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Wenzhi Y, Xiangyi L, Dongsheng F. The prion-like effect and prion-like protein targeting strategy in amyotrophic lateral sclerosis. Heliyon 2024; 10:e34963. [PMID: 39170125 PMCID: PMC11336370 DOI: 10.1016/j.heliyon.2024.e34963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/09/2024] [Accepted: 07/19/2024] [Indexed: 08/23/2024] Open
Abstract
Pathological proteins in amyotrophic lateral sclerosis (ALS), such as superoxide dismutase 1, TAR DNA-binding protein 43, and fused in sarcoma, exhibit a prion-like pattern. All these proteins have a low-complexity domain and seeding activity in cells. In this review, we summarize the studies on the prion-like effect of these proteins and list six prion-like protein targeting strategies that we believe have potential for ALS therapy, including antisense oligonucleotides, antibody-based technology, peptide, protein chaperone, autophagy enhancement, and heteromultivalent compounds. Considering the pathological complexity and heterogeneity of ALS, we believe that the final solution to ALS therapy is most likely to be an individualized cocktail therapy, including clearance of toxicity, blockage of pathological progress, and protection of neurons.
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Affiliation(s)
- Yang Wenzhi
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
| | - Liu Xiangyi
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
| | - Fan Dongsheng
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
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2
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Roth GV, Gengaro IR, Qi LS. Precision epigenetic editing: Technological advances, enduring challenges, and therapeutic applications. Cell Chem Biol 2024:S2451-9456(24)00309-X. [PMID: 39137782 DOI: 10.1016/j.chembiol.2024.07.007] [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: 03/04/2024] [Revised: 05/31/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024]
Abstract
The epigenome is a complex framework through which gene expression is precisely and flexibly modulated to incorporate heritable memory and responses to environmental stimuli. It governs diverse cellular processes, including cell fate, disease, and aging. The need to understand this system and precisely control gene expression outputs for therapeutic purposes has precipitated the development of a diverse set of epigenetic editing tools. Here, we review the existing toolbox for targeted epigenetic editing, technical considerations of the current technologies, and opportunities for future development. We describe applications of therapeutic epigenetic editing and their potential for treating disease, with a discussion of ongoing delivery challenges that impede certain clinical interventions, particularly in the brain. With simultaneous advancements in available engineering tools and appropriate delivery technologies, we predict that epigenetic editing will increasingly cement itself as a powerful approach for safely treating a wide range of disorders in all tissues of the body.
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Affiliation(s)
- Goldie V Roth
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Isabella R Gengaro
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Lei S Qi
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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3
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Ni Y, Qiao Y, Tian X, Li H, Meng Y, Li C, Du W, Sun T, Zhu K, Huang W, Yan H, Li J, Zhou R, Ding C, Gao X. Unraveling the mechanism of thermotolerance by Set302 in Cryptococcus neoformans. Microbiol Spectr 2024; 12:e0420223. [PMID: 38874428 PMCID: PMC11302353 DOI: 10.1128/spectrum.04202-23] [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: 12/28/2023] [Accepted: 05/12/2024] [Indexed: 06/15/2024] Open
Abstract
The underlying mechanism of thermotolerance, which is a key virulence factor essential for pathogenic fungi such as Cryptococcus neoformans, is largely unexplored. In this study, our findings suggest that Set302, a homolog of Set3 and a subunit of histone deacetylase complex Set3C, contributes to thermotolerance in C. neoformans. Specifically, the deletion of the predicted Set3C core subunit, Set302, resulted in further reduction in the growth of C. neoformans at 39°C, and survival of transient incubation at 50°C. Transcriptomics analysis revealed that the expression levels of numerous heat stress-responsive genes altered at both 30°C and 39°C due to the lack of Set302. Notably, at 39°C, the absence of Set302 led to the downregulation of gene expression related to the ubiquitin-proteasome system (UPS). Based on the GFP-α-synuclein overexpression model to characterize misfolded proteins, we observed a pronounced accumulation of misfolded GFP-α-synuclein at 39°C, consequently inhibiting C. neoformans thermotolerance. Furthermore, the loss of Set302 exacerbated the accumulation of misfolded GFP-α-synuclein during heat stress. Interestingly, the set302∆ strain exhibited a similar phenotype under proteasome stress as it did at 39°C. Moreover, the absence of Set302 led to reduced production of capsule and melanin. set302∆ strain also displayed significantly reduced pathogenicity and colonization ability compared to the wild-type strain in the murine infection model. Collectively, our findings suggest that Set302 modulates thermotolerance by affecting the degradation of misfolded proteins and multiple virulence factors to mediate the pathogenicity of C. neoformans.IMPORTANCECryptococcus neoformans is a pathogenic fungus that poses a potential and significant threat to public health. Thermotolerance plays a crucial role in the wide distribution in natural environments and host colonization of this fungus. Herein, Set302, a critical core subunit for the integrity of histone deacetylase complex Set3C and widely distributed in various fungi and mammals, governs thermotolerance and affects survival at extreme temperatures as well as the formation of capsule and melanin in C. neoformans. Additionally, Set302 participates in regulating the expression of multiple genes associated with the ubiquitin-proteasome system (UPS). By eliminating misfolded proteins under heat stress, Set302 significantly contributes to the thermotolerance of C. neoformans. Moreover, Set302 regulates the pathogenicity and colonization ability of C. neoformans in a murine model. Overall, this study provides new insight into the mechanism of thermotolerance in C. neoformans.
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Affiliation(s)
- Yue Ni
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Yue Qiao
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Xing Tian
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Hailong Li
- NHC Key Laboratory of AIDS Immunology, National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yang Meng
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Chao Li
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Wei Du
- Department of Clinical Laboratory, National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tianshu Sun
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Medical Research Centre, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Keting Zhu
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Wei Huang
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - He Yan
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Jia Li
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Renjie Zhou
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Chen Ding
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Xindi Gao
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
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4
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Garai S, Raizada A, Kumar V, Sopory SK, Pareek A, Singla-Pareek SL, Kaur C. In silico analysis of fungal prion-like proteins for elucidating their role in plant-fungi interactions. Arch Microbiol 2024; 206:308. [PMID: 38896139 DOI: 10.1007/s00203-024-04040-1] [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: 04/03/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/21/2024]
Abstract
Prion-like proteins (PrLPs) have emerged as beneficial molecules with implications in adaptive responses. These proteins possess a conserved prion-like domain (PrLD) which is an intrinsically disordered region capable of adopting different conformations upon perceiving external stimuli. Owing to changes in protein conformation, functional characteristics of proteins harboring PrLDs get altered thereby, providing a unique mode of protein-based regulation. Since PrLPs are ubiquitous in nature and involved in diverse functions, through this study, we aim to explore the role of such domains in yet another important physiological process viz. plant-microbe interactions to get insights into the mechanisms dictating cross-kingdom interactions. We have evaluated the presence and functions of PrLPs in 18 different plant-associated fungi of agricultural importance to unravel their role in plant-microbe interactions. Of the 241,997 proteins scanned, 3,820 (~ 1.6%) were identified as putative PrLPs with pathogenic fungi showing significantly higher PrLP density than their beneficial counterparts. Further, through GO enrichment analysis, we could predict several PrLPs from pathogenic fungi to be involved in virulence and formation of stress granules. Notably, PrLPs involved in (retro)transposition were observed exclusively in pathogenic fungi. We even analyzed publicly available data for the expression alterations of fungal PrLPs upon their interaction with their respective hosts which revealed perturbation in the levels of some PrLP-encoding genes during interactions with plants. Overall, our work sheds light into the probable role of prion-like candidates in plant-fungi interaction, particularly in context of pathogenesis, paving way for more focused studies for validating their role.
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Affiliation(s)
- Sampurna Garai
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Avi Raizada
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India
| | - Vijay Kumar
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India
| | - Sudhir K Sopory
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ashwani Pareek
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Charanpreet Kaur
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
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5
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Akilli N, Cheutin T, Cavalli G. Phase separation and inheritance of repressive chromatin domains. Curr Opin Genet Dev 2024; 86:102201. [PMID: 38701672 DOI: 10.1016/j.gde.2024.102201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024]
Abstract
Polycomb-associated chromatin and pericentromeric heterochromatin form genomic domains important for the epigenetic regulation of gene expression. Both Polycomb complexes and heterochromatin factors rely on 'read and write' mechanisms, which, on their own, are not sufficient to explain the formation and the maintenance of these epigenetic domains. Microscopy has revealed that they form specific nuclear compartments separated from the rest of the genome. Recently, some subunits of these molecular machineries have been shown to undergo phase separation, both in vitro and in vivo, suggesting that phase separation might play important roles in the formation and the function of these two kinds of repressive chromatin. In this review, we will present the recent advances in the field of facultative and constitutive heterochromatin formation and maintenance through phase separation.
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Affiliation(s)
- Nazli Akilli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France. https://twitter.com/@sinmerank
| | - Thierry Cheutin
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
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6
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Fallet M, Wilson R, Sarkies P. Cisplatin exposure alters tRNA-derived small RNAs but does not affect epimutations in C. elegans. BMC Biol 2023; 21:276. [PMID: 38031056 PMCID: PMC10688063 DOI: 10.1186/s12915-023-01767-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND The individual lifestyle and environment of an organism can influence its phenotype and potentially the phenotype of its offspring. The different genetic and non-genetic components of the inheritance system and their mutual interactions are key mechanisms to generate inherited phenotypic changes. Epigenetic changes can be transmitted between generations independently from changes in DNA sequence. In Caenorhabditis elegans, epigenetic differences, i.e. epimutations, mediated by small non-coding RNAs, particularly 22G-RNAs, as well as chromatin have been identified, and their average persistence is three to five generations. In addition, previous research showed that some epimutations had a longer duration and concerned genes that were enriched for multiple components of xenobiotic response pathways. These results raise the possibility that environmental stresses might change the rate at which epimutations occur, with potential significance for adaptation. RESULTS In this work, we explore this question by propagating C. elegans lines either in control conditions or in moderate or high doses of cisplatin, which introduces genotoxic stress by damaging DNA. Our results show that cisplatin has a limited effect on global small non-coding RNA epimutations and epimutations in gene expression levels. However, cisplatin exposure leads to increased fluctuations in the levels of small non-coding RNAs derived from tRNA cleavage. We show that changes in tRNA-derived small RNAs may be associated with gene expression changes. CONCLUSIONS Our work shows that epimutations are not substantially altered by cisplatin exposure but identifies transient changes in tRNA-derived small RNAs as a potential source of variation induced by genotoxic stress.
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Affiliation(s)
- Manon Fallet
- Department of Biochemistry, Evolutionary Epigenetics Group, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd., Oxford, OX1 3QU, UK.
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182, Örebro, Sweden.
| | - Rachel Wilson
- Department of Biochemistry, Evolutionary Epigenetics Group, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd., Oxford, OX1 3QU, UK
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Peter Sarkies
- Department of Biochemistry, Evolutionary Epigenetics Group, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd., Oxford, OX1 3QU, UK.
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7
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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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Tehrani SSH, Kogan A, Mikulski P, Jansen LET. Remembering foods and foes: emerging principles of transcriptional memory. Cell Death Differ 2023:10.1038/s41418-023-01200-6. [PMID: 37563261 DOI: 10.1038/s41418-023-01200-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/20/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Transcriptional memory is characterized by a primed cellular state, induced by an external stimulus that results in an altered expression of primed genes upon re-exposure to the inducing signal. Intriguingly, the primed state is heritably maintained across somatic cell divisions even after the initial stimulus and target gene transcription cease. This phenomenon is widely observed across various organisms and appears to enable cells to retain a memory of external signals, thereby adapting to environmental changes. Signals range from nutrient supplies (food) to a variety of stress signals, including exposure to pathogens (foes), leading to long-term memory such as in the case of trained immunity in plants and mammals. Here, we review these priming phenomena and our current understanding of transcriptional memory. We consider different mechanistic models for how memory can work and discuss existing evidence for potential carriers of memory. Key molecular signatures include: the poising of RNA polymerase II machinery, maintenance of histone marks, as well as alterations in nuclear positioning and long-range chromatin interactions. Finally, we discuss the potential adaptive roles of transcriptional memory in the organismal response to its environment from nutrient sensing to trained immunity.
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Affiliation(s)
- Sahar S H Tehrani
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Anna Kogan
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Pawel Mikulski
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK.
| | - Lars E T Jansen
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK.
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9
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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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10
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Jay-Garcia LM, Cornell JL, Howie RL, Faber QL, Salas A, Chernova TA, Chernoff YO. Yeast Chaperone Hsp70-Ssb Modulates a Variety of Protein-Based Heritable Elements. Int J Mol Sci 2023; 24:ijms24108660. [PMID: 37240005 DOI: 10.3390/ijms24108660] [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: 04/11/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Prions are transmissible self-perpetuating protein isoforms associated with diseases and heritable traits. Yeast prions and non-transmissible protein aggregates (mnemons) are frequently based on cross-β ordered fibrous aggregates (amyloids). The formation and propagation of yeast prions are controlled by chaperone machinery. Ribosome-associated chaperone Hsp70-Ssb is known (and confirmed here) to modulate formation and propagation of the prion form of the Sup35 protein [PSI+]. Our new data show that both formation and mitotic transmission of the stress-inducible prion form of the Lsb2 protein ([LSB+]) are also significantly increased in the absence of Ssb. Notably, heat stress leads to a massive accumulation of [LSB+] cells in the absence of Ssb, implicating Ssb as a major downregulator of the [LSB+]-dependent memory of stress. Moreover, the aggregated form of Gγ subunit Ste18, [STE+], behaving as a non-heritable mnemon in the wild-type strain, is generated more efficiently and becomes heritable in the absence of Ssb. Lack of Ssb also facilitates mitotic transmission, while lack of the Ssb cochaperone Hsp40-Zuo1 facilitates both spontaneous formation and mitotic transmission of the Ure2 prion, [URE3]. These results demonstrate that Ssb is a general modulator of cytosolic amyloid aggregation, whose effect is not restricted only to [PSI+].
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Affiliation(s)
- Lina M Jay-Garcia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joseph L Cornell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Rebecca L Howie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Quincy L Faber
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Abigail Salas
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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11
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Wilson R, Le Bourgeois M, Perez M, Sarkies P. Fluctuations in chromatin state at regulatory loci occur spontaneously under relaxed selection and are associated with epigenetically inherited variation in C. elegans gene expression. PLoS Genet 2023; 19:e1010647. [PMID: 36862744 PMCID: PMC10013927 DOI: 10.1371/journal.pgen.1010647] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/14/2023] [Accepted: 02/01/2023] [Indexed: 03/03/2023] Open
Abstract
Some epigenetic information can be transmitted between generations without changes in the underlying DNA sequence. Changes in epigenetic regulators, termed epimutations, can occur spontaneously and be propagated in populations in a manner reminiscent of DNA mutations. Small RNA-based epimutations occur in C. elegans and persist for around 3-5 generations on average. Here, we explored whether chromatin states also undergo spontaneous change and whether this could be a potential alternative mechanism for transgenerational inheritance of gene expression changes. We compared the chromatin and gene expression profiles at matched time points from three independent lineages of C. elegans propagated at minimal population size. Spontaneous changes in chromatin occurred in around 1% of regulatory regions each generation. Some were heritable epimutations and were significantly enriched for heritable changes in expression of nearby protein-coding genes. Most chromatin-based epimutations were short-lived but a subset had longer duration. Genes subject to long-lived epimutations were enriched for multiple components of xenobiotic response pathways. This points to a possible role for epimutations in adaptation to environmental stressors.
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Affiliation(s)
- Rachel Wilson
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London, United Kingdom.,Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Marcos Perez
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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12
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Chou JY, Hsu PC, Leu JY. Enforcement of Postzygotic Species Boundaries in the Fungal Kingdom. Microbiol Mol Biol Rev 2022; 86:e0009822. [PMID: 36098649 PMCID: PMC9769731 DOI: 10.1128/mmbr.00098-22] [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] [Indexed: 01/01/2023] Open
Abstract
Understanding the molecular basis of speciation is a primary goal in evolutionary biology. The formation of the postzygotic reproductive isolation that causes hybrid dysfunction, thereby reducing gene flow between diverging populations, is crucial for speciation. Using various advanced approaches, including chromosome replacement, hybrid introgression and transcriptomics, population genomics, and experimental evolution, scientists have revealed multiple mechanisms involved in postzygotic barriers in the fungal kingdom. These results illuminate both unique and general features of fungal speciation. Our review summarizes experiments on fungi exploring how Dobzhansky-Muller incompatibility, killer meiotic drive, chromosome rearrangements, and antirecombination contribute to postzygotic reproductive isolation. We also discuss possible evolutionary forces underlying different reproductive isolation mechanisms and the potential roles of the evolutionary arms race under the Red Queen hypothesis and epigenetic divergence in speciation.
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Affiliation(s)
- Jui-Yu Chou
- Department of Biology, National Changhua University of Education, Changhua, Taiwan
| | - Po-Chen Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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13
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Sun B, Sherrin M, Roy R. Unscheduled epigenetic modifications cause genome instability and sterility through aberrant R-loops following starvation. Nucleic Acids Res 2022; 51:84-98. [PMID: 36504323 PMCID: PMC9841415 DOI: 10.1093/nar/gkac1155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
During starvation, organisms modify both gene expression and metabolism to adjust to the energy stress. We previously reported that Caenorhabditis elegans lacing AMP-activated protein kinase (AMPK) exhibit transgenerational reproductive defects associated with abnormally elevated trimethylated histone H3 at lysine 4 (H3K4me3) levels in the germ line following recovery from acute starvation. Here, we show that these H3K4me3 marks are significantly increased at promoters, driving aberrant transcription elongation resulting in the accumulation of R-loops in starved AMPK mutants. DNA-RNA immunoprecipitation followed by high-throughput sequencing (DRIP-seq) analysis demonstrated that a significant proportion of the genome was affected by R-loop formation. This was most pronounced in the promoter-transcription start site regions of genes, in which the chromatin was modified by H3K4me3. Like H3K4me3, the R-loops were also found to be heritable, likely contributing to the transgenerational reproductive defects typical of these mutants following starvation. Strikingly, AMPK mutant germ lines show considerably more RAD-51 (the RecA recombinase) foci at sites of R-loop formation, potentially sequestering them from their roles at meiotic breaks or at sites of induced DNA damage. Our study reveals a previously unforeseen role of AMPK in maintaining genome stability following starvation. The downstream effects of R-loops on DNA damage sensitivity and germline stem cell integrity may account for inappropriate epigenetic modification that occurs in numerous human disorders, including various cancers.
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Affiliation(s)
- Bing Sun
- To whom correspondence should be addressed.
| | - McLean Sherrin
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Richard Roy
- Correspondence may also be addressed to Richard Roy. Tel: +1 514 398 6437;
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14
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Cobos SN, Janani C, Cruz G, Rana N, Son E, Frederic R, Paredes Casado J, Khan M, Bennett SA, Torrente MP. [PRION +] States Are Associated with Specific Histone H3 Post-Translational Modification Changes. Pathogens 2022; 11:pathogens11121436. [PMID: 36558770 PMCID: PMC9786042 DOI: 10.3390/pathogens11121436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
Prions are proteins able to take on alternative conformations and propagate them in a self-templating process. In Saccharomyces cerevisiae, prions enable heritable responses to environmental conditions through bet-hedging mechanisms. Hence, [PRION+] states may serve as an atypical form of epigenetic control, producing heritable phenotypic change via protein folding. However, the connections between prion states and the epigenome remain unknown. Do [PRION+] states link to canonical epigenetic channels, such as histone post-translational modifications? Here, we map out the histone H3 modification landscape in the context of the [SWI+] and [PIN+] prion states. [SWI+] is propagated by Swi1, a subunit of the SWI/SNF chromatin remodeling complex, while [PIN+] is propagated by Rnq1, a protein of unknown function. We find [SWI+] yeast display decreases in the levels of H3K36me2 and H3K56ac compared to [swi-] yeast. In contrast, decreases in H3K4me3, H3K36me2, H3K36me3 and H3K79me3 are connected to the [PIN+] state. Curing of the prion state by treatment with guanidine hydrochloride restored histone PTM to [prion-] state levels. We find histone PTMs in the [PRION+] state do not match those in loss-of-function models. Our findings shed light into the link between prion states and histone modifications, revealing novel insight into prion function in yeast.
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Affiliation(s)
- Samantha N. Cobos
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Chaim Janani
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Gabriel Cruz
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Navin Rana
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Elizaveta Son
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Rania Frederic
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | | | - Maliha Khan
- Biology Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Seth A. Bennett
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
- Graduate Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Mariana P. Torrente
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
- Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Correspondence:
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15
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Epigenetic Changes in Prion and Prion-like Neurodegenerative Diseases: Recent Advances, Potential as Biomarkers, and Future Perspectives. Int J Mol Sci 2022; 23:ijms232012609. [PMID: 36293477 PMCID: PMC9604074 DOI: 10.3390/ijms232012609] [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: 09/06/2022] [Revised: 10/09/2022] [Accepted: 10/18/2022] [Indexed: 12/01/2022] Open
Abstract
Prion diseases are transmissible spongiform encephalopathies (TSEs) caused by a conformational conversion of the native cellular prion protein (PrPC) to an abnormal, infectious isoform called PrPSc. Amyotrophic lateral sclerosis, Alzheimer’s, Parkinson’s, and Huntington’s diseases are also known as prion-like diseases because they share common features with prion diseases, including protein misfolding and aggregation, as well as the spread of these misfolded proteins into different brain regions. Increasing evidence proposes the involvement of epigenetic mechanisms, namely DNA methylation, post-translational modifications of histones, and microRNA-mediated post-transcriptional gene regulation in the pathogenesis of prion-like diseases. Little is known about the role of epigenetic modifications in prion diseases, but recent findings also point to a potential regulatory role of epigenetic mechanisms in the pathology of these diseases. This review highlights recent findings on epigenetic modifications in TSEs and prion-like diseases and discusses the potential role of such mechanisms in disease pathology and their use as potential biomarkers.
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16
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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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17
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Yamamoto R, Sato G, Amai T, Ueda M, Kuroda K. Development of Artificial System to Induce Chromatin Loosening in Saccharomyces cerevisiae. Biomolecules 2022; 12:1138. [PMID: 36009033 PMCID: PMC9406041 DOI: 10.3390/biom12081138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 12/05/2022] Open
Abstract
In eukaryotic cells, loosening of chromatin causes changes in transcription and DNA replication. The artificial conversion of tightly packed chromatin (heterochromatin) to loosely packed chromatin (euchromatin) enables gene expression and regulates cell differentiation. Although some chemicals convert chromatin structures through histone modifications, they lack sequence specificity. This study attempted to establish a novel technology for inducing chromatin loosening in target regions of Saccharomyces cerevisiae. We focused on histone acetylation, which is one of the mechanisms of euchromatin induction. The sequence-recognizing ability of the dead Cas9 (dCas9) and guide RNA (gRNA) complex was used to promote histone acetylation at a targeted genomic locus. We constructed a plasmid to produce a fusion protein consisting of dCas9 and histone acetyltransferase Gcn5 and a plasmid to express gRNA recognizing the upstream region of heterochromatic URA3. Confocal microscopy revealed that the fusion proteins were localized in the nucleus. The yeast strain producing the fusion protein and gRNA grew well in the uracil-deficient medium, while the strain harboring empty plasmids or the strain containing the mutations that cause loss of nucleosomal histone acetylation activity of Gcn5 did not. This suggests that the heterochromatin was loosened as much as euchromatin through nucleosomal histone acetylation. The amount of euchromatic DNA at the target locus increased, indicating that chromatin loosening was induced by our system. Nucleosomal histone acetylation in heterochromatic loci by our developed system is a promising method for inducing euchromatic state in a target locus.
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Affiliation(s)
| | | | | | | | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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18
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Memory of plants: present understanding. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00399-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
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19
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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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20
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Tikhodeyev ON. Prions as Non-Canonical Hereditary Factors. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422060126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Du Z, Cho B, Li L. Identifying Endogenous Cellular Proteins Destabilizing the Propagation of Swi1 Prion upon Overproduction. Viruses 2022; 14:1366. [PMID: 35891348 PMCID: PMC9321512 DOI: 10.3390/v14071366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/07/2022] [Accepted: 06/21/2022] [Indexed: 01/25/2023] Open
Abstract
(1) Background: Numerous prions exist in the budding yeast, including [SWI+], the prion form of Swi1-a subunit of the chromatin-remodeling complex SWI/SNF. Despite decades of research, the molecular mechanisms underlying prion initiation and propagation are not fully understood. In this study, we aimed to identify endogenous cellular proteins that destabilize [SWI+]. (2) Methods: We screened the MoBY-ORF 2.0 library for proteins that destabilize [SWI+] upon overproduction. We further explored the effects of the identified candidates against other yeast prions and analyzed their potential prion-curing mechanisms. (3) Results: Eighty-two [SWI+] suppressors were identified, and their effects were shown to be [SWI+]-specific. Interestingly, a few documented [SWI+] suppressors were not among the identified hits. Further experiments indicate that, for some of these [SWI+] suppressors, their overproduction, and thus their prion-curing activities, are regulated by environmental conditions. Bioinformatics analyses show that our identified [SWI+] suppressors are involved in diverse biological functions, with gene ontology term enrichments specifically for transcriptional regulation and translation. Competition for Swi1 monomers between [SWI+] and Swi1 interactors, including the SWI/SNF complex, is a potential prion-curing mechanism. (4) Conclusions: We identified a number of [SWI+]-specific suppressors that highlight unique features of [SWI+] in maintaining its self-perpetuating conformations.
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Affiliation(s)
- Zhiqiang Du
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | | | - Liming Li
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
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22
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Dennis EM, Garcia DM. Biochemical Principles in Prion-Based Inheritance. EPIGENOMES 2022; 6:4. [PMID: 35225957 PMCID: PMC8883993 DOI: 10.3390/epigenomes6010004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/13/2022] [Accepted: 01/20/2022] [Indexed: 12/14/2022] Open
Abstract
Prions are proteins that can stably fold into alternative structures that frequently alter their activities. They can self-template their alternate structures and are inherited across cell divisions and generations. While they have been studied for more than four decades, their enigmatic nature has limited their discovery. In the last decade, we have learned just how widespread they are in nature, the many beneficial phenotypes that they confer, while also learning more about their structures and modes of inheritance. Here, we provide a brief review of the biochemical principles of prion proteins, including their sequences, characteristics and structures, and what is known about how they self-template, citing examples from multiple organisms. Prion-based inheritance is the most understudied segment of epigenetics. Here, we lay a biochemical foundation and share a framework for how to define these molecules, as new examples are unearthed throughout nature.
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Affiliation(s)
- Emily M. Dennis
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA;
| | - David M. Garcia
- Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
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23
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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: 5] [Impact Index Per Article: 2.5] [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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24
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Loh D, Reiter RJ. Melatonin: Regulation of Prion Protein Phase Separation in Cancer Multidrug Resistance. Molecules 2022; 27:705. [PMID: 35163973 PMCID: PMC8839844 DOI: 10.3390/molecules27030705] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/13/2022] Open
Abstract
The unique ability to adapt and thrive in inhospitable, stressful tumor microenvironments (TME) also renders cancer cells resistant to traditional chemotherapeutic treatments and/or novel pharmaceuticals. Cancer cells exhibit extensive metabolic alterations involving hypoxia, accelerated glycolysis, oxidative stress, and increased extracellular ATP that may activate ancient, conserved prion adaptive response strategies that exacerbate multidrug resistance (MDR) by exploiting cellular stress to increase cancer metastatic potential and stemness, balance proliferation and differentiation, and amplify resistance to apoptosis. The regulation of prions in MDR is further complicated by important, putative physiological functions of ligand-binding and signal transduction. Melatonin is capable of both enhancing physiological functions and inhibiting oncogenic properties of prion proteins. Through regulation of phase separation of the prion N-terminal domain which targets and interacts with lipid rafts, melatonin may prevent conformational changes that can result in aggregation and/or conversion to pathological, infectious isoforms. As a cancer therapy adjuvant, melatonin could modulate TME oxidative stress levels and hypoxia, reverse pH gradient changes, reduce lipid peroxidation, and protect lipid raft compositions to suppress prion-mediated, non-Mendelian, heritable, but often reversible epigenetic adaptations that facilitate cancer heterogeneity, stemness, metastasis, and drug resistance. This review examines some of the mechanisms that may balance physiological and pathological effects of prions and prion-like proteins achieved through the synergistic use of melatonin to ameliorate MDR, which remains a challenge in cancer treatment.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health San Antonio, San Antonio, TX 78229, USA
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25
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Yao Y, Wen Q, Zhang T, Yu C, Chan KM, Gan H. Advances in Approaches to Study Chromatin-Mediated Epigenetic Memory. ACS Synth Biol 2022; 11:16-25. [PMID: 34965084 DOI: 10.1021/acssynbio.1c00394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chromatin structure contains critical epigenetic information in various forms, such as histone post-translational modifications (PTMs). The deposition of certain histone PTMs can remodel the chromatin structure, resulting in gene expression alteration. The epigenetic information carried by histone PTMs could be inherited by daughter cells to maintain the gene expression status. Recently, studies revealed that several conserved replisome proteins regulate the recycling of parental histones carrying epigenetic information in Saccharomyces cerevisiae. Hence, the proper recycling and deposition of parental histones onto newly synthesized DNA strands is presumed to be essential for epigenetic inheritance. Here, we first reviewed the fundamental mechanisms of epigenetic modification establishment and maintenance discovered within fungal models. Next, we discussed the functions of parental histone chaperones and the potential impacts of the parental histone recycling process on heterochromatin-mediated transcriptional silencing inheritance. Subsequently, we summarized novel synthetic biology approaches developed to analyze individual epigenetic components during epigenetic inheritance in fungal and mammalian systems. These newly emerged research paradigms enable us to dissect epigenetic systems in a bottom-up manner. Furthermore, we highlighted the approaches developed in this emerging field and discussed the potential applications of these engineered regulators to building synthetic epigenetic systems.
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Affiliation(s)
- Yuan Yao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qing Wen
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tianjun Zhang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Chuanhe Yu
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR 999077, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518172, China
| | - Haiyun Gan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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26
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Jethmalani Y, Tran K, Negesse MY, Sun W, Ramos M, Jaiswal D, Jezek M, Amos S, Garcia EJ, Park D, Green EM. Set4 regulates stress response genes and coordinates histone deacetylases within yeast subtelomeres. Life Sci Alliance 2021; 4:e202101126. [PMID: 34625508 PMCID: PMC8507492 DOI: 10.26508/lsa.202101126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/25/2022] Open
Abstract
The yeast chromatin protein Set4 is a member of the Set3-subfamily of SET domain proteins which play critical roles in the regulation of gene expression in diverse developmental and environmental contexts. We previously reported that Set4 promotes survival during oxidative stress and regulates expression of stress response genes via stress-dependent chromatin localization. In this study, global gene expression analysis and investigation of histone modification status identified a role for Set4 in maintaining gene repressive mechanisms within yeast subtelomeres under both normal and stress conditions. We show that Set4 works in a partially overlapping pathway to the SIR complex and the histone deacetylase Rpd3 to maintain proper levels of histone acetylation and expression of stress response genes encoded in subtelomeres. This role for Set4 is particularly critical for cells under hypoxic conditions, where the loss of Set4 decreases cell fitness and cell wall integrity. These findings uncover a new regulator of subtelomeric chromatin that is key to stress defense pathways and demonstrate a function for Set4 in regulating repressive, heterochromatin-like environments.
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Affiliation(s)
- Yogita Jethmalani
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Khoa Tran
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Maraki Y Negesse
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Winny Sun
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Mark Ramos
- Department of Mathematics and Statistics, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Deepika Jaiswal
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Meagan Jezek
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Shandon Amos
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Eric Joshua Garcia
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - DoHwan Park
- Department of Mathematics and Statistics, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Erin M Green
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
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27
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Ghai M, Kader F. A Review on Epigenetic Inheritance of Experiences in Humans. Biochem Genet 2021; 60:1107-1140. [PMID: 34792705 DOI: 10.1007/s10528-021-10155-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022]
Abstract
If genetics defines the inheritance of DNA, epigenetics aims to regulate and make it adaptable. Epigenetic alterations include DNA methylation, chromatin remodelling, post-translational modifications of histone proteins and activity of non-coding RNAs. Several studies, especially in animal models, have reported transgenerational inheritance of epigenetic marks. However, evidence of transgenerational inheritance in humans via germline in the absence of any direct exposure to the driving external stimulus remains controversial. Most of the epimutations exist in relation with genetic variants. The present review looks at intergenerational and transgenerational inheritance in humans, (both father and mother) in response to diet, exposure to chemicals, stress, exercise, and disease status. If not transgenerational, at least intergenerational human studies could help to understand early processes of inheritance. In humans, female and male germline development follow separate paths of epigenetic events and both oocyte and sperm possess their own unique epigenomes. While DNA methylation alterations are reset during epigenetic reprogramming, non-coding RNAs via human sperm provide evidence of being reliable carriers for transgenerational inheritance. Human studies reveal that one mechanism of epigenetic inheritance cannot be applied to the complete human genome. Multiple factors including time, type, and tissue of exposure determine if the modified epigenetic mark could be transmissible and till which generation. Population-specific differences should also be taken into consideration while associating inheritance to an environmental exposure. A longitudinal study targeting one environmental factor, but different population groups should be conducted at a specific geographical location to pinpoint heritable epigenetic changes.
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Affiliation(s)
- Meenu Ghai
- Discipline of Genetics, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, KwaZulu Natal, South Africa.
| | - Farzeen Kader
- Discipline of Genetics, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, KwaZulu Natal, South Africa
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28
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Bauer I, Graessle S. Fungal Lysine Deacetylases in Virulence, Resistance, and Production of Small Bioactive Compounds. Genes (Basel) 2021; 12:1470. [PMID: 34680865 PMCID: PMC8535771 DOI: 10.3390/genes12101470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
The growing number of immunocompromised patients begs for efficient therapy strategies against invasive fungal infections. As conventional antifungal treatment is increasingly hampered by resistance to commonly used antifungals, development of novel therapy regimens is required. On the other hand, numerous fungal species are industrially exploited as cell factories of enzymes and chemicals or as producers of medically relevant pharmaceuticals. Consequently, there is immense interest in tapping the almost inexhaustible fungal portfolio of natural products for potential medical and industrial applications. Both the pathogenicity and production of those small metabolites are significantly dependent on the acetylation status of distinct regulatory proteins. Thus, classical lysine deacetylases (KDACs) are crucial virulence determinants and important regulators of natural products of fungi. In this review, we present an overview of the members of classical KDACs and their complexes in filamentous fungi. Further, we discuss the impact of the genetic manipulation of KDACs on the pathogenicity and production of bioactive molecules. Special consideration is given to inhibitors of these enzymes and their role as potential new antifungals and emerging tools for the discovery of novel pharmaceutical drugs and antibiotics in fungal producer strains.
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Affiliation(s)
| | - Stefan Graessle
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria;
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29
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Gil‐Garcia M, Iglesias V, Pallarès I, Ventura S. Prion-like proteins: from computational approaches to proteome-wide analysis. FEBS Open Bio 2021; 11:2400-2417. [PMID: 34057308 PMCID: PMC8409284 DOI: 10.1002/2211-5463.13213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/07/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
Prions are self-perpetuating proteins able to switch between a soluble state and an aggregated-and-transmissible conformation. These proteinaceous entities have been widely studied in yeast, where they are involved in hereditable phenotypic adaptations. The notion that such proteins could play functional roles and be positively selected by evolution has triggered the development of computational tools to identify prion-like proteins in different kingdoms of life. These algorithms have succeeded in screening multiple proteomes, allowing the identification of prion-like proteins in a diversity of unrelated organisms, evidencing that the prion phenomenon is well conserved among species. Interestingly enough, prion-like proteins are not only connected with the formation of functional membraneless protein-nucleic acid coacervates, but are also linked to human diseases. This review addresses state-of-the-art computational approaches to identify prion-like proteins, describes proteome-wide analysis efforts, discusses these unique proteins' functional role, and illustrates recently validated examples in different domains of life.
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Affiliation(s)
- Marcos Gil‐Garcia
- Departament de Bioquímica i Biologia MolecularInstitut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaSpain
| | - Valentín Iglesias
- Departament de Bioquímica i Biologia MolecularInstitut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaSpain
| | - Irantzu Pallarès
- Departament de Bioquímica i Biologia MolecularInstitut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaSpain
| | - Salvador Ventura
- Departament de Bioquímica i Biologia MolecularInstitut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaSpain
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30
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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: 9] [Impact Index Per Article: 3.0] [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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31
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Leng H, Liu S, Lei Y, Tang Y, Gu S, Hu J, Chen S, Feng J, Li Q. FACT interacts with Set3 HDAC and fine-tunes GAL1 transcription in response to environmental stimulation. Nucleic Acids Res 2021; 49:5502-5519. [PMID: 33963860 PMCID: PMC8191775 DOI: 10.1093/nar/gkab312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 01/22/2023] Open
Abstract
The histone chaperone facilitates chromatin transactions (FACT) functions in various DNA transactions. How FACT performs these multiple functions remains largely unknown. Here, we found, for the first time, that the N-terminal domain of its Spt16 subunit interacts with the Set3 histone deacetylase complex (Set3C) and that FACT and Set3C function in the same pathway to regulate gene expression in some settings. We observed that Spt16-G132D mutant proteins show defects in binding to Set3C but not other reported FACT interactors. At the permissive temperature, induction of the GAL1 and GAL10 genes is reduced in both spt16-G132D and set3Δ cells, whereas transient upregulation of GAL10 noncoding RNA (ncRNA), which is transcribed from the 3′ end of the GAL10 gene, is elevated. Mutations that inhibit GAL10 ncRNA transcription reverse the GAL1 and GAL10 induction defects in spt16-G132D and set3Δ mutant cells. Mechanistically, set3Δ and FACT (spt16-G132D) mutants show reduced histone acetylation and increased nucleosome occupancy at the GAL1 promoter under inducing conditions and inhibition of GAL10 ncRNA transcription also partially reverses these chromatin changes. These results indicate that FACT interacts with Set3C, which in turn prevents uncontrolled GAL10 ncRNA expression and fine-tunes the expression of GAL genes upon a change in carbon source.
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Affiliation(s)
- He Leng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shaofeng Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yang Lei
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuantao Tang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shijia Gu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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32
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Portz B, Lee BL, Shorter J. FUS and TDP-43 Phases in Health and Disease. Trends Biochem Sci 2021; 46:550-563. [PMID: 33446423 PMCID: PMC8195841 DOI: 10.1016/j.tibs.2020.12.005] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/24/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022]
Abstract
The distinct prion-like domains (PrLDs) of FUS and TDP-43, modulate phase transitions that result in condensates with a range of material states. These assemblies are implicated in both health and disease. In this review, we examine how sequence, structure, post-translational modifications, and RNA can affect the self-assembly of these RNA-binding proteins (RBPs). We discuss how our emerging understanding of FUS and TDP-43 liquid-liquid phase separation (LLPS) and aggregation, could be leveraged to design new therapies for neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and limbic-predominant age-related TDP-43 encephalopathy (LATE).
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Affiliation(s)
- Bede Portz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bo Lim Lee
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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33
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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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34
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Stajic D, Jansen LET. Empirical evidence for epigenetic inheritance driving evolutionary adaptation. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200121. [PMID: 33866813 DOI: 10.1098/rstb.2020.0121] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The cellular machinery that regulates gene expression can be self-propagated across cell division cycles and even generations. This renders gene expression states and their associated phenotypes heritable, independently of genetic changes. These phenotypic states, in turn, can be subject to selection and may influence evolutionary adaptation. In this review, we will discuss the molecular basis of epigenetic inheritance, the extent of its transmission and mechanisms of evolutionary adaptation. The current work shows that heritable gene expression can facilitate the process of adaptation through the increase of survival in a novel environment and by enlarging the size of beneficial mutational targets. Moreover, epigenetic control of gene expression enables stochastic switching between different phenotypes in populations that can potentially facilitate adaptation in rapidly fluctuating environments. Ecological studies of the variation of epigenetic markers (e.g. DNA methylation patterns) in wild populations show a potential contribution of this mode of inheritance to local adaptation in nature. However, the extent of the adaptive contribution of the naturally occurring variation in epi-alleles compared to genetic variation remains unclear. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Dragan Stajic
- Department of Zoology, University of Stockholm, 106 91 Stockholm, Sweden
| | - Lars E T Jansen
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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35
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Gui Q, Deng S, Zhou Z, Cao W, Zhang X, Shi W, Cai X, Jiang W, Cui Z, Hu Z, Chen X. Transcriptome Analysis in Yeast Reveals the Externality of Position Effects. Mol Biol Evol 2021; 38:3294-3307. [PMID: 33871622 PMCID: PMC8321525 DOI: 10.1093/molbev/msab104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The activity of a gene newly integrated into a chromosome depends on the genomic context of the integration site. This “position effect” has been widely reported, although the other side of the coin, that is, how integration affects the local chromosomal environment, has remained largely unexplored, as have the mechanism and phenotypic consequences of this “externality” of the position effect. Here, we examined the transcriptome profiles of approximately 250 Saccharomyces cerevisiae strains, each with GFP integrated into a different locus of the wild-type strain. We found that in genomic regions enriched in essential genes, GFP expression tended to be lower, and the genes near the integration site tended to show greater expression reduction. Further joint analysis with public genome-wide histone modification profiles indicated that this effect was associated with H3K4me2. More importantly, we found that changes in the expression of neighboring genes, but not GFP expression, significantly altered the cellular growth rate. As a result, genomic loci that showed high GFP expression immediately after integration were associated with growth disadvantages caused by elevated expression of neighboring genes, ultimately leading to a low total yield of GFP in the long run. Our results were consistent with competition for transcriptional resources among neighboring genes and revealed a previously unappreciated facet of position effects. This study highlights the impact of position effects on the fate of exogenous gene integration and has significant implications for biological engineering and the pathology of viral integration into the host genome.
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Affiliation(s)
- Qian Gui
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shuyun Deng
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - ZhenZhen Zhou
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Waifang Cao
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xin Zhang
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wenjun Shi
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiujuan Cai
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wenbing Jiang
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zifeng Cui
- Department of Obstetrics and Gynecology, Precision Medicine Institute, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zheng Hu
- Department of Obstetrics and Gynecology, Precision Medicine Institute, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoshu Chen
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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36
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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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37
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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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38
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Elsherbiny A, Dobreva G. Epigenetic memory of cell fate commitment. Curr Opin Cell Biol 2021; 69:80-87. [PMID: 33535129 DOI: 10.1016/j.ceb.2020.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/23/2022]
Abstract
During development, discrete cell fates are established in precise spatiotemporal order guided by morphogen signals. These signals converge in the nucleus to induce transcriptional and epigenetic programming that determines cell fate. Once cell identity is established, cell programs have to be accurately sustained through multiple rounds of cell division, during which DNA replication serves as a window of opportunity for altering cell fate. In this review, we summarize recent advances in understanding the molecular players that underlie epigenetic memory of cell fate decisions, with a particular focus on histone modifications and mitotic bookmarking factors. We also discuss the different mechanisms of inheritance of repressed and active chromatin states.
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Affiliation(s)
- Adel Elsherbiny
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; German Centre for Cardiovascular Research (DZHK), Germany
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; German Centre for Cardiovascular Research (DZHK), Germany.
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39
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Parental nucleosome segregation and the inheritance of cellular identity. Nat Rev Genet 2021; 22:379-392. [PMID: 33500558 DOI: 10.1038/s41576-020-00312-w] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2020] [Indexed: 12/20/2022]
Abstract
Gene expression programmes conferring cellular identity are achieved through the organization of chromatin structures that either facilitate or impede transcription. Among the key determinants of chromatin organization are the histone modifications that correlate with a given transcriptional status and chromatin state. Until recently, the details for the segregation of nucleosomes on DNA replication and their implications in re-establishing heritable chromatin domains remained unclear. Here, we review recent findings detailing the local segregation of parental nucleosomes and highlight important advances as to how histone methyltransferases associated with the establishment of repressive chromatin domains facilitate epigenetic inheritance.
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40
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Lei B, Capella M, Montgomery SA, Borg M, Osakabe A, Goiser M, Muhammad A, Braun S, Berger F. A Synthetic Approach to Reconstruct the Evolutionary and Functional Innovations of the Plant Histone Variant H2A.W. Curr Biol 2021; 31:182-191.e5. [PMID: 33096036 DOI: 10.1016/j.cub.2020.09.080] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/28/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022]
Abstract
Diversification of histone variants is marked by the acquisition of distinct motifs and functional properties through convergent evolution.1-4 H2A variants are distinguished by specific C-terminal motifs and tend to be segregated within defined domains of the genome.5,6 Whether evolution of these motifs pre-dated the evolution of segregation mechanisms or vice versa has remained unclear. A suitable model to address this question is the variant H2A.W, which evolved in plants through acquisition of a KSPK motif7 and is tightly associated with heterochromatin.4 We used fission yeast, where chromatin is naturally devoid of H2A.W, to study the impact of engineered chimeras combining yeast H2A with the KSPK motif. Biochemical assays showed that the KSPK motif conferred nucleosomes with specific properties. Despite uniform incorporation of the engineered H2A chimeras in the yeast genome, the KSPK motif specifically affected heterochromatin composition and function. We conclude that the KSPK motif promotes chromatin properties in yeast that are comparable to the properties and function of H2A.W in plant heterochromatin. We propose that the selection of functional motifs confer histone variants with properties that impact primarily a specific chromatin state. The association between a new histone variant and a preferred chromatin state can thus provide a setting for the evolution of mechanisms that segregate the new variant to this state, thereby enhancing the impact of the selected properties of the variant on genome activity.
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Affiliation(s)
- Bingkun Lei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Matías Capella
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany
| | - Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael Borg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Akihisa Osakabe
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Malgorzata Goiser
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Abubakar Muhammad
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany; International Max Planck Research School for Molecular and Cellular Life Sciences, Am Klopferspitz 18, 82152 Planegg-Martinsried, Germany
| | - Sigurd Braun
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany; International Max Planck Research School for Molecular and Cellular Life Sciences, Am Klopferspitz 18, 82152 Planegg-Martinsried, Germany.
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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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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42
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Skinner MK, Nilsson EE. Role of environmentally induced epigenetic transgenerational inheritance in evolutionary biology: Unified Evolution Theory. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab012. [PMID: 34729214 PMCID: PMC8557805 DOI: 10.1093/eep/dvab012] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 05/15/2023]
Abstract
The current evolutionary biology theory primarily involves genetic alterations and random DNA sequence mutations to generate the phenotypic variation required for Darwinian natural selection to act. This neo-Darwinian evolution is termed the Modern Evolution Synthesis and has been the primary paradigm for nearly 100 years. Although environmental factors have a role in neo-Darwinian natural selection, Modern Evolution Synthesis does not consider environment to impact the basic molecular processes involved in evolution. An Extended Evolutionary Synthesis has recently developed that extends the modern synthesis to consider non-genetic processes. Over the past few decades, environmental epigenetics research has been demonstrated to regulate genetic processes and directly generate phenotypic variation independent of genetic sequence alterations. Therefore, the environment can on a molecular level through non-genetic (i.e. epigenetic) mechanisms directly influence phenotypic variation, genetic variation, inheritance and adaptation. This direct action of the environment to alter phenotype that is heritable is a neo-Lamarckian concept that can facilitate neo-Darwinian (i.e. Modern Synthesis) evolution. The integration of genetics, epigenetics, Darwinian theory, Lamarckian concepts, environment, and epigenetic inheritance provides a paradigm shift in evolution theory. The role of environmental-induced epigenetic transgenerational inheritance in evolution is presented to describe a more unified theory of evolutionary biology.
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Affiliation(s)
- Michael K Skinner
- **Correspondence address. Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA. Tel: +1 509-335-1524; E-mail:
| | - Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
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43
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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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44
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Du Z, Regan J, Bartom E, Wu WS, Zhang L, Goncharoff DK, Li L. Elucidating the regulatory mechanism of Swi1 prion in global transcription and stress responses. Sci Rep 2020; 10:21838. [PMID: 33318504 PMCID: PMC7736884 DOI: 10.1038/s41598-020-77993-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/18/2020] [Indexed: 01/16/2023] Open
Abstract
Transcriptional regulators are prevalent among identified prions in Saccharomyces cerevisiae, however, it is unclear how prions affect genome-wide transcription. We show here that the prion ([SWI+]) and mutant (swi1∆) forms of Swi1, a subunit of the SWI/SNF chromatin-remodeling complex, confer dramatically distinct transcriptomic profiles. In [SWI+] cells, genes encoding for 34 transcription factors (TFs) and 24 Swi1-interacting proteins can undergo transcriptional modifications. Several TFs show enhanced aggregation in [SWI+] cells. Further analyses suggest that such alterations are key factors in specifying the transcriptomic signatures of [SWI+] cells. Interestingly, swi1∆ and [SWI+] impose distinct and oftentimes opposite effects on cellular functions. Translation-associated activities, in particular, are significantly reduced in swi1∆ cells. Although both swi1∆ and [SWI+] cells are similarly sensitive to thermal, osmotic and drought stresses, harmful, neutral or beneficial effects were observed for a panel of tested chemical stressors. Further analyses suggest that the environmental stress response (ESR) is mechanistically different between swi1∆ and [SWI+] cells—stress-inducible ESR (iESR) are repressed by [SWI+] but unchanged by swi1∆ while stress-repressible ESR (rESR) are induced by [SWI+] but repressed by swi1∆. Our work thus demonstrates primarily gain-of-function outcomes through transcriptomic modifications by [SWI+] and highlights a prion-mediated regulation of transcription and phenotypes in yeast.
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Affiliation(s)
- Zhiqiang Du
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, 60011, USA.
| | - Jeniece Regan
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, 60011, USA
| | - Elizabeth Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, 60011, USA
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan City, 701, Taiwan
| | - Li Zhang
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, 60011, USA.,Chinese Institute for Brain Research, Genomics Center and HPC Core, Beijing, 102206, China
| | | | - Liming Li
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, 60011, USA.
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45
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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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46
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Madhani HD. Unbelievable but True: Epigenetics and Chromatin in Fungi. Trends Genet 2020; 37:12-20. [PMID: 33092902 DOI: 10.1016/j.tig.2020.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/22/2022]
Abstract
Evolutionary innovations in chromatin biology have been recently discovered through the study of fungi. In Saccharomyces cerevisiae, a prion form of a deacetylase complex assembles over subtelomeric domains that produces a heritable gene expression state that enables resistance to stress. In Candida albicans, stress triggers adaptive chromosome destabilization via erasure a centromeric histone H3, CENP-A; a process that cooperates with a newly evolved H2A variant lacking a mitotic phosphorylation site. Finally, in Cryptococcus neoformans, the loss of a cytosine DNA methyltransferase at least 50 million years ago has enabled the Darwinian evolution of methylation patterns over geological timescales. These studies reveal a remarkable genetic and epigenetic evolutionary plasticity of the chromatin fiber, despite the highly conserved structure of the nucleosome.
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Affiliation(s)
- Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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47
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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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Abstract
The term “prion” was originally coined to describe the proteinaceous infectious agents involved in mammalian neurological disorders. More recently, a prion has been defined as a nonchromosomal, protein-based genetic element that is capable of converting the copies of its own benign variant into the prion form, with the new phenotypic effects that can be transmitted through the cytoplasm. Some prions are toxic to the cell, are able to aggregate and/or form amyloid structures, and may be infectious in the wild, but none of those traits are seen as an integral property of all prions. The term “prion” was originally coined to describe the proteinaceous infectious agents involved in mammalian neurological disorders. More recently, a prion has been defined as a nonchromosomal, protein-based genetic element that is capable of converting the copies of its own benign variant into the prion form, with the new phenotypic effects that can be transmitted through the cytoplasm. Some prions are toxic to the cell, are able to aggregate and/or form amyloid structures, and may be infectious in the wild, but none of those traits are seen as an integral property of all prions. We propose that the definition of prion should be expanded, to include the inducible transmissible entities undergoing autocatalytic conversion and consisting of RNA rather than protein. We show that when seen in this framework, some naturally occurring RNAs, including ribozymes, riboswitches, viroids, viroid-like retroelements, and PIWI-interacting RNAs (piRNAs), possess several of the characteristic properties of prions.
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