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Soleimani A, Alizadeh H. Unlocking the potential of Extensin Signal peptide and Elastin-like polypeptide tag fused to Shigella dysenteriae's IpaDSTxB to improve protein expression and purification in Nicotiana tabacum and Medicagosativa. Protein Expr Purif 2024; 222:106521. [PMID: 38852714 DOI: 10.1016/j.pep.2024.106521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
Plants are often seen as a potent tool in the recombinant protein production industry. However, unlike bacterial expression, it is not a popular method due to the low yield and difficulty of protein extraction and purification. Therefore, developing a new high efficient and easy to purify platform is crucial. One of the best approaches to make extraction easier is to utilize the Extensin Signal peptide (EXT) to translocate the recombinant protein to the outside of the cell, along with incorporating an Elastin-like polypeptide tag (ELP) to enhance purification and accumulation rates. In this research, we transiently expressed Shigella dysenteriae's IpaDSTxB fused to both NtEXT and ELP in both Nicotiana tabacum and Medicago sativa. Our results demonstrated that N. tabacum, with an average yield of 6.39 ng/μg TSP, outperforms M. sativa, which had an average yield of 3.58 ng/μg TSP. On the other hand, analyzing NtEXT signal peptide indicated that merging EXT to the constructs facilitates translocation of IpaDSTxB to the apoplast by 78.4% and 65.9% in N. tabacum and M. sativa, respectively. Conversely, the mean level for constructs without EXT was below 25% for both plants. Furthermore, investigation into the orientation of ELP showed that merging it to the C-terminal of IpaDSTxB leads to a higher accumulation rate in both N. tabacum and M. sativa by 1.39 and 1.28 times, respectively. It also facilitates purification rate by over 70% in comparison to 20% of the 6His tag. The results show a highly efficient and easy to purify platform for the expression of heterologous proteins in plant.
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Affiliation(s)
- AmirMohammad Soleimani
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.
| | - Houshang Alizadeh
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
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Qi A, Wang K, Li Y, Hu R, Hu G, Li Y, Shi G, Huang M. The degradation of α--synuclein is limited by dynein to drive the AALP pathway through HDAC6 upon paraquat exposure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116841. [PMID: 39128448 DOI: 10.1016/j.ecoenv.2024.116841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 07/26/2024] [Accepted: 08/02/2024] [Indexed: 08/13/2024]
Abstract
Lewy body disease (LBD), one of the most common neurodegenerative diseases (NDDs), is characterized by excessive accumulation of α-synuclein (α-syn) in neurons. In recent years, environmental factors such as exposure to herbicides and pesticides have been attributed to the development of this condition. While majority of the studies on neurotoxic effects of paraquat (PQ) have focused on α-syn-mediated neuronal damage in the early stages of α-syn accumulation in neurons, efforts to explore the key target for α-syn degradation are limited. Recent research has suggested that histone deacetylase 6 (HDAC6) might possibly regulate amyloid clearance, and that the metabolism of compounds in neurons is also directly affected by axonal transport in neurons. Dynein predominantly mediates reverse transportation of metabolites and uptake of signal molecules and other compounds at the end of axons, which is conducive to the reuse of cell components. However, the role of interaction of dynein with HDAC6 in metabolites transport is still unclear. Therefore, this study aimed to investigate the role of HDAC6 in α-syn accumulation/clearance in neurons and the associated possible influencing factors. The results revealed that HDAC6 could transport ubiquitinated α-syn, bind to dynein, form an aggresome, and relocate to the center of the microtubule tissue, ultimately reducing abnormal accumulation of α-syn. However, PQ treatment resulted in HDAC6 upregulation, causing abnormal aggregation of α-syn. Taken together, these findings indicated that PQ exposure caused abnormal accumulation of α-syn and decreased effective degradation of α-syn by HDAC6-mediated aggresome-autophagy-lysosome pathway.
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Affiliation(s)
- Ai Qi
- School of Public Health, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China; Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China
| | - Kaidong Wang
- School of Public Health, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China; Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China
| | - Yujing Li
- School of Public Health, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China; Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China
| | - Rong Hu
- School of Public Health, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China; Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China
| | - Guiling Hu
- School of Public Health, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China; Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China
| | - Yang Li
- School of Public Health, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China; Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China
| | - Ge Shi
- School of Public Health, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China; Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China.
| | - Min Huang
- School of Public Health, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China; Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, No.1160, Shengli Street, Xingqing District, Yinchuan, Ningxia, China.
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Ni Y, Qiao Y, Tian X, Li H, Meng Y, Li C, Du W, Sun T, Zhu K, Huang W, Yan H, Li J, Zhou R, Ding C, Gao X. Unraveling the mechanism of thermotolerance by Set302 in Cryptococcus neoformans. Microbiol Spectr 2024; 12:e0420223. [PMID: 38874428 PMCID: PMC11302353 DOI: 10.1128/spectrum.04202-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 05/12/2024] [Indexed: 06/15/2024] Open
Abstract
The underlying mechanism of thermotolerance, which is a key virulence factor essential for pathogenic fungi such as Cryptococcus neoformans, is largely unexplored. In this study, our findings suggest that Set302, a homolog of Set3 and a subunit of histone deacetylase complex Set3C, contributes to thermotolerance in C. neoformans. Specifically, the deletion of the predicted Set3C core subunit, Set302, resulted in further reduction in the growth of C. neoformans at 39°C, and survival of transient incubation at 50°C. Transcriptomics analysis revealed that the expression levels of numerous heat stress-responsive genes altered at both 30°C and 39°C due to the lack of Set302. Notably, at 39°C, the absence of Set302 led to the downregulation of gene expression related to the ubiquitin-proteasome system (UPS). Based on the GFP-α-synuclein overexpression model to characterize misfolded proteins, we observed a pronounced accumulation of misfolded GFP-α-synuclein at 39°C, consequently inhibiting C. neoformans thermotolerance. Furthermore, the loss of Set302 exacerbated the accumulation of misfolded GFP-α-synuclein during heat stress. Interestingly, the set302∆ strain exhibited a similar phenotype under proteasome stress as it did at 39°C. Moreover, the absence of Set302 led to reduced production of capsule and melanin. set302∆ strain also displayed significantly reduced pathogenicity and colonization ability compared to the wild-type strain in the murine infection model. Collectively, our findings suggest that Set302 modulates thermotolerance by affecting the degradation of misfolded proteins and multiple virulence factors to mediate the pathogenicity of C. neoformans.IMPORTANCECryptococcus neoformans is a pathogenic fungus that poses a potential and significant threat to public health. Thermotolerance plays a crucial role in the wide distribution in natural environments and host colonization of this fungus. Herein, Set302, a critical core subunit for the integrity of histone deacetylase complex Set3C and widely distributed in various fungi and mammals, governs thermotolerance and affects survival at extreme temperatures as well as the formation of capsule and melanin in C. neoformans. Additionally, Set302 participates in regulating the expression of multiple genes associated with the ubiquitin-proteasome system (UPS). By eliminating misfolded proteins under heat stress, Set302 significantly contributes to the thermotolerance of C. neoformans. Moreover, Set302 regulates the pathogenicity and colonization ability of C. neoformans in a murine model. Overall, this study provides new insight into the mechanism of thermotolerance in C. neoformans.
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Affiliation(s)
- Yue Ni
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Yue Qiao
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Xing Tian
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Hailong Li
- NHC Key Laboratory of AIDS Immunology, National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yang Meng
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Chao Li
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Wei Du
- Department of Clinical Laboratory, National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tianshu Sun
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Medical Research Centre, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Keting Zhu
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Wei Huang
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - He Yan
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Jia Li
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Renjie Zhou
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Chen Ding
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Xindi Gao
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
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Bosch E, Güse E, Kirchner P, Winterpacht A, Walther M, Alders M, Kerkhof J, Ekici AB, Sticht H, Sadikovic B, Reis A, Vasileiou G. The missing link: ARID1B non-truncating variants causing Coffin-Siris syndrome due to protein aggregation. Hum Genet 2024; 143:965-978. [PMID: 39028335 PMCID: PMC11303441 DOI: 10.1007/s00439-024-02688-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/07/2024] [Indexed: 07/20/2024]
Abstract
ARID1B is the most frequently mutated gene in Coffin-Siris syndrome (CSS). To date, the vast majority of causative variants reported in ARID1B are truncating, leading to nonsense-mediated mRNA decay. In the absence of experimental data, only few ARID1B amino acid substitutions have been classified as pathogenic, mainly based on clinical data and their de novo occurrence, while most others are currently interpreted as variants of unknown significance. The present study substantiates the pathogenesis of ARID1B non-truncating/NMD-escaping variants located in the SMARCA4-interacting EHD2 and DNA-binding ARID domains. Overexpression assays in cell lines revealed that the majority of EHD2 variants lead to protein misfolding and formation of cytoplasmic aggresomes surrounded by vimentin cage-like structures and co-localizing with the microtubule organisation center. ARID domain variants exhibited not only aggresomes, but also nuclear aggregates, demonstrating robust pathological effects. Protein levels were not compromised, as shown by quantitative western blot analysis. In silico structural analysis predicted the exposure of amylogenic segments in both domains due to the nearby variants, likely causing this aggregation. Genome-wide transcriptome and methylation analysis in affected individuals revealed expression and methylome patterns consistent with those of the pathogenic haploinsufficiency ARID1B alterations in CSS cases. These results further support pathogenicity and indicate two approaches for disambiguation of such variants in everyday practice. The few affected individuals harbouring EHD2 non-truncating variants described to date exhibit mild CSS clinical traits. In summary, this study paves the way for the re-evaluation of previously unclear ARID1B non-truncating variants and opens a new era in CSS genetic diagnosis.
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Affiliation(s)
- Elisabeth Bosch
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Esther Güse
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Philipp Kirchner
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Andreas Winterpacht
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Mona Walther
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Arif B Ekici
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
- Centre for Rare Diseases Erlangen (ZSEER), Universitätsklinikum Erlangen, Erlangen, Germany
| | - Georgia Vasileiou
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany.
- Centre for Rare Diseases Erlangen (ZSEER), Universitätsklinikum Erlangen, Erlangen, Germany.
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5
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Begar E, Seyrek E, Firat-Karalar EN. Navigating centriolar satellites: the role of PCM1 in cellular and organismal processes. FEBS J 2024. [PMID: 38825736 DOI: 10.1111/febs.17194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/20/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024]
Abstract
Centriolar satellites are ubiquitous membrane-less organelles that play critical roles in numerous cellular and organismal processes. They were initially discovered through electron microscopy as cytoplasmic granules surrounding centrosomes in vertebrate cells. These structures remained enigmatic until the identification of pericentriolar material 1 protein (PCM1) as their molecular marker, which has enabled their in-depth characterization. Recently, centriolar satellites have come into the spotlight due to their links to developmental and neurodegenerative disorders. This review presents a comprehensive summary of the major advances in centriolar satellite biology, with a focus on studies that investigated their biology associated with the essential scaffolding protein PCM1. We begin by exploring the molecular, cellular, and biochemical properties of centriolar satellites, laying the groundwork for a deeper understanding of their functions and mechanisms at both cellular and organismal levels. We then examine the implications of their dysregulation in various diseases, particularly highlighting their emerging roles in neurodegenerative and developmental disorders, as revealed by organismal models of PCM1. We conclude by discussing the current state of knowledge and posing questions about the adaptable nature of these organelles, thereby setting the stage for future research.
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Affiliation(s)
- Efe Begar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Ece Seyrek
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
- School of Medicine, Koç University, Istanbul, Turkey
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Körschgen H, Behl C. Aggresome-aggrephagy transition process: getting closer to the functional roles of HDAC6 and BAG3. Neural Regen Res 2024; 19:1181-1182. [PMID: 37905854 DOI: 10.4103/1673-5374.386407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/21/2023] [Indexed: 11/02/2023] Open
Affiliation(s)
- Hagen Körschgen
- The Autophagy Lab, Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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7
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Stahl F, Evert BO, Han X, Breuer P, Wüllner U. Spinocerebellar Ataxia Type 3 Pathophysiology-Implications for Translational Research and Clinical Studies. Int J Mol Sci 2024; 25:3984. [PMID: 38612794 PMCID: PMC11012515 DOI: 10.3390/ijms25073984] [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: 02/14/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
The spinocerebellar ataxias (SCA) comprise a group of inherited neurodegenerative diseases. Machado-Joseph Disease (MJD) or spinocerebellar ataxia 3 (SCA3) is the most common autosomal dominant form, caused by the expansion of CAG repeats within the ataxin-3 (ATXN3) gene. This mutation results in the expression of an abnormal protein containing long polyglutamine (polyQ) stretches that confers a toxic gain of function and leads to misfolding and aggregation of ATXN3 in neurons. As a result of the neurodegenerative process, SCA3 patients are severely disabled and die prematurely. Several screening approaches, e.g., druggable genome-wide and drug library screenings have been performed, focussing on the reduction in stably overexpressed ATXN3(polyQ) protein and improvement in the resultant toxicity. Transgenic overexpression models of toxic ATXN3, however, missed potential modulators of endogenous ATXN3 regulation. In another approach to identify modifiers of endogenous ATXN3 expression using a CRISPR/Cas9-modified SK-N-SH wild-type cell line with a GFP-T2A-luciferase (LUC) cassette under the control of the endogenous ATXN3 promotor, four statins were identified as potential activators of expression. We here provide an overview of the high throughput screening approaches yet performed to find compounds or genomic modifiers of ATXN3(polyQ) toxicity in different SCA3 model organisms and cell lines to ameliorate and halt SCA3 progression in patients. Furthermore, the putative role of cholesterol in neurodegenerative diseases (NDDs) in general and SCA3 in particular is discussed.
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Affiliation(s)
- Fabian Stahl
- German Centre for Neurodegenerative Disease (DZNE), 53127 Bonn, Germany;
| | - Bernd O. Evert
- Departments of Neurology and Neurodegenerative Diseases, University of Bonn, 53127 Bonn, Germany; (B.O.E.); (X.H.); (P.B.)
| | - Xinyu Han
- Departments of Neurology and Neurodegenerative Diseases, University of Bonn, 53127 Bonn, Germany; (B.O.E.); (X.H.); (P.B.)
| | - Peter Breuer
- Departments of Neurology and Neurodegenerative Diseases, University of Bonn, 53127 Bonn, Germany; (B.O.E.); (X.H.); (P.B.)
| | - Ullrich Wüllner
- German Centre for Neurodegenerative Disease (DZNE), 53127 Bonn, Germany;
- Departments of Neurology and Neurodegenerative Diseases, University of Bonn, 53127 Bonn, Germany; (B.O.E.); (X.H.); (P.B.)
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8
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Goralski TM, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse DJ, Henderson MX. Spatial transcriptomics reveals molecular dysfunction associated with cortical Lewy pathology. Nat Commun 2024; 15:2642. [PMID: 38531900 PMCID: PMC10966039 DOI: 10.1038/s41467-024-47027-8] [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: 01/30/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
A key hallmark of Parkinson's disease (PD) is Lewy pathology. Composed of α-synuclein, Lewy pathology is found both in dopaminergic neurons that modulate motor function, and cortical regions that control cognitive function. Recent work has established the molecular identity of dopaminergic neurons susceptible to death, but little is known about cortical neurons susceptible to Lewy pathology or molecular changes induced by aggregates. In the current study, we use spatial transcriptomics to capture whole transcriptome signatures from cortical neurons with α-synuclein pathology compared to neurons without pathology. We find, both in PD and related PD dementia, dementia with Lewy bodies and in the pre-formed fibril α-synucleinopathy mouse model, that specific classes of excitatory neurons are vulnerable to developing Lewy pathology. Further, we identify conserved gene expression changes in aggregate-bearing neurons that we designate the Lewy-associated molecular dysfunction from aggregates (LAMDA) signature. Neurons with aggregates downregulate synaptic, mitochondrial, ubiquitin-proteasome, endo-lysosomal, and cytoskeletal genes and upregulate DNA repair and complement/cytokine genes. Our results identify neurons vulnerable to Lewy pathology in the PD cortex and describe a conserved signature of molecular dysfunction in both mice and humans.
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Affiliation(s)
- Thomas M Goralski
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lindsay Meyerdirk
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Libby Breton
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Laura Brasseur
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Kevin Kurgat
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Daniella DeWeerd
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lisa Turner
- Van Andel Institute Pathology Core, Grand Rapids, MI, 49503, USA
| | - Katelyn Becker
- Van Andel Institute Genomics Core, Grand Rapids, MI, 49503, USA
| | - Marie Adams
- Van Andel Institute Genomics Core, Grand Rapids, MI, 49503, USA
| | | | - Michael X Henderson
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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Vasudevan S, Senapati S, Pendergast M, Park PSH. Aggregation of rhodopsin mutants in mouse models of autosomal dominant retinitis pigmentosa. Nat Commun 2024; 15:1451. [PMID: 38365903 PMCID: PMC10873427 DOI: 10.1038/s41467-024-45748-4] [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: 04/07/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
Mutations in rhodopsin can cause it to misfold and lead to retinal degeneration. A distinguishing feature of these mutants in vitro is that they mislocalize and aggregate. It is unclear whether or not these features contribute to retinal degeneration observed in vivo. The effect of P23H and G188R misfolding mutations were examined in a heterologous expression system and knockin mouse models, including a mouse model generated here expressing the G188R rhodopsin mutant. In vitro characterizations demonstrate that both mutants aggregate, with the G188R mutant exhibiting a more severe aggregation profile compared to the P23H mutant. The potential for rhodopsin mutants to aggregate in vivo was assessed by PROTEOSTAT, a dye that labels aggregated proteins. Both mutants mislocalize in photoreceptor cells and PROTEOSTAT staining was detected surrounding the nuclei of photoreceptor cells. The G188R mutant promotes a more severe retinal degeneration phenotype and greater PROTEOSTAT staining compared to that promoted by the P23H mutant. Here, we show that the level of PROTEOSTAT positive cells mirrors the progression and level of photoreceptor cell death, which suggests a potential role for rhodopsin aggregation in retinal degeneration.
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Affiliation(s)
- Sreelakshmi Vasudevan
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Subhadip Senapati
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
- Prayoga Institute of Education Research, Bengaluru, KA, 560116, India
| | - Maryanne Pendergast
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
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10
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Sweeney KM, Chantarawong S, Barbieri EM, Cajka G, Liu M, Spruce L, Fazelinia H, Portz B, Copley K, Lapidot T, Duhamel L, Greenwald P, Saida N, Shalgi R, Shorter J, Shalem O. CRISPR screen for protein inclusion formation uncovers a role for SRRD in the regulation of intermediate filament dynamics and aggresome assembly. PLoS Genet 2024; 20:e1011138. [PMID: 38315730 PMCID: PMC10868785 DOI: 10.1371/journal.pgen.1011138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 02/15/2024] [Accepted: 01/15/2024] [Indexed: 02/07/2024] Open
Abstract
The presence of large protein inclusions is a hallmark of neurodegeneration, and yet the precise molecular factors that contribute to their formation remain poorly understood. Screens using aggregation-prone proteins have commonly relied on downstream toxicity as a readout rather than the direct formation of aggregates. Here, we combined a genome-wide CRISPR knockout screen with Pulse Shape Analysis, a FACS-based method for inclusion detection, to identify direct modifiers of TDP-43 aggregation in human cells. Our screen revealed both canonical and novel proteostasis genes, and unearthed SRRD, a poorly characterized protein, as a top regulator of protein inclusion formation. APEX biotin labeling reveals that SRRD resides in proximity to proteins that are involved in the formation and breakage of disulfide bonds and to intermediate filaments, suggesting a role in regulation of the spatial dynamics of the intermediate filament network. Indeed, loss of SRRD results in aberrant intermediate filament fibrils and the impaired formation of aggresomes, including blunted vimentin cage structure, during proteotoxic stress. Interestingly, SRRD also localizes to aggresomes and unfolded proteins, and rescues proteotoxicity in yeast whereby its N-terminal low complexity domain is sufficient to induce this affect. Altogether this suggests an unanticipated and broad role for SRRD in cytoskeletal organization and cellular proteostasis.
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Affiliation(s)
- Katelyn M. Sweeney
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sapanna Chantarawong
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Edward M. Barbieri
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Greg Cajka
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew Liu
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lynn Spruce
- Proteomics Core Facility, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Hossein Fazelinia
- Proteomics Core Facility, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Bede Portz
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katie Copley
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tomer Lapidot
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lauren Duhamel
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Phoebe Greenwald
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Naseeb Saida
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Reut Shalgi
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ophir Shalem
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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11
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Vuletić A, Mirjačić Martinović K, Spasić J. Role of Histone Deacetylase 6 and Histone Deacetylase 6 Inhibition in Colorectal Cancer. Pharmaceutics 2023; 16:54. [PMID: 38258065 PMCID: PMC10818982 DOI: 10.3390/pharmaceutics16010054] [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: 11/28/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Histone deacetylase 6 (HDAC6), by deacetylation of multiple substrates and association with interacting proteins, regulates many physiological processes that are involved in cancer development and invasiveness such as cell proliferation, apoptosis, motility, epithelial to mesenchymal transition, and angiogenesis. Due to its ability to remove misfolded proteins, induce autophagy, and regulate unfolded protein response, HDAC6 plays a protective role in responses to stress and enables tumor cell survival. The scope of this review is to discuss the roles of HDCA6 and its implications for the therapy of colorectal cancer (CRC). As HDAC6 is overexpressed in CRC, correlates with poor disease prognosis, and is not essential for normal mammalian development, it represents a good therapeutic target. Selective inhibition of HDAC6 impairs growth and progression without inducing major adverse events in experimental animals. In CRC, HDAC6 inhibitors have shown the potential to reduce tumor progression and enhance the therapeutic effect of other drugs. As HDAC6 is involved in the regulation of immune responses, HDAC6 inhibitors have shown the potential to improve antitumor immunity by increasing the immunogenicity of tumor cells, augmenting immune cell activity, and alleviating immunosuppression in the tumor microenvironment. Therefore, HDAC6 inhibitors may represent promising candidates to improve the effect of and overcome resistance to immunotherapy.
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Affiliation(s)
- Ana Vuletić
- Department of Experimental Oncology, Institute of Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
| | - Katarina Mirjačić Martinović
- Department of Experimental Oncology, Institute of Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
| | - Jelena Spasić
- Clinic for Medical Oncology, Institute of Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
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12
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Furthmann N, Bader V, Angersbach L, Blusch A, Goel S, Sánchez-Vicente A, Krause LJ, Chaban SA, Grover P, Trinkaus VA, van Well EM, Jaugstetter M, Tschulik K, Damgaard RB, Saft C, Ellrichmann G, Gold R, Koch A, Englert B, Westenberger A, Klein C, Jungbluth L, Sachse C, Behrends C, Glatzel M, Hartl FU, Nakamura K, Christine CW, Huang EJ, Tatzelt J, Winklhofer KF. NEMO reshapes the α-Synuclein aggregate interface and acts as an autophagy adapter by co-condensation with p62. Nat Commun 2023; 14:8368. [PMID: 38114471 PMCID: PMC10730909 DOI: 10.1038/s41467-023-44033-0] [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: 02/08/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
NEMO is a ubiquitin-binding protein which regulates canonical NF-κB pathway activation in innate immune signaling, cell death regulation and host-pathogen interactions. Here we identify an NF-κB-independent function of NEMO in proteostasis regulation by promoting autophagosomal clearance of protein aggregates. NEMO-deficient cells accumulate misfolded proteins upon proteotoxic stress and are vulnerable to proteostasis challenges. Moreover, a patient with a mutation in the NEMO-encoding IKBKG gene resulting in defective binding of NEMO to linear ubiquitin chains, developed a widespread mixed brain proteinopathy, including α-synuclein, tau and TDP-43 pathology. NEMO amplifies linear ubiquitylation at α-synuclein aggregates and promotes the local concentration of p62 into foci. In vitro, NEMO lowers the threshold concentrations required for ubiquitin-dependent phase transition of p62. In summary, NEMO reshapes the aggregate surface for efficient autophagosomal clearance by providing a mobile phase at the aggregate interphase favoring co-condensation with p62.
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Affiliation(s)
- Nikolas Furthmann
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Lena Angersbach
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Alina Blusch
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, 44791, Bochum, Germany
| | - Simran Goel
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Ana Sánchez-Vicente
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Laura J Krause
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
- Cluster of Excellence RESOLV, 44801, Bochum, Germany
| | - Sarah A Chaban
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Prerna Grover
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Victoria A Trinkaus
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Eva M van Well
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Maximilian Jaugstetter
- Analytical Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Kristina Tschulik
- Cluster of Excellence RESOLV, 44801, Bochum, Germany
- Analytical Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Rune Busk Damgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Carsten Saft
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, 44791, Bochum, Germany
| | - Gisa Ellrichmann
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, 44791, Bochum, Germany
- Department of Neurology, Klinikum Dortmund, University Witten/Herdecke, 44135, Dortmund, Germany
| | - Ralf Gold
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, 44791, Bochum, Germany
| | - Arend Koch
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Benjamin Englert
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, 10117, Berlin, Germany
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University, 81377, Munich, Germany
| | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Lisa Jungbluth
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Information Processing (IBI-6/Cellular Structural Biology), Forschungszentrum Jülich, Jülich, Germany
| | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Information Processing (IBI-6/Cellular Structural Biology), Forschungszentrum Jülich, Jülich, Germany
- Department of Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251, Hamburg, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377, Munich, Germany
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Chadwick W Christine
- Department of Neurology, University of California, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Eric J Huang
- Department of Neurology, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
- Cluster of Excellence RESOLV, 44801, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany.
- Cluster of Excellence RESOLV, 44801, Bochum, Germany.
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13
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Christie J, Anthony CM, Harish M, Mudartha D, Ud Din Farooqee SB, Venkatraman P. The interaction network of the proteasome assembly chaperone PSMD9 regulates proteostasis. FEBS J 2023; 290:5581-5604. [PMID: 37665644 DOI: 10.1111/febs.16948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/09/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Functional networks in cells are created by physical, genetic, and regulatory interactions. Mapping them and annotating their functions by available methods remains a challenge. We use affinity purification mass spectrometry (AP-MS) coupled with SLiMFinder to discern such a network involving 26S proteasome non-ATPase regulatory subunit 9 (PSMD9), a chaperone of proteasome assembly. Approximately 20% of proteins within the PSMD9 interactome carry a short linear motif (SLiM) of the type 'EXKK'. The binding of purified PSMD9 with the peptide sequence ERKK, proteins heterogeneous nuclear ribonucleoproteins A2/B1 (hnRNPA2B1; containing ERKK), and peroxiredoxin-6 (PRDX6; containing EAKK) provided proof of principle for this motif-driven network. The EXKK motif in the peptide primarily interacts with the coiled-coil N domain of PSMD9, a unique interaction not reported for any coiled-coil domain. PSMD9 knockout (KO) HEK293 cells experience endoplasmic reticulum (ER) stress and respond by increasing the unfolded protein response (UPR) and reducing the formation of aggresomes and lipid droplets. Trans-expression of PSMD9 in the KO cells rescues lipid droplet formation. Overexpression of PSMD9 in HEK293 cells results in reduced UPR, and increased lipid droplet and aggresome formation. The outcome argues for the prominent role of PSMD9 in maintaining proteostasis. Probable mechanisms involve the binding of PSMD9 to binding immunoglobulin protein (BIP/GRP78; containing EDKK), an endoplasmic reticulum chaperone and key regulator of the UPR, and fatty acid synthase (FASN; containing ELKK), involved in fatty acid synthesis/lipid biogenesis. We propose that PSMD9 acts as a buffer in the cellular milieu by moderating the UPR and enhancing aggresome formation to reduce stress-induced proteotoxicity. Akin to waves created in ponds that perpetuate to a distance, perturbing the levels of PSMD9 would cause ripples down the networks, affecting final reactions in the pathway, one of which is altered proteostasis.
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Affiliation(s)
- Joel Christie
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - C Merlyn Anthony
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Mahalakshmi Harish
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Deepti Mudartha
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Sheikh Burhan Ud Din Farooqee
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Prasanna Venkatraman
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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14
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Castro V, Pérez-Berna AJ, Calvo G, Pereiro E, Gastaminza P. Three-Dimensional Remodeling of SARS-CoV2-Infected Cells Revealed by Cryogenic Soft X-ray Tomography. ACS NANO 2023; 17:22708-22721. [PMID: 37939169 PMCID: PMC10690842 DOI: 10.1021/acsnano.3c07265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023]
Abstract
Plus-strand RNA viruses are proficient at remodeling host cell membranes for optimal viral genome replication and the production of infectious progeny. These ultrastructural alterations result in the formation of viral membranous organelles and may be observed by different imaging techniques, providing nanometric resolution. Guided by confocal and electron microscopy, this study describes the generation of wide-field volumes using cryogenic soft-X-ray tomography (cryo-SXT) on SARS-CoV-2-infected human lung adenocarcinoma cells. Confocal microscopy showed accumulation of double-stranded RNA (dsRNA) and nucleocapsid (N) protein in compact perinuclear structures, preferentially found around centrosomes at late stages of the infection. Transmission electron microscopy (TEM) showed accumulation of membranous structures in the vicinity of the infected cell nucleus, forming a viral replication organelle containing characteristic double-membrane vesicles and virus-like particles within larger vesicular structures. Cryo-SXT revealed viral replication organelles very similar to those observed by TEM but indicated that the vesicular organelle observed in TEM sections is indeed a vesiculo-tubular network that is enlarged and elongated at late stages of the infection. Overall, our data provide additional insight into the molecular architecture of the SARS-CoV-2 replication organelle.
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Affiliation(s)
- Victoria Castro
- Centro
Nacional de Biotecnología. Calle Darwin, 3, 28049 Madrid, Spain
| | | | - Gema Calvo
- Centro
Nacional de Biotecnología. Calle Darwin, 3, 28049 Madrid, Spain
| | - Eva Pereiro
- ALBA
Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Valles, Spain
| | - Pablo Gastaminza
- Centro
Nacional de Biotecnología. Calle Darwin, 3, 28049 Madrid, Spain
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15
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Takanezawa Y, Ishikawa K, Nakayama S, Nakamura R, Ohshiro Y, Uraguchi S, Kiyono M. Conversion of methylmercury into inorganic mercury via organomercurial lyase (MerB) activates autophagy and aggresome formation. Sci Rep 2023; 13:19958. [PMID: 37968352 PMCID: PMC10651920 DOI: 10.1038/s41598-023-47110-y] [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: 06/16/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023] Open
Abstract
Methylmercury (MeHg) is converted to inorganic mercury (iHg) in several organs; however, its impact on tissues and cells remains poorly understood. Previously, we established a bacterial organomercury lyase (MerB)-expressing mammalian cell line to overcome the low cell permeability of iHg and investigate its effects. Here, we elucidated the cytotoxic effects of the resultant iHg on autophagy and deciphered their relationship. Treatment of MerB-expressing cells with MeHg significantly increases the mRNA and protein levels of LC3B and p62, which are involved in autophagosome formation and substrate recognition, respectively. Autophagic flux assays using the autophagy inhibitor chloroquine (CQ) revealed that MeHg treatment activates autophagy in MerB-expressing cells but not in wild-type cells. Additionally, MeHg treatment induces the accumulation of ubiquitinated proteins and p62, specifically in MerB-expressing cells. Confocal microscopy revealed that large ubiquitinated protein aggregates (aggresomes) associated with p62 are formed transiently in the perinuclear region of MerB-expressing cells upon MeHg exposure. Meanwhile, inhibition of autophagic flux decreases the MeHg-induced cell viability of MerB-expressing cells. Overall, our results imply that cells regulate aggresome formation and autophagy activation by activating LC3B and p62 to prevent cytotoxicity caused by iHg. These findings provide insights into the role of autophagy against iHg-mediated toxicity.
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Affiliation(s)
- Yasukazu Takanezawa
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Kouhei Ishikawa
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Shunsuke Nakayama
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Ryosuke Nakamura
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Yuka Ohshiro
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Shimpei Uraguchi
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Masako Kiyono
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
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16
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Marquardt L, Montino M, Mühe Y, Schlotterhose P, Thumm M. Topology and Function of the S. cerevisiae Autophagy Protein Atg15. Cells 2023; 12:2056. [PMID: 37626866 PMCID: PMC10453639 DOI: 10.3390/cells12162056] [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: 07/11/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
The putative phospholipase Atg15 is required for the intravacuolar lysis of autophagic bodies and MVB vesicles. Intracellular membrane lysis is a highly sophisticated mechanism that is not fully understood. The amino-terminal transmembrane domain of Atg15 contains the sorting signal for entry into the MVB pathway. By replacing this domain, we generated chimeras located in the cytosol, the vacuole membrane, and the lumen. The variants at the vacuole membrane and in the lumen were highly active. Together with the absence of Atg15 from the phagophore and autophagic bodies, this suggests that, within the vacuole, Atg15 can lyse vesicles where it is not embedded. In-depth topological analyses showed that Atg15 is a single membrane-spanning protein with the amino-terminus in the cytosol and the rest, including the active site motif, in the ER lumen. Remarkably, only membrane-embedded Atg15 variants affected growth when overexpressed. The growth defects depended on its active site serine 332, showing that it was linked to the enzymatic activity of Atg15. Interestingly, the growth defects were independent of vacuolar proteinase A and vacuolar acidification.
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Affiliation(s)
| | | | | | | | - Michael Thumm
- Institute of Cellular Biochemistry, University Medicine, Humboldtallee 23, D-37073 Goettingen, Germany
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17
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Kim MJ, O'Connor MB. Expression of Drosophila VDRC GD RNAi lines in larval skeletal muscle often leads to abnormal proteostasis. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000904. [PMID: 37602283 PMCID: PMC10436074 DOI: 10.17912/micropub.biology.000904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/31/2023] [Accepted: 07/31/2023] [Indexed: 08/22/2023]
Abstract
In Drosophila , multiple transgenic RNAi libraries have been generated to facilitate large-scale genetic screens in vivo . Although those libraries have helped generate many new discoveries, certain libraries are associated with technical drawbacks requiring caution in interpreting the results. Here, we report an unexpected effect of VDRC GD lines on proteostasis. When expressed in the larval skeletal muscle, 17 out of 20 GD lines induced protein aggregates enriched around the myonuclei while VDRC KK or TRiP counterparts had no effect. By contrast, the same GD lines failed to induce protein aggregates when expressed in the epidermal cells. Because the GD lines tested in this study target diverse classes of molecules and since the KK or TRiP counterparts exhibited no effect, we conclude that VDRC GD lines, for unknown reasons, tend to interfere with proteostasis in a tissue-specific and target-independent manner.
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Affiliation(s)
- Myung-Jun Kim
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Michael B. O'Connor
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
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18
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Arnold ML, Cooper J, Androwski R, Ardeshna S, Melentijevic I, Smart J, Guasp RJ, Nguyen KCQ, Bai G, Hall DH, Grant BD, Driscoll M. Intermediate filaments associate with aggresome-like structures in proteostressed C. elegans neurons and influence large vesicle extrusions as exophers. Nat Commun 2023; 14:4450. [PMID: 37488107 PMCID: PMC10366101 DOI: 10.1038/s41467-023-39700-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/19/2023] [Indexed: 07/26/2023] Open
Abstract
Toxic protein aggregates can spread among neurons to promote human neurodegenerative disease pathology. We found that in C. elegans touch neurons intermediate filament proteins IFD-1 and IFD-2 associate with aggresome-like organelles and are required cell-autonomously for efficient production of neuronal exophers, giant vesicles that can carry aggregates away from the neuron of origin. The C. elegans aggresome-like organelles we identified are juxtanuclear, HttPolyQ aggregate-enriched, and dependent upon orthologs of mammalian aggresome adaptor proteins, dynein motors, and microtubule integrity for localized aggregate collection. These key hallmarks indicate that conserved mechanisms drive aggresome formation. Furthermore, we found that human neurofilament light chain (NFL) can substitute for C. elegans IFD-2 in promoting exopher extrusion. Taken together, our results suggest a conserved influence of intermediate filament association with aggresomes and neuronal extrusions that eject potentially toxic material. Our findings expand understanding of neuronal proteostasis and suggest implications for neurodegenerative disease progression.
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Affiliation(s)
- Meghan Lee Arnold
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08855, USA
| | - Jason Cooper
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08855, USA
| | - Rebecca Androwski
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08855, USA
| | - Sohil Ardeshna
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08855, USA
| | - Ilija Melentijevic
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08855, USA
| | - Joelle Smart
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08855, USA
| | - Ryan J Guasp
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08855, USA
| | - Ken C Q Nguyen
- Department of Neuroscience, Albert Einstein College of Medicine, Rose F. Kennedy Center, Bronx, NY, 10461, USA
| | - Ge Bai
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08855, USA
| | - David H Hall
- Department of Neuroscience, Albert Einstein College of Medicine, Rose F. Kennedy Center, Bronx, NY, 10461, USA
| | - Barth D Grant
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08855, USA.
| | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08855, USA.
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19
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Halder R, Nissley DA, Sitarik I, Jiang Y, Rao Y, Vu QV, Li MS, Pritchard J, O'Brien EP. How soluble misfolded proteins bypass chaperones at the molecular level. Nat Commun 2023; 14:3689. [PMID: 37344452 DOI: 10.1038/s41467-023-38962-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2023] [Indexed: 06/23/2023] Open
Abstract
Subpopulations of soluble, misfolded proteins can bypass chaperones within cells. The extent of this phenomenon and how it happens at the molecular level are unknown. Through a meta-analysis of the experimental literature we find that in all quantitative protein refolding studies there is always a subpopulation of soluble but misfolded protein that does not fold in the presence of one or more chaperones, and can take days or longer to do so. Thus, some misfolded subpopulations commonly bypass chaperones. Using multi-scale simulation models we observe that the misfolded structures that bypass various chaperones can do so because their structures are highly native like, leading to a situation where chaperones do not distinguish between the folded and near-native-misfolded states. More broadly, these results provide a mechanism by which long-time scale changes in protein structure and function can persist in cells because some misfolded states can bypass components of the proteostasis machinery.
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Affiliation(s)
- Ritaban Halder
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Daniel A Nissley
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yiyun Rao
- Molecular, Cellular and Integrative Biosciences Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Quyen V Vu
- Institute of Physics, Polish Academy of Sciences; Al. Lotnikow 32/46, 02-668, Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences; Al. Lotnikow 32/46, 02-668, Warsaw, Poland
- Institute for Computational Sciences and Technology; Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Justin Pritchard
- Department of Biomedical Engineering, Pennsylvania State University, State College, PA, 16802, USA
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, 16802, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA.
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
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20
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Goralski T, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse D, Henderson MX. Spatial transcriptomics reveals molecular dysfunction associated with Lewy pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541144. [PMID: 37292685 PMCID: PMC10245657 DOI: 10.1101/2023.05.17.541144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lewy pathology composed of α-synuclein is the key pathological hallmark of Parkinson's disease (PD), found both in dopaminergic neurons that control motor function, and throughout cortical regions that control cognitive function. Recent work has investigated which dopaminergic neurons are most susceptible to death, but little is known about which neurons are vulnerable to developing Lewy pathology and what molecular changes an aggregate induces. In the current study, we use spatial transcriptomics to selectively capture whole transcriptome signatures from cortical neurons with Lewy pathology compared to those without pathology in the same brains. We find, both in PD and in a mouse model of PD, that there are specific classes of excitatory neurons that are vulnerable to developing Lewy pathology in the cortex. Further, we identify conserved gene expression changes in aggregate-bearing neurons that we designate the Lewy-associated molecular dysfunction from aggregates (LAMDA) signature. This gene signature indicates that neurons with aggregates downregulate synaptic, mitochondrial, ubiquitin-proteasome, endo-lysosomal, and cytoskeletal genes and upregulate DNA repair and complement/cytokine genes. However, beyond DNA repair gene upregulation, we find that neurons also activate apoptotic pathways, suggesting that if DNA repair fails, neurons undergo programmed cell death. Our results identify neurons vulnerable to Lewy pathology in the PD cortex and identify a conserved signature of molecular dysfunction in both mice and humans.
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Affiliation(s)
- Thomas Goralski
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Lindsay Meyerdirk
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Libby Breton
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Laura Brasseur
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
| | - Kevin Kurgat
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Daniella DeWeerd
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | | | | | | | | | - Michael X. Henderson
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
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21
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Jolly RD, Perrott MR, Alley MR, Hunter SA, Pas A, Beard H, Hemsley KM, Greaves G. A lower motor neuron disease in takahē ( Porphyrio hochstetteri) is an endoplasmic reticulum storage disease. N Z Vet J 2023:1-8. [PMID: 36938644 DOI: 10.1080/00480169.2023.2190549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
AIMS To investigate the pathogenesis of a disease in takahē with intracytoplasmic inclusion bodies in lower motor neurons. METHODS Four cases aged between 5 and 12 years, from three different wildlife sanctuaries in New Zealand were examined. Of these, only one had signs of spinal dysfunction in the form of paresis. Stained paraffin sections of tissues were examined by light microscopy and immunostained sections of the ventral horn of the spinal cord by confocal microscopy. Epoxy resin sections of the bird with spinal dysfunction were examined by electron microscopy. RESULTS Two types of inclusion bodies were noted, but only in motor neurons of the ventral spinal cord and brain stem. These were large globoid eosinophilic bodies up to 5 µm in diameter, and yellow/brown granular inclusions mostly at the pole of the cell. The globoid bodies stained with Luxol fast blue but not with periodic acid Schiff (PAS), or Sudan black. The granular inclusions stained with Luxol fast blue, PAS and Sudan black. Both bodies were slightly autofluorescent. On electron microscopy the globoid bodies had an even electron-dense texture and were bound by a membrane. Beneath the membrane were large numbers of small intraluminal vesicles. The smaller granular bodies were more heterogeneous, irregularly rounded and membrane-bound accumulations of granular electron-dense material, often with electron-lucent vacuoles. Others were more vesicular but contained varying amounts of electron-dense material. The large globoid bodies did not immunostain for lysosomal markers lysosomal associated protein 1 (LAMP1) or cathepsin D so they were not lysosomal. The small granular bodies stained for cathepsin D by a chromogenic method. A kindred matrix analysis showed two cases to be as closely related as first cousins, and another case was almost as closely related to one of them, but the fourth bird was unrelated to any other. CONCLUSIONS It was concluded that this was an endoplasmic reticulum storage disease due to a specific protein misfolding within endoplasmic reticulum. It was rationalised that the two types of inclusions reflected the same aetiology, but that misfolded protein in the smaller granular bodies had entered the lysosomal system via endoplasmic reticulum autophagy. Although the cause was unclear, it most likely had a genetic aetiology or predisposition and, as such, has clinical relevance.
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Affiliation(s)
- R D Jolly
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - M R Perrott
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - M R Alley
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - S A Hunter
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - A Pas
- New Zealand Centre for Conservation Medicine, Auckland Zoo, Auckland, New Zealand
| | - H Beard
- Childhood Dementia Research Group, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - K M Hemsley
- Childhood Dementia Research Group, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - G Greaves
- Department of Conservation, Wellington, New Zealand
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22
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Tseng CS, Chao YW, Liu YH, Huang YS, Chao HW. Dysregulated proteostasis network in neuronal diseases. Front Cell Dev Biol 2023; 11:1075215. [PMID: 36910151 PMCID: PMC9998692 DOI: 10.3389/fcell.2023.1075215] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
Long-term maintenance of synaptic connections is important for brain function, which depends on varying proteostatic regulations to govern the functional integrity of neuronal proteomes. Proteostasis supports an interconnection of pathways that regulates the fate of proteins from synthesis to degradation. Defects in proteostatic signaling are associated with age-related functional decline and neurodegenerative diseases. Recent studies have advanced our knowledge of how cells have evolved distinct mechanisms to safely control protein homeostasis during synthesis, folding and degradation, and in different subcellular organelles and compartments. Neurodegeneration occurs when these protein quality controls are compromised by accumulated pathogenic proteins or aging to an irreversible state. Consequently, several therapeutic strategies, such as targeting the unfolded protein response and autophagy pathways, have been developed to reduce the burden of misfolded proteins and proved useful in animal models. Here, we present a brief overview of the molecular mechanisms involved in maintaining proteostatic networks, along with some examples linking dysregulated proteostasis to neuronal diseases.
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Affiliation(s)
- Ching-San Tseng
- Department of Anatomy, School of Medicine, China Medical University, Taichung, Taiwan
| | - Yu-Wen Chao
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Hsiang Liu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsu-Wen Chao
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
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23
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Liao W, Nielsen ME, Pedersen C, Xie W, Thordal-Christensen H. Barley endosomal MONENSIN SENSITIVITY1 is a target of the powdery mildew effector CSEP0162 and plays a role in plant immunity. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:118-129. [PMID: 36227010 PMCID: PMC9786837 DOI: 10.1093/jxb/erac403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Encasements formed around haustoria and biotrophic hyphae as well as hypersensitive reaction (HR) cell death are essential plant immune responses to filamentous pathogens. In this study we examine the components that may contribute to the absence of these responses in susceptible barley attacked by the powdery mildew fungus. We find that the effector CSEP0162 from this pathogen targets plant MONENSIN SENSITIVITY1 (MON1), which is important for the fusion of multivesicular bodies to their target membranes. Overexpression of CSEP0162 and silencing of barley MON1 both inhibit encasement formation. We find that the Arabidopsis ecotype No-0 has resistance to powdery mildew, and that this is partially dependent on MON1. Surprisingly, we find the MON1-dependent resistance in No-0 not only includes an encasement response, but also an effective HR. Similarly, silencing of MON1 in barley also blocks Mla3-mediated HR-based powdery mildew resistance. Our results indicate that MON1 is a vital plant immunity component, and we speculate that the barley powdery mildew fungus introduces the effector CSEP0162 to target MON1 and hence reduce encasement formation and HR.
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Affiliation(s)
- Wenlin Liao
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Mads E Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Carsten Pedersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Wenjun Xie
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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24
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Ci Y, Yao B, Yue K, Yang Y, Xu C, Li DF, Qin CF, Shi L. Bortezomib inhibits ZIKV/DENV by interfering with viral polyprotein cleavage via the ERAD pathway. Cell Chem Biol 2022; 30:527-539.e5. [DOI: 10.1016/j.chembiol.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 09/08/2022] [Accepted: 09/30/2022] [Indexed: 11/09/2022]
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25
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Bouzón-Arnáiz I, Avalos-Padilla Y, Biosca A, Caño-Prades O, Román-Álamo L, Valle J, Andreu D, Moita D, Prudêncio M, Arce EM, Muñoz-Torrero D, Fernàndez-Busquets X. The protein aggregation inhibitor YAT2150 has potent antimalarial activity in Plasmodium falciparum in vitro cultures. BMC Biol 2022; 20:197. [PMID: 36271358 PMCID: PMC9587658 DOI: 10.1186/s12915-022-01374-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 07/12/2022] [Indexed: 11/25/2022] Open
Abstract
Background By 2016, signs of emergence of Plasmodium falciparum resistance to artemisinin and partner drugs were detected in the Greater Mekong Subregion. Recently, the independent evolution of artemisinin resistance has also been reported in Africa and South America. This alarming scenario calls for the urgent development of new antimalarials with novel modes of action. We investigated the interference with protein aggregation, which is potentially toxic for the cell and occurs abundantly in all Plasmodium stages, as a hitherto unexplored drug target in the pathogen. Results Attempts to exacerbate the P. falciparum proteome’s propensity to aggregation by delivering endogenous aggregative peptides to in vitro cultures of this parasite did not significantly affect their growth. In contrast, protein aggregation inhibitors clearly reduced the pathogen’s viability. One such compound, the bis(styrylpyridinium) salt YAT2150, exhibited potent antiplasmodial activity with an in vitro IC50 of 90 nM for chloroquine- and artemisinin-resistant lines, arresting asexual blood parasites at the trophozoite stage, as well as interfering with the development of both sexual and hepatic forms of Plasmodium. At its IC50, this compound is a powerful inhibitor of the aggregation of the model amyloid β peptide fragment 1-40, and it reduces the amount of aggregated proteins in P. falciparum cultures, suggesting that the underlying antimalarial mechanism consists in a generalized impairment of proteostasis in the pathogen. YAT2150 has an easy, rapid, and inexpensive synthesis, and because it fluoresces when it accumulates in its main localization in the Plasmodium cytosol, it is a theranostic agent. Conclusions Inhibiting protein aggregation in Plasmodium significantly reduces the parasite’s viability in vitro. Since YAT2150 belongs to a novel structural class of antiplasmodials with a mode of action that potentially targets multiple gene products, rapid evolution of resistance to this drug is unlikely to occur, making it a promising compound for the post-artemisinin era. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01374-4.
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Affiliation(s)
- Inés Bouzón-Arnáiz
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-University of Barcelona), Rosselló 149-153, 08036, Barcelona, Spain.,Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| | - Yunuen Avalos-Padilla
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-University of Barcelona), Rosselló 149-153, 08036, Barcelona, Spain.,Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| | - Arnau Biosca
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-University of Barcelona), Rosselló 149-153, 08036, Barcelona, Spain.,Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| | - Omar Caño-Prades
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-University of Barcelona), Rosselló 149-153, 08036, Barcelona, Spain.,Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| | - Lucía Román-Álamo
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-University of Barcelona), Rosselló 149-153, 08036, Barcelona, Spain.,Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| | - Javier Valle
- Department of Medicine and Life Sciences, Barcelona Biomedical Research Park, Pompeu Fabra University, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - David Andreu
- Department of Medicine and Life Sciences, Barcelona Biomedical Research Park, Pompeu Fabra University, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Diana Moita
- Instituto de Medicina Molecular, Fac. Medicina Univ. Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Miguel Prudêncio
- Instituto de Medicina Molecular, Fac. Medicina Univ. Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Elsa M Arce
- Laboratory of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, 08028, Barcelona, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, 08028, Barcelona, Spain
| | - Xavier Fernàndez-Busquets
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-University of Barcelona), Rosselló 149-153, 08036, Barcelona, Spain. .,Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain. .,Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain.
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26
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Morrow CS, Arndt ZP, Klosa PC, Peng B, Zewdie EY, Benayoun BA, Moore DL. Adult fibroblasts use aggresomes only in distinct cell-states. Sci Rep 2022; 12:15001. [PMID: 36056070 PMCID: PMC9440096 DOI: 10.1038/s41598-022-19055-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
The aggresome is a protein turnover system in which proteins are trafficked along microtubules to the centrosome for degradation. Despite extensive focus on aggresomes in immortalized cell lines, it remains unclear if the aggresome is conserved in all primary cells and all cell-states. Here we examined the aggresome in primary adult mouse dermal fibroblasts shifted into four distinct cell-states. We found that in response to proteasome inhibition, quiescent and immortalized fibroblasts formed aggresomes, whereas proliferating and senescent fibroblasts did not. Using this model, we generated a resource to provide a characterization of the proteostasis networks in which the aggresome is used and transcriptomic features associated with the presence or absence of aggresome formation. Using this resource, we validate a previously reported role for p38 MAPK signaling in aggresome formation and identify TAK1 as a novel driver of aggresome formation upstream of p38 MAPKs. Together, our data demonstrate that the aggresome is a non-universal protein degradation system which can be used cell-state specifically and provide a resource for studying aggresome formation and function.
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Affiliation(s)
| | - Zachary P Arndt
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Payton C Klosa
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Bo Peng
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Eden Y Zewdie
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Darcie L Moore
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA.
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27
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Höllerhage M, Klietz M, Höglinger GU. Disease modification in Parkinsonism: obstacles and ways forward. J Neural Transm (Vienna) 2022; 129:1133-1153. [PMID: 35695938 PMCID: PMC9463344 DOI: 10.1007/s00702-022-02520-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/21/2022] [Indexed: 12/19/2022]
Abstract
To date, the diagnoses of Parkinson syndromes are based on clinical examination. Therefore, these specific diagnoses are made, when the neuropathological process is already advanced. However, disease modification or neuroprotection, is considered to be most effective before marked neurodegeneration has occurred. In recent years, early clinical or prodromal stages of Parkinson syndromes came into focus. Moreover, subtypes of distinct diseases will allow predictions of the individual course of the diseases more precisely. Thereby, patients will be enrolled into clinical trials with more specific disease entities and endpoints. Furthermore, novel fluid and imaging biomarkers that allow biochemical diagnoses are under development. These will lead to earlier diagnoses and earlier therapy in the future as consequence. Furthermore, therapeutic approaches will take the underlying neuropathological process of neurodegenerative Parkinson syndromes more specific into account. Specifically, future therapies will target the aggregation of aggregation-prone proteins such as alpha-synuclein and tau, the degradation of pathological aggregates, and the spreading of pathological protein aggregates throughout the brain. Many of these approaches are already in (pre)clinical development. In addition, anti-inflammatory approaches are in development. Furthermore, drug-repurposing is a feasible approach to shorten the developmental process of new drugs.
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Affiliation(s)
- M Höllerhage
- Department of Neurology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - M Klietz
- Department of Neurology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - G U Höglinger
- Department of Neurology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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28
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Prakash P, Pradhan AK, Sheeba V. Hsp40 overexpression in pacemaker neurons delays circadian dysfunction in a Drosophila model of Huntington's disease. Dis Model Mech 2022; 15:275556. [PMID: 35645202 PMCID: PMC9254228 DOI: 10.1242/dmm.049447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 05/24/2022] [Indexed: 12/13/2022] Open
Abstract
Circadian disturbances are early features of neurodegenerative diseases, including Huntington's disease (HD). Emerging evidence suggests that circadian decline feeds into neurodegenerative symptoms, exacerbating them. Therefore, we asked whether known neurotoxic modifiers can suppress circadian dysfunction. We performed a screen of neurotoxicity-modifier genes to suppress circadian behavioural arrhythmicity in a Drosophila circadian HD model. The molecular chaperones Hsp40 and HSP70 emerged as significant suppressors in the circadian context, with Hsp40 being the more potent mitigator. Upon Hsp40 overexpression in the Drosophila circadian ventrolateral neurons (LNv), the behavioural rescue was associated with neuronal rescue of loss of circadian proteins from small LNv soma. Specifically, there was a restoration of the molecular clock protein Period and its oscillations in young flies and a long-lasting rescue of the output neuropeptide Pigment dispersing factor. Significantly, there was a reduction in the expanded Huntingtin inclusion load, concomitant with the appearance of a spot-like Huntingtin form. Thus, we provide evidence implicating the neuroprotective chaperone Hsp40 in circadian rehabilitation. The involvement of molecular chaperones in circadian maintenance has broader therapeutic implications for neurodegenerative diseases. This article has an associated First Person interview with the first author of the paper. Summary: This study shows, for the first time, a neuroprotective role of chaperone Hsp40 in suppressing circadian dysfunction associated with Huntington's disease in a Drosophila model.
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Affiliation(s)
- Pavitra Prakash
- Evolutionary and Integrative Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Arpit Kumar Pradhan
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Vasu Sheeba
- Evolutionary and Integrative Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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Perazza LR, Brown-Borg HM, Thompson LV. Physiological Systems in Promoting Frailty. Compr Physiol 2022; 12:3575-3620. [PMID: 35578945 DOI: 10.1002/cphy.c210034] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Frailty is a complex syndrome affecting a growing sector of the global population as medical developments have advanced human mortality rates across the world. Our current understanding of frailty is derived from studies conducted in the laboratory as well as the clinic, which have generated largely phenotypic information. Far fewer studies have uncovered biological underpinnings driving the onset and progression of frailty, but the stage is set to advance the field with preclinical and clinical assessment tools, multiomics approaches together with physiological and biochemical methodologies. In this article, we provide comprehensive coverage of topics regarding frailty assessment, preclinical models, interventions, and challenges as well as clinical frameworks and prevalence. We also identify central biological mechanisms that may be at play including mitochondrial dysfunction, epigenetic alterations, and oxidative stress that in turn, affect metabolism, stress responses, and endocrine and neuromuscular systems. We review the role of metabolic syndrome, insulin resistance and visceral obesity, focusing on glucose homeostasis, adenosine monophosphate-activated protein kinase (AMPK), mammalian target of rapamycin (mTOR), and nicotinamide adenine dinucleotide (NAD+ ) as critical players influencing the age-related loss of health. We further focus on how immunometabolic dysfunction associates with oxidative stress in promoting sarcopenia, a key contributor to slowness, weakness, and fatigue. We explore the biological mechanisms involved in stem cell exhaustion that affect regeneration and may contribute to the frailty-associated decline in resilience and adaptation to stress. Together, an overview of the interplay of aging biology with genetic, lifestyle, and environmental factors that contribute to frailty, as well as potential therapeutic targets to lower risk and slow the progression of ongoing disease is covered. © 2022 American Physiological Society. Compr Physiol 12:1-46, 2022.
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Affiliation(s)
- Laís R Perazza
- Department of Physical Therapy and Athletic Training, Boston University, Boston, Massachusetts, USA
| | - Holly M Brown-Borg
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, North Dakota, USA
| | - LaDora V Thompson
- Department of Physical Therapy and Athletic Training, Boston University, Boston, Massachusetts, USA
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Esfandiary A, Finkelstein DI, Voelcker NH, Rudd D. Clinical Sphingolipids Pathway in Parkinson’s Disease: From GCase to Integrated-Biomarker Discovery. Cells 2022; 11:cells11081353. [PMID: 35456032 PMCID: PMC9028315 DOI: 10.3390/cells11081353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 02/01/2023] Open
Abstract
Alterations in the sphingolipid metabolism of Parkinson’s Disease (PD) could be a potential diagnostic feature. Only around 10–15% of PD cases can be diagnosed through genetic alterations, while the remaining population, idiopathic PD (iPD), manifest without validated and specific biomarkers either before or after motor symptoms appear. Therefore, clinical diagnosis is reliant on the skills of the clinician, which can lead to misdiagnosis. IPD cases present with a spectrum of non-specific symptoms (e.g., constipation and loss of the sense of smell) that can occur up to 20 years before motor function loss (prodromal stage) and formal clinical diagnosis. Prodromal alterations in metabolites and proteins from the pathways underlying these symptoms could act as biomarkers if they could be differentiated from the broad values seen in a healthy age-matched control population. Additionally, these shifts in metabolites could be integrated with other emerging biomarkers/diagnostic tests to give a PD-specific signature. Here we provide an up-to-date review of the diagnostic value of the alterations in sphingolipids pathway in PD by focusing on the changes in definitive PD (postmortem confirmed brain data) and their representation in “probable PD” cerebrospinal fluid (CSF) and blood. We conclude that the trend of holistic changes in the sphingolipid pathway in the PD brain seems partly consistent in CSF and blood, and could be one of the most promising pathways in differentiating PD cases from healthy controls, with the potential to improve early-stage iPD diagnosis and distinguish iPD from other Parkinsonism when combined with other pathological markers.
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Affiliation(s)
- Ali Esfandiary
- Drug Delivery, Disposition and Dynamics, Monash University, Parkville, VIC 3052, Australia; (A.E.); (N.H.V.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
| | | | - Nicolas Hans Voelcker
- Drug Delivery, Disposition and Dynamics, Monash University, Parkville, VIC 3052, Australia; (A.E.); (N.H.V.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Clayton, VIC 3168, Australia
- Materials Science and Engineering, Monash University, Clayton, VIC 3168, Australia
| | - David Rudd
- Drug Delivery, Disposition and Dynamics, Monash University, Parkville, VIC 3052, Australia; (A.E.); (N.H.V.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
- Correspondence: ; Tel.: +61-3-9903-9581
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Aggresome assembly at the centrosome is driven by CP110–CEP97–CEP290 and centriolar satellites. Nat Cell Biol 2022; 24:483-496. [PMID: 35411088 PMCID: PMC9033585 DOI: 10.1038/s41556-022-00869-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/10/2022] [Indexed: 12/30/2022]
Abstract
Protein degradation is critical to maintaining cellular homeostasis, and perturbation of the ubiquitin proteasome system leads to the accumulation of protein aggregates. These aggregates are either directed towards autophagy for destruction or sequestered into an inclusion, termed the aggresome, at the centrosome. Utilizing high-resolution quantitative analysis, here, we define aggresome assembly at the centrosome in human cells. Centriolar satellites are proteinaceous granules implicated in the trafficking of proteins to the centrosome. During aggresome assembly, satellites were required for the growth of the aggresomal structure from an initial ring of phosphorylated HSP27 deposited around the centrioles. The seeding of this phosphorylated HSP27 ring depended on the centrosomal proteins CP110, CEP97 and CEP290. Owing to limiting amounts of CP110, senescent cells, which are characterized by the accumulation of protein aggregates, were defective in aggresome formation. Furthermore, satellites and CP110–CEP97–CEP290 were required for the aggregation of mutant huntingtin. Together, these data reveal roles for CP110–CEP97–CEP290 and satellites in the control of cellular proteostasis and the aggregation of disease-relevant proteins. Prosser et al. report that centriolar satellite and centrosomal proteins seed aggresomes, perinuclear inclusions of misfolded proteins, and may play a role in aggresome formation during senescence and huntingtin aggregation.
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Vitiello E, Gergely F. Centrosomes grow aggresomes to clear waste. Nat Cell Biol 2022; 24:408-410. [PMID: 35411087 DOI: 10.1038/s41556-022-00891-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Elisa Vitiello
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Fanni Gergely
- Department of Biochemistry, University of Oxford, Oxford, UK.
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Abstract
Ageing, death, and potential immortality lie at the heart of biology, but two seemingly incompatible paradigms coexist in different research communities and have done since the nineteenth century. The universal senescence paradigm sees senescence as inevitable in all cells. Damage accumulates. The potential immortality paradigm sees some cells as potentially immortal, especially unicellular organisms, germ cells and cancerous cells. Recent research with animal cells, yeasts and bacteria show that damaged cell constituents do in fact build up, but can be diluted by growth and cell division, especially by asymmetric cell division. By contrast, mammalian embryonic stem cells and many cancerous and 'immortalized' cell lines divide symmetrically, and yet replicate indefinitely. How do they acquire their potential immortality? I suggest they are rejuvenated by excreting damaged cell constituents in extracellular vesicles. If so, our understanding of cellular senescence, rejuvenation and potential immortality could be brought together in a new synthesis, which I call the cellular rejuvenation hypothesis: damaged cell constituents build up in all cells, but cells can be rejuvenated either by growth and cell division or, in 'immortal' cell lines, by excreting damaged cell constituents. In electronic supplementary material, appendix, I outline nine ways in which this hypothesis could be tested.
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Ferrari V, Cristofani R, Tedesco B, Crippa V, Chierichetti M, Casarotto E, Cozzi M, Mina F, Piccolella M, Galbiati M, Rusmini P, Poletti A. Valosin Containing Protein (VCP): A Multistep Regulator of Autophagy. Int J Mol Sci 2022; 23:1939. [PMID: 35216053 PMCID: PMC8878954 DOI: 10.3390/ijms23041939] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/03/2022] [Accepted: 02/06/2022] [Indexed: 02/04/2023] Open
Abstract
Valosin containing protein (VCP) has emerged as a central protein in the regulation of the protein quality control (PQC) system. VCP mutations are causative of multisystem proteinopathies, which include neurodegenerative diseases (NDs), and share various signs of altered proteostasis, mainly associated with autophagy malfunctioning. Autophagy is a complex multistep degradative system essential for the maintenance of cell viability, especially in post-mitotic cells as neurons and differentiated skeletal muscle cells. Interestingly, many studies concerning NDs have focused on autophagy impairment as a pathological mechanism or autophagy activity boosting to rescue the pathological phenotype. The role of VCP in autophagy has been widely debated, but recent findings have defined new mechanisms associated with VCP activity in the regulation of autophagy, showing that VCP is involved in different steps of this pathway. Here we will discuss the multiple activity of VCP in the autophagic pathway underlying its leading role either in physiological or pathological conditions. A better understanding of VCP complexes and mechanisms in regulating autophagy could define the altered mechanisms by which VCP directly or indirectly causes or modulates different human diseases and revealing possible new therapeutic approaches for NDs.
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Affiliation(s)
- Veronica Ferrari
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy; (V.F.); (R.C.); (V.C.); (M.C.); (E.C.); (M.C.); (F.M.); (M.P.); (M.G.); (P.R.)
| | - Riccardo Cristofani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy; (V.F.); (R.C.); (V.C.); (M.C.); (E.C.); (M.C.); (F.M.); (M.P.); (M.G.); (P.R.)
| | - Barbara Tedesco
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS—Istituto Neurologico Carlo Besta, Via Celoria 11, 20133 Milan, Italy;
| | - Valeria Crippa
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy; (V.F.); (R.C.); (V.C.); (M.C.); (E.C.); (M.C.); (F.M.); (M.P.); (M.G.); (P.R.)
| | - Marta Chierichetti
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy; (V.F.); (R.C.); (V.C.); (M.C.); (E.C.); (M.C.); (F.M.); (M.P.); (M.G.); (P.R.)
| | - Elena Casarotto
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy; (V.F.); (R.C.); (V.C.); (M.C.); (E.C.); (M.C.); (F.M.); (M.P.); (M.G.); (P.R.)
| | - Marta Cozzi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy; (V.F.); (R.C.); (V.C.); (M.C.); (E.C.); (M.C.); (F.M.); (M.P.); (M.G.); (P.R.)
| | - Francesco Mina
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy; (V.F.); (R.C.); (V.C.); (M.C.); (E.C.); (M.C.); (F.M.); (M.P.); (M.G.); (P.R.)
| | - Margherita Piccolella
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy; (V.F.); (R.C.); (V.C.); (M.C.); (E.C.); (M.C.); (F.M.); (M.P.); (M.G.); (P.R.)
| | - Mariarita Galbiati
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy; (V.F.); (R.C.); (V.C.); (M.C.); (E.C.); (M.C.); (F.M.); (M.P.); (M.G.); (P.R.)
| | - Paola Rusmini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy; (V.F.); (R.C.); (V.C.); (M.C.); (E.C.); (M.C.); (F.M.); (M.P.); (M.G.); (P.R.)
| | - Angelo Poletti
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy; (V.F.); (R.C.); (V.C.); (M.C.); (E.C.); (M.C.); (F.M.); (M.P.); (M.G.); (P.R.)
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Arghavani P, Pirhaghi M, Moosavi-Movahedi F, Mamashli F, Hosseini E, Moosavi-Movahedi AA. Amyloid management by chaperones: The mystery underlying protein oligomers’ dual functions. Curr Res Struct Biol 2022; 4:356-364. [DOI: 10.1016/j.crstbi.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
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Batnasan E, Koivukoski S, Kärkkäinen M, Latonen L. Nuclear Organization in Response to Stress: A Special Focus on Nucleoli. Results Probl Cell Differ 2022; 70:469-494. [PMID: 36348119 DOI: 10.1007/978-3-031-06573-6_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In this chapter, we discuss the nuclear organization and how it responds to different types of stress. A key component in these responses is molecular traffic between the different sub-nucleolar compartments, such as nucleoplasm, chromatin, nucleoli, and various speckle and body compartments. This allows specific repair and response activities in locations where they normally are not active and serve to halt sensitive functions until the stress insult passes and inflicted damage has been repaired. We focus on mammalian cells and their nuclear organization, especially describing the central role of the nucleolus in nuclear stress responses. We describe events after multiple stress types, including DNA damage, various drugs, and toxic compounds, and discuss the involvement of macromolecular traffic between dynamic, phase-separated nuclear organelles and foci. We delineate the key proteins and non-coding RNA in the formation of stress-responsive, non-membranous nuclear organelles, many of which are relevant to the formation of and utilization in cancer treatment.
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Affiliation(s)
- Enkhzaya Batnasan
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Sonja Koivukoski
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Minttu Kärkkäinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.
- Foundation for the Finnish Cancer Institute, Helsinki, Finland.
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Baldan S, Meriin AB, Yaglom J, Alexandrov I, Varelas X, Xiao ZXJ, Sherman MY. The Hsp70-Bag3 complex modulates the phosphorylation and nuclear translocation of Hippo pathway protein Yap. J Cell Sci 2021; 134:273417. [PMID: 34761265 DOI: 10.1242/jcs.259107] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/28/2021] [Indexed: 11/20/2022] Open
Abstract
Protein abnormalities can accelerate aging causing protein misfolding diseases, and various adaptive responses have evolved to relieve proteotoxicity. To trigger these responses, cells must detect the buildup of aberrant proteins. Previously we demonstrated that the Hsp70-Bag3 (HB) complex senses the accumulation of defective ribosomal products, stimulating signaling pathway proteins, such as stress kinases or the Hippo pathway kinase LATS1. Here, we studied how Bag3 regulates the ability for LATS1 to regulate its key downstream target YAP (also known as YAP1). In naïve cells, Bag3 recruited a complex of LATS1, YAP and the scaffold AmotL2, which links LATS1 and YAP. Upon inhibition of the proteasome, AmotL2 dissociated from Bag3, which prevented phosphorylation of YAP by LATS1, and led to consequent nuclear YAP localization together with Bag3. Mutations in Bag3 that enhanced its translocation into nucleus also facilitated nuclear translocation of YAP. Interestingly, Bag3 also controlled YAP nuclear localization in response to cell density, indicating broader roles beyond proteotoxic signaling responses for Bag3 in the regulation of YAP. These data implicate Bag3 as a regulator of Hippo pathway signaling, and suggest mechanisms by which proteotoxic stress signals are propagated.
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Affiliation(s)
- Simone Baldan
- Department of Molecular Biology, Ariel University, Ariel 4077625, Israel
| | - Anatoli B Meriin
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02215, USA
| | - Julia Yaglom
- Department of Molecular Biology, Ariel University, Ariel 4077625, Israel
| | | | - Xaralabos Varelas
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02215, USA
| | | | - Michael Y Sherman
- Department of Molecular Biology, Ariel University, Ariel 4077625, Israel
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Chang P, Li H, Hu H, Li Y, Wang T. The Role of HDAC6 in Autophagy and NLRP3 Inflammasome. Front Immunol 2021; 12:763831. [PMID: 34777380 PMCID: PMC8578992 DOI: 10.3389/fimmu.2021.763831] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022] Open
Abstract
Autophagy fights against harmful stimuli and degrades cytosolic macromolecules, organelles, and intracellular pathogens. Autophagy dysfunction is associated with many diseases, including infectious and inflammatory diseases. Recent studies have identified the critical role of the NACHT, LRR, and PYD domain-containing protein 3 (NLRP3) inflammasomes activation in the innate immune system, which mediates the secretion of proinflammatory cytokines IL-1β/IL-18 and cleaves Gasdermin D to induce pyroptosis in response to pathogenic and sterile stimuli. Accumulating evidence has highlighted the crosstalk between autophagy and NLRP3 inflammasome in multifaceted ways to influence host defense and inflammation. However, the underlying mechanisms require further clarification. Histone deacetylase 6 (HDAC6) is a class IIb deacetylase among the 18 mammalian HDACs, which mainly localizes in the cytoplasm. It is involved in two functional deacetylase domains and a ubiquitin-binding zinc finger domain (ZnF-BUZ). Due to its unique structure, HDAC6 regulates various physiological processes, including autophagy and NLRP3 inflammasome, and may play a role in the crosstalk between them. In this review, we provide insight into the mechanisms by which HDAC6 regulates autophagy and NLRP3 inflammasome and we explored the possibility and challenges of HDAC6 in the crosstalk between autophagy and NLRP3 inflammasome. Finally, we discuss HDAC6 inhibitors as a potential therapeutic approach targeting either autophagy or NLRP3 inflammasome as an anti-inflammatory strategy, although further clarification is required regarding their crosstalk.
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Affiliation(s)
- Panpan Chang
- Trauma Medicine Center, Peking University People's Hospital, Key Laboratory of Trauma and Neural Regeneration (Peking University), National Center for Trauma Medicine of China, Beijing, China
| | - Hao Li
- Department of Emergency, First Hospital of China Medical University, Shenyang, China
| | - Hui Hu
- Department of Traumatology, Central Hospital of Chongqing University, Chongqing Emergency Medical Center, Chongqing, China
| | - Yongqing Li
- Department of Surgery, University of Michigan, Ann Arbor, MI, United States
| | - Tianbing Wang
- Trauma Medicine Center, Peking University People's Hospital, Key Laboratory of Trauma and Neural Regeneration (Peking University), National Center for Trauma Medicine of China, Beijing, China
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Messa L, Celegato M, Bertagnin C, Mercorelli B, Alvisi G, Banks L, Palù G, Loregian A. The Dimeric Form of HPV16 E6 Is Crucial to Drive YAP/TAZ Upregulation through the Targeting of hScrib. Cancers (Basel) 2021; 13:cancers13164083. [PMID: 34439242 PMCID: PMC8393709 DOI: 10.3390/cancers13164083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 01/22/2023] Open
Abstract
Simple Summary Understanding the mechanisms of action of HPV oncoproteins is pivotal for the rationale development of anti-cancer drugs to treat HPV-related malignancies. The aim of the present study was to explore more in detail the mechanism of action of the HPV16 oncoprotein E6 that directly fosters the YAP/TAZ signaling pathway, a conserved cascade highly active in HPV-related cancers. We confirmed previous evidence about the importance of the PDZ-protein targeting in this process, highlighting here the importance of hScrib degradation, and discovered that the targeting of the Scribble module involves the dimeric form of HPV16 E6. The findings here presented extend our knowledge about the mechanism through which the oncoprotein E6 targets a PDZ-host factor to degradation in cancer cells. Abstract Human papillomavirus is the most common viral infectious agent responsible for cancer development in humans. High-risk strains are known to induce cancer through the expression of the viral oncogenes E6 and E7, yet we have only a partial understanding of the precise mechanisms of action of these viral proteins. Here we investigated the molecular mechanism through which the oncoprotein E6 alters the Hippo-YAP/TAZ pathway to trigger YAP/TAZ induction in cancer cells. By employing E6 overexpression systems combined with protein–protein interaction studies and loss-of-function approaches, we discovered that the E6-mediated targeting of hScrib, which supports YAP/TAZ upregulation, intimately requires E6 homodimerization. We show that the self-association of E6, previously reported only in vitro, takes place in the cytoplasm and, as a dimer, E6 targets the fraction of hScrib at the cell cortex for proteasomal degradation. Thus, E6 homodimerization emerges as an important event in the mechanism of E6-mediated hScrib targeting to sustain downstream YAP/TAZ upregulation, unraveling for the first time the key role of E6 homodimerization in the context of its transforming functions and thus paving the way for the possible development of E6 dimerization inhibitors.
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Affiliation(s)
- Lorenzo Messa
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (L.M.); (M.C.); (C.B.); (B.M.); (G.A.); (G.P.)
| | - Marta Celegato
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (L.M.); (M.C.); (C.B.); (B.M.); (G.A.); (G.P.)
| | - Chiara Bertagnin
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (L.M.); (M.C.); (C.B.); (B.M.); (G.A.); (G.P.)
| | - Beatrice Mercorelli
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (L.M.); (M.C.); (C.B.); (B.M.); (G.A.); (G.P.)
| | - Gualtiero Alvisi
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (L.M.); (M.C.); (C.B.); (B.M.); (G.A.); (G.P.)
| | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy;
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (L.M.); (M.C.); (C.B.); (B.M.); (G.A.); (G.P.)
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (L.M.); (M.C.); (C.B.); (B.M.); (G.A.); (G.P.)
- Correspondence: ; Tel.: +39-049-8272363
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UPF1: From mRNA Surveillance to Protein Quality Control. Biomedicines 2021; 9:biomedicines9080995. [PMID: 34440199 PMCID: PMC8392595 DOI: 10.3390/biomedicines9080995] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 12/20/2022] Open
Abstract
Selective recognition and removal of faulty transcripts and misfolded polypeptides are crucial for cell viability. In eukaryotic cells, nonsense-mediated mRNA decay (NMD) constitutes an mRNA surveillance pathway for sensing and degrading aberrant transcripts harboring premature termination codons (PTCs). NMD functions also as a post-transcriptional gene regulatory mechanism by downregulating naturally occurring mRNAs. As NMD is activated only after a ribosome reaches a PTC, PTC-containing mRNAs inevitably produce truncated and potentially misfolded polypeptides as byproducts. To cope with the emergence of misfolded polypeptides, eukaryotic cells have evolved sophisticated mechanisms such as chaperone-mediated protein refolding, rapid degradation of misfolded polypeptides through the ubiquitin–proteasome system, and sequestration of misfolded polypeptides to the aggresome for autophagy-mediated degradation. In this review, we discuss how UPF1, a key NMD factor, contributes to the selective removal of faulty transcripts via NMD at the molecular level. We then highlight recent advances on UPF1-mediated communication between mRNA surveillance and protein quality control.
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A Novel Nanobody Precisely Visualizes Phosphorylated Histone H2AX in Living Cancer Cells under Drug-Induced Replication Stress. Cancers (Basel) 2021; 13:cancers13133317. [PMID: 34282773 PMCID: PMC8267817 DOI: 10.3390/cancers13133317] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary γ-H2AX, a phosphorylated variant of histone H2A, is a widely used biomarker of DNA replication stress. To develop an immunological probe able to detect and track γ-H2AX in live cancer cells, we have isolated single domain antibodies (called nanobodies) that are easily expressed as functional recombinant proteins and here we report the extensive characterization of a novel nanobody that specifically recognizes γ-H2AX. The interaction of this nanobody with the C-terminal end of γ-H2AX was determined by X-ray crystallography. Moreover, the generation of a bivalent nanobody allowed us to precisely detect γ-H2AX foci in drug-treated cells as efficiently as with commercially available conventional antibodies. Furthermore, we tracked γ-H2AX foci in live cells upon intracellular delivery of the bivalent nanobody fused to the red fluorescent protein dTomato, making, consequently, this new cost-effective reagent useful for studying drug-induced replication stress in both fixed and living cancer cells. Abstract Histone H2AX phosphorylated at serine 139 (γ-H2AX) is a hallmark of DNA damage, signaling the presence of DNA double-strand breaks and global replication stress in mammalian cells. While γ-H2AX can be visualized with antibodies in fixed cells, its detection in living cells was so far not possible. Here, we used immune libraries and phage display to isolate nanobodies that specifically bind to γ-H2AX. We solved the crystal structure of the most soluble nanobody in complex with the phosphopeptide corresponding to the C-terminus of γ-H2AX and show the atomic constituents behind its specificity. We engineered a bivalent version of this nanobody and show that bivalency is essential to quantitatively visualize γ-H2AX in fixed drug-treated cells. After labelling with a chemical fluorophore, we were able to detect γ-H2AX in a single-step assay with the same sensitivity as with validated antibodies. Moreover, we produced fluorescent nanobody-dTomato fusion proteins and applied a transduction strategy to visualize with precision γ-H2AX foci present in intact living cells following drug treatment. Together, this novel tool allows performing fast screenings of genotoxic drugs and enables to study the dynamics of this particular chromatin modification in individual cancer cells under a variety of conditions.
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Chargui A, Belaid A, Ndiaye PD, Imbert V, Samson M, Guigonis JM, Tauc M, Peyron JF, Poujeol P, Brest P, Hofman P, Mograbi B. The Carcinogen Cadmium Activates Lysine 63 (K63)-Linked Ubiquitin-Dependent Signaling and Inhibits Selective Autophagy. Cancers (Basel) 2021; 13:2490. [PMID: 34065348 PMCID: PMC8161291 DOI: 10.3390/cancers13102490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/11/2021] [Indexed: 01/18/2023] Open
Abstract
Signaling, proliferation, and inflammation are dependent on K63-linked ubiquitination-conjugation of a chain of ubiquitin molecules linked via lysine 63. However, very little information is currently available about how K63-linked ubiquitination is subverted in cancer. The present study provides, for the first time, evidence that cadmium (Cd), a widespread environmental carcinogen, is a potent activator of K63-linked ubiquitination, independently of oxidative damage, activation of ubiquitin ligase, or proteasome impairment. We show that Cd induces the formation of protein aggregates that sequester and inactivate cylindromatosis (CYLD) and selective autophagy, two tumor suppressors that deubiquitinate and degrade K63-ubiquitinated proteins, respectively. The aggregates are constituted of substrates of selective autophagy-SQSTM1, K63-ubiquitinated proteins, and mitochondria. These protein aggregates also cluster double-membrane remnants, which suggests an impairment in autophagosome maturation. However, failure to eliminate these selective cargos is not due to alterations in the general autophagy process, as degradation of long-lived proteins occurs normally. We propose that the simultaneous disruption of CYLD and selective autophagy by Cd feeds a vicious cycle that further amplifies K63-linked ubiquitination and downstream activation of the NF-κB pathway, processes that support cancer progression. These novel findings link together impairment of selective autophagy, K63-linked ubiquitination, and carcinogenesis.
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Affiliation(s)
- Abderrahman Chargui
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
- Higher School of Agriculture of Kef, University Jendouba, Le Kef and Laboratory of Histology, Embryology and Cell Biology, Faculty of Medicine Tunis, 7110 Le Kef, Tunisia
| | - Amine Belaid
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| | - Papa Diogop Ndiaye
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| | - Véronique Imbert
- Université Côte d’Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Institut National de la Santé et de la Recherche Médicale (INSERM), F-06204 Nice, France; (V.I.); (J.-F.P.)
| | - Michel Samson
- Université Côte d’Azur, Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des sciences du vivant Fréderic Joliot, Commissariat à l’Energie Atomique et aux énergies alternatives (CEA), F-06107 Nice, France; (M.S.); (J.-M.G.)
| | - Jean-Marie Guigonis
- Université Côte d’Azur, Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des sciences du vivant Fréderic Joliot, Commissariat à l’Energie Atomique et aux énergies alternatives (CEA), F-06107 Nice, France; (M.S.); (J.-M.G.)
| | - Michel Tauc
- Université Côte d’Azur, Laboratoire de Physiomédecine Moléculaire, LP2M, Labex ICST, Centre National de la Recherche Scientifique (CNRS), F-06107 Nice, France; (M.T.); (P.P.)
| | - Jean-François Peyron
- Université Côte d’Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Institut National de la Santé et de la Recherche Médicale (INSERM), F-06204 Nice, France; (V.I.); (J.-F.P.)
| | - Philippe Poujeol
- Université Côte d’Azur, Laboratoire de Physiomédecine Moléculaire, LP2M, Labex ICST, Centre National de la Recherche Scientifique (CNRS), F-06107 Nice, France; (M.T.); (P.P.)
| | - Patrick Brest
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| | - Paul Hofman
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
- Université Côte d’Azur, Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Hospital-Integrated Biobank (BB-0033-00025), Centre Hospitalier Universitaire (CHU) de Nice, F-06001 Nice, France
| | - Baharia Mograbi
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
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Hickey CM, Breckel C, Zhang M, Theune WC, Hochstrasser M. Protein quality control degron-containing substrates are differentially targeted in the cytoplasm and nucleus by ubiquitin ligases. Genetics 2021; 217:1-19. [PMID: 33683364 PMCID: PMC8045714 DOI: 10.1093/genetics/iyaa031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022] Open
Abstract
Intracellular proteolysis by the ubiquitin-proteasome system regulates numerous processes and contributes to protein quality control (PQC) in all eukaryotes. Covalent attachment of ubiquitin to other proteins is specified by the many ubiquitin ligases (E3s) expressed in cells. Here we determine the E3s in Saccharomyces cerevisiae that function in degradation of proteins bearing various PQC degradation signals (degrons). The E3 Ubr1 can function redundantly with several E3s, including nuclear-localized San1, endoplasmic reticulum/nuclear membrane-embedded Doa10, and chromatin-associated Slx5/Slx8. Notably, multiple degrons are targeted by more ubiquitylation pathways if directed to the nucleus. Degrons initially assigned as exclusive substrates of Doa10 were targeted by Doa10, San1, and Ubr1 when directed to the nucleus. By contrast, very short hydrophobic degrons-typical targets of San1-are shown here to be targeted by Ubr1 and/or San1, but not Doa10. Thus, distinct types of PQC substrates are differentially recognized by the ubiquitin system in a compartment-specific manner. In human cells, a representative short hydrophobic degron appended to the C-terminus of GFP-reduced protein levels compared with GFP alone, consistent with a recent study that found numerous natural hydrophobic C-termini of human proteins can act as degrons. We also report results of bioinformatic analyses of potential human C-terminal degrons, which reveal that most peptide substrates of Cullin-RING ligases (CRLs) are of low hydrophobicity, consistent with previous data showing CRLs target degrons with specific sequences. These studies expand our understanding of PQC in yeast and human cells, including the distinct but overlapping PQC E3 substrate specificity of the cytoplasm and nucleus.
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Affiliation(s)
- Christopher M Hickey
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Carolyn Breckel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Mengwen Zhang
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - William C Theune
- Department of Biology and Environmental Science, University of New Haven, West Haven, CT 06516, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
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It's not just a phase; ubiquitination in cytosolic protein quality control. Biochem Soc Trans 2021; 49:365-377. [PMID: 33634825 PMCID: PMC7924994 DOI: 10.1042/bst20200694] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 02/04/2023]
Abstract
The accumulation of misfolded proteins is associated with numerous degenerative conditions, cancers and genetic diseases. These pathological imbalances in protein homeostasis (termed proteostasis), result from the improper triage and disposal of damaged and defective proteins from the cell. The ubiquitin-proteasome system is a key pathway for the molecular control of misfolded cytosolic proteins, co-opting a cascade of ubiquitin ligases to direct terminally damaged proteins to the proteasome via modification with chains of the small protein, ubiquitin. Despite the evidence for ubiquitination in this critical pathway, the precise complement of ubiquitin ligases and deubiquitinases that modulate this process remains under investigation. Whilst chaperones act as the first line of defence against protein misfolding, the ubiquitination machinery has a pivotal role in targeting terminally defunct cytosolic proteins for destruction. Recent work points to a complex assemblage of chaperones, ubiquitination machinery and subcellular quarantine as components of the cellular arsenal against proteinopathies. In this review, we examine the contribution of these pathways and cellular compartments to the maintenance of the cytosolic proteome. Here we will particularly focus on the ubiquitin code and the critical enzymes which regulate misfolded proteins in the cytosol, the molecular point of origin for many neurodegenerative and genetic diseases.
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Nuclear Ubiquitin-Proteasome Pathways in Proteostasis Maintenance. Biomolecules 2021; 11:biom11010054. [PMID: 33406777 PMCID: PMC7824755 DOI: 10.3390/biom11010054] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/19/2022] Open
Abstract
Protein homeostasis, or proteostasis, is crucial for the functioning of a cell, as proteins that are mislocalized, present in excessive amounts, or aberrant due to misfolding or other type of damage can be harmful. Proteostasis includes attaining the correct protein structure, localization, and the formation of higher order complexes, and well as the appropriate protein concentrations. Consequences of proteostasis imbalance are evident in a range of neurodegenerative diseases characterized by protein misfolding and aggregation, such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis. To protect the cell from the accumulation of aberrant proteins, a network of protein quality control (PQC) pathways identifies the substrates and direct them towards refolding or elimination via regulated protein degradation. The main pathway for degradation of misfolded proteins is the ubiquitin-proteasome system. PQC pathways have been first described in the cytoplasm and the endoplasmic reticulum, however, accumulating evidence indicates that the nucleus is an important PQC compartment for ubiquitination and proteasomal degradation of not only nuclear, but also cytoplasmic proteins. In this review, we summarize the nuclear ubiquitin-proteasome pathways involved in proteostasis maintenance in yeast, focusing on inner nuclear membrane-associated degradation (INMAD) and San1-mediated protein quality control.
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