1
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Harel I, Chen YR, Ziv I, Singh PP, Heinzer D, Navarro Negredo P, Goshtchevsky U, Wang W, Astre G, Moses E, McKay A, Machado BE, Hebestreit K, Yin S, Sánchez Alvarado A, Jarosz DF, Brunet A. Identification of protein aggregates in the aging vertebrate brain with prion-like and phase-separation properties. Cell Rep 2024; 43:112787. [PMID: 38810650 DOI: 10.1016/j.celrep.2023.112787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/23/2023] [Accepted: 06/26/2023] [Indexed: 05/31/2024] Open
Abstract
Protein aggregation, which can sometimes spread in a prion-like manner, is a hallmark of neurodegenerative diseases. However, whether prion-like aggregates form during normal brain aging remains unknown. Here, we use quantitative proteomics in the African turquoise killifish to identify protein aggregates that accumulate in old vertebrate brains. These aggregates are enriched for prion-like RNA-binding proteins, notably the ATP-dependent RNA helicase DDX5. We validate that DDX5 forms aggregate-like puncta in the brains of old killifish and mice. Interestingly, DDX5's prion-like domain allows these aggregates to propagate across many generations in yeast. In vitro, DDX5 phase separates into condensates. Mutations that abolish DDX5 prion propagation also impair the protein's ability to phase separate. DDX5 condensates exhibit enhanced enzymatic activity, but they can mature into inactive, solid aggregates. Our findings suggest that protein aggregates with prion-like properties form during normal brain aging, which could have implications for the age-dependency of cognitive decline.
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Affiliation(s)
- Itamar Harel
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel.
| | - 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
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Daniel Heinzer
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Uri Goshtchevsky
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Wei Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Gwendoline Astre
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Eitan Moses
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Andrew McKay
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ben E Machado
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Katja Hebestreit
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sifei Yin
- 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.
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, CA 94305, USA.
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2
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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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3
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Nazeen S, Wang X, Zielinski D, Lam I, Hallacli E, Xu P, Ethier E, Strom R, Zanella CA, Nithianandam V, Ritter D, Henderson A, Saurat N, Afroz J, Nutter-Upham A, Benyamini H, Copty J, Ravishankar S, Morrow A, Mitchel J, Neavin D, Gupta R, Farbehi N, Grundman J, Myers RH, Scherzer CR, Trojanowski JQ, Van Deerlin VM, Cooper AA, Lee EB, Erlich Y, Lindquist S, Peng J, Geschwind DH, Powell J, Studer L, Feany MB, Sunyaev SR, Khurana V. Deep sequencing of proteotoxicity modifier genes uncovers a Presenilin-2/beta-amyloid-actin genetic risk module shared among alpha-synucleinopathies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583145. [PMID: 38496508 PMCID: PMC10942362 DOI: 10.1101/2024.03.03.583145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Whether neurodegenerative diseases linked to misfolding of the same protein share genetic risk drivers or whether different protein-aggregation pathologies in neurodegeneration are mechanistically related remains uncertain. Conventional genetic analyses are underpowered to address these questions. Through careful selection of patients based on protein aggregation phenotype (rather than clinical diagnosis) we can increase statistical power to detect associated variants in a targeted set of genes that modify proteotoxicities. Genetic modifiers of alpha-synuclein (ɑS) and beta-amyloid (Aβ) cytotoxicity in yeast are enriched in risk factors for Parkinson's disease (PD) and Alzheimer's disease (AD), respectively. Here, along with known AD/PD risk genes, we deeply sequenced exomes of 430 ɑS/Aβ modifier genes in patients across alpha-synucleinopathies (PD, Lewy body dementia and multiple system atrophy). Beyond known PD genes GBA1 and LRRK2, rare variants AD genes (CD33, CR1 and PSEN2) and Aβ toxicity modifiers involved in RhoA/actin cytoskeleton regulation (ARGHEF1, ARHGEF28, MICAL3, PASK, PKN2, PSEN2) were shared risk factors across synucleinopathies. Actin pathology occurred in iPSC synucleinopathy models and RhoA downregulation exacerbated ɑS pathology. Even in sporadic PD, the expression of these genes was altered across CNS cell types. Genome-wide CRISPR screens revealed the essentiality of PSEN2 in both human cortical and dopaminergic neurons, and PSEN2 mutation carriers exhibited diffuse brainstem and cortical synucleinopathy independent of AD pathology. PSEN2 contributes to a common-risk signal in PD GWAS and regulates ɑS expression in neurons. Our results identify convergent mechanisms across synucleinopathies, some shared with AD.
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Affiliation(s)
- Sumaiya Nazeen
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Xinyuan Wang
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Dina Zielinski
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Whitehead Institute of Biomedical Research, Cambridge, MA, USA
| | - Isabel Lam
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Erinc Hallacli
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ping Xu
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth Ethier
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ronya Strom
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Camila A Zanella
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Vanitha Nithianandam
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Dylan Ritter
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Alexander Henderson
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Nathalie Saurat
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Jalwa Afroz
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | | | - Hadar Benyamini
- Whitehead Institute of Biomedical Research, Cambridge, MA, USA
| | - Joseph Copty
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Autumn Morrow
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jonathan Mitchel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA
| | - Drew Neavin
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Renuka Gupta
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Nona Farbehi
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Jennifer Grundman
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Clemens R Scherzer
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Vivianna M Van Deerlin
- Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Antony A Cooper
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Edward B Lee
- Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Yaniv Erlich
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Susan Lindquist
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jian Peng
- Department of Computer Science, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, Semel Institute, Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joseph Powell
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vikram Khurana
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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4
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Tomaszewski A, Wang R, Sandoval E, Zhu J, Liu J, Li R. Solid-to-liquid phase transition in the dissolution of cytosolic misfolded-protein aggregates. iScience 2023; 26:108334. [PMID: 38025775 PMCID: PMC10663836 DOI: 10.1016/j.isci.2023.108334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/08/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
Accumulation of protein aggregates is a hallmark of cellular aging and degenerative disorders. This could result from either increased protein misfolding and aggregation or impaired dissolution of aggregates formed under stress, the latter of which is poorly understood. In this study, we employed quantitative live-cell imaging to investigate the dynamic process of protein disaggregation in yeast. We show that protein aggregates formed upon heat stress are solid condensates, but after stress attenuation these protein aggregates first transition into a liquid-like state during their dissolution. This solid-to-liquid phase transition (SLPT) accompanies the reduction in aggregate number due to the fusion of the liquid condensates. The chaperone activity of Hsp104, a Clp/HSP100 family chaperone, is required for both SLPT and subsequent dispersal of the liquid condensates. Sse1, a yeast HSP110 chaperone, also facilitates SLPT. These results illuminate an unexpected mechanistic framework of cellular control over protein disaggregation upon stress attenuation.
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Affiliation(s)
- Alexis Tomaszewski
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Rebecca Wang
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Eduardo Sandoval
- Department of Neuroscience, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jin Zhu
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Jian Liu
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
- Department of Biological Science, National University of Singapore, Singapore 117411, Singapore
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5
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Zajkowski T, Lee MD, Sharma S, Vallota-Eastman A, Kuska M, Malczewska M, Rothschild LJ. Conserved functions of prion candidates suggest a primeval role of protein self-templating. Proteins 2023; 91:1298-1315. [PMID: 37519023 DOI: 10.1002/prot.26558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
Amyloid-based prions have simple structures, a wide phylogenetic distribution, and a plethora of functions in contemporary organisms, suggesting they may be an ancient phenomenon. However, this hypothesis has yet to be addressed with a systematic, computational, and experimental approach. Here we present a framework to help guide future experimental verification of candidate prions with conserved functions to understand their role in the early stages of evolution and potentially in the origins of life. We identified candidate prions in all high-quality proteomes available in UniProt computationally, assessed their phylogenomic distributions, and analyzed candidate-prion functional annotations. Of the 27 980 560 proteins scanned, 228 561 were identified as candidate prions (~0.82%). Among these candidates, there were 84 Gene Ontology (GO) terms conserved across the three domains of life. We found that candidate prions with a possible role in adaptation were particularly well-represented within this group. We discuss unifying features of candidate prions to elucidate the primeval roles of prions and their associated functions. Candidate prions annotated as transcription factors, DNA binding, and kinases are particularly well suited to generating diverse responses to changes in their environment and could allow for adaptation and population expansion into more diverse environments. We hypothesized that a relationship between these functions and candidate prions could be evolutionarily ancient, even if individual prion domains themselves are not evolutionarily conserved. Candidate prions annotated with these universally occurring functions potentially represent the oldest extant prions on Earth and are therefore excellent experimental targets.
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Affiliation(s)
- Tomasz Zajkowski
- Universities Space Research Association at NASA Ames Research Center, Mountain View, California, USA
- Polish Astrobiology Society, Warsaw, Poland
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- KBR, NASA Ames Research Center, Mountain View, California, USA
| | - Siddhant Sharma
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Alec Vallota-Eastman
- Department of Earth Science, University of California, Santa Barbara, California, USA
| | - Mikołaj Kuska
- Polish Astrobiology Society, Warsaw, Poland
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Małgorzata Malczewska
- Polish Astrobiology Society, Warsaw, Poland
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Lynn J Rothschild
- Space Science and Astrobiology Division, NASA Ames Research Center, Mountain View, California, USA
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6
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Howard MK, Miller KR, Sohn BS, Ryan JJ, Xu A, Jackrel ME. Probing the drivers of Staphylococcus aureus biofilm protein amyloidogenesis and disrupting biofilms with engineered protein disaggregases. mBio 2023; 14:e0058723. [PMID: 37195208 PMCID: PMC10470818 DOI: 10.1128/mbio.00587-23] [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: 03/14/2023] [Accepted: 04/05/2023] [Indexed: 05/18/2023] Open
Abstract
Phenol-soluble modulins (PSMs) are the primary proteinaceous component of Staphylococcus aureus biofilms. Residence in the protective environment of biofilms allows bacteria to rapidly evolve and acquire antimicrobial resistance, which can lead to persistent infections such as those caused by methicillin-resistant S. aureus (MRSA). In their soluble form, PSMs hinder the immune response of the host and can increase the virulence potential of MRSA. PSMs also self-assemble into insoluble functional amyloids that contribute to the structural scaffold of biofilms. The specific roles of PSM peptides in biofilms remain poorly understood. Here, we report the development of a genetically tractable yeast model system for studying the properties of PSMα peptides. Expression of PSMα peptides in yeast drives the formation of toxic insoluble aggregates that adopt vesicle-like structures. Using this system, we probed the molecular drivers of PSMα aggregation to delineate key similarities and differences among the PSMs and identified a crucial residue that drives PSM features. Biofilms are a major public health threat; thus, biofilm disruption is a key goal. To solubilize aggregates comprised of a diverse range of amyloid and amyloid-like species, we have developed engineered variants of Hsp104, a hexameric AAA+ protein disaggregase from yeast. Here, we demonstrate that potentiated Hsp104 variants counter the toxicity and aggregation of PSMα peptides. Further, we demonstrate that a potentiated Hsp104 variant can drive the disassembly of preformed S. aureus biofilms. We suggest that this new yeast model can be a powerful platform for screening for agents that disrupt PSM aggregation and that Hsp104 disaggregases could be a promising tool for the safe enzymatic disruption of biofilms. IMPORTANCE Biofilms are complex mixtures secreted by bacteria that form a material in which the bacteria can become embedded. This process transforms the properties of the bacteria, and they become more resistant to removal, which can give rise to multidrug-resistant strains, such as methicillin-resistant Staphylococcus aureus (MRSA). Here, we study phenol-soluble modulins (PSMs), which are amyloidogenic proteins secreted by S. aureus, that become incorporated into biofilms. Biofilms are challenging to study, so we have developed a new genetically tractable yeast model to study the PSMs. We used our system to learn about several key features of the PSMs. We also demonstrate that variants of an amyloid disaggregase, Hsp104, can disrupt the PSMs and, more importantly, dissolve preformed S. aureus biofilms. We propose that our system can be a powerful screening tool and that Hsp104 disaggregases may be a new avenue to explore for biofilm disruption agents.
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Affiliation(s)
- Matthew K. Howard
- Department of Chemistry, Washington University, St. Louis, Missouri, USA
| | - Karlie R. Miller
- Department of Chemistry, Washington University, St. Louis, Missouri, USA
| | - Brian S. Sohn
- Department of Chemistry, Washington University, St. Louis, Missouri, USA
| | - Jeremy J. Ryan
- Department of Chemistry, Washington University, St. Louis, Missouri, USA
| | - Andy Xu
- Department of Chemistry, Washington University, St. Louis, Missouri, USA
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7
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Hallacli E, Kayatekin C, Nazeen S, Wang XH, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, Di Maio R, Wang W, Keeney MT, Felsky D, Sandoe J, Vahdatshoar A, Udeshi ND, Mani DR, Carr SA, Lindquist S, De Jager PL, Bartel DP, Myers CL, Greenamyre JT, Feany MB, Sunyaev SR, Chung CY, Khurana V. The Parkinson's disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability. Cell 2022; 185:2035-2056.e33. [PMID: 35688132 DOI: 10.1016/j.cell.2022.05.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/05/2022] [Accepted: 05/06/2022] [Indexed: 12/13/2022]
Abstract
Alpha-synuclein (αS) is a conformationally plastic protein that reversibly binds to cellular membranes. It aggregates and is genetically linked to Parkinson's disease (PD). Here, we show that αS directly modulates processing bodies (P-bodies), membraneless organelles that function in mRNA turnover and storage. The N terminus of αS, but not other synucleins, dictates mutually exclusive binding either to cellular membranes or to P-bodies in the cytosol. αS associates with multiple decapping proteins in close proximity on the Edc4 scaffold. As αS pathologically accumulates, aberrant interaction with Edc4 occurs at the expense of physiologic decapping-module interactions. mRNA decay kinetics within PD-relevant pathways are correspondingly disrupted in PD patient neurons and brain. Genetic modulation of P-body components alters αS toxicity, and human genetic analysis lends support to the disease-relevance of these interactions. Beyond revealing an unexpected aspect of αS function and pathology, our data highlight the versatility of conformationally plastic proteins with high intrinsic disorder.
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Affiliation(s)
- Erinc Hallacli
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Can Kayatekin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sumaiya Nazeen
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Xiou H Wang
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Zoe Sheinkopf
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shubhangi Sathyakumar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Souvarish Sarkar
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Xin Jiang
- Yumanity Therapeutics, Boston, MA 02135, USA
| | - Xianjun Dong
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Genomics and Bioinformatics Hub, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Roberto Di Maio
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew T Keeney
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics and Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON M5T 3M7, Canada
| | - Jackson Sandoe
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Aazam Vahdatshoar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David P Bartel
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - J Timothy Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | | | - Vikram Khurana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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8
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Huang Y, Chang Y, Liu L, Wang J. Nanomaterials for Modulating the Aggregation of β-Amyloid Peptides. Molecules 2021; 26:4301. [PMID: 34299575 PMCID: PMC8305396 DOI: 10.3390/molecules26144301] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022] Open
Abstract
The aberrant aggregation of amyloid-β (Aβ) peptides in the brain has been recognized as the major hallmark of Alzheimer's disease (AD). Thus, the inhibition and dissociation of Aβ aggregation are believed to be effective therapeutic strategiesforthe prevention and treatment of AD. When integrated with traditional agents and biomolecules, nanomaterials can overcome their intrinsic shortcomings and boost their efficiency via synergistic effects. This article provides an overview of recent efforts to utilize nanomaterials with superior properties to propose effective platforms for AD treatment. The underlying mechanismsthat are involved in modulating Aβ aggregation are discussed. The summary of nanomaterials-based modulation of Aβ aggregation may help researchers to understand the critical roles in therapeutic agents and provide new insight into the exploration of more promising anti-amyloid agents and tactics in AD theranostics.
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Affiliation(s)
- Yaliang Huang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China;
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China;
| | - Yong Chang
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China;
| | - Lin Liu
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China;
| | - Jianxiu Wang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China;
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9
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Sprunger ML, Jackrel ME. Prion-Like Proteins in Phase Separation and Their Link to Disease. Biomolecules 2021; 11:biom11071014. [PMID: 34356638 PMCID: PMC8301953 DOI: 10.3390/biom11071014] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/28/2021] [Accepted: 07/06/2021] [Indexed: 02/01/2023] Open
Abstract
Aberrant protein folding underpins many neurodegenerative diseases as well as certain myopathies and cancers. Protein misfolding can be driven by the presence of distinctive prion and prion-like regions within certain proteins. These prion and prion-like regions have also been found to drive liquid-liquid phase separation. Liquid-liquid phase separation is thought to be an important physiological process, but one that is prone to malfunction. Thus, aberrant liquid-to-solid phase transitions may drive protein aggregation and fibrillization, which could give rise to pathological inclusions. Here, we review prions and prion-like proteins, their roles in phase separation and disease, as well as potential therapeutic approaches to counter aberrant phase transitions.
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10
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Fanning S, Selkoe D, Dettmer U. Vesicle trafficking and lipid metabolism in synucleinopathy. Acta Neuropathol 2021; 141:491-510. [PMID: 32607605 DOI: 10.1007/s00401-020-02177-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 12/12/2022]
Abstract
The neuronal protein α-synuclein (αS) is central to the pathogenesis of Parkinson's disease and other progressive brain diseases such as Lewy body dementia and multiple system atrophy. These diseases, collectively referred to as 'synucleinopathies', have long been considered purely proteinopathies: diseases characterized by the misfolding of a protein into small and large aggregates mainly consisting of that protein (in this case: α-synuclein). However, recent morphological insights into Lewy bodies, the hallmark neuropathology of human synucleinopathies, suggests these lesions are also rich in vesicles and other membranous organelles. Moreover, αS physiology and pathology are both strongly associated with various aspects of intracellular vesicle trafficking and lipid biology. αS physiologically binds to synaptic and other small vesicles, and several functions of αS in regulating vesicle biology have been proposed. Familial PD-linked αS excess and missense mutations have been shown to impair vesicle trafficking and alter lipid homeostasis. On the other hand, vesicle trafficking and lipid-related genes have emerged as Parkinson's risk factors, suggesting a bidirectional relationship. The answer to the question "Does abnormal αS accumulation cause impaired vesicle trafficking and lipid dyshomeostasis or is αS aggregation the consequence of such impairments?" may be "Both". Here, we review current knowledge of the αS-lipid and αS-vesicle trafficking interplay, with a special focus on Parkinson's disease and Lewy body dementia.
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11
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Alberti S, Hyman AA. Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing. Nat Rev Mol Cell Biol 2021; 22:196-213. [PMID: 33510441 DOI: 10.1038/s41580-020-00326-6] [Citation(s) in RCA: 439] [Impact Index Per Article: 146.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2020] [Indexed: 12/14/2022]
Abstract
Biomolecular condensates are membraneless intracellular assemblies that often form via liquid-liquid phase separation and have the ability to concentrate biopolymers. Research over the past 10 years has revealed that condensates play fundamental roles in cellular organization and physiology, and our understanding of the molecular principles, components and forces underlying their formation has substantially increased. Condensate assembly is tightly regulated in the intracellular environment, and failure to control condensate properties, formation and dissolution can lead to protein misfolding and aggregation, which are often the cause of ageing-associated diseases. In this Review, we describe the mechanisms and regulation of condensate assembly and dissolution, highlight recent advances in understanding the role of biomolecular condensates in ageing and disease, and discuss how cellular stress, ageing-related loss of homeostasis and a decline in protein quality control may contribute to the formation of aberrant, disease-causing condensates. Our improved understanding of condensate pathology provides a promising path for the treatment of protein aggregation diseases.
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Affiliation(s)
- Simon Alberti
- Technische Universität Dresden, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Engineering (CMCB), Dresden, Germany.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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12
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Systematic review and meta-analysis of human transcriptomics reveals neuroinflammation, deficient energy metabolism, and proteostasis failure across neurodegeneration. Neurobiol Dis 2020; 149:105225. [PMID: 33347974 PMCID: PMC7856076 DOI: 10.1016/j.nbd.2020.105225] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative disorders such as Alzheimer's disease (AD), Lewy body diseases (LBD), and the amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD) spectrum are defined by the accumulation of specific misfolded protein aggregates. However, the mechanisms by which each proteinopathy leads to neurodegeneration remain elusive. We hypothesized that there is a common "pan-neurodegenerative" gene expression signature driving pathophysiology across these clinically and pathologically diverse proteinopathies. To test this hypothesis, we performed a systematic review of human CNS transcriptomics datasets from AD, LBD, and ALS-FTD patients and age-matched controls in the Gene Expression Omnibus (GEO) and ArrayExpress databases, followed by consistent processing of each dataset, meta-analysis, pathway enrichment, and overlap analyses. After applying pre-specified eligibility criteria and stringent data pre-processing, a total of 2600 samples from 26 AD, 21 LBD, and 13 ALS-FTD datasets were included in the meta-analysis. The pan-neurodegenerative gene signature is characterized by an upregulation of innate immunity, cytoskeleton, and transcription and RNA processing genes, and a downregulation of the mitochondrial electron transport chain. Pathway enrichment analyses also revealed the upregulation of neuroinflammation (including Toll-like receptor, TNF, and NFκB signaling) and phagocytosis, and the downregulation of mitochondrial oxidative phosphorylation, lysosomal acidification, and ubiquitin-proteasome pathways. Our findings suggest that neuroinflammation and a failure in both neuronal energy metabolism and protein degradation systems are consistent features underlying neurodegenerative diseases, despite differences in the extent of neuronal loss and brain regions involved.
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13
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March ZM, Sweeney K, Kim H, Yan X, Castellano LM, Jackrel ME, Lin J, Chuang E, Gomes E, Willicott CW, Michalska K, Jedrzejczak RP, Joachimiak A, Caldwell KA, Caldwell GA, Shalem O, Shorter J. Therapeutic genetic variation revealed in diverse Hsp104 homologs. eLife 2020; 9:e57457. [PMID: 33319748 PMCID: PMC7785292 DOI: 10.7554/elife.57457] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
The AAA+ protein disaggregase, Hsp104, increases fitness under stress by reversing stress-induced protein aggregation. Natural Hsp104 variants might exist with enhanced, selective activity against neurodegenerative disease substrates. However, natural Hsp104 variation remains largely unexplored. Here, we screened a cross-kingdom collection of Hsp104 homologs in yeast proteotoxicity models. Prokaryotic ClpG reduced TDP-43, FUS, and α-synuclein toxicity, whereas prokaryotic ClpB and hyperactive variants were ineffective. We uncovered therapeutic genetic variation among eukaryotic Hsp104 homologs that specifically antagonized TDP-43 condensation and toxicity in yeast and TDP-43 aggregation in human cells. We also uncovered distinct eukaryotic Hsp104 homologs that selectively antagonized α-synuclein condensation and toxicity in yeast and dopaminergic neurodegeneration in C. elegans. Surprisingly, this therapeutic variation did not manifest as enhanced disaggregase activity, but rather as increased passive inhibition of aggregation of specific substrates. By exploring natural tuning of this passive Hsp104 activity, we elucidated enhanced, substrate-specific agents that counter proteotoxicity underlying neurodegeneration.
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Affiliation(s)
- Zachary M March
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Department of Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - Katelyn Sweeney
- Department of Genetics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Hanna Kim
- Department of Biological Sciences, The University of AlabamaTuscaloosaUnited States
| | - Xiaohui Yan
- Department of Biological Sciences, The University of AlabamaTuscaloosaUnited States
| | - Laura M Castellano
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Pharmacology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - Meredith E Jackrel
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - JiaBei Lin
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - Edward Chuang
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Pharmacology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - Edward Gomes
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - Corey W Willicott
- Department of Biological Sciences, The University of AlabamaTuscaloosaUnited States
| | - Karolina Michalska
- Structural Biology Center, X-ray Science Division, Argonne National LaboratoryArgonneUnited States
- Department of Biochemistry and Molecular Biology, University of ChicagoChicagoUnited States
| | - Robert P Jedrzejczak
- Structural Biology Center, X-ray Science Division, Argonne National LaboratoryArgonneUnited States
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National LaboratoryArgonneUnited States
- Department of Biochemistry and Molecular Biology, University of ChicagoChicagoUnited States
| | - Kim A Caldwell
- Department of Biological Sciences, The University of AlabamaTuscaloosaUnited States
| | - Guy A Caldwell
- Department of Biological Sciences, The University of AlabamaTuscaloosaUnited States
| | - Ophir Shalem
- Department of Genetics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Department of Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Pharmacology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
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14
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Martins PM, Navarro S, Silva A, Pinto MF, Sárkány Z, Figueiredo F, Pereira PJB, Pinheiro F, Bednarikova Z, Burdukiewicz M, Galzitskaya OV, Gazova Z, Gomes CM, Pastore A, Serpell LC, Skrabana R, Smirnovas V, Ziaunys M, Otzen DE, Ventura S, Macedo-Ribeiro S. MIRRAGGE - Minimum Information Required for Reproducible AGGregation Experiments. Front Mol Neurosci 2020; 13:582488. [PMID: 33328883 PMCID: PMC7729192 DOI: 10.3389/fnmol.2020.582488] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. The information conveyed by these reports can be used directly in translational investigation, e.g., for the design of better drug screening strategies, or be compiled in databases for benchmarking novel aggregation-predicting algorithms. Given that minute protocol variations determine different outcomes of protein aggregation assays, there is a strong urge for standardized descriptions of the different types of aggregates and the detailed methods used in their production. In an attempt to address this need, we assembled the Minimum Information Required for Reproducible Aggregation Experiments (MIRRAGGE) guidelines, considering first-principles and the established literature on protein self-assembly and aggregation. This consensus information aims to cover the major and subtle determinants of experimental reproducibility while avoiding excessive technical details that are of limited practical interest for non-specialized users. The MIRRAGGE table (template available in Supplementary Information) is useful as a guide for the design of new studies and as a checklist during submission of experimental reports for publication. Full disclosure of relevant information also enables other researchers to reproduce results correctly and facilitates systematic data deposition into curated databases.
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Affiliation(s)
- Pedro M Martins
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Susanna Navarro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alexandra Silva
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria F Pinto
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Zsuzsa Sárkány
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisco Figueiredo
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.,International Iberian Nanotechnology Laboratory - Department of Atomic Structure - Composition of Materials, Braga, Portugal
| | - Pedro José Barbosa Pereira
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisca Pinheiro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Zuzana Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Michał Burdukiewicz
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Annalisa Pastore
- UK-DRI Centre at King's College London, the Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Rostislav Skrabana
- Department of Neuroimmunology, Axon Neuroscience R&D Services SE, Bratislava, Slovakia.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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15
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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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16
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Chavali S, Singh AK, Santhanam B, Babu MM. Amino acid homorepeats in proteins. Nat Rev Chem 2020; 4:420-434. [PMID: 37127972 DOI: 10.1038/s41570-020-0204-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 12/16/2022]
Abstract
Amino acid homorepeats, or homorepeats, are polypeptide segments found in proteins that contain stretches of identical amino acid residues. Although abnormal homorepeat expansions are linked to pathologies such as neurodegenerative diseases, homorepeats are prevalent in eukaryotic proteomes, suggesting that they are important for normal physiology. In this Review, we discuss recent advances in our understanding of the biological functions of homorepeats, which range from facilitating subcellular protein localization to mediating interactions between proteins across diverse cellular pathways. We explore how the functional diversity of homorepeat-containing proteins could be linked to the ability of homorepeats to adopt different structural conformations, an ability influenced by repeat composition, repeat length and the nature of flanking sequences. We conclude by highlighting how an understanding of homorepeats will help us better characterize and develop therapeutics against the human diseases to which they contribute.
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Affiliation(s)
- Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India.
| | - Anjali K Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Balaji Santhanam
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA.
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17
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Sachsenhauser V, Deng X, Kim HH, Jankovic M, Bardwell JC. Yeast Tripartite Biosensors Sensitive to Protein Stability and Aggregation Propensity. ACS Chem Biol 2020; 15:1078-1088. [PMID: 32105441 DOI: 10.1021/acschembio.0c00083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In contrast to the myriad approaches available to study protein misfolding and aggregation in vitro, relatively few tools are available for the study of these processes in the cellular context. This is in part due to the complexity of the cellular environment which, for instance, interferes with many spectroscopic approaches. Here, we describe a tripartite fusion approach that can be used to assess in vivo protein stability and solubility in the cytosol of Saccharomyces cerevisiae. Our biosensors contain tripartite fusions in which a protein of interest is inserted into antibiotic resistance markers. These fusions act to directly link the aggregation susceptibility and stability of the inserted protein to antibiotic resistance. We demonstrate a linear relationship between the thermodynamic stabilities of variants of the model folding protein immunity protein 7 (Im7) fused into the resistance markers and their antibiotic resistance readouts. We also use this system to investigate the in vivo properties of the yeast prion proteins Sup35 and Rnq1 and proteins whose aggregation is associated with some of the most prevalent neurodegenerative misfolding disorders, including peptide amyloid beta 1-42 (Aβ42), which is involved in Alzheimer's disease, and protein α-synuclein, which is linked to Parkinson's disease.
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Affiliation(s)
- Veronika Sachsenhauser
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109-1085, United States
- Department of Chemistry, Technical University Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Xiexiong Deng
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109-1085, United States
| | - Hyun-hee Kim
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109-1085, United States
| | - Maja Jankovic
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109-1085, United States
| | - James C.A. Bardwell
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109-1085, United States
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18
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Abstract
The traditional view of protein aggregation as being strictly disease-related has been challenged by many examples of cellular aggregates that regulate beneficial biological functions. When coupled with the emerging view that many regulatory proteins undergo phase separation to form dynamic cellular compartments, it has become clear that supramolecular assembly plays wide-ranging and critical roles in cellular regulation. This presents opportunities to develop new tools to probe and illuminate this biology, and to harness the unique properties of these self-assembling systems for synthetic biology for the purposeful manipulation of biological function.
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Affiliation(s)
- Giulio Chiesa
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Szilvia Kiriakov
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, 02215, USA. .,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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19
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Harvey ZH, Chakravarty AK, Futia RA, Jarosz DF. A Prion Epigenetic Switch Establishes an Active Chromatin State. Cell 2020; 180:928-940.e14. [PMID: 32109413 PMCID: PMC7195540 DOI: 10.1016/j.cell.2020.02.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/10/2019] [Accepted: 02/05/2020] [Indexed: 01/24/2023]
Abstract
Covalent modifications to histones are essential for development, establishing distinct and functional chromatin domains from a common genetic sequence. Whereas repressed chromatin is robustly inherited, no mechanism that facilitates inheritance of an activated domain has been described. Here, we report that the Set3C histone deacetylase scaffold Snt1 can act as a prion that drives the emergence and transgenerational inheritance of an activated chromatin state. This prion, which we term [ESI+] for expressed sub-telomeric information, is triggered by transient Snt1 phosphorylation upon cell cycle arrest. Once engaged, the prion reshapes the activity of Snt1 and the Set3C complex, recruiting RNA pol II and interfering with Rap1 binding to activate genes in otherwise repressed sub-telomeric domains. This transcriptional state confers broad resistance to environmental stress, including antifungal drugs. Altogether, our results establish a robust means by which a prion can facilitate inheritance of an activated chromatin state to provide adaptive benefit.
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Affiliation(s)
- Zachary H Harvey
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anupam K Chakravarty
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Raymond A Futia
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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20
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Lam I, Hallacli E, Khurana V. Proteome-Scale Mapping of Perturbed Proteostasis in Living Cells. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a034124. [PMID: 30910772 DOI: 10.1101/cshperspect.a034124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteinopathies are degenerative diseases in which specific proteins adopt deleterious conformations, leading to the dysfunction and demise of distinct cell types. They comprise some of the most significant diseases of aging-from Alzheimer's disease to Parkinson's disease to type 2 diabetes-for which not a single disease-modifying or preventative strategy exists. Here, we survey approaches in tractable cellular and organismal models that bring us toward a more complete understanding of the molecular consequences of protein misfolding. These include proteome-scale profiling of genetic modifiers, as well as transcriptional and proteome changes. We describe assays that can capture protein interactomes in situ and distinct protein conformational states. A picture of cellular drivers and responders to proteotoxicity emerges from this work, distinguishing general alterations of proteostasis from cellular events that are deeply tied to the intrinsic function of the misfolding protein. These distinctions have consequences for the understanding and treatment of proteinopathies.
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Affiliation(s)
- Isabel Lam
- Ann Romney Center for Neurologic Disease, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Erinc Hallacli
- Ann Romney Center for Neurologic Disease, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Vikram Khurana
- Ann Romney Center for Neurologic Disease, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138.,New York Stem Cell Foundation - Robertson Investigator
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21
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Parkinson's disease: proteinopathy or lipidopathy? NPJ PARKINSONS DISEASE 2020; 6:3. [PMID: 31909184 PMCID: PMC6941970 DOI: 10.1038/s41531-019-0103-7] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/02/2019] [Indexed: 12/16/2022]
Abstract
Lipids play a more significant role in Parkinson’s disease and its related brain disorders than is currently recognized, supporting a “lipid cascade”. The 14 kDa protein α-synuclein (αS) is strongly associated with Parkinson’s disease (PD), dementia with Lewy bodies (DLB), other synucleinopathies such as multiple system atrophy, and even certain forms of Alzheimer’s disease. Rigorously deciphering the biochemistry of αS in native systems is the key to developing treatments. αS is highly expressed in the brain, the second most lipid-rich organ, and has been proposed to be a lipid-binding protein that physiologically interacts with phospholipids and fatty acids (FAs). αS-rich cytoplasmic inclusions called Lewy bodies and Lewy neurites are the hallmark lesions of synucleinopathies. Excess αS–membrane interactions may trigger proteinaceous αS aggregation by stimulating its primary nucleation. However, αS may also exert its toxicity prior to or independent of its self-aggregation, e.g., via excessive membrane interactions, which may be promoted by certain lipids and FAs. A complex αS-lipid landscape exists, which comprises both physiological and pathological states of αS. As novel insights about the composition of Lewy lesions occur, new lipid-related PD drug candidates emerge, and genome-wide association studies (GWAS) increasingly validate new hits in lipid-associated pathways, it seems timely to review our current knowledge of lipids in PD and consider the roles for these pathways in synucleinopathies.αS ↔ lipid interplay: aspects of cellular αS homeostasis (blue oval), aspects of lipid homeostasis (green oval), and overlapping aspects. Pathological states are labeled in red. Simplified schematic of both select αS and select lipid species. Several existing publications suggest αS effects on lipids and vice versa, as indicated by arrows. DG diglyceride, ER endoplasmic reticulum, FA fatty acid, LD, lipid droplet, TG triglyceride. ![]()
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22
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Chakravarty AK, Smejkal T, Itakura AK, Garcia DM, Jarosz DF. A Non-amyloid Prion Particle that Activates a Heritable Gene Expression Program. Mol Cell 2019; 77:251-265.e9. [PMID: 31757755 PMCID: PMC6980676 DOI: 10.1016/j.molcel.2019.10.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/29/2019] [Accepted: 10/17/2019] [Indexed: 11/16/2022]
Abstract
Spatiotemporal gene regulation is often driven by RNA-binding proteins that harbor long intrinsically disordered regions in addition to folded RNA-binding domains. We report that the disordered region of the evolutionarily ancient developmental regulator Vts1/Smaug drives self-assembly into gel-like condensates. These proteinaceous particles are not composed of amyloid, yet they are infectious, allowing them to act as a protein-based epigenetic element: a prion [SMAUG+]. In contrast to many amyloid prions, condensation of Vts1 enhances its function in mRNA decay, and its self-assembly properties are conserved over large evolutionary distances. Yeast cells harboring [SMAUG+] downregulate a coherent network of mRNAs and exhibit improved growth under nutrient limitation. Vts1 condensates formed from purified protein can transform naive cells to acquire [SMAUG+]. Our data establish that non-amyloid self-assembly of RNA-binding proteins can drive a form of epigenetics beyond the chromosome, instilling adaptive gene expression programs that are heritable over long biological timescales.
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Affiliation(s)
- Anupam K Chakravarty
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, USA
| | - Tina Smejkal
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, USA
| | - Alan K Itakura
- Department of Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, USA
| | - David M Garcia
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, USA.
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23
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Eguchi Y, Bilolikar G, Geiler-Samerotte K. Why and how to study genetic changes with context-dependent effects. Curr Opin Genet Dev 2019; 58-59:95-102. [PMID: 31593884 DOI: 10.1016/j.gde.2019.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/21/2019] [Accepted: 08/29/2019] [Indexed: 01/18/2023]
Abstract
The phenotypic impacts of a genetic change can depend on genetic background (e.g. epistasis), as well as other contexts including environment, developmental stage, cell type, disease state, and higher-order combinations thereof. Recent advances in high-throughput phenotyping are uncovering examples of context dependence faster than genotype-phenotype maps and other core concepts are changing to reflect the dynamic nature of biological systems. Here, we review several approaches to study context dependence and their findings. In our opinion, these findings encourage more studies that examine the spectrum of effects a genetic change may have, as opposed to studies that exclusively measure the impact of a genetic change in a particular context. Studies that elucidate the mechanisms that cause the effects of genetic change to vary with context are of special interest. Previous studies of the mechanisms underlying context dependence have improved predictions of phenotype from genotype and have provided insight about how biological systems function and evolve.
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Affiliation(s)
- Yuichi Eguchi
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Gaurav Bilolikar
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Kerry Geiler-Samerotte
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States.
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24
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Schattling B, Engler JB, Volkmann C, Rothammer N, Woo MS, Petersen M, Winkler I, Kaufmann M, Rosenkranz SC, Fejtova A, Thomas U, Bose A, Bauer S, Träger S, Miller KK, Brück W, Duncan KE, Salinas G, Soba P, Gundelfinger ED, Merkler D, Friese MA. Bassoon proteinopathy drives neurodegeneration in multiple sclerosis. Nat Neurosci 2019; 22:887-896. [PMID: 31011226 DOI: 10.1038/s41593-019-0385-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 03/13/2019] [Indexed: 12/21/2022]
Abstract
Multiple sclerosis (MS) is characterized by inflammatory insults that drive neuroaxonal injury. However, knowledge about neuron-intrinsic responses to inflammation is limited. By leveraging neuron-specific messenger RNA profiling, we found that neuroinflammation leads to induction and toxic accumulation of the synaptic protein bassoon (Bsn) in the neuronal somata of mice and patients with MS. Neuronal overexpression of Bsn in flies resulted in reduction of lifespan, while genetic disruption of Bsn protected mice from inflammation-induced neuroaxonal injury. Notably, pharmacological proteasome activation boosted the clearance of accumulated Bsn and enhanced neuronal survival. Our study demonstrates that neuroinflammation initiates toxic protein accumulation in neuronal somata and advocates proteasome activation as a potential remedy.
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Affiliation(s)
- Benjamin Schattling
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Jan Broder Engler
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Constantin Volkmann
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Rothammer
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Marcel S Woo
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Meike Petersen
- Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Iris Winkler
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Max Kaufmann
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Sina C Rosenkranz
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Fejtova
- Leibniz-Institute für Neurobiologie, Magdeburg, Germany.,Psychiatrische und Psychotherapeutische Klinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ulrich Thomas
- Leibniz-Institute für Neurobiologie, Magdeburg, Germany
| | - Aparajita Bose
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Simone Bauer
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Simone Träger
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Katharine K Miller
- Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Wolfgang Brück
- Institut für Neuropathologie, Universitätsmedizin Göttingen, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Kent E Duncan
- Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriela Salinas
- Transkriptomanalyselabor, Institut für Entwicklungsbiochemie, Universitätsmedizin Göttingen, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Peter Soba
- Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Eckart D Gundelfinger
- Leibniz-Institute für Neurobiologie, Magdeburg, Germany.,Center for Behavioral Brain Sciences and Medical Faculty, Otto von Guericke Universität, Magdeburg, Germany
| | - Doron Merkler
- Department of Pathology and Immunology, Service of Clinical Pathology, Geneva Faculty of Medicine, Geneva, Switzerland
| | - Manuel A Friese
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.
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25
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Kulkarni V, Kulkarni P. Intrinsically disordered proteins and phenotypic switching: Implications in cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:63-84. [PMID: 31521237 DOI: 10.1016/bs.pmbts.2019.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It is now well established that intrinsically disordered proteins (IDPs) that constitute a large part of the proteome across the three kingdoms, play critical roles in several biological processes including phenotypic switching. However, dysregulated expression of IDPs that engage in promiscuous interactions can lead to pathological states. In this chapter, using cancer as a paradigm, we discuss how IDP conformational dynamics and the resultant conformational noise can modulate phenotypic switching. Thus, contrary to the prevailing wisdom that phenotypic switching is highly deterministic (has a genetic underpinning) in cancer, emerging evidence suggests that non-genetic mechanisms, at least in part due to the conformational noise, may also be a confounding factor in phenotypic switching.
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Affiliation(s)
- Vivek Kulkarni
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, United States.
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26
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Tariq A, Lin J, Noll MM, Torrente MP, Mack KL, Murillo OH, Jackrel ME, Shorter J. Potentiating Hsp104 activity via phosphomimetic mutations in the middle domain. FEMS Yeast Res 2019; 18:4969683. [PMID: 29788207 DOI: 10.1093/femsyr/foy042] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/10/2018] [Indexed: 12/13/2022] Open
Abstract
Hsp104 is a hexameric AAA + ATPase and protein disaggregase found in yeast, which can be potentiated via mutations in its middle domain (MD) to counter toxic phase separation by TDP-43, FUS and α-synuclein connected to devastating neurodegenerative disorders. Subtle missense mutations in the Hsp104 MD can enhance activity, indicating that post-translational modification of specific MD residues might also potentiate Hsp104. Indeed, several serine and threonine residues throughout Hsp104 can be phosphorylated in vivo. Here, we introduce phosphomimetic aspartate or glutamate residues at these positions and assess Hsp104 activity. Remarkably, phosphomimetic T499D/E and S535D/E mutations in the MD enable Hsp104 to counter TDP-43, FUS and α-synuclein aggregation and toxicity in yeast, whereas T499A/V/I and S535A do not. Moreover, Hsp104T499E and Hsp104S535E exhibit enhanced ATPase activity and Hsp70-independent disaggregase activity in vitro. We suggest that phosphorylation of T499 or S535 may elicit enhanced Hsp104 disaggregase activity in a reversible and regulated manner.
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Affiliation(s)
| | - JiaBei Lin
- Department of Biochemistry and Biophysics
| | | | | | - Korrie L Mack
- Department of Biochemistry and Biophysics
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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27
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Metabolic switching of sake yeast by kimoto lactic acid bacteria through the [GAR] non-genetic element. J Biosci Bioeng 2018; 126:624-629. [DOI: 10.1016/j.jbiosc.2018.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/08/2018] [Accepted: 05/15/2018] [Indexed: 12/11/2022]
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28
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Dettmer U. Rationally Designed Variants of α-Synuclein Illuminate Its in vivo Structural Properties in Health and Disease. Front Neurosci 2018; 12:623. [PMID: 30319334 PMCID: PMC6167557 DOI: 10.3389/fnins.2018.00623] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/20/2018] [Indexed: 12/11/2022] Open
Abstract
α-Synuclein (αS) is a conserved and abundant neuronal protein with unusual structural properties. It appears to partition between folded and unstructured states as well as between membrane-bound and aqueously soluble states. In addition, a switch between monomeric and tetrameric/multimeric states has been observed recently. The precise composition, localization and abundance of the multimeric species are under study and remain unsettled. Yet to interfere with disease pathogenesis, we must dissect how small changes in αS homeostasis may give rise to Parkinson’s disease (PD), dementia with Lewy bodies (DLB) and other human synucleinopathies. Rationally designed αS point mutations that prevent the protein from populating all states within its normal folding repertoire have continued to be instrumental in bringing new insights into its biochemistry in vivo. This review summarizes biochemical and cell biological findings about αS homeostasis from different labs, with a special emphasis on intact-cell approaches that may preserve the complex, metastable native states of αS.
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Affiliation(s)
- Ulf Dettmer
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
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29
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Abstract
From bacteria to humans, ancient stress responses enable organisms to contend with damage to both the genome and the proteome. These pathways have long been viewed as fundamentally separate responses. Yet recent discoveries from multiple fields have revealed surprising links between the two. Many DNA-damaging agents also target proteins, and mutagenesis induced by DNA damage produces variant proteins that are prone to misfolding, degradation, and aggregation. Likewise, recent studies have observed pervasive engagement of a p53-mediated response, and other factors linked to maintenance of genomic integrity, in response to misfolded protein stress. Perhaps most remarkably, protein aggregation and self-assembly has now been observed in multiple proteins that regulate the DNA damage response. The importance of these connections is highlighted by disease models of both cancer and neurodegeneration, in which compromised DNA repair machinery leads to profound defects in protein quality control, and vice versa.
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30
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Chakravarty AK, Jarosz DF. More than Just a Phase: Prions at the Crossroads of Epigenetic Inheritance and Evolutionary Change. J Mol Biol 2018; 430:4607-4618. [PMID: 30031007 DOI: 10.1016/j.jmb.2018.07.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/08/2018] [Accepted: 07/16/2018] [Indexed: 12/11/2022]
Abstract
A central tenet of molecular biology is that heritable information is stored in nucleic acids. However, this paradigm has been overturned by a group of proteins called "prions." Prion proteins, many of which are intrinsically disordered, can adopt multiple conformations, at least one of which has the capacity to self-template. This unusual folding landscape drives a form of extreme epigenetic inheritance that can be stable through both mitotic and meiotic cell divisions. Although the first prion discovered-mammalian PrP-is the causative agent of debilitating neuropathies, many additional prions have now been identified that are not obviously detrimental and can even be adaptive. Intrinsically disordered regions, which endow proteins with the bulk property of "phase-separation," can also be drivers of prion formation. Indeed, many protein domains that promote phase separation have been described as prion-like. In this review, we describe how prions lie at the crossroads of phase separation, epigenetic inheritance, and evolutionary adaptation.
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Affiliation(s)
- Anupam K Chakravarty
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, United States
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, United States; Department of Developmental Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, United States.
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31
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Abstract
Self-assembled peptide nanostructures have been increasingly exploited as functional materials for applications in biomedicine and energy. The emergent properties of these nanomaterials determine the applications for which they can be exploited. It has recently been appreciated that nanomaterials composed of multicomponent coassembled peptides often display unique emergent properties that have the potential to dramatically expand the functional utility of peptide-based materials. This review presents recent efforts in the development of multicomponent peptide assemblies. The discussion includes multicomponent assemblies derived from short low molecular weight peptides, peptide amphiphiles, coiled coil peptides, collagen, and β-sheet peptides. The design, structure, emergent properties, and applications for these multicomponent assemblies are presented in order to illustrate the potential of these formulations as sophisticated next-generation bio-inspired materials.
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Affiliation(s)
- Danielle M Raymond
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
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32
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Mentlein L, Thorlacius GE, Meneghel L, Aqrawi LA, Ramírez Sepúlveda JI, Grunewald J, Espinosa A, Wahren-Herlenius M. The rheumatic disease-associated FAM167A-BLK locus encodes DIORA-1, a novel disordered protein expressed highly in bronchial epithelium and alveolar macrophages. Clin Exp Immunol 2018; 193:167-177. [PMID: 29663334 DOI: 10.1111/cei.13138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/30/2018] [Accepted: 04/03/2018] [Indexed: 12/11/2022] Open
Abstract
Triggering of autoimmunity that leads to rheumatic disease has been suggested to depend upon gene-environment interactions occurring in epithelial barriers and associated immune cells. Genetic studies have identified associations of the FAM167A-BLK locus with rheumatoid arthritis, systemic lupus erythematosus (SLE) and Sjögren's syndrome. While BLK (B lymphocyte kinase) has a well-established role in B cells, family with sequence similarity to 167 member A (FAM167A) and its gene family remain uncharacterized. To begin to understand the role of FAM167A in rheumatic disease pathogenesis, we explored this gene family and cloned and investigated the gene products. Expression of quantitative trait locus analysis was performed in immune cells. FAM167A and FAM167B were cloned from human peripheral blood mononuclear cells (PBMC). Gene conservation and protein properties were analysed by online tools, mRNA expression measured in mouse organs by quantitative polymerase chain reaction (qPCR) and protein expression investigated in human tissues by immunohistochemistry. We found that autoimmune risk genotypes within the FAM167A-BLK locus lead to increased expression of FAM167A. The FAM167 gene family includes two members, FAM167A and FAM167B, which are not homologous to any other annotated gene but are evolutionarily conserved. The encoded proteins, which we denote 'disordered autoimmunity' (DIORA)-1 and DIORA-2, respectively, are characterized by a high content of intrinsic disorder. Notably, DIORA-1 has its highest expression in the lung, detectable in both bronchial epithelium and alveolar macrophages with an endosomal localization pattern. In summary, the FAM167A gene is associated with several rheumatic diseases and encodes a novel disordered protein, DIORA-1, which is expressed highly in the lung, consistent with a potential role in disease pathogenesis.
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Affiliation(s)
| | | | | | | | | | - J Grunewald
- Respiratory Medicine Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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33
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Abstract
Amyloid fibrils are protein homopolymers that adopt diverse cross-β conformations. Some amyloid fibrils are associated with the pathogenesis of devastating neurodegenerative disorders, including Alzheimer's disease and Parkinson's disease. Conversely, functional amyloids play beneficial roles in melanosome biogenesis, long-term memory formation and release of peptide hormones. Here, we showcase advances in our understanding of amyloid assembly and structure, and how distinct amyloid strains formed by the same protein can cause distinct neurodegenerative diseases. We discuss how mutant steric zippers promote deleterious amyloidogenesis and aberrant liquid-to-gel phase transitions. We also highlight effective strategies to combat amyloidogenesis and related toxicity, including: (1) small-molecule drugs (e.g. tafamidis) to inhibit amyloid formation or (2) stimulate amyloid degradation by the proteasome and autophagy, and (3) protein disaggregases that disassemble toxic amyloid and soluble oligomers. We anticipate that these advances will inspire therapeutics for several fatal neurodegenerative diseases. Summary: This Review showcases important advances in our understanding of amyloid structure, assembly and disassembly, which are inspiring novel therapeutic strategies for amyloid disorders.
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Affiliation(s)
- Edward Chuang
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Pharmacology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Acacia M Hori
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christina D Hesketh
- 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 .,Pharmacology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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34
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Conformation Polymorphism of Polyglutamine Proteins. Trends Biochem Sci 2018; 43:424-435. [PMID: 29636213 DOI: 10.1016/j.tibs.2018.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/05/2018] [Accepted: 03/12/2018] [Indexed: 01/29/2023]
Abstract
Expanded polyglutamine (polyQ) stretches within endogenous proteins cause at least nine human diseases. The structural basis of polyQ pathogenesis is the key to understanding fundamental mechanisms of these diseases, but it remains unclear and controversial due to a lack of polyQ protein structures at the single-atom level. Various hypotheses have been proposed to explain the structure-cytotoxicity relationship of pathogenic proteins with polyQ expansion, largely based on indirect evidence. Here we review these hypotheses and their supporting evidence, along with additional insights from recent structural biology and chemical biology studies, with a focus on Huntingtin (HTT), the most extensively studied polyQ disease protein. Lastly, we propose potential novel strategies that may further clarify the conformation-cytotoxicity relationship of polyQ proteins.
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