoughts about how progress may be made to further our understanding of the widespread roles of condensates in cell biology.
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Oamen HP, Lau Y, Caudron F. Prion-like proteins as epigenetic devices of stress adaptation. Exp Cell Res 2020; 396:112262. [DOI: 10.1016/j.yexcr.2020.112262] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/26/2020] [Accepted: 08/30/2020] [Indexed: 01/03/2023]
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Jakobson CM, Jarosz DF. What Has a Century of Quantitative Genetics Taught Us About Nature's Genetic Tool Kit? Annu Rev Genet 2020; 54:439-464. [PMID: 32897739 DOI: 10.1146/annurev-genet-021920-102037] [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] [Indexed: 11/09/2022]
Abstract
The complexity of heredity has been appreciated for decades: Many traits are controlled not by a single genetic locus but instead by polymorphisms throughout the genome. The importance of complex traits in biology and medicine has motivated diverse approaches to understanding their detailed genetic bases. Here, we focus on recent systematic studies, many in budding yeast, which have revealed that large numbers of all kinds of molecular variation, from noncoding to synonymous variants, can make significant contributions to phenotype. Variants can affect different traits in opposing directions, and their contributions can be modified by both the environment and the epigenetic state of the cell. The integration of prospective (synthesizing and analyzing variants) and retrospective (examining standing variation) approaches promises to reveal how natural selection shapes quantitative traits. Only by comprehensively understanding nature's genetic tool kit can we predict how phenotypes arise from the complex ensembles of genetic variants in living organisms.
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Affiliation(s)
- Christopher M Jakobson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA; .,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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Dixson JD, Azad RK. Prions: Roles in Development and Adaptive Evolution. J Mol Evol 2020; 88:427-434. [PMID: 32388713 DOI: 10.1007/s00239-020-09944-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/28/2020] [Indexed: 12/14/2022]
Abstract
Prions are often considered as anomalous proteins associated primarily with disease rather than as a fundamental source of diversity within biological proteomes. Whereas this longstanding viewpoint has its genesis in the discovery of the original namesake prions as causative agents of several complex diseases, the underlying assumption of a strict disease basis for prions could not be further from the truth. Prions and the spectrum of functions they comprise, likely represent one of the largest paradigm shifts concerning molecular-encoded phenotypic diversity since identification of DNA as the principle molecule of heredity. The ability of prions to recruit similar proteins to alternate conformations may engender a reservoir of diversity supplementing the genetic diversity resulting from stochastic mutations of DNA and subsequent natural selection. Here we present several currently known prions and how many of their functions as well as modes of transmission are intricately linked to adaptation from an evolutionary perspective. Further, the stability of some prion conformations across generations indicates that heritable prion-based adaptation is a reality.
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Affiliation(s)
- Jamie D Dixson
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA.
- Department of Mathematics, University of North Texas, Denton, TX, 76203, USA.
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Widespread Prion-Based Control of Growth and Differentiation Strategies in Saccharomyces cerevisiae. Mol Cell 2019; 77:266-278.e6. [PMID: 31757756 DOI: 10.1016/j.molcel.2019.10.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/29/2019] [Accepted: 10/17/2019] [Indexed: 02/08/2023]
Abstract
Theory and experiments suggest that organisms would benefit from pre-adaptation to future stressors based on reproducible environmental fluctuations experienced by their ancestors, but the mechanisms driving pre-adaptation remain enigmatic. We report that the [SMAUG+] prion allows yeast to anticipate nutrient repletion after periods of starvation, providing a strong selective advantage. By transforming the landscape of post-transcriptional gene expression, [SMAUG+] regulates the decision between two broad growth and survival strategies: mitotic proliferation or meiotic differentiation into a stress-resistant state. [SMAUG+] is common in laboratory yeast strains, where standard propagation practice produces regular cycles of nutrient scarcity followed by repletion. Distinct [SMAUG+] variants are also widespread in wild yeast isolates from multiple niches, establishing that prion polymorphs can be utilized in natural populations. Our data provide a striking example of how protein-based epigenetic switches, hidden in plain sight, can establish a transgenerational memory that integrates adaptive prediction into developmental decisions.
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