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Halder B, Ghosh S, Khan T, Pal S, Das N, Sen P. Tracking heterogenous protein aggregation at nanoscale through fluorescence correlation spectroscopy. Photochem Photobiol 2024; 100:989-999. [PMID: 39032082 DOI: 10.1111/php.14004] [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: 02/21/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/22/2024]
Abstract
Various biophysical techniques have been extensively employed to study protein aggregation due to its significance. Traditionally, these methods detect aggregation at micrometer length scales and micromolar concentrations. However, unlike in vitro, protein aggregation typically occurs at nanomolar concentrations in vivo. Here, using fluorescence correlation spectroscopy (FCS), we captured bromelain aggregation at concentrations as low as ~20 nM, surpassing the detection limit of traditional methods like thioflavin T fluorescence, scattering, and fluorescence microscopy by more than one order of magnitude. Moreover, using thioflavin T fluorescence-based FCS, we have detected larger aggregates at higher bromelain concentrations, which is undetectable in FCS otherwise. Importantly, our study reveals inherent heterogeneity in bromelain aggregation, inaccessible to ensemble-averaged techniques. The presented report may provide a platform for the characterization of premature aggregates at very low protein concentrations, which are thought to be functionally significant species in protein aggregation-induced diseases.
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Affiliation(s)
- Bisal Halder
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Shreya Ghosh
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Subhendu Pal
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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2
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Sankaran J, Wohland T. Current capabilities and future perspectives of FCS: super-resolution microscopy, machine learning, and in vivo applications. Commun Biol 2023; 6:699. [PMID: 37419967 PMCID: PMC10328937 DOI: 10.1038/s42003-023-05069-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule sensitive tool for the quantitative measurement of biomolecular dynamics and interactions. Improvements in biology, computation, and detection technology enable real-time FCS experiments with multiplexed detection even in vivo. These new imaging modalities of FCS generate data at the rate of hundreds of MB/s requiring efficient data processing tools to extract information. Here, we briefly review FCS's capabilities and limitations before discussing recent directions that address these limitations with a focus on imaging modalities of FCS, their combinations with super-resolution microscopy, new evaluation strategies, especially machine learning, and applications in vivo.
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Affiliation(s)
- Jagadish Sankaran
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138632, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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3
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Kinetic analysis reveals that independent nucleation events determine the progression of polyglutamine aggregation in C. elegans. Proc Natl Acad Sci U S A 2021; 118:2021888118. [PMID: 33836595 PMCID: PMC7980373 DOI: 10.1073/pnas.2021888118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Protein aggregation is associated with a wide range of degenerative human diseases with devastating consequences, as exemplified by Alzheimer's, Parkinson's, and Huntington's diseases. In vitro kinetic studies have provided a mechanistic understanding of the aggregation process at the molecular level. However, it has so far remained largely unclear to what extent the biophysical principles of amyloid formation learned in vitro translate to the complex environment of living organisms. Here, we take advantage of the unique properties of a Caenorhabditis elegans model expressing a fluorescently tagged polyglutamine (polyQ) protein, which aggregates into discrete micrometer-sized inclusions that can be directly visualized in real time. We provide a quantitative analysis of protein aggregation in this system and show that the data are described by a molecular model where stochastic nucleation occurs independently in each cell, followed by rapid aggregate growth. Global fitting of the image-based aggregation kinetics reveals a nucleation rate corresponding to 0.01 h-1 per cell at 1 mM intracellular protein concentration, and shows that the intrinsic molecular stochasticity of nucleation accounts for a significant fraction of the observed animal-to-animal variation. Our results highlight how independent, stochastic nucleation events in individual cells control the overall progression of polyQ aggregation in a living animal. The key finding that the biophysical principles associated with protein aggregation in small volumes remain the governing factors, even in the complex environment of a living organism, will be critical for the interpretation of in vivo data from a wide range of protein aggregation diseases.
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4
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Fluorescence-based techniques for the detection of the oligomeric status of proteins: implication in amyloidogenic diseases. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:671-685. [PMID: 33564930 DOI: 10.1007/s00249-021-01505-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/10/2020] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
Intrinsically disordered proteins (IDPs) have captured attention in the last couple of decades due to their functional roles despite a lack of specific structure. Moreover, these proteins are found to be highly aggregation prone depending on the mutational and environmental changes to which they are subjected. The aggregation of such proteins either in the intracellular context or extracellular matrix is associated with several adverse pathophysiological conditions such as Alzheimer's, Parkinson's, and Huntington's diseases, Spinocerebellar ataxia, and Type-II diabetes. Interestingly, it has been noted that the smaller oligomers formed by IDPs are more toxic to cells than their larger aggregates. This necessitates the development of techniques that can detect the smaller oligomers formed by IDPs for diagnosis of such diseases during their early onset. Fluorescence-based spectroscopic and microscopic techniques are highly effective as compared to other techniques for the evaluation of protein oligomerization, organization, and dynamics. In this review, we discuss several fluorescence-based techniques including fluorescence/Förster resonance energy transfer (FRET), homo-FRET, fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), fluorescence lifetime imaging (FLIM), and photobleaching image correlation spectroscopy (pbICS) that are routinely used to identify protein oligomers in extracellular and intracellular matrices.
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5
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Fu R, Huang Z, Li H, Zhu Y, Zhang H. A Hemidesmosome-to-Cytoplasm Translocation of Small Heat Shock Proteins Provides Immediate Protection against Heat Stress. Cell Rep 2020; 33:108410. [DOI: 10.1016/j.celrep.2020.108410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/28/2020] [Accepted: 10/29/2020] [Indexed: 02/08/2023] Open
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6
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Dawes ML, Soeller C, Scholpp S. Studying molecular interactions in the intact organism: fluorescence correlation spectroscopy in the living zebrafish embryo. Histochem Cell Biol 2020; 154:507-519. [PMID: 33067656 PMCID: PMC7609432 DOI: 10.1007/s00418-020-01930-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
Cell behaviour and function is determined through the interactions of a multitude of molecules working in concert. To observe these molecular dynamics, biophysical studies have been developed that track single interactions. Fluorescence correlation spectroscopy (FCS) is an optical biophysical technique that non-invasively resolves single molecules through recording the signal intensity at the femtolitre scale. However, recording the behaviour of these biomolecules using in vitro-based assays often fails to recapitulate the full range of variables in vivo that directly confer dynamics. Therefore, there has been an increasing interest in observing the state of these biomolecules within living organisms such as the zebrafish Danio rerio. In this review, we explore the advancements of FCS within the zebrafish and compare and contrast these findings to those found in vitro.
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Affiliation(s)
- Michael L Dawes
- Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Christian Soeller
- Living Systems Institute, College of Engineering, Mathematics, and Physical Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Steffen Scholpp
- Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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7
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Jung KH, Zhang X. Fluorogenic detection of protein aggregates in live cells using the AggTag method. Methods Enzymol 2020; 639:1-22. [PMID: 32475397 DOI: 10.1016/bs.mie.2020.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein aggregation is a process that occurs through the self-assembly of misfolded proteins to form soluble oligomers and insoluble aggregates. While there has been significant interest in protein aggregation for neurodegenerative diseases, progress in this field of research has been limited by the lack of effective methods to detect and interrogate these species in live cells. To resolve this issue, we have developed a new imaging method named the AggTag to report on protein aggregation in live cells with fluorescence microscopy. The AggTag method utilizes a genetic fusion of a protein of interest (POI) to a protein tag to conjugate with the AggTag probe, which contains a fluorophore that turns on its fluorescence upon interaction with protein aggregates. Unlike the conventional methods, this method enables one to detect soluble misfolded oligomers that were previously invisible. Furthermore, the AggTag method has been applied for the simultaneous detection of co-aggregation between two different POIs by a dual-color and orthogonal tagging system. This chapter aims to provide step-by-step procedures of the AggTag method for researchers who intend to study aggregation of POIs in mammalian cell lines.
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Affiliation(s)
- Kwan Ho Jung
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States.
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8
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Pohl F, Teixeira-Castro A, Costa MD, Lindsay V, Fiúza-Fernandes J, Goua M, Bermano G, Russell W, Maciel P, Kong Thoo Lin P. GST-4-Dependent Suppression of Neurodegeneration in C. elegans Models of Parkinson's and Machado-Joseph Disease by Rapeseed Pomace Extract Supplementation. Front Neurosci 2019; 13:1091. [PMID: 31680826 PMCID: PMC6811615 DOI: 10.3389/fnins.2019.01091] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/27/2019] [Indexed: 12/13/2022] Open
Abstract
Genetic mutations and aging-associated oxidative damage underlie the onset and progression of neurodegenerative diseases, like Parkinson’s disease (PD) and Machado-Joseph disease (MJD). Natural products derived from plants have been regarded as important sources of novel bioactive compounds to counteract neurodegeneration. Here, we tested the neuroprotective effect of an ethanolic extract of rapeseed pomace (RSP), a rapeseed (canola) oil production by-product, in C. elegans models of MJD and PD. The extract, containing sinapine and other phenolics, restored motor function of mutant ataxin-3 (ATXN3) animals (MJD) and prevented degeneration of dopaminergic neurons in one toxin-induced and two genetic models of PD. Whole-organism sensors of antioxidant and xenobiotic response activation revealed the induction of phase II detoxification enzymes, including glutathione S- transferase (GST-4) upon RSP extract supplementation. Furthermore in vivo pharmacogenetic studies confirmed gst-4 is required for the therapeutic effect of RSP extract in the two disease models. The results suggest that GST-4-mediated antioxidant pathways may constitute promising therapeutic co-targets for neurodegenerative diseases and confirm the utility of searching for bioactive compounds in novel sources, including food and agricultural waste/by-products, such as RSP.
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Affiliation(s)
- Franziska Pohl
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
| | - Andreia Teixeira-Castro
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal
| | - Marta Daniela Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal
| | - Victoria Lindsay
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
| | - Juliana Fiúza-Fernandes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal
| | - Marie Goua
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
| | - Giovanna Bermano
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
| | - Wendy Russell
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Patrícia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal
| | - Paul Kong Thoo Lin
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
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9
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Laine RF, Sinnige T, Ma KY, Haack AJ, Poudel C, Gaida P, Curry N, Perni M, Nollen EA, Dobson CM, Vendruscolo M, Kaminski Schierle GS, Kaminski CF. Fast Fluorescence Lifetime Imaging Reveals the Aggregation Processes of α-Synuclein and Polyglutamine in Aging Caenorhabditis elegans. ACS Chem Biol 2019; 14:1628-1636. [PMID: 31246415 PMCID: PMC7612977 DOI: 10.1021/acschembio.9b00354] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The nematode worm Caenorhabditis elegans has emerged as an important model organism in the study of the molecular mechanisms of protein misfolding diseases associated with amyloid formation because of its small size, ease of genetic manipulation, and optical transparency. Obtaining a reliable and quantitative read-out of protein aggregation in this system, however, remains a challenge. To address this problem, we here present a fast time-gated fluorescence lifetime imaging (TG-FLIM) method and show that it provides functional insights into the process of protein aggregation in living animals by enabling the rapid characterization of different types of aggregates. Specifically, in longitudinal studies of C. elegans models of Parkinson's and Huntington's diseases, we observed marked differences in the aggregation kinetics and the nature of the protein inclusions formed by α-synuclein and polyglutamine. In particular, we found that α-synuclein inclusions do not display amyloid-like features until late in the life of the worms, whereas polyglutamine forms amyloid characteristics rapidly in early adulthood. Furthermore, we show that the TG-FLIM method is capable of imaging live and non-anaesthetized worms moving in specially designed agarose microchambers. Taken together, our results show that the TG-FLIM method enables high-throughput functional imaging of living C. elegans that can be used to study in vivo mechanisms of protein aggregation and that has the potential to aid the search for therapeutic modifiers of protein aggregation and toxicity.
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Affiliation(s)
- Romain F. Laine
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Tessa Sinnige
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Kai Yu Ma
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Amanda J. Haack
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Chetan Poudel
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Peter Gaida
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Nathan Curry
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Ellen A.A. Nollen
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, 9700 AD Groningen, The Netherlands
| | - Christopher M. Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Gabriele S. Kaminski Schierle
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Clemens F. Kaminski
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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10
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Wilson JW, Rolland AD, Klausen GM, Prell JS. Ion Mobility-Mass Spectrometry Reveals That α-Hemolysin from Staphylococcus aureus Simultaneously Forms Hexameric and Heptameric Complexes in Detergent Micelle Solutions. Anal Chem 2019; 91:10204-10211. [PMID: 31282652 DOI: 10.1021/acs.analchem.9b02243] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many soluble and membrane proteins form symmetrical homooligomeric complexes. However, determining the oligomeric state of protein complexes can be difficult. Alpha-hemolysin (αHL) from Staphylococcus aureus is a symmetrical homooligomeric protein toxin that forms transmembrane β-barrel pores in host cell membranes. The stable pore structure of αHL has also been exploited in vitro as a nanopore tool. Early structural experiments suggested αHL forms a hexameric pore, while more recent X-ray crystal structure and solution studies have identified a heptameric pore structure. Here, using native ion mobility-mass spectrometry (IM-MS) we find that αHL simultaneously forms hexameric and heptameric oligomers in both tetraethylene glycol monooctyl ether (C8E4) and tetradecylphosphocholine (FOS-14) detergent solutions. We also analyze intact detergent micelle-embedded αHL porelike complexes by native IM-MS without the need to fully strip the detergent micelle, which can cause significant gas-phase unfolding. The highly congested native mass spectra are deconvolved using Fourier- and Gábor-transform (FT and GT) methods to determine charge states and detergent stoichiometry distributions. The intact αHL micelle complexes are found to contain oligomeric state-proportional numbers of detergent molecules. This evidence, combined with IM data and results from vacuum molecular dynamics simulations, is consistent with both the hexamer and the heptamer forming porelike complexes. The ability of αHL to form both oligomeric states simultaneously has implications for its use as a nanopore tool and its pore formation mechanism in vivo. This study also demonstrates more generally the power of FT and GT to deconvolve the charge state and stoichiometry distributions of polydisperse ions.
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Affiliation(s)
- Jesse W Wilson
- Department of Chemistry and Biochemistry , University of Oregon , 1253 University of Oregon , Eugene , Oregon 97403-1253 , United States
| | - Amber D Rolland
- Department of Chemistry and Biochemistry , University of Oregon , 1253 University of Oregon , Eugene , Oregon 97403-1253 , United States
| | - Grant M Klausen
- Department of Chemistry and Biochemistry , University of Oregon , 1253 University of Oregon , Eugene , Oregon 97403-1253 , United States
| | - James S Prell
- Department of Chemistry and Biochemistry , University of Oregon , 1253 University of Oregon , Eugene , Oregon 97403-1253 , United States.,Materials Science Institute , University of Oregon , 1252 University of Oregon , Eugene , Oregon 97403-1252 , United States
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11
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State-of-the-Art Fluorescence Fluctuation-Based Spectroscopic Techniques for the Study of Protein Aggregation. Int J Mol Sci 2018; 19:ijms19040964. [PMID: 29570669 PMCID: PMC5979297 DOI: 10.3390/ijms19040964] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/17/2018] [Accepted: 03/21/2018] [Indexed: 02/07/2023] Open
Abstract
Neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease, are devastating proteinopathies with misfolded protein aggregates accumulating in neuronal cells. Inclusion bodies of protein aggregates are frequently observed in the neuronal cells of patients. Investigation of the underlying causes of neurodegeneration requires the establishment and selection of appropriate methodologies for detailed investigation of the state and conformation of protein aggregates. In the current review, we present an overview of the principles and application of several methodologies used for the elucidation of protein aggregation, specifically ones based on determination of fluctuations of fluorescence. The discussed methods include fluorescence correlation spectroscopy (FCS), imaging FCS, image correlation spectroscopy (ICS), photobleaching ICS (pbICS), number and brightness (N&B) analysis, super-resolution optical fluctuation imaging (SOFI), and transient state (TRAST) monitoring spectroscopy. Some of these methodologies are classical protein aggregation analyses, while others are not yet widely used. Collectively, the methods presented here should help the future development of research not only into protein aggregation but also neurodegenerative diseases.
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12
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Chongtham A, Barbaro B, Filip T, Syed A, Huang W, Smith MR, Marsh JL. Nonmammalian Models of Huntington's Disease. Methods Mol Biol 2018; 1780:75-96. [PMID: 29856015 DOI: 10.1007/978-1-4939-7825-0_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Flies, worms, yeast and more recently zebra fish have all been engineered to express expanded polyglutamine repeat versions of Huntingtin with various resulting pathologies including early death, neurodegeneration, and loss of motor function. Each of these models present particular features that make it useful in studying the mechanisms of polyglutamine pathology. However, one particular unbiased readout of mHTT pathology is functional loss of motor control. Loss of motor control is prominent in patients, but it remains unresolved whether pathogenic symptoms in patients result from overt degeneration and loss of neurons or from malfunctioning of surviving neurons as the pathogenic insult builds up. This is why a functional assay such as motor control can be uniquely powerful in revealing early as well as late neurological deficits and does not rely on assumptions such as that the level of inclusions or the degree of neuronal loss can be equated with the level of pathology. Drosophila is well suited for such assays because it contains a functioning nervous system with many parallels to the human condition. In addition, the ability to readily express mHTT transgenes in different tissues and subsets of neurons allows one the possibility of isolating a particular effect to a subset of neurons where one can correlate subcellular events in response to mHTT challenge with pathology at both the cellular and organismal levels. Here we describe methods to monitor the degree of motor function disruption in Drosophila models of HD and we include a brief summary of other nonmammalian models of HD and discussion of their unique strengths.
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Affiliation(s)
- Anjalika Chongtham
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, 92697, CA, USA
| | - Brett Barbaro
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, 92697, CA, USA.,The Scripps Research Institute, La Jolla, CA, USA
| | - Tomas Filip
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, 92697, CA, USA.,Biology Centre Czech Acad. Sci., Ceske Budejovice, Czech Republic
| | - Adeela Syed
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, 92697, CA, USA
| | - Weijian Huang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, 92697, CA, USA
| | - Marianne R Smith
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, 92697, CA, USA.,University Advancement, UC Irvine, Irvine, CA, USA
| | - J Lawrence Marsh
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, 92697, CA, USA.
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13
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Tungtur SK, Nishimune N, Radel J, Nishimune H. Mouse Behavior Tracker: An economical method for tracking behavior in home cages. Biotechniques 2017; 63:215-220. [PMID: 29185921 PMCID: PMC5910027 DOI: 10.2144/000114607] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 10/06/2017] [Indexed: 02/02/2023] Open
Abstract
Analysis of mouse behavior often requires expensive equipment and transfer of the mice to new test environments, which could trigger confounding behavior alterations. Here, we describe a system for tracking mouse behavior in home cages using a low-cost USB webcam and free software (Fiji and wrMTrck). We demonstrate the effectiveness of this method by tracking differences in distance traveled, speed, and movement tracks between wild-type mice and amyotrophic lateral sclerosis (ALS) model mice (SOD1G93A).
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Affiliation(s)
- Sudheer K. Tungtur
- Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Natsuko Nishimune
- Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Jeff Radel
- Department of Occupational Therapy Education, University of Kansas School of Health Professions, Kansas City, KS, 66160, USA
| | - Hiroshi Nishimune
- Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, KS, 66160, USA
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14
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Kim SA, D'Acunto VF, Kokona B, Hofmann J, Cunningham NR, Bistline EM, Garcia FJ, Akhtar NM, Hoffman SH, Doshi SH, Ulrich KM, Jones NM, Bonini NM, Roberts CM, Link CD, Laue TM, Fairman R. Sedimentation Velocity Analysis with Fluorescence Detection of Mutant Huntingtin Exon 1 Aggregation in Drosophila melanogaster and Caenorhabditis elegans. Biochemistry 2017; 56:4676-4688. [PMID: 28786671 DOI: 10.1021/acs.biochem.7b00518] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
At least nine neurodegenerative diseases that are caused by the aggregation induced by long tracts of glutamine sequences have been identified. One such polyglutamine-containing protein is huntingtin, which is the primary factor responsible for Huntington's disease. Sedimentation velocity with fluorescence detection is applied to perform a comparative study of the aggregation of the huntingtin exon 1 protein fragment upon transgenic expression in Drosophila melanogaster and Caenorhabditis elegans. This approach allows the detection of aggregation in complex mixtures under physiologically relevant conditions. Complementary methods used to support this biophysical approach included fluorescence microscopy and semidenaturing detergent agarose gel electrophoresis, as a point of comparison with earlier studies. New analysis tools developed for the analytical ultracentrifuge have made it possible to readily identify a wide range of aggregating species, including the monomer, a set of intermediate aggregates, and insoluble inclusion bodies. Differences in aggregation in the two animal model systems are noted, possibly because of differences in levels of expression of glutamine-rich sequences. An increased level of aggregation is shown to correlate with increased toxicity for both animal models. Co-expression of the human Hsp70 in D. melanogaster showed some mitigation of aggregation and toxicity, correlating best with inclusion body formation. The comparative study emphasizes the value of the analytical ultracentrifuge equipped with fluorescence detection as a useful and rigorous tool for in situ aggregation analysis to assess commonalities in aggregation across animal model systems.
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Affiliation(s)
- Surin A Kim
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Victoria F D'Acunto
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Bashkim Kokona
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Jennifer Hofmann
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Nicole R Cunningham
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Emily M Bistline
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - F Jay Garcia
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Nabeel M Akhtar
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Susanna H Hoffman
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Seema H Doshi
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Kathleen M Ulrich
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Nicholas M Jones
- Department of Psychology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Nancy M Bonini
- Department of Biology, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Christine M Roberts
- Integrative Physiology, University of Colorado Boulder , Boulder, Colorado 80309, United States
| | - Christopher D Link
- Integrative Physiology, University of Colorado Boulder , Boulder, Colorado 80309, United States
| | - Thomas M Laue
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire , Durham, New Hampshire 03824, United States
| | - Robert Fairman
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
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15
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Kokona B, May CA, Cunningham NR, Richmond L, Jay Garcia F, Durante JC, Ulrich KM, Roberts CM, Link CD, Stafford WF, Laue TM, Fairman R. Studying polyglutamine aggregation in Caenorhabditis elegans using an analytical ultracentrifuge equipped with fluorescence detection. Protein Sci 2015; 25:605-17. [PMID: 26647351 DOI: 10.1002/pro.2854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/01/2015] [Indexed: 11/11/2022]
Abstract
This work explores the heterogeneity of aggregation of polyglutamine fusion constructs in crude extracts of transgenic Caenorhabditis elegans animals. The work takes advantage of the recent technical advances in fluorescence detection for the analytical ultracentrifuge. Further, new sedimentation velocity methods, such as the multi-speed method for data capture and wide distribution analysis for data analysis, are applied to improve the resolution of the measures of heterogeneity over a wide range of sizes. The focus here is to test the ability to measure sedimentation of polyglutamine aggregates in complex mixtures as a prelude to future studies that will explore the effects of genetic manipulation and environment on aggregation and toxicity. Using sedimentation velocity methods, we can detect a wide range of aggregates, ranging from robust analysis of the monomer species through an intermediate and quite heterogeneous population of oligomeric species, and all the way up to detecting species that likely represent intact inclusion bodies based on comparison to an analysis of fluorescent puncta in living worms by confocal microscopy. Our results support the hypothesis that misfolding of expanded polyglutamine tracts into insoluble aggregates involves transitions through a number of stable intermediate structures, a model that accounts for how an aggregation pathway can lead to intermediates that can have varying toxic or protective attributes. An understanding of the details of intermediate and large-scale aggregation for polyglutamine sequences, as found in neurodegenerative diseases such as Huntington's Disease, will help to more precisely identify which aggregated species may be involved in toxicity and disease.
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Affiliation(s)
- Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041
| | - Carrie A May
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824
| | | | - Lynn Richmond
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041
| | - F Jay Garcia
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041
| | - Julia C Durante
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041
| | - Kathleen M Ulrich
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041
| | - Christine M Roberts
- Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, 80309
| | - Christopher D Link
- Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, 80309
| | - Walter F Stafford
- Boston Biomedical Research Institute, Watertown, Massachusetts, 02472
| | - Thomas M Laue
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041
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16
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Ruff KM, Khan SJ, Pappu RV. A coarse-grained model for polyglutamine aggregation modulated by amphipathic flanking sequences. Biophys J 2015; 107:1226-1235. [PMID: 25185558 DOI: 10.1016/j.bpj.2014.07.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 06/25/2014] [Accepted: 07/09/2014] [Indexed: 02/06/2023] Open
Abstract
The aggregation of proteins with expanded polyglutamine (polyQ) tracts is directly relevant to the formation of neuronal intranuclear inclusions in Huntington's disease. In vitro studies have uncovered the effects of flanking sequences as modulators of the driving forces and mechanisms of polyQ aggregation in sequence segments associated with HD. Specifically, a seventeen-residue amphipathic stretch (N17) that is directly N-terminal to the polyQ tract in huntingtin decreases the overall solubility, destabilizes nonfibrillar aggregates, and accelerates fibril formation. Published results from atomistic simulations showed that the N17 module reduces the frequency of intermolecular association. Our reanalysis of these simulation results demonstrates that the N17 module also reduces interchain entanglements between polyQ domains. These two effects, which are observed on the smallest lengthscales, are incorporated into phenomenological pair potentials and used in coarse-grained Brownian dynamics simulations to investigate their impact on large-scale aggregation. We analyze the results from Brownian dynamics simulations using the framework of diffusion-limited cluster aggregation. When entanglements prevail, which is true in the absence of N17, small spherical clusters and large linear aggregates form on distinct timescales, in accord with in vitro experiments. Conversely, when entanglements are quenched and a barrier to intermolecular associations is introduced, both of which are attributable to N17, the timescales for forming small species and large linear aggregates become similar. Therefore, the combination of a reduction of interchain entanglements through homopolymeric polyQ and barriers to intermolecular associations appears to be sufficient for providing a minimalist phenomenological rationalization of in vitro observations regarding the effects of N17 on polyQ aggregation.
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Affiliation(s)
- Kiersten M Ruff
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri; Division of Biology and Biomedical Sciences, Computational and Systems Biology Program, Washington University in St. Louis, St. Louis, Missouri
| | - Siddique J Khan
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri.
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17
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Theillet FX, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley PB, Gierasch L, Pielak GJ, Elcock AH, Gershenson A, Selenko P. Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev 2014; 114:6661-714. [PMID: 24901537 PMCID: PMC4095937 DOI: 10.1021/cr400695p] [Citation(s) in RCA: 338] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Francois-Xavier Theillet
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Andres Binolfi
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Tamara Frembgen-Kesner
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Karan Hingorani
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Mohona Sarkar
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Ciara Kyne
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Conggang Li
- Key Laboratory
of Magnetic Resonance in Biological Systems, State Key Laboratory
of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center
for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P.R. China
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Lila Gierasch
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Gary J. Pielak
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Adrian H. Elcock
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Anne Gershenson
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Philipp Selenko
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
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18
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Calamini B, Lo DC, Kaltenbach LS. Experimental models for identifying modifiers of polyglutamine-induced aggregation and neurodegeneration. Neurotherapeutics 2013; 10:400-15. [PMID: 23700210 PMCID: PMC3701774 DOI: 10.1007/s13311-013-0195-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Huntington's disease (HD) typifies a class of inherited neurodegenerative disorders in which a CAG expansion in a single gene leads to an extended polyglutamine tract and misfolding of the expressed protein, driving cumulative neural dysfunction and degeneration. HD is invariably fatal with symptoms that include progressive neuropsychiatric and cognitive impairments, and eventual motor disability. No curative therapies yet exist for HD and related polyglutamine diseases; therefore, substantial efforts have been made in the drug discovery field to identify potential drug and drug target candidates for disease-modifying treatment. In this context, we review here a range of early-stage screening approaches based in in vitro, cellular, and invertebrate models to identify pharmacological and genetic modifiers of polyglutamine aggregation and induced neurodegeneration. In addition, emerging technologies, including high-content analysis, three-dimensional culture models, and induced pluripotent stem cells are increasingly being incorporated into drug discovery screening pipelines for protein misfolding disorders. Together, these diverse screening strategies are generating novel and exciting new probes for understanding the disease process and for furthering development of therapeutic candidates for eventual testing in the clinical setting.
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Affiliation(s)
- Barbara Calamini
- Department of Neurobiology and Center for Drug Discovery, Duke University Medical Center, 4321 Medical Park Drive, Durham, NC 27704 USA
| | - Donald C. Lo
- Department of Neurobiology and Center for Drug Discovery, Duke University Medical Center, 4321 Medical Park Drive, Durham, NC 27704 USA
| | - Linda S. Kaltenbach
- Department of Neurobiology and Center for Drug Discovery, Duke University Medical Center, 4321 Medical Park Drive, Durham, NC 27704 USA
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19
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Affiliation(s)
- Yves Engelborghs
- University of Leuven, Biomolecular Dynamics, Celestijnenlaan, Belgium.
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20
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Cohen A, Ross L, Nachman I, Bar-Nun S. Aggregation of polyQ proteins is increased upon yeast aging and affected by Sir2 and Hsf1: novel quantitative biochemical and microscopic assays. PLoS One 2012; 7:e44785. [PMID: 22970306 PMCID: PMC3435303 DOI: 10.1371/journal.pone.0044785] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 08/13/2012] [Indexed: 11/18/2022] Open
Abstract
Aging-related neurodegenerative disorders, such as Parkinson's, Alzheimer's and Huntington's diseases, are characterized by accumulation of protein aggregates in distinct neuronal cells that eventually die. In Huntington's disease, the protein huntingtin forms aggregates, and the age of disease onset is inversely correlated to the length of the protein's poly-glutamine tract. Using quantitative assays to estimate microscopically and capture biochemically protein aggregates, here we study in Saccharomyces cerevisiae aging-related aggregation of GFP-tagged, huntingtin-derived proteins with different polyQ lengths. We find that the short 25Q protein never aggregates whereas the long 103Q version always aggregates. However, the mid-size 47Q protein is soluble in young logarithmically growing yeast but aggregates as the yeast cells enter the stationary phase and age, allowing us to plot an “aggregation timeline”. This aging-dependent aggregation was associated with increased cytotoxicity. We also show that two aging-related genes, SIR2 and HSF1, affect aggregation of the polyQ proteins. In Δsir2 strain the aging-dependent aggregation of the 47Q protein is aggravated, while overexpression of the transcription factor Hsf1 attenuates aggregation. Thus, the mid-size 47Q protein and our quantitative aggregation assays provide valuable tools to unravel the roles of genes and environmental conditions that affect aging-related aggregation.
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Affiliation(s)
- Aviv Cohen
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Liron Ross
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Iftach Nachman
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shoshana Bar-Nun
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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