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Pradhan SS, R SS, Kanikaram SP, V M DD, Pargaonkar A, Dandamudi RB, Sivaramakrishnan V. Metabolic deregulation associated with aging modulates protein aggregation in the yeast model of Huntington's disease. J Biomol Struct Dyn 2023:1-18. [PMID: 37732342 DOI: 10.1080/07391102.2023.2257322] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 09/05/2023] [Indexed: 09/22/2023]
Abstract
Huntington's disease is associated with increased CAG repeat resulting in an expanded polyglutamine tract in the protein Huntingtin (HTT) leading to its aggregation resulting in neurodegeneration. Previous studies have shown that N-terminal HTT with 46Q aggregated in the stationary phase but not the logarithmic phase in the yeast model of HD. We carried out a metabolomic analysis of logarithmic and stationary phase yeast model of HD expressing different polyQ lengths attached to N-terminal HTT tagged with enhanced green fluorescent protein (EGFP). The results show significant changes in the metabolic profile and deregulated pathways in stationary phase cells compared to logarithmic phase cells. Comparison of metabolic pathways obtained from logarithmic phase 46Q versus 25Q with those obtained for presymptomatic HD patients from our previous study and drosophila model of HD showed considerable overlap. The arginine biosynthesis pathway emerged as one of the key pathways that is common in stationary phase yeast compared to logarithmic phase and HD patients. Treatment of yeast with arginine led to a significant decrease, while transfer to arginine drop-out media led to a significant increase in the size of protein aggregates in both logarithmic and stationary phase yeast model of HD. Knockout of arginine transporters in the endoplasmic reticulum and vacuole led to a significant decrease in mutant HTT aggregation. Overall our results highlight arginine as a critical metabolite that modulates the aggregation of mutant HTT and disease progression in HD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Sai Swaroop R
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Sai Phalguna Kanikaram
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Ashish Pargaonkar
- Application Division, Agilent Technologies Ltd., Bengaluru, Karnataka, India
| | | | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
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2
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Pradhan SS, Thota SM, Rajaratnam S, Bhagavatham SKS, Pulukool SK, Rathnakumar S, Phalguna KS, Dandamudi RB, Pargaonkar A, Joseph P, Joshy EV, Sivaramakrishnan V. Integrated multi-omics analysis of Huntington disease identifies pathways that modulate protein aggregation. Dis Model Mech 2022; 15:dmm049492. [PMID: 36052548 PMCID: PMC10655815 DOI: 10.1242/dmm.049492] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Huntington disease (HD) is a neurodegenerative disease associated with polyglutamine expansion in the protein huntingtin (HTT). Although the length of the polyglutamine repeat correlates with age at disease onset and severity, psychological, cognitive and behavioral complications point to the existence of disease modifiers. Mitochondrial dysfunction and metabolic deregulation are both associated with the HD but, despite multi-omics characterization of patients and model systems, their mechanisms have remained elusive. Systems analysis of multi-omics data and its validation by using a yeast model could help to elucidate pathways that modulate protein aggregation. Metabolomics analysis of HD patients and of a yeast model of HD was, therefore, carried out. Our analysis showed a considerable overlap of deregulated metabolic pathways. Further, the multi-omics analysis showed deregulated pathways common in human, mice and yeast model systems, and those that are unique to them. The deregulated pathways include metabolic pathways of various amino acids, glutathione metabolism, longevity, autophagy and mitophagy. The addition of certain metabolites as well as gene knockouts targeting the deregulated metabolic and autophagy pathways in the yeast model system showed that these pathways do modulate protein aggregation. Taken together, our results showed that the modulation of deregulated pathways influences protein aggregation in HD, and has implications for progression and prognosis. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Sai S. Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Sai M. Thota
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Saiswaroop Rajaratnam
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Sai K. S. Bhagavatham
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Sujith K. Pulukool
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Sriram Rathnakumar
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Kanikaram S. Phalguna
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Rajesh B. Dandamudi
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515 134, India
| | - Ashish Pargaonkar
- Application Division, Agilent Technologies Ltd., Bengaluru 560048, India
| | - Prasanth Joseph
- Application Division, Agilent Technologies Ltd., Bengaluru 560048, India
| | - E. V. Joshy
- Department of Neurology, Sri Sathya Sai Institute of Higher Medical Sciences, Whitefield, Bengaluru, Karnataka 560066, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
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Akinniyi OT, Reese JC. DEF1: Much more than an RNA polymerase degradation factor. DNA Repair (Amst) 2021; 107:103202. [PMID: 34419700 DOI: 10.1016/j.dnarep.2021.103202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 01/14/2023]
Abstract
Degradation Factor 1 was discovered 20 years ago as a yeast protein copurifying with Rad26, a helicase involved in transcription-coupled DNA repair. It was subsequently shown to control the ubiquitylation and destruction of the large subunit of DNA damage-arrested RNA Polymerase II. Since that time, much has been learned about Def1's role in polymerase destruction and new functions of the protein have been revealed. We now understand that Def1 is involved in more than just RNA polymerase II regulation. Most of its known functions are associated with maintaining chromosome and genomic integrity, but other exciting activities outside this realm have been suggested. Here we review this fascinating protein, describe its regulation and present a hypothesis that Def1 is a central coordinator of ubiquitin signaling pathways in cells.
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Affiliation(s)
- Oluwasegun T Akinniyi
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Joseph C Reese
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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Cheng W, Ng CA. Using Machine Learning to Classify Bioactivity for 3486 Per- and Polyfluoroalkyl Substances (PFASs) from the OECD List. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:13970-13980. [PMID: 31661253 DOI: 10.1021/acs.est.9b04833] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A recent OECD report estimated that more than 4000 per- and polyfluorinated alkyl substances (PFASs) have been produced and used in a broad range of industrial and consumer applications. However, little is known about the potential hazards (e.g., bioactivity, bioaccumulation, and toxicity) of most PFASs. Here, we built machine-learning-based quantitative structure-activity relationship (QSAR) models to predict the bioactivity of those PFASs. By examining a number of available molecular data sets, we constructed the first PFAS-specific database that contains the bioactivity information on 1012 PFASs for 26 bioassays. On the basis of the collected PFAS data set, we trained 5 different machine learning models that cover a variety of conventional models (e.g., random forest and multitask neural network (MNN)) and advanced graph-based models (e.g., graph convolutional network). Those models were evaluated based on the validation data set. Both MNN and graph-based models demonstrated the best performance. The average of the best area-under-the-curve score for each bioassay is 0.916. For predictions on the OECD list, most of the biologically active PFASs have perfluoroalkyl chain lengths less than 12 and are categorized into fluorotelomer-related compounds and perfluoroalkyl acids and their precursors.
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Affiliation(s)
- Weixiao Cheng
- Department of Civil and Environmental Engineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Carla A Ng
- Department of Civil and Environmental Engineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
- Secondary Appointment, Department of Environmental and Occupational Health, Graduate School of Public Health , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
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Tuite MF. Yeast models of neurodegenerative diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 168:351-379. [DOI: 10.1016/bs.pmbts.2019.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Hofer S, Kainz K, Zimmermann A, Bauer MA, Pendl T, Poglitsch M, Madeo F, Carmona-Gutierrez D. Studying Huntington's Disease in Yeast: From Mechanisms to Pharmacological Approaches. Front Mol Neurosci 2018; 11:318. [PMID: 30233317 PMCID: PMC6131589 DOI: 10.3389/fnmol.2018.00318] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder that leads to progressive neuronal loss, provoking impaired motor control, cognitive decline, and dementia. So far, HD remains incurable, and available drugs are effective only for symptomatic management. HD is caused by a mutant form of the huntingtin protein, which harbors an elongated polyglutamine domain and is highly prone to aggregation. However, many aspects underlying the cytotoxicity of mutant huntingtin (mHTT) remain elusive, hindering the efficient development of applicable interventions to counteract HD. An important strategy to obtain molecular insights into human disorders in general is the use of eukaryotic model organisms, which are easy to genetically manipulate and display a high degree of conservation regarding disease-relevant cellular processes. The budding yeast Saccharomyces cerevisiae has a long-standing and successful history in modeling a plethora of human maladies and has recently emerged as an effective tool to study neurodegenerative disorders, including HD. Here, we summarize some of the most important contributions of yeast to HD research, specifically concerning the elucidation of mechanistic features of mHTT cytotoxicity and the potential of yeast as a platform to screen for pharmacological agents against HD.
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Affiliation(s)
- Sebastian Hofer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Katharina Kainz
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Andreas Zimmermann
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Maria A. Bauer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Tobias Pendl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Michael Poglitsch
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Frank Madeo
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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Stepchenkova EI, Shiriaeva AA, Pavlov YI. Deletion of the DEF1 gene does not confer UV-immutability but frequently leads to self-diploidization in yeast Saccharomyces cerevisiae. DNA Repair (Amst) 2018; 70:49-54. [PMID: 30172224 DOI: 10.1016/j.dnarep.2018.08.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/19/2018] [Accepted: 08/21/2018] [Indexed: 11/18/2022]
Abstract
In yeast Saccharomyces cerevisiae, the DEF1 gene is responsible for regulation of many cellular processes including ubiquitin-dependent degradation of DNA metabolism proteins. Recently it has been proposed that Def1 promotes degradation of the catalytic subunit of DNA polymerase δ at sites of DNA damage and regulates a switch to specialized polymerases and, as a consequence, DNA-damage induced mutagenesis. The idea was based substantially on the severe defects in induced mutagenesis observed in the def1 mutants. We describe that UV mutability of def1Δ strains is actually only moderately affected, while the virtual absence of UV mutagenesis in many def1Δ clones is caused by a novel phenotype of the def1 mutants, proneness to self-diploidization. Diploids are extremely frequent (90%) after transformation of wild-type haploids with def1::kanMX disruption cassette and are frequent (2.3%) in vegetative haploid def1 cultures. Such diploids look "UV immutable" when assayed for recessive forward mutations but have normal UV mutability when assayed for dominant reverse mutations. The propensity for frequent self-diploidization in def1Δ mutants should be taken into account in studies of the def1Δ effect on mutagenesis. The true haploids with def1Δ mutation are moderately UV sensitive but retain substantial UV mutagenesis for forward mutations: they are fully proficient at lower doses and only partially defective at higher doses of UV. We conclude that Def1 does not play a critical role in damage-induced mutagenesis.
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Affiliation(s)
- E I Stepchenkova
- Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, Saint-Petersburg, 199034, Russia; Department of Genetics, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - A A Shiriaeva
- Department of Genetics, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143028, Russia; Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, Saint-Petersburg, 195251, Russia; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Y I Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA; Departments of Microbiology and Pathology, Biochemistry and Molecular Biology, Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
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Bondarev SA, Antonets KS, Kajava AV, Nizhnikov AA, Zhouravleva GA. Protein Co-Aggregation Related to Amyloids: Methods of Investigation, Diversity, and Classification. Int J Mol Sci 2018; 19:ijms19082292. [PMID: 30081572 PMCID: PMC6121665 DOI: 10.3390/ijms19082292] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/29/2018] [Accepted: 08/02/2018] [Indexed: 01/04/2023] Open
Abstract
Amyloids are unbranched protein fibrils with a characteristic spatial structure. Although the amyloids were first described as protein deposits that are associated with the diseases, today it is becoming clear that these protein fibrils play multiple biological roles that are essential for different organisms, from archaea and bacteria to humans. The appearance of amyloid, first of all, causes changes in the intracellular quantity of the corresponding soluble protein(s), and at the same time the aggregate can include other proteins due to different molecular mechanisms. The co-aggregation may have different consequences even though usually this process leads to the depletion of a functional protein that may be associated with different diseases. The protein co-aggregation that is related to functional amyloids may mediate important biological processes and change of protein functions. In this review, we survey the known examples of the amyloid-related co-aggregation of proteins, discuss their pathogenic and functional roles, and analyze methods of their studies from bacteria and yeast to mammals. Such analysis allow for us to propose the following co-aggregation classes: (i) titration: deposition of soluble proteins on the amyloids formed by their functional partners, with such interactions mediated by a specific binding site; (ii) sequestration: interaction of amyloids with certain proteins lacking a specific binding site; (iii) axial co-aggregation of different proteins within the same amyloid fibril; and, (iv) lateral co-aggregation of amyloid fibrils, each formed by different proteins.
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Affiliation(s)
- Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
| | - Kirill S Antonets
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh., 3, Pushkin, St. Petersburg 196608, Russia.
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France.
- Institut de Biologie Computationnelle (IBC), 34095 Montpellier, France.
- University ITMO, Institute of Bioengineering, Kronverksky Pr. 49, St. Petersburg 197101, Russia.
| | - Anton A Nizhnikov
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh., 3, Pushkin, St. Petersburg 196608, Russia.
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
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Masnata M, Cicchetti F. The Evidence for the Spread and Seeding Capacities of the Mutant Huntingtin Protein in in Vitro Systems and Their Therapeutic Implications. Front Neurosci 2017; 11:647. [PMID: 29234268 PMCID: PMC5712341 DOI: 10.3389/fnins.2017.00647] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/07/2017] [Indexed: 12/22/2022] Open
Abstract
Neurodegenerative disorders are not only characterized by specific patterns of cell loss but the presence and accumulation of various pathological proteins—both of which correlate with disease evolution. There is now mounting evidence to suggest that these pathological proteins present with toxic, at times prion-like, properties and can therefore seed pathology in neighboring as well remotely connected healthy neurons as they spread across the brain. What is less clear, at this stage, is how much this actually contributes to, and drives, the core pathogenic events. In this review, we present a comprehensive, up-to-date summary of the reported in vitro studies that support the spreading and seeding capacities of pathological proteins, with an emphasis on mutant huntingtin protein in the context of Huntington's disease, although in vivo work remains to be performed to validate this theory in this particular disease. We have further reviewed these findings in light of their potential implications for the development of novel therapeutic approaches.
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Affiliation(s)
- Maria Masnata
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Quebec, QC, Canada
| | - Francesca Cicchetti
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Quebec, QC, Canada.,Département de Psychiatrie & Neurosciences, Université Laval, Quebec, QC, Canada
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