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Ruger-Herreros C, Svoboda L, Mogk A, Bukau B. Role of J-domain Proteins in Yeast Physiology and Protein Quality Control. J Mol Biol 2024; 436:168484. [PMID: 38331212 DOI: 10.1016/j.jmb.2024.168484] [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: 10/20/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
The Hsp70 chaperone system is a central component of cellular protein quality control (PQC) by acting in a multitude of protein folding processes ranging from the folding of newly synthesized proteins to the disassembly and refolding of protein aggregates. This multifunctionality of Hsp70 is governed by J-domain proteins (JDPs), which act as indispensable co-chaperones that target specific substrates to Hsp70. The number of distinct JDPs present in a species always outnumbers Hsp70, documenting JDP function in functional diversification of Hsp70. In this review, we describe the physiological roles of JDPs in the Saccharomyces cerevisiae PQC system, with a focus on the abundant JDP generalists, Zuo1, Ydj1 and Sis1, which function in fundamental cellular processes. Ribosome-bound Zuo1 cooperates with the Hsp70 chaperones Ssb1/2 in folding and assembly of nascent polypeptides. Ydj1 and Sis1 cooperate with the Hsp70 members Ssa1 to Ssa4 to exert overlapping functions in protein folding and targeting of newly synthesized proteins to organelles including mitochondria and facilitating the degradation of aberrant proteins by E3 ligases. Furthermore, they act in protein disaggregation reactions, though Ydj1 and Sis1 differ in their modes of Hsp70 cooperation and substrate specificities. This results in functional specialization as seen in prion propagation and the underlying dominant role of Sis1 in targeting Hsp70 for shearing of prion amyloid fibrils.
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Affiliation(s)
- Carmen Ruger-Herreros
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot, s/n, E-41013 Sevilla, Spain
| | - Lucia Svoboda
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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2
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Rinaldi E, Drenkhahn C, Gebel B, Saleh K, Tönnies H, von Loewenich FD, Thoma N, Baier C, Boeker M, Hinske LC, Diaz LAP, Behnke M, Ingenerf J, Thun S. Towards interoperability in infection control: a standard data model for microbiology. Sci Data 2023; 10:654. [PMID: 37741862 PMCID: PMC10517923 DOI: 10.1038/s41597-023-02560-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
The COVID-19 pandemic has made it clear: sharing and exchanging data among research institutions is crucial in order to efficiently respond to global health threats. This can be facilitated by defining health data models based on interoperability standards. In Germany, a national effort is in progress to create common data models using international healthcare IT standards. In this context, collaborative work on a data set module for microbiology is of particular importance as the WHO has declared antimicrobial resistance one of the top global public health threats that humanity is facing. In this article, we describe how we developed a common model for microbiology data in an interdisciplinary collaborative effort and how we make use of the standard HL7 FHIR and terminologies such as SNOMED CT or LOINC to ensure syntactic and semantic interoperability. The use of international healthcare standards qualifies our data model to be adopted beyond the environment where it was first developed and used at an international level.
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Affiliation(s)
- Eugenia Rinaldi
- Berlin Institute of Health, Charité Universitätsmedizin, Berlin, Germany.
| | - Cora Drenkhahn
- Institute of Medical Informatics (IMI), University of Lübeck, Lübeck, Germany
| | - Benjamin Gebel
- Klinik für Infektiologie und Mikrobiologie, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Kutaiba Saleh
- Data Integration Center, Jena University Hospital, Jena, Germany
| | | | | | - Norbert Thoma
- Institute for Hygiene and Environmental Medicine, Charité Universitätsmedizin, Berlin, Germany
| | - Claas Baier
- Hannover Medical School, Institute for Medical Microbiology and Hospital Epidemiology, Hannover, Germany
| | | | | | - Luis Alberto Peña Diaz
- Institute for Hygiene and Environmental Medicine, Charité Universitätsmedizin, Berlin, Germany
| | - Michael Behnke
- Institute for Hygiene and Environmental Medicine, Charité Universitätsmedizin, Berlin, Germany
| | - Josef Ingenerf
- Institute of Medical Informatics (IMI), University of Lübeck, Lübeck, Germany
| | - Sylvia Thun
- Berlin Institute of Health, Charité Universitätsmedizin, Berlin, Germany
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3
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Jay-Garcia LM, Cornell JL, Howie RL, Faber QL, Salas A, Chernova TA, Chernoff YO. Yeast Chaperone Hsp70-Ssb Modulates a Variety of Protein-Based Heritable Elements. Int J Mol Sci 2023; 24:ijms24108660. [PMID: 37240005 DOI: 10.3390/ijms24108660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Prions are transmissible self-perpetuating protein isoforms associated with diseases and heritable traits. Yeast prions and non-transmissible protein aggregates (mnemons) are frequently based on cross-β ordered fibrous aggregates (amyloids). The formation and propagation of yeast prions are controlled by chaperone machinery. Ribosome-associated chaperone Hsp70-Ssb is known (and confirmed here) to modulate formation and propagation of the prion form of the Sup35 protein [PSI+]. Our new data show that both formation and mitotic transmission of the stress-inducible prion form of the Lsb2 protein ([LSB+]) are also significantly increased in the absence of Ssb. Notably, heat stress leads to a massive accumulation of [LSB+] cells in the absence of Ssb, implicating Ssb as a major downregulator of the [LSB+]-dependent memory of stress. Moreover, the aggregated form of Gγ subunit Ste18, [STE+], behaving as a non-heritable mnemon in the wild-type strain, is generated more efficiently and becomes heritable in the absence of Ssb. Lack of Ssb also facilitates mitotic transmission, while lack of the Ssb cochaperone Hsp40-Zuo1 facilitates both spontaneous formation and mitotic transmission of the Ure2 prion, [URE3]. These results demonstrate that Ssb is a general modulator of cytosolic amyloid aggregation, whose effect is not restricted only to [PSI+].
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Affiliation(s)
- Lina M Jay-Garcia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joseph L Cornell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Rebecca L Howie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Quincy L Faber
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Abigail Salas
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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4
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Bezsonov E, Khotina V, Glanz V, Sobenin I, Orekhov A. Lipids and Lipoproteins in Atherosclerosis. Biomedicines 2023; 11:biomedicines11051424. [PMID: 37239095 DOI: 10.3390/biomedicines11051424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Atherosclerosis is a chronic inflammatory disease [...].
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Affiliation(s)
- Evgeny Bezsonov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiiskaya Street, 125315 Moscow, Russia
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution " Petrovsky National Research Centre of Surgery", 3 Tsyurupa Street, 117418 Moscow, Russia
- Department of Biology and General Genetics, I. M. Sechenov First Moscow State Medical University, 8 Izmailovsky Boulevard, 105043 Moscow, Russia
| | - Victoria Khotina
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiiskaya Street, 125315 Moscow, Russia
| | - Victor Glanz
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution " Petrovsky National Research Centre of Surgery", 3 Tsyurupa Street, 117418 Moscow, Russia
| | - Igor Sobenin
- Laboratory of Medical Genetics, Institute of Experimental Cardiology, National Medical Research Center of Cardiology, 15a 3rd Cherepkovskaya Street, 121552 Moscow, Russia
| | - Alexander Orekhov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiiskaya Street, 125315 Moscow, Russia
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution " Petrovsky National Research Centre of Surgery", 3 Tsyurupa Street, 117418 Moscow, Russia
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5
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Ajmal MR. Protein Misfolding and Aggregation in Proteinopathies: Causes, Mechanism and Cellular Response. Diseases 2023; 11:diseases11010030. [PMID: 36810544 PMCID: PMC9944956 DOI: 10.3390/diseases11010030] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/02/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
Proteins are central to life functions. Alterations in the structure of proteins are reflected in their function. Misfolded proteins and their aggregates present a significant risk to the cell. Cells have a diverse but integrated network of protection mechanisms. Streams of misfolded proteins that cells are continuously exposed to must be continually monitored by an elaborated network of molecular chaperones and protein degradation factors to control and contain protein misfolding problems. Aggregation inhibition properties of small molecules such as polyphenols are important as they possess other beneficial properties such as antioxidative, anti-inflammatory, and pro-autophagic properties and help neuroprotection. A candidate with such desired features is important for any possible treatment development for protein aggregation diseases. There is a need to study the protein misfolding phenomenon so that we can treat some of the worst kinds of human ailments related to protein misfolding and aggregation.
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Affiliation(s)
- Mohammad Rehan Ajmal
- Physical Biochemistry Research Laboratory, Biochemistry Department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
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6
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Kumar A, Sudevan ST, Nair AS, Singh AK, Kumar S, Jose J, Behl T, Mangalathillam S, Mathew B, Kim H. Current and Future Nano-Carrier-Based Approaches in the Treatment of Alzheimer's Disease. Brain Sci 2023; 13:brainsci13020213. [PMID: 36831756 PMCID: PMC9953820 DOI: 10.3390/brainsci13020213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
It is a very alarming situation for the globe because 55 million humans are estimated to be affected by Alzheimer's disease (AD) worldwide, and still it is increasing at the rapid speed of 10 million cases per year worldwide. This is an urgent reminder for better research and treatment due to the unavailability of a permanent medication for neurodegenerative disorders like AD. The lack of drugs for neurodegenerative disorder treatment is due to the complexity of the structure of the brain, mainly due to blood-brain barrier, because blood-brain drug molecules must enter the brain compartment. There are several novel and conventional formulation approaches that can be employed for the transportation of drug molecules to the target site in the brain, such as oral, intravenous, gene delivery, surgically implanted intraventricular catheter, nasal and liposomal hydrogels, and repurposing old drugs. A drug's lipophilicity influences metabolic activity in addition to membrane permeability because lipophilic substances have a higher affinity for metabolic enzymes. As a result, the higher a drug's lipophilicity is, the higher its permeability and metabolic clearance. AD is currently incurable, and the medicines available merely cure the symptoms or slow the illness's progression. In the next 20 years, the World Health Organization (WHO) predicts that neurodegenerative illnesses affecting motor function will become the second-leading cause of mortality. The current article provides a brief overview of recent advances in brain drug delivery for AD therapy.
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Affiliation(s)
- Astik Kumar
- Department of Pharmaceutics, Amrita School of Pharmacy, AIMS Health Sciences Campus, Amrita Vishwa Vidyapeetham, Kochi 682041, India
| | - Sachithra Thazhathuveedu Sudevan
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, AIMS Health Sciences Campus, Amrita Vishwa Vidyapeetham, Kochi 682041, India
| | - Aathira Sujathan Nair
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, AIMS Health Sciences Campus, Amrita Vishwa Vidyapeetham, Kochi 682041, India
| | - Ashutosh Kumar Singh
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, AIMS Health Sciences Campus, Amrita Vishwa Vidyapeetham, Kochi 682041, India
| | - Sunil Kumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, AIMS Health Sciences Campus, Amrita Vishwa Vidyapeetham, Kochi 682041, India
| | - Jobin Jose
- Department of Pharmaceutics, NGSM Institute of Pharmaceutical Science, NITTE Deemed to be University, Mangalore 575018, India
| | - Tapan Behl
- School of Health Science and Technology, University of Petroleum and Energy Studies, Dehradun 248007, India
| | - Sabitha Mangalathillam
- Department of Pharmaceutics, Amrita School of Pharmacy, AIMS Health Sciences Campus, Amrita Vishwa Vidyapeetham, Kochi 682041, India
- Correspondence: (S.M.); or (B.M.); (H.K.)
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, AIMS Health Sciences Campus, Amrita Vishwa Vidyapeetham, Kochi 682041, India
- Correspondence: (S.M.); or (B.M.); (H.K.)
| | - Hoon Kim
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
- Correspondence: (S.M.); or (B.M.); (H.K.)
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7
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Noori L, Filip K, Nazmara Z, Mahakizadeh S, Hassanzadeh G, Caruso Bavisotto C, Bucchieri F, Marino Gammazza A, Cappello F, Wnuk M, Scalia F. Contribution of Extracellular Vesicles and Molecular Chaperones in Age-Related Neurodegenerative Disorders of the CNS. Int J Mol Sci 2023; 24:ijms24020927. [PMID: 36674442 PMCID: PMC9861359 DOI: 10.3390/ijms24020927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Many neurodegenerative disorders are characterized by the abnormal aggregation of misfolded proteins that form amyloid deposits which possess prion-like behavior such as self-replication, intercellular transmission, and consequent induction of native forms of the same protein in surrounding cells. The distribution of the accumulated proteins and their correlated toxicity seem to be involved in the progression of nervous system degeneration. Molecular chaperones are known to maintain proteostasis, contribute to protein refolding to protect their function, and eliminate fatally misfolded proteins, prohibiting harmful effects. However, chaperone network efficiency declines during aging, prompting the onset and the development of neurological disorders. Extracellular vesicles (EVs) are tiny membranous structures produced by a wide range of cells under physiological and pathological conditions, suggesting their significant role in fundamental processes particularly in cellular communication. They modulate the behavior of nearby and distant cells through their biological cargo. In the pathological context, EVs transport disease-causing entities, including prions, α-syn, and tau, helping to spread damage to non-affected areas and accelerating the progression of neurodegeneration. However, EVs are considered effective for delivering therapeutic factors to the nervous system, since they are capable of crossing the blood-brain barrier (BBB) and are involved in the transportation of a variety of cellular entities. Here, we review the neurodegeneration process caused mainly by the inefficiency of chaperone systems as well as EV performance in neuropathies, their potential as diagnostic biomarkers and a promising EV-based therapeutic approach.
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Affiliation(s)
- Leila Noori
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653761, Iran
| | - Kamila Filip
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35959 Rzeszow, Poland
| | - Zohreh Nazmara
- Department of Neuroscience and Addiction Studies, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1417653761, Iran
| | - Simin Mahakizadeh
- Department of Anatomy, School of Medicine, Alborz University of Medical Sciences, Karaj 3149779453, Iran
| | - Gholamreza Hassanzadeh
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653761, Iran
- Department of Neuroscience and Addiction Studies, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1417653761, Iran
| | - Celeste Caruso Bavisotto
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
- Correspondence: (C.C.B.); (F.S.)
| | - Fabio Bucchieri
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Antonella Marino Gammazza
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Francesco Cappello
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Maciej Wnuk
- Department of Biotechnology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35959 Rzeszow, Poland
| | - Federica Scalia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
- Correspondence: (C.C.B.); (F.S.)
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8
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Processing of Fluorescent Proteins May Prevent Detection of Prion Particles in [ PSI+] Cells. BIOLOGY 2022; 11:biology11121688. [PMID: 36552198 PMCID: PMC9774836 DOI: 10.3390/biology11121688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022]
Abstract
Yeast is a convenient model for studying protein aggregation as it is known to propagate amyloid prions. [PSI+] is the prion form of the release factor eRF3 (Sup35). Aggregated Sup35 causes defects in termination of translation, which results in nonsense suppression in strains carrying premature stop codons. N-terminal and middle (M) domains of Sup35 are necessary and sufficient for maintaining [PSI+] in cells while preserving the prion strain's properties. For this reason, Sup35NM fused to fluorescent proteins is often used for [PSI+] detection and investigation. However, we found that in such chimeric constructs, not all fluorescent proteins allow the reliable detection of Sup35 aggregates. Particularly, transient overproduction of Sup35NM-mCherry resulted in a diffuse fluorescent pattern in the [PSI+] cells, while no loss of prions and no effect on the Sup35NM prion properties could be observed. This effect was reproduced in various unrelated strain backgrounds and prion variants. In contrast, Sup35NM fused to another red fluorescent protein, TagRFP-T, allowed the detection of [PSI+] aggregates. Analysis of protein lysates showed that Sup35NM-mCherry is actively degraded in the cell. This degradation was not caused by vacuolar proteases and the ubiquitin-proteasomal system implicated in the Sup35 processing. Even though the intensity of this proteolysis was higher than that of Sup35NM-GFP, it was roughly the same as in the case of Sup35NM-TagRFP-T. Thus, it is possible that, in contrast to TagRFP-T, degradation products of Sup35NM-mCherry still preserve their fluorescent properties while losing the ability to decorate pre-existing Sup35 aggregates. This results in diffuse fluorescence despite the presence of the prion aggregates in the cell. Thus, tagging with fluorescent proteins should be used with caution, as such proteolysis may increase the rate of false-negative results when detecting prion-bearing cells.
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9
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Alzheimer's Disease: Treatment Strategies and Their Limitations. Int J Mol Sci 2022; 23:ijms232213954. [PMID: 36430432 PMCID: PMC9697769 DOI: 10.3390/ijms232213954] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Alzheimer's disease (AD) is the most frequent case of neurodegenerative disease and is becoming a major public health problem all over the world. Many therapeutic strategies have been explored for several decades; however, there is still no curative treatment, and the priority remains prevention. In this review, we present an update on the clinical and physiological phase of the AD spectrum, modifiable and non-modifiable risk factors for AD treatment with a focus on prevention strategies, then research models used in AD, followed by a discussion of treatment limitations. The prevention methods can significantly slow AD evolution and are currently the best strategy possible before the advanced stages of the disease. Indeed, current drug treatments have only symptomatic effects, and disease-modifying treatments are not yet available. Drug delivery to the central nervous system remains a complex process and represents a challenge for developing therapeutic and preventive strategies. Studies are underway to test new techniques to facilitate the bioavailability of molecules to the brain. After a deep study of the literature, we find the use of soft nanoparticles, in particular nanoliposomes and exosomes, as an innovative approach for preventive and therapeutic strategies in reducing the risk of AD and solving problems of brain bioavailability. Studies show the promising role of nanoliposomes and exosomes as smart drug delivery systems able to penetrate the blood-brain barrier and target brain tissues. Finally, the different drug administration techniques for neurological disorders are discussed. One of the promising therapeutic methods is the intranasal administration strategy which should be used for preclinical and clinical studies of neurodegenerative diseases.
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10
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Garcia DM, Campbell EA, Jakobson CM, Tsuchiya M, Shaw EA, DiNardo AL, Kaeberlein M, Jarosz DF. A prion accelerates proliferation at the expense of lifespan. eLife 2021; 10:e60917. [PMID: 34545808 PMCID: PMC8455135 DOI: 10.7554/elife.60917] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/12/2021] [Indexed: 12/23/2022] Open
Abstract
In fluctuating environments, switching between different growth strategies, such as those affecting cell size and proliferation, can be advantageous to an organism. Trade-offs arise, however. Mechanisms that aberrantly increase cell size or proliferation-such as mutations or chemicals that interfere with growth regulatory pathways-can also shorten lifespan. Here we report a natural example of how the interplay between growth and lifespan can be epigenetically controlled. We find that a highly conserved RNA-modifying enzyme, the pseudouridine synthase Pus4/TruB, can act as a prion, endowing yeast with greater proliferation rates at the cost of a shortened lifespan. Cells harboring the prion grow larger and exhibit altered protein synthesis. This epigenetic state, [BIG+] (better in growth), allows cells to heritably yet reversibly alter their translational program, leading to the differential synthesis of dozens of proteins, including many that regulate proliferation and aging. Our data reveal a new role for prion-based control of an RNA-modifying enzyme in driving heritable epigenetic states that transform cell growth and survival.
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Affiliation(s)
- David M Garcia
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Edgar A Campbell
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Christopher M Jakobson
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Mitsuhiro Tsuchiya
- Department of Pathology, University of Washington, Seattle, United States
| | - Ethan A Shaw
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Acadia L DiNardo
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, United States
| | - Daniel F Jarosz
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
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11
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Dyrka W, Coustou V, Daskalov A, Lends A, Bardin T, Berbon M, Kauffmann B, Blancard C, Salin B, Loquet A, Saupe SJ. Identification of NLR-associated Amyloid Signaling Motifs in Bacterial Genomes. J Mol Biol 2020; 432:6005-6027. [PMID: 33058872 DOI: 10.1016/j.jmb.2020.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023]
Abstract
In filamentous fungi, amyloid signaling sequences allow Nod-like receptors (NLRs) to activate downstream cell-death inducing proteins with HeLo and HeLo-like (HELL) domains and amyloid RHIM and RHIM-related motifs control immune defense pathways in mammals and flies. Herein, we show bioinformatically that analogous amyloid signaling motifs exist in bacteria. These short motifs are found at the N terminus of NLRs and at the C terminus of proteins with a domain we term BELL. The corresponding NLR and BELL proteins are encoded by adjacent genes. We identify 10 families of such bacterial amyloid signaling sequences (BASS), one of which (BASS3) is homologous to RHIM and a fungal amyloid motif termed PP. BASS motifs occur nearly exclusively in bacteria forming multicellular structures (mainly in Actinobacteria and Cyanobacteria). We analyze experimentally a subset of seven of these motifs (from the most common BASS1 family and the RHIM-related BASS3 family) and find that these sequences form fibrils in vitro. Using a fungal in vivo model, we show that all tested BASS-motifs form prions and that the NLR-side motifs seed prion-formation of the corresponding BELL-side motif. We find that BASS3 motifs show partial prion cross-seeding with mammalian RHIM and fungal PP-motifs and that proline mutations on key positions of the BASS3 core motif, conserved in RHIM and PP-motifs, abolish prion formation. This work expands the paradigm of prion amyloid signaling to multicellular prokaryotes and suggests a long-term evolutionary conservation of these motifs from bacteria, to fungi and animals.
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Affiliation(s)
- Witold Dyrka
- Politechnika Wrocławska, Wydział Podstawowych Problemów Techniki, Katedra Inżynierii Biomedycznej, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Virginie Coustou
- Non-self Recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Asen Daskalov
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248 CBMN, IECB, CNRS, Université de Bordeaux, Allee Geoffroy Saint-Hilaire, 33607 Pessac, France
| | - Alons Lends
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248 CBMN, IECB, CNRS, Université de Bordeaux, Allee Geoffroy Saint-Hilaire, 33607 Pessac, France
| | - Thierry Bardin
- Non-self Recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Mélanie Berbon
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Brice Kauffmann
- IECB, UMS 3033, US 001, CNRS, Université de Bordeaux, 2 Rue Robert Escarpit, 33607 Pessac, France
| | - Corinne Blancard
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Bénédicte Salin
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248 CBMN, IECB, CNRS, Université de Bordeaux, Allee Geoffroy Saint-Hilaire, 33607 Pessac, France
| | - Sven J Saupe
- Non-self Recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France.
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12
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Chernoff YO, Grizel AV, Rubel AA, Zelinsky AA, Chandramowlishwaran P, Chernova TA. Application of yeast to studying amyloid and prion diseases. ADVANCES IN GENETICS 2020; 105:293-380. [PMID: 32560789 PMCID: PMC7527210 DOI: 10.1016/bs.adgen.2020.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Amyloids are fibrous cross-β protein aggregates that are capable of proliferation via nucleated polymerization. Amyloid conformation likely represents an ancient protein fold and is linked to various biological or pathological manifestations. Self-perpetuating amyloid-based protein conformers provide a molecular basis for transmissible (infectious or heritable) protein isoforms, termed prions. Amyloids and prions, as well as other types of misfolded aggregated proteins are associated with a variety of devastating mammalian and human diseases, such as Alzheimer's, Parkinson's and Huntington's diseases, transmissible spongiform encephalopathies (TSEs), amyotrophic lateral sclerosis (ALS) and transthyretinopathies. In yeast and fungi, amyloid-based prions control phenotypically detectable heritable traits. Simplicity of cultivation requirements and availability of powerful genetic approaches makes yeast Saccharomyces cerevisiae an excellent model system for studying molecular and cellular mechanisms governing amyloid formation and propagation. Genetic techniques allowing for the expression of mammalian or human amyloidogenic and prionogenic proteins in yeast enable researchers to capitalize on yeast advantages for characterization of the properties of disease-related proteins. Chimeric constructs employing mammalian and human aggregation-prone proteins or domains, fused to fluorophores or to endogenous yeast proteins allow for cytological or phenotypic detection of disease-related protein aggregation in yeast cells. Yeast systems are amenable to high-throughput screening for antagonists of amyloid formation, propagation and/or toxicity. This review summarizes up to date achievements of yeast assays in application to studying mammalian and human disease-related aggregating proteins, and discusses both limitations and further perspectives of yeast-based strategies.
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Affiliation(s)
- Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States; Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia.
| | - Anastasia V Grizel
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Aleksandr A Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia; Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia; Sirius University of Science and Technology, Sochi, Russia
| | - Andrew A Zelinsky
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | | | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
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13
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Saijo E, Metrick MA, Koga S, Parchi P, Litvan I, Spina S, Boxer A, Rojas JC, Galasko D, Kraus A, Rossi M, Newell K, Zanusso G, Grinberg LT, Seeley WW, Ghetti B, Dickson DW, Caughey B. 4-Repeat tau seeds and templating subtypes as brain and CSF biomarkers of frontotemporal lobar degeneration. Acta Neuropathol 2020; 139:63-77. [PMID: 31616982 PMCID: PMC7192393 DOI: 10.1007/s00401-019-02080-2] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/08/2019] [Accepted: 09/26/2019] [Indexed: 10/25/2022]
Abstract
To address the need for more meaningful biomarkers of tauopathies, we have developed an ultrasensitive tau seed amplification assay (4R RT-QuIC) for the 4-repeat (4R) tau aggregates of progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), and other diseases with 4R tauopathy. The assay detected seeds in 106-109-fold dilutions of 4R tauopathy brain tissue but was orders of magnitude less responsive to brain with other types of tauopathy, such as from Alzheimer's disease cases. The analytical sensitivity for synthetic 4R tau fibrils was ~ 50 fM or 2 fg/sample. A novel dimension of this tau RT-QuIC testing was the identification of three disease-associated classes of 4R tau seeds; these classes were revealed by conformational variations in the in vitro amplified tau fibrils as detected by thioflavin T fluorescence amplitudes and FTIR spectroscopy. Tau seeds were detected in postmortem cerebrospinal fluid (CSF) from all neuropathologically confirmed PSP and CBD cases but not in controls. CSF from living subjects had weaker seeding activities; however, mean assay responses for cases clinically diagnosed as PSP and CBD/corticobasal syndrome were significantly higher than those from control cases. Altogether, 4R RT-QuIC provides a practical cell-free method of detecting and subtyping pathologic 4R tau aggregates as biomarkers.
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Affiliation(s)
- Eri Saijo
- LPVD, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, USA
| | | | - Shunsuke Koga
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Piero Parchi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139, Bologna, Italy
- Department of Experimental Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40138, Bologna, Italy
| | - Irene Litvan
- Department of Neurosciences, Parkinson and Other Movement Disorders Center, University of California, San Diego, CA, USA
| | - Salvatore Spina
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | - Adam Boxer
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | - Julio C Rojas
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | - Douglas Galasko
- Department of Neurosciences, University of California, San Diego, CA, USA
| | - Allison Kraus
- LPVD, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, USA
| | - Marcello Rossi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139, Bologna, Italy
| | - Kathy Newell
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Lea T Grinberg
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
- Department of Pathology, LIM-22, University of Sao Paulo, Sao Paulo, Brazil
| | - William W Seeley
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | | | | | - Byron Caughey
- LPVD, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, USA.
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14
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Killian AN, Miller SC, Hines JK. Impact of Amyloid Polymorphism on Prion-Chaperone Interactions in Yeast. Viruses 2019; 11:v11040349. [PMID: 30995727 PMCID: PMC6521183 DOI: 10.3390/v11040349] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/12/2019] [Accepted: 04/14/2019] [Indexed: 12/22/2022] Open
Abstract
Yeast prions are protein-based genetic elements found in the baker's yeast Saccharomyces cerevisiae, most of which are amyloid aggregates that propagate by fragmentation and spreading of small, self-templating pieces called propagons. Fragmentation is carried out by molecular chaperones, specifically Hsp104, Hsp70, and Hsp40. Like other amyloid-forming proteins, amyloid-based yeast prions exhibit structural polymorphisms, termed "strains" in mammalian systems and "variants" in yeast, which demonstrate diverse phenotypes and chaperone requirements for propagation. Here, the known differential interactions between chaperone proteins and yeast prion variants are reviewed, specifically those of the yeast prions [PSI+], [RNQ+]/[PIN+], and [URE3]. For these prions, differences in variant-chaperone interactions (where known) with Hsp104, Hsp70s, Hsp40s, Sse1, and Hsp90 are summarized, as well as some interactions with chaperones of other species expressed in yeast. As amyloid structural differences greatly impact chaperone interactions, understanding and accounting for these variations may be crucial to the study of chaperones and both prion and non-prion amyloids.
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Affiliation(s)
- Andrea N Killian
- Department of Chemistry, Lafayette College, Easton, PA 18042, USA.
| | - Sarah C Miller
- Department of Chemistry, Lafayette College, Easton, PA 18042, USA.
| | - Justin K Hines
- Department of Chemistry, Lafayette College, Easton, PA 18042, USA.
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15
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Hashimoto M, Ho G, Sugama S, Takamatsu Y, Shimizu Y, Takenouchi T, Waragai M, Masliah E. Evolvability of Amyloidogenic Proteins in Human Brain. J Alzheimers Dis 2018; 62:73-83. [PMID: 29439348 PMCID: PMC5817905 DOI: 10.3233/jad-170894] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2017] [Indexed: 12/29/2022]
Abstract
Currently, the physiological roles of amyloidogenic proteins (APs) in human brain, such as amyloid-β and α-synuclein, are elusive. Given that many APs arose by gene duplication and have been resistant against the pressures of natural selection, APs may be associated with some functions that are advantageous for survival of offspring. Nonetheless, evolvability is the sole physiological quality of APs that has been characterized in microorganisms such as yeast. Since yeast and human brain may share similar strategies in coping with diverse range of critical environmental stresses, the objective of this paper was to discuss the potential role of evolvability of APs in aging-associated neurodegenerative disorders, including Alzheimer's disease and Parkinson's disease. Given the heterogeneity of APs in terms of structure and cytotoxicity, it is argued that APs might be involved in preconditioning against diverse stresses in human brain. It is further speculated that these stress-related APs, most likely protofibrillar forms, might be transmitted to offspring via the germline, conferring preconditioning against forthcoming stresses. Thus, APs might represent a vehicle for the inheritance of the acquired characteristics against environmental stresses. Curiously, such a characteristic of APs is reminiscent of Charles Darwin's 'gemmules', imagined molecules of heritability described in his pangenesis theory. We propose that evolvability might be a physiological function of APs during the reproductive stage and neurodegenerative diseases could be a by-product effect manifested later in aging. Collectively, our evolvability hypothesis may play a complementary role in the pathophysiology of APs with the conventional amyloid cascade hypothesis.
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Affiliation(s)
- Makoto Hashimoto
- Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Gilbert Ho
- PCND Neuroscience Research Institute, Poway, CA, USA
| | - Shuei Sugama
- Department of Physiology, Nippon Medical School, Tokyo, Japan
| | - Yoshiki Takamatsu
- Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Yuka Shimizu
- Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Takato Takenouchi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Masaaki Waragai
- Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Eliezer Masliah
- Division of Neurosciences, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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16
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Chernova TA, Kiktev DA, Romanyuk AV, Shanks JR, Laur O, Ali M, Ghosh A, Kim D, Yang Z, Mang M, Chernoff YO, Wilkinson KD. Yeast Short-Lived Actin-Associated Protein Forms a Metastable Prion in Response to Thermal Stress. Cell Rep 2017; 18:751-761. [PMID: 28099852 DOI: 10.1016/j.celrep.2016.12.082] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/18/2016] [Accepted: 12/23/2016] [Indexed: 12/11/2022] Open
Abstract
Self-perpetuating ordered protein aggregates (amyloids and prions) are associated with a variety of neurodegenerative disorders. Although environmental agents have been linked to certain amyloid diseases, the molecular basis of their action remains unclear. We have employed endogenous yeast prions as a model system to study environmental control of amyloid formation. A short-lived actin-associated yeast protein Lsb2 can trigger prion formation by other proteins in a mode regulated by the cytoskeleton and ubiquitin-dependent processes. Here, we show that such a heterologous prion induction is due to the ability of Lsb2 to form a transient prion state, generated in response to thermal stress. Evolutionary acquisition of prion-inducing activity by Lsb2 is traced to a single amino acid change, coinciding with the acquisition of thermotolerance in the Saccharomyces yeast lineage. This raises the intriguing possibility that the transient prion formation could aid in functioning of Lsb2 at higher temperatures.
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Affiliation(s)
- Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Denis A Kiktev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA; Laboratory of Amyloid Biology and Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Andrey V Romanyuk
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - John R Shanks
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Oskar Laur
- Division of Microbiology, Yerkes Research Center, Emory University, Atlanta, GA 30322, USA
| | - Moiez Ali
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Abheek Ghosh
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dami Kim
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zhen Yang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Maggie Mang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA; Laboratory of Amyloid Biology and Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia.
| | - Keith D Wilkinson
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
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17
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Fernández MR, Batlle C, Gil-García M, Ventura S. Amyloid cores in prion domains: Key regulators for prion conformational conversion. Prion 2017; 11:31-39. [PMID: 28281928 DOI: 10.1080/19336896.2017.1282020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Despite the significant efforts devoted to decipher the particular protein features that encode for a prion or prion-like behavior, they are still poorly understood. The well-characterized yeast prions constitute an ideal model system to address this question, because, in these proteins, the prion activity can be univocally assigned to a specific region of their sequence, known as the prion forming domain (PFD). These PFDs are intrinsically disordered, relatively long and, in many cases, of low complexity, being enriched in glutamine/asparagine residues. Computational analyses have identified a significant number of proteins having similar domains in the human proteome. The compositional bias of these regions plays an important role in the transition of the prions to the amyloid state. However, it is difficult to explain how composition alone can account for the formation of specific contacts that position correctly PFDs and provide the enthalpic force to compensate for the large entropic cost of immobilizing these domains in the initial assemblies. We have hypothesized that short, sequence-specific, amyloid cores embedded in PFDs can perform these functions and, accordingly, act as preferential nucleation centers in both spontaneous and seeded aggregation. We have shown that the implementation of this concept in a prediction algorithm allows to score the prion propensities of putative PFDs with high accuracy. Recently, we have provided experimental evidence for the existence of such amyloid cores in the PFDs of Sup35, Ure2, Swi1, and Mot3 yeast prions. The fibrils formed by these short stretches may recognize and promote the aggregation of the complete proteins inside cells, being thus a promising tool for targeted protein inactivation.
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Affiliation(s)
- María Rosario Fernández
- a Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular , Universitat Autonoma de Barcelona , Bellaterra (Barcelona) , Spain
| | - Cristina Batlle
- a Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular , Universitat Autonoma de Barcelona , Bellaterra (Barcelona) , Spain
| | - Marcos Gil-García
- a Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular , Universitat Autonoma de Barcelona , Bellaterra (Barcelona) , Spain
| | - Salvador Ventura
- a Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular , Universitat Autonoma de Barcelona , Bellaterra (Barcelona) , Spain
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18
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Abstract
Prions are infectious protein polymers that have been found to cause fatal diseases in mammals. Prions have also been identified in fungi (yeast and filamentous fungi), where they behave as cytoplasmic non-Mendelian genetic elements. Fungal prions correspond in most cases to fibrillary β-sheet-rich protein aggregates termed amyloids. Fungal prion models and, in particular, yeast prions were instrumental in the description of fundamental aspects of prion structure and propagation. These models established the "protein-only" nature of prions, the physical basis of strain variation, and the role of a variety of chaperones in prion propagation and amyloid aggregate handling. Yeast and fungal prions do not necessarily correspond to harmful entities but can have adaptive roles in these organisms.
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19
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Abstract
TDP-43 is a dimeric nuclear protein that plays a central role in RNA metabolism. In recent years, this protein has become a focal point of research in the amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD) disease spectrum, as pathognomonic inclusions within affected neurons contain post-translationally modified TDP-43. A key question in TDP-43 research involves determining the mechanisms and triggers that cause TDP-43 to form pathological aggregates. This review gives a brief overview of the physiological and pathological roles of TDP-43 and focuses on the structural features of its protein domains and how they may contribute to normal protein function and to disease. A special emphasis is placed on the C-terminal prion-like region thought to be implicated in pathology, as it is where nearly all ALS/FTD-associated mutations reside. Recent structural studies of this domain revealed its crucial role in the formation of phase-separated liquid droplets through a partially populated α-helix. This new discovery provides further support for the theory that liquid droplets such as stress granules may be precursors to pathological aggregates, linking environmental effects such as stress to the potential etiology of the disease. The transition of TDP-43 among soluble, droplet, and aggregate phases and the implications of these transitions for pathological aggregation are summarized and discussed.
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Affiliation(s)
- Yulong Sun
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G1L7, Canada
| | - Avijit Chakrabartty
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G1L7, Canada.,Department of Biochemistry, University of Toronto , Toronto, Ontario M5G1L7, Canada
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20
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MacLea KS. What Makes a Prion: Infectious Proteins From Animals to Yeast. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:227-276. [PMID: 28109329 DOI: 10.1016/bs.ircmb.2016.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
While philosophers in ancient times had many ideas for the cause of contagion, the modern study of infective agents began with Fracastoro's 1546 proposal that invisible "spores" spread infectious disease. However, firm categorization of the pathogens of the natural world would need to await a mature germ theory that would not arise for 300 years. In the 19th century, the earliest pathogens described were bacteria and other cellular microbes. By the close of that century, the work of Ivanovsky and Beijerinck introduced the concept of a virus, an infective particle smaller than any known cell. Extending into the early-mid-20th century there was an explosive growth in pathogenic microbiology, with a cellular or viral cause identified for nearly every transmissible disease. A few occult pathogens remained to be discovered, including the infectious proteins (prions) proposed by Prusiner in 1982. This review discusses the prions identified in mammals, yeasts, and other organisms, focusing on the amyloid-based prions. I discuss the essential biochemical properties of these agents and the application of this knowledge to diseases of protein misfolding and aggregation, as well as the utility of yeast as a model organism to study prion and amyloid proteins that affect human and animal health. Further, I summarize the ideas emerging out of these studies that the prion concept may go beyond proteinaceous infectious particles and that prions may be a subset of proteins having general nucleating or seeding functions involved in noninfectious as well as infectious pathogenic protein aggregation.
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Affiliation(s)
- K S MacLea
- University of New Hampshire, Manchester, NH, United States.
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21
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Characterization of Amyloid Cores in Prion Domains. Sci Rep 2016; 6:34274. [PMID: 27686217 PMCID: PMC5043269 DOI: 10.1038/srep34274] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/09/2016] [Indexed: 11/09/2022] Open
Abstract
Amyloids consist of repetitions of a specific polypeptide chain in a regular cross-β-sheet conformation. Amyloid propensity is largely determined by the protein sequence, the aggregation process being nucleated by specific and short segments. Prions are special amyloids that become self-perpetuating after aggregation. Prions are responsible for neuropathology in mammals, but they can also be functional, as in yeast prions. The conversion of these last proteins to the prion state is driven by prion forming domains (PFDs), which are generally large, intrinsically disordered, enriched in glutamines/asparagines and depleted in hydrophobic residues. The self-assembly of PFDs has been thought to rely mostly on their particular amino acid composition, rather than on their sequence. Instead, we have recently proposed that specific amyloid-prone sequences within PFDs might be key to their prion behaviour. Here, we demonstrate experimentally the existence of these amyloid stretches inside the PFDs of the canonical Sup35, Swi1, Mot3 and Ure2 prions. These sequences self-assemble efficiently into highly ordered amyloid fibrils, that are functionally competent, being able to promote the PFD amyloid conversion in vitro and in vivo. Computational analyses indicate that these kind of amyloid stretches may act as typical nucleating signals in a number of different prion domains.
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22
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A Decentralized Approach to the Formulation of Hypotheses: A Hierarchical Structural Model for a Prion Self-Assembled System. Sci Rep 2016; 6:30633. [PMID: 27464832 PMCID: PMC4964355 DOI: 10.1038/srep30633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/06/2016] [Indexed: 11/13/2022] Open
Abstract
Innovation in hypotheses is a key transformative driver for scientific development.
The conventional centralized hypothesis formulation approach, where a dominant
hypothesis is typically derived from a primary phenomenon, can, inevitably, impose
restriction on the range of conceivable experiments and legitimate hypotheses, and
ultimately impede understanding of the system of interest. We report herein the
proposal of a decentralized approach for the formulation of hypotheses, through
initial preconception-free phenomenon accumulation and subsequent reticular logical
reasoning processes. The two-step approach can provide an unbiased, panoramic view
of the system and as such should enable the generation of a set of more coherent and
therefore plausible hypotheses. As a proof-of-concept demonstration of the utility
of this open-ended approach, a hierarchical model has been developed for a prion
self-assembled system, allowing insight into hitherto elusive static and dynamic
features associated with this intriguing structure.
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