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Cheng W, Wei B, Liu W, Jin L, Guo S, Ding M, Liu Y, Fan H, Li R, Zhang X, He X, Li X, Duan C. p97 inhibits integrated stress response-induced neuronal apoptosis after subarachnoid hemorrhage in mice by enhancing proteasome function. Exp Neurol 2024; 377:114778. [PMID: 38609045 DOI: 10.1016/j.expneurol.2024.114778] [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: 11/10/2023] [Revised: 03/19/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024]
Abstract
Neuronal apoptosis is a common pathological change in early brain injury after subarachnoid hemorrhage (SAH), and it is closely associated with neurological deficits. According to previous research, p97 exhibits a remarkable anti-cardiomyocyte apoptosis effect. p97 is a critical molecule in the growth and development of the nervous system. However, it remains unknown whether p97 can exert an anti-neuronal apoptosis effect in SAH. In the present study, we examined the role of p97 in neuronal apoptosis induced after SAH and investigated the underlying mechanism. We established an in vivo SAH mice model and overexpressed the p97 protein through transfection of the mouse cerebral cortex. We analyzed the protective effect of p97 on neurons and evaluated short-term and long-term neurobehavior in mice after SAH. p97 was found to be significantly downregulated in the cerebral cortex of the affected side in mice after SAH. The site showing reduced p97 expression also exhibited a high level of neuronal apoptosis. Adeno-associated virus-mediated overexpression of p97 significantly reduced the extent of neuronal apoptosis, improved early and long-term neurological function, and repaired the neuronal damage in the long term. These neuroprotective effects were accompanied by enhanced proteasome function and inhibition of the integrated stress response (ISR) apoptotic pathway involving eIF2α/CHOP. The administration of the p97 inhibitor NMS-873 induced a contradictory effect. Subsequently, we observed that inhibiting the function of the proteasome with the proteasome inhibitor PS-341 blocked the anti-neuronal apoptosis effect of p97 and enhanced the activation of the ISR apoptotic pathway. However, the detrimental effects of NMS-873 and PS-341 in mice with SAH were mitigated by the administration of the ISR inhibitor ISRIB. These results suggest that p97 can promote neuronal survival and improve neurological function in mice after SAH. The anti-neuronal apoptosis effect of p97 is achieved by enhancing proteasome function and inhibiting the overactivation of the ISR apoptotic pathway.
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Affiliation(s)
- Wenping Cheng
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Boyang Wei
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Wenchao Liu
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lei Jin
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shenquan Guo
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Mingxiang Ding
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yanchao Liu
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Haiyan Fan
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ran Li
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xin Zhang
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xuying He
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xifeng Li
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
| | - Chuanzhi Duan
- Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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Hao M, Lu P, Sotropa S, Manupati K, Yeo SK, Guan JL. In vivo CRISPR knockout screen identifies p47 as a suppressor of HER2+ breast cancer metastasis by regulating NEMO trafficking and autophagy flux. Cell Rep 2024; 43:113780. [PMID: 38363674 DOI: 10.1016/j.celrep.2024.113780] [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: 08/29/2023] [Revised: 12/14/2023] [Accepted: 01/26/2024] [Indexed: 02/18/2024] Open
Abstract
Autophagy is a conserved cellular process, and its dysfunction is implicated in cancer and other diseases. Here, we employ an in vivo CRISPR screen targeting genes implicated in the regulation of autophagy to identify the Nsfl1c gene encoding p47 as a suppressor of human epidermal growth factor receptor 2 (HER2)+ breast cancer metastasis. p47 ablation specifically increases metastasis without promoting primary mammary tumor growth. Analysis of human breast cancer patient databases and tissue samples indicates a correlation of lower p47 expression levels with metastasis and decreased survival. Mechanistic studies show that p47 functions in the repair of lysosomal damage for autophagy flux and in the endosomal trafficking of nuclear factor κB essential modulator for lysosomal degradation to promote metastasis. Our results demonstrate a role and mechanisms of p47 in the regulation of breast cancer metastasis. They highlight the potential to exploit p47 as a suppressor of metastasis through multiple pathways in HER2+ breast cancer cells.
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Affiliation(s)
- Mingang Hao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Peixin Lu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Sarah Sotropa
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Kanakaraju Manupati
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Syn Kok Yeo
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
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3
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Inès D, Courty PE, Wendehenne D, Rosnoblet C. CDC48 in plants and its emerging function in plant immunity. TRENDS IN PLANT SCIENCE 2024:S1360-1385(23)00398-9. [PMID: 38218650 DOI: 10.1016/j.tplants.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/15/2024]
Abstract
Protein homeostasis, namely the balance between protein synthesis and degradation, must be finely controlled to ensure cell survival, notably through the ubiquitin-proteasome system (UPS). In all species, including plants, homeostasis is disrupted by biotic and abiotic stresses. A key player in the maintenance of protein balance, the protein CDC48, shows emerging functions in plants, particularly in response to biotic stress. In this review on CDC48 in plants, we detail its highly conserved structure, describe a gene expansion that is only present in Viridiplantae, discuss its various functions and regulations, and finally highlight its recruitment, still not clear, during the plant immune response.
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Affiliation(s)
- Damien Inès
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - David Wendehenne
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - Claire Rosnoblet
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France.
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4
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Nakayama S, Kondo H. VCIP135 associates with both the N- and C-terminal regions of p97 ATPase. J Biol Chem 2024; 300:105540. [PMID: 38072049 PMCID: PMC10805704 DOI: 10.1016/j.jbc.2023.105540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 01/02/2024] Open
Abstract
Two distinct p97ATPase-mediated membrane fusion pathways are required for Golgi and endoplasmic reticulum (ER) biogenesis, namely, the p97/p47 pathway and the p97/p37 pathway. p97 (VCP)/p47 complex-interacting protein p135 (VCIP135) is necessary for both of these pathways. Although VCIP135 is known to form a complex with p97 in the cytosol, the role of this complex in Golgi and ER biogenesis has remained unclear. In this study, we demonstrated that VCIP135 has two distinct p97-binding sites at its N- and C-terminal regions. In particular, the C-terminal binding site includes the SHP motif, which is also found in other p97-binding proteins, such as p47, p37, and Ufd1. We also clarified that VCIP135 binds to both the N- and C-terminal regions of p97; that is, the N- and C-terminal binding sites in VCIP135 interact with the C- and N-terminal regions of p97, respectively. These two interactions within the complex are synchronously controlled by the nucleotide state of p97. We next generated VCIP135 mutants lacking each of the p97-binding sites to investigate their functions in living cells and clarified that VCIP135 is involved in Golgi and ER biogenesis through its two distinct interactions with p97. VCIP135 is hence a unique p97-binding protein that functions by interacting with both the N-and C-terminal regions of p97, which strongly suggests that it plays crucial roles in p97-mediated events.
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Affiliation(s)
- Suzune Nakayama
- Department of Molecular Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hisao Kondo
- Department of Molecular Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
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5
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Luthuli SD, Shonhai A. The multi-faceted roles of R2TP complex span across regulation of gene expression, translation, and protein functional assembly. Biophys Rev 2023; 15:1951-1965. [PMID: 38192347 PMCID: PMC10771493 DOI: 10.1007/s12551-023-01127-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/27/2023] [Indexed: 01/10/2024] Open
Abstract
Macromolecular complexes play essential roles in various cellular processes. The assembly of macromolecular assemblies within the cell must overcome barriers imposed by a crowded cellular environment which is characterized by an estimated concentration of biological macromolecules amounting to 100-450 g/L that take up approximately 5-40% of the cytoplasmic volume. The formation of the macromolecular assemblies is facilitated by molecular chaperones in cooperation with their co-chaperones. The R2TP protein complex has emerged as a co-chaperone of Hsp90 that plays an important role in macromolecular assembly. The R2TP complex is composed of a heterodimer of RPAP3:P1H1DI that is in turn complexed to members of the ATPase associated with diverse cellular activities (AAA +), RUVBL1 and RUVBL2 (R1 and R2) families. What makes the R2TP co-chaperone complex particularly important is that it is involved in a wide variety of cellular processes including gene expression, translation, co-translational complex assembly, and posttranslational protein complex formation. The functional versatility of the R2TP co-chaperone complex makes it central to cellular development; hence, it is implicated in various human diseases. In addition, their roles in the development of infectious disease agents has become of interest. In the current review, we discuss the roles of these proteins as co-chaperones regulating Hsp90 and its partnership with Hsp70. Furthermore, we highlight the structure-function features of the individual proteins within the R2TP complex and describe their roles in various cellular processes.
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Affiliation(s)
- Sifiso Duncan Luthuli
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Addmore Shonhai
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
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6
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Braxton JR, Southworth DR. Structural insights of the p97/VCP AAA+ ATPase: How adapter interactions coordinate diverse cellular functionality. J Biol Chem 2023; 299:105182. [PMID: 37611827 PMCID: PMC10641518 DOI: 10.1016/j.jbc.2023.105182] [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: 05/30/2023] [Revised: 08/05/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
p97/valosin-containing protein is an essential eukaryotic AAA+ ATPase with diverse functions including protein homeostasis, membrane remodeling, and chromatin regulation. Dysregulation of p97 function causes severe neurodegenerative disease and is associated with cancer, making this protein a significant therapeutic target. p97 extracts polypeptide substrates from macromolecular assemblies by hydrolysis-driven translocation through its central pore. Growing evidence indicates that this activity is highly coordinated by "adapter" partner proteins, of which more than 30 have been identified and are commonly described to facilitate translocation through substrate recruitment or modification. In so doing, these adapters enable critical p97-dependent functions such as extraction of misfolded proteins from the endoplasmic reticulum or mitochondria, and are likely the reason for the extreme functional diversity of p97 relative to other AAA+ translocases. Here, we review the known functions of adapter proteins and highlight recent structural and biochemical advances that have begun to reveal the diverse molecular bases for adapter-mediated regulation of p97 function. These studies suggest that the range of mechanisms by which p97 activity is controlled is vastly underexplored with significant advances possible for understanding p97 regulation by the most known adapters.
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Affiliation(s)
- Julian R Braxton
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, California, USA; Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California, USA
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California, USA.
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7
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Cordes CN, Gouge MM, Morgan H, Porter C, Siders J, Bacab E, Barin B, Becerra IA, Castillo J, Church J, Condo-Hicks S, Conroy KJ, Curbelo-Navarro I, DePrest BJ, Eady A, Edmead T, Farouk V, Flores-Torres A, Girmai M, Gutierrez Navarro CI, Guzman S, Harris AB, Healy K, Jaafar A, Khadr A, Kiboi MN, Korte SN, Lopez C, Mahdi H, Mendoza Avalos J, Miranda K, Patel D, Lopez C, Mahdi H, Mendoza Avalos J, Miranda K, Patel D, Patel R, Pechulis S, Plachta V, Rhodes K, Sandoval AM, Thomas C, Valadez-Mendoza JA, Vora H, Yousif J, Bieser KL, Kagey JD. Genetic mapping of the p47 L.3.2 mutation in Drosophilamelanogaster. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000783. [PMID: 37799208 PMCID: PMC10550376 DOI: 10.17912/micropub.biology.000783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/17/2023] [Accepted: 08/09/2023] [Indexed: 10/07/2023]
Abstract
An EMS-based forward genetic screen was conducted in an apoptotic null background to identify genetic aberrations that contribute to regulation of cell growth in Drosophila melanogaster . The current work maps the genomic location of one of the identified mutants, L.3.2 . Genetic crosses conducted through the Fly-CURE consortium determined that the gene locus for the L.3.2 mutation is p47 on chromosome 2R.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Hyder Mahdi
- University of Detroit Mercy, Detroit, MI, USA
| | | | | | | | | | - Hyder Mahdi
- University of Detroit Mercy, Detroit, MI, USA
| | | | | | | | - Rishi Patel
- University of Detroit Mercy, Detroit, MI, USA
| | | | | | | | | | | | | | - Hannah Vora
- University of Detroit Mercy, Detroit, MI, USA
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8
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Elkholi IE, Boulais J, Thibault MP, Phan HD, Robert A, Lai LB, Faubert D, Smith MJ, Gopalan V, Côté JF. Mapping the MOB proteins' proximity network reveals a unique interaction between human MOB3C and the RNase P complex. J Biol Chem 2023; 299:105123. [PMID: 37536630 PMCID: PMC10480535 DOI: 10.1016/j.jbc.2023.105123] [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: 05/09/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023] Open
Abstract
Distinct functions mediated by members of the monopolar spindle-one-binder (MOB) family of proteins remain elusive beyond the evolutionarily conserved and well-established roles of MOB1 (MOB1A/B) in regulating tissue homeostasis within the Hippo pathway. Since MOB proteins are adaptors, understanding how they engage in protein-protein interactions and help assemble complexes is essential to define the full scope of their biological functions. To address this, we undertook a proximity-dependent biotin identification approach to define the interactomes of all seven human MOB proteins in HeLa and human embryonic kidney 293 cell lines. We uncovered >200 interactions, of which at least 70% are unreported on BioGrid. The generated dataset reliably recalled the bona fide interactors of the well-studied MOBs. We further defined the common and differential interactome between different MOBs on a subfamily and an individual level. We discovered a unique association between MOB3C and 7 of 10 protein subunits of the RNase P complex, an endonuclease that catalyzes tRNA 5' maturation. As a proof of principle for the robustness of the generated dataset, we validated the specific interaction of MOB3C with catalytically active RNase P by using affinity purification-mass spectrometry and pre-tRNA cleavage assays of MOB3C pulldowns. In summary, our data provide novel insights into the biology of MOB proteins and reveal the first interactors of MOB3C, components of the RNase P complex, and hence an exciting nexus with RNA biology.
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Affiliation(s)
- Islam E Elkholi
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada; Molecular Biology Programs, Université de Montréal, Montreal, Quebec, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada.
| | - Jonathan Boulais
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | | | - Hong-Duc Phan
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Amélie Robert
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Lien B Lai
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Denis Faubert
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Matthew J Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Venkat Gopalan
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jean-Franҫois Côté
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada; Molecular Biology Programs, Université de Montréal, Montreal, Quebec, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada.
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9
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Valimehr S, Sethi A, Shukla M, Bhattacharyya S, Kazemi M, Rouiller I. Molecular Mechanisms Driving and Regulating the AAA+ ATPase VCP/p97, an Important Therapeutic Target for Treating Cancer, Neurological and Infectious Diseases. Biomolecules 2023; 13:biom13050737. [PMID: 37238606 DOI: 10.3390/biom13050737] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/15/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
p97/VCP, a highly conserved type II ATPase associated with diverse cellular activities (AAA+ ATPase), is an important therapeutic target in the treatment of neurodegenerative diseases and cancer. p97 performs a variety of functions in the cell and facilitates virus replication. It is a mechanochemical enzyme that generates mechanical force from ATP-binding and hydrolysis to perform several functions, including unfolding of protein substrates. Several dozens of cofactors/adaptors interact with p97 and define the multifunctionality of p97. This review presents the current understanding of the molecular mechanism of p97 during the ATPase cycle and its regulation by cofactors and small-molecule inhibitors. We compare detailed structural information obtained in different nucleotide states in the presence and absence of substrates and inhibitors. We also review how pathogenic gain-of-function mutations modify the conformational changes of p97 during the ATPase cycle. Overall, the review highlights how the mechanistic knowledge of p97 helps in designing pathway-specific modulators and inhibitors.
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Affiliation(s)
- Sepideh Valimehr
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Ian Holmes Imaging Centre, Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Ashish Sethi
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- Australian Nuclear Science Technology Organisation, The Australian Synchrotron, 800 Blackburn Rd, Clayton, VIC 3168, Australia
| | - Manjari Shukla
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jodhpur 342030, Rajasthan, India
| | - Sudipta Bhattacharyya
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jodhpur 342030, Rajasthan, India
| | - Mohsen Kazemi
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Isabelle Rouiller
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, The University of Melbourne, Melbourne, VIC 3010, Australia
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10
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Meyer H, van den Boom J. Targeting of client proteins to the VCP/p97/Cdc48 unfolding machine. Front Mol Biosci 2023; 10:1142989. [PMID: 36825201 PMCID: PMC9941556 DOI: 10.3389/fmolb.2023.1142989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
The AAA+ ATPase p97 (also called VCP or Cdc48) is a major protein unfolding machine with hundreds of clients in diverse cellular pathways that are critical for cell homeostasis, proliferation and signaling. In this review, we summarize recent advances in understanding how diverse client proteins are targeted to the p97 machine to facilitate client degradation or to strip clients from binding partners for regulation. We describe an elaborate system that is governed by at least two types of alternative adapters. The Ufd1-Npl4 adapter along with accessory adapters targets ubiquitylated clients in the majority of pathways and uses ubiquitin as a universal unfolding tag. In contrast, the family of SEP-domain adapters such as p37 can target clients directly to p97 in a ubiquitin-independent manner. Despite the different targeting strategies, both pathways converge by inserting the client into the p97 pore to initiate a peptide threading mechanism through the central channel of p97 that drives client protein unfolding, protein extraction from membranes and protein complex disassembly processes.
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Affiliation(s)
| | - Johannes van den Boom
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
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11
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Kilgas S, Ramadan K. Inhibitors of the ATPase p97/VCP: From basic research to clinical applications. Cell Chem Biol 2023; 30:3-21. [PMID: 36640759 DOI: 10.1016/j.chembiol.2022.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/13/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Abstract
Protein homeostasis deficiencies underlie various cancers and neurodegenerative diseases. The ubiquitin-proteasome system (UPS) and autophagy are responsible for most of the protein degradation in mammalian cells and, therefore, represent attractive targets for cancer therapy and that of neurodegenerative diseases. The ATPase p97, also known as VCP, is a central component of the UPS that extracts and disassembles its substrates from various cellular locations and also regulates different steps in autophagy. Several UPS- and autophagy-targeting drugs are in clinical trials. In this review, we focus on the development of various p97 inhibitors, including the ATPase inhibitors CB-5083 and CB-5339, which reached clinical trials by demonstrating effective anti-tumor activity across various tumor models, providing an effective alternative to targeting protein degradation for cancer therapy. Here, we provide an overview of how different p97 inhibitors have evolved over time both as basic research tools and effective UPS-targeting cancer therapies in the clinic.
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Affiliation(s)
- Susan Kilgas
- Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
| | - Kristijan Ramadan
- Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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12
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Park E, Yang CR, Raghuram V, Deshpande V, Datta A, Poll BG, Leo KT, Kikuchi H, Chen L, Chou CL, Knepper MA. Data resource: vasopressin-regulated protein phosphorylation sites in the collecting duct. Am J Physiol Renal Physiol 2023; 324:F43-F55. [PMID: 36264882 PMCID: PMC9762968 DOI: 10.1152/ajprenal.00229.2022] [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: 08/29/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 02/04/2023] Open
Abstract
Vasopressin controls renal water excretion through actions to regulate aquaporin-2 (AQP2) trafficking, transcription, and degradation. These actions are in part dependent on vasopressin-induced phosphorylation changes in collecting duct cells. Although most efforts have focused on the phosphorylation of AQP2 itself, phosphoproteomic studies have identified many vasopressin-regulated phosphorylation sites in proteins other than AQP2. The goal of this bioinformatics-based review is to create a compendium of vasopressin-regulated phosphorylation sites with a focus on those that are seen in both native rat inner medullary collecting ducts and cultured collecting duct cells from the mouse (mpkCCD), arguing that these sites are the best candidates for roles in AQP2 regulation. This analysis identified 51 vasopressin-regulated phosphorylation sites in 45 proteins. We provide resource web pages at https://esbl.nhlbi.nih.gov/Databases/AVP-Phos/ and https://esbl.nhlbi.nih.gov/AVP-Network/, listing the phosphorylation sites and describing annotated functions of each of the vasopressin-targeted phosphoproteins. Among these sites are 23 consensus protein kinase A (PKA) sites that are increased in response to vasopressin, consistent with a central role for PKA in vasopressin signaling. The remaining sites are predicted to be phosphorylated by other kinases, most notably ERK1/2, which accounts for decreased phosphorylation at sites with a X-p(S/T)-P-X motif. Additional protein kinases that undergo vasopressin-induced changes in phosphorylation are Camkk2, Cdk18, Erbb3, Mink1, and Src, which also may be activated directly or indirectly by PKA. The regulated phosphoproteins are mapped to processes that hypothetically can account for vasopressin-mediated control of AQP2 trafficking, cytoskeletal alterations, and Aqp2 gene expression, providing grist for future studies.NEW & NOTEWORTHY Vasopressin regulates renal water excretion through control of the aquaporin-2 water channel in collecting duct cells. Studies of vasopressin-induced protein phosphorylation have focused mainly on the phosphorylation of aquaporin-2. This study describes 44 phosphoproteins other than aquaporin-2 that undergo vasopressin-mediated phosphorylation changes and summarizes potential physiological roles of each.
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Affiliation(s)
- Euijung Park
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Chin-Rang Yang
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Viswanathan Raghuram
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Venkatesh Deshpande
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Arnab Datta
- Laboratory of Translational Neuroscience, Division of Neuroscience, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Brian G Poll
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Kirby T Leo
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Hiroaki Kikuchi
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Lihe Chen
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Chung-Lin Chou
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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13
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Geng T, Yang D, Lin T, Cahoon JG, Wang P. UBXN3B Controls Immunopathogenesis of Arthritogenic Alphaviruses by Maintaining Hematopoietic Homeostasis. mBio 2022; 13:e0268722. [PMID: 36377866 PMCID: PMC9765034 DOI: 10.1128/mbio.02687-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
Ubiquitin regulatory X domain-containing proteins (UBXN) might be involved in diverse cellular processes. However, their in vivo physiological functions remain largely elusive. We recently showed that UBXN3B positively regulated stimulator-of-interferon-genes (STING)-mediated innate immune responses to DNA viruses. Herein, we reported the essential role of UBXN3B in the control of infection and immunopathogenesis of two arthritogenic RNA viruses, Chikungunya (CHIKV) and O'nyong'nyong (ONNV) viruses. Ubxn3b deficient (Ubxn3b-/-) mice presented higher viral loads, more severe foot swelling and immune infiltrates, and slower clearance of viruses and resolution of inflammation than the Ubxn3b+/+ littermates. While the serum cytokine levels were intact, the virus-specific immunoglobulin G and neutralizing antibody levels were lower in the Ubxn3b-/- mice. The Ubxn3b-/- mice had more neutrophils and macrophages, but much fewer B cells in the ipsilateral feet. Of note, this immune dysregulation was also observed in the spleens and blood of uninfected Ubxn3b-/- mice. UBXN3B restricted CHIKV replication in a cell-intrinsic manner but independent of type I IFN signaling. These results demonstrated a dual role of UBXN3B in the maintenance of immune homeostasis and control of RNA virus replication. IMPORTANCE The human genome encodes 13 ubiquitin regulatory X (UBX) domain-containing proteins (UBXN) that might participate in diverse cellular processes. However, their in vivo physiological functions remain largely elusive. Herein, we reported an essential role of UBXN3B in the control of infection and immunopathogenesis of arthritogenic alphaviruses, including Chikungunya virus (CHIKV), which causes acute and chronic crippling arthralgia, long-term neurological disorders, and poses a significant public health problem in the tropical and subtropical regions worldwide. However, there are no approved vaccines or specific antiviral drugs. This was partly due to a poor understanding of the protective and detrimental immune responses elicited by CHIKV. We showed that UBXN3B was critical for the control of CHIKV replication in a cell-intrinsic manner in the acute phase and persistent immunopathogenesis in the post-viremic stage. Mechanistically, UBXN3B was essential for the maintenance of hematopoietic homeostasis during viral infection and in steady-state.
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Affiliation(s)
- Tingting Geng
- Department of Immunology, School of Medicine, the University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Duomeng Yang
- Department of Immunology, School of Medicine, the University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Tao Lin
- Department of Immunology, School of Medicine, the University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Jason G. Cahoon
- Department of Immunology, School of Medicine, the University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Penghua Wang
- Department of Immunology, School of Medicine, the University of Connecticut Health Center, Farmington, Connecticut, USA
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14
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Mirzadeh A, Kobakhidze G, Vuillemot R, Jonic S, Rouiller I. In silico prediction, characterization, docking studies and molecular dynamics simulation of human p97 in complex with p37 cofactor. BMC Mol Cell Biol 2022; 23:39. [PMID: 36088301 PMCID: PMC9464413 DOI: 10.1186/s12860-022-00437-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/13/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The AAA + ATPase p97 is an essential unfoldase/segragase involved in a multitude of cellular processes. It functions as a molecular machine critical for protein homeostasis, homotypic membrane fusion events and organelle biogenesis during mitosis in which it acts in concert with cofactors p47 and p37. Cofactors assist p97 in extracting and unfolding protein substrates through ATP hydrolysis. In contrast to other p97ʼs cofactors, p37 uniquely increases the ATPase activity of p97. Disease-causing mutations in p97, including mutations that cause neurodegenerative diseases, increase cofactor association with its N-domain, ATPase activity and improper substrate processing. Upregulation of p97 has also been observed in various cancers. This study aims towards the characterization of the protein–protein interaction between p97 and p37 at the atomic level. We defined the interacting residues in p97 and p37. The knowledge will facilitate the design of unique small molecules inhibiting this interaction with insights into cancer therapy and drug design.
Results
The homology model of human p37 UBX domain was built from the X-ray crystal structure of p47 C-terminus from rat (PDB code:1S3S, G) as a template and assessed by model validation analysis. According to the HDOCK, HAWKDOCK, MM-GBSA binding free energy calculations and Arpeggio, we found that there are several hydrophobic and two hydrogen-bonding interactions between p37 UBX and p97 N-D1 domain. Residues of p37 UBX predicted to be involved in the interactions with p97 N-D1 domain interface are highly conserved among UBX cofactors.
Conclusion
This study provides a reliable structural insight into the p37-p97 complex binding sites at the atomic level though molecular docking coupled with molecular dynamics simulation. This can guide the rational design of small molecule drugs for inhibiting mutant p97 activity.
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15
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Nguyen TQ, My Le LT, Kim DH, Ko KS, Lee HT, Kim Nguyen YT, Kim HS, Han BW, Kang W, Yang JK. Structural basis for the interaction between human Npl4 and Npl4-binding motif of human Ufd1. Structure 2022; 30:1530-1537.e3. [PMID: 36087575 DOI: 10.1016/j.str.2022.08.005] [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] [Received: 04/23/2022] [Revised: 07/19/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022]
Abstract
The heterodimer of human ubiquitin fusion degradation 1 (hUfd1) and human nuclear protein localization 4 (hNpl4) is a major cofactor of human p97 adenosine triphosphatase (ATPase). The p97-Ufd1-Npl4 complex translocates the ubiquitin-conjugated proteins from the endoplasmic reticulum membrane to the cytoplasm. Ubiquitinated proteins are then degraded by the proteasome. The structures of Npl4 and Ufd1-Npl4 (UN) complex in Saccharomyces cerevisiae have been recently reported; however, the structures of hNpl4 and the human UN complex remain unknown. Here, we report the crystal structures of the human UN complex at a resolution of 2.7 Å and hNpl4 at a resolution of 3.0 Å. We also present atomic details and characterization of the human UN complex. Crystallographic studies and site-directed mutagenesis of the hUfd1 residues involved in the interaction with hNpl4 revealed the atomic details of the two proteins.
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Affiliation(s)
- Thang Quyet Nguyen
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Le Thi My Le
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Do Hyeon Kim
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Kyung Soo Ko
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Hee Taek Lee
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Yen Thi Kim Nguyen
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyoun Sook Kim
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Byung Woo Han
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Wonchull Kang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea; Department of Physics and Integrative Institute of Basic Science, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea; Department of Green Chemistry and Material Engineering, Soongsil University, Seoul 06798, Republic of Korea.
| | - Jin Kuk Yang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea.
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16
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Cavalcanti RRM, Lira RB, Riske KA. Membrane Fusion Biophysical Analysis of Fusogenic Liposomes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:10430-10441. [PMID: 35977420 DOI: 10.1021/acs.langmuir.2c01169] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Liposomes represent important drug carrier vehicles in biological systems. A fusogenic liposomal system composed of equimolar mixtures of the cationic lipid DOTAP and the phospholipid DOPE showed high fusion and delivery efficiencies with cells and lipid vesicles. However, aspects of the thermodynamics involving the interaction of these fusogenic liposomes and biomimetic systems remain unclear. Here, we investigate the fusion of this system with large unilamellar vesicles (LUVs) composed of the zwitterionic lipid POPC and increasing fractions of the anionic lipid POPG and up to 30 mol % cholesterol. The focus here is to concomitantly follow changes in size, zeta-potential, and enthalpy binding upon membrane interaction and fusion. Isothermal titration calorimetry (ITC) data showed that membrane fusion in our system is an exothermic process in the absence of cholesterol, suggesting that electrostatic attraction is the driving force for fusion. An endothermic component appeared and eventually dominated the titration at 30 mol % cholesterol, which we propose is caused by membrane fluidification when cholesterol is diluted upon fusion. The inflection points of the ITC data occurred around 0.5-0.7 POPG/DOTAP for all systems, the same stoichiometry for which zeta-potential and dynamic light scattering measurements showed an increase in size coupled with charge neutralization of the system, which is consistent with the fact that fusion in our system is charge-mediated. Microscopy observations of the final mixtures revealed the presence of giant vesicles, which is a clear indication of fusion, coexisting with intermediate-sized objects that could be the result of both fusion and/or aggregation. The results show that the fusion efficiency of the DOTAP:DOPE fusogenic system is modulated by the charge and membrane packing of the acceptor membrane and explain why the system fuses very efficiently with cells.
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Affiliation(s)
- Rafaela R M Cavalcanti
- Departamento de Biofísica, Universidade Federal de São Paulo, CEP 04039-032, São Paulo, Brazil
| | - Rafael B Lira
- Departamento de Biofísica, Universidade Federal de São Paulo, CEP 04039-032, São Paulo, Brazil
| | - Karin A Riske
- Departamento de Biofísica, Universidade Federal de São Paulo, CEP 04039-032, São Paulo, Brazil
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17
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Alimogullari E, Akcan G, Ari O, Cayli S. The determination of the relationship between p97/VCP, small VCP-interacting protein, two ERAD proteins and steroidogenesis in Leydig cell lines. Mol Biol Rep 2022; 49:9159-9170. [DOI: 10.1007/s11033-022-07740-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/22/2022] [Indexed: 10/15/2022]
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18
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Jiang Z, Kuo YH, Zhong M, Zhang J, Zhou XX, Xing L, Wells JA, Wang Y, Arkin MR. Adaptor-Specific Antibody Fragment Inhibitors for the Intracellular Modulation of p97 (VCP) Protein-Protein Interactions. J Am Chem Soc 2022; 144:13218-13225. [PMID: 35819848 PMCID: PMC9335864 DOI: 10.1021/jacs.2c03665] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein-protein interactions (PPIs) form complex networks to drive cellular signaling and cellular functions. Precise modulation of a target PPI helps explain the role of the PPI in cellular events and possesses therapeutic potential. For example, valosin-containing protein (VCP/p97) is a hub protein that interacts with more than 30 adaptor proteins involved in various cellular functions. However, the role of each p97 PPI during the relevant cellular event is underexplored. The development of small-molecule PPI modulators remains challenging due to a lack of grooves and pockets in the relatively large PPI interface and the fact that a common binding groove in p97 binds to multiple adaptors. Here, we report an antibody fragment-based modulator for the PPI between p97 and its adaptor protein NSFL1C (p47). We engineered these antibody modulators by phage display against the p97-interacting domain of p47 and minimizing binding to other p97 adaptors. The selected antibody fragment modulators specifically disrupt the intracellular p97/p47 interaction. The potential of this antibody platform to develop PPI inhibitors in therapeutic applications was demonstrated through the inhibition of Golgi reassembly, which requires the p97/p47 interaction. This study presents a unique approach to modulate specific intracellular PPIs using engineered antibody fragments, demonstrating a method to dissect the function of a PPI within a convoluted PPI network.
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Affiliation(s)
- Ziwen Jiang
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, California 94158, United States,Small
Molecule Discovery Center, University of
California, San Francisco, California 94158, United States
| | - Yu-Hsuan Kuo
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, California 94158, United States,Small
Molecule Discovery Center, University of
California, San Francisco, California 94158, United States
| | - Mengqi Zhong
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, California 94158, United States,Small
Molecule Discovery Center, University of
California, San Francisco, California 94158, United States
| | - Jianchao Zhang
- Department
of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1085, United States
| | - Xin X. Zhou
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, California 94158, United States,Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States,Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115 United States
| | - Lijuan Xing
- Department
of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1085, United States
| | - James A. Wells
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, California 94158, United States
| | - Yanzhuang Wang
- Department
of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1085, United States
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, California 94158, United States,Small
Molecule Discovery Center, University of
California, San Francisco, California 94158, United States,
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19
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Abstract
The p97 AAA+ATPase is an essential and abundant regulator of protein homeostasis that plays a central role in unfolding ubiquitylated substrates. Here we report two cryo-EM structures of human p97 in complex with its p47 adaptor. One of the conformations is six-fold symmetric, corresponds to previously reported structures of p97, and lacks bound substrate. The other structure adopts a helical conformation, displays substrate running in an extended conformation through the pore of the p97 hexamer, and resembles structures reported for other AAA unfoldases. These findings support the model that p97 utilizes a "hand-over-hand" mechanism in which two residues of the substrate are translocated for hydrolysis of two ATPs, one in each of the two p97 AAA ATPase rings. Proteomics analysis supports the model that one p97 complex can bind multiple substrate adaptors or binding partners, and can process substrates with multiple types of ubiquitin modification.
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20
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Prophet SM, Naughton BS, Schlieker C. p97/UBXD1 Generate Ubiquitylated Proteins That Are Sequestered into Nuclear Envelope Herniations in Torsin-Deficient Cells. Int J Mol Sci 2022; 23:4627. [PMID: 35563018 PMCID: PMC9100061 DOI: 10.3390/ijms23094627] [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: 02/26/2022] [Revised: 04/14/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023] Open
Abstract
DYT1 dystonia is a debilitating neurological movement disorder that arises upon Torsin ATPase deficiency. Nuclear envelope (NE) blebs that contain FG-nucleoporins (FG-Nups) and K48-linked ubiquitin are the hallmark phenotype of Torsin manipulation across disease models of DYT1 dystonia. While the aberrant deposition of FG-Nups is caused by defective nuclear pore complex assembly, the source of K48-ubiquitylated proteins inside NE blebs is not known. Here, we demonstrate that the characteristic K48-ubiquitin accumulation inside blebs requires p97 activity. This activity is highly dependent on the p97 adaptor UBXD1. We show that p97 does not significantly depend on the Ufd1/Npl4 heterodimer to generate the K48-ubiquitylated proteins inside blebs, nor does inhibiting translation affect the ubiquitin sequestration in blebs. However, stimulating global ubiquitylation by heat shock greatly increases the amount of K48-ubiquitin sequestered inside blebs. These results suggest that blebs have an extraordinarily high capacity for sequestering ubiquitylated protein generated in a p97-dependent manner. The p97/UBXD1 axis is thus a major factor contributing to cellular DYT1 dystonia pathology and its modulation represents an unexplored potential for therapeutic development.
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Affiliation(s)
- Sarah M. Prophet
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA; (S.M.P.); (B.S.N.)
| | - Brigitte S. Naughton
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA; (S.M.P.); (B.S.N.)
| | - Christian Schlieker
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA; (S.M.P.); (B.S.N.)
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
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21
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Calvanese E, Gu Y. Towards understanding inner nuclear membrane protein degradation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2266-2274. [PMID: 35139191 DOI: 10.1093/jxb/erac037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
The inner nuclear membrane (INM) hosts a unique set of membrane proteins that play essential roles in various aspects of the nuclear function. However, overaccumulation or malfunction of INM protein has been associated with a range of rare genetic diseases; therefore, maintaining the homeostasis and integrity of INM proteins by active removal of aberrantly accumulated proteins and replacing defective molecules through proteolysis is of critical importance. Within the last decade, it has been shown that INM proteins are degraded in yeasts by a process very similar to endoplasmic reticulum-associated degradation (ERAD), which is accomplished by retrotranslocation of membrane substrates followed by proteasome-dependent proteolysis, and this process was named inner nuclear membrane-associated degradation (INMAD). INMAD is distinguished from ERAD by specific INM-localized E3 ubiquitin ligases and proteolysis regulators. While much is yet to be determined about the INMAD pathway in yeasts, virtually no knowledge of it exists for higher eukaryotes, and only very recently have several critical regulators that participate in INM protein degradation been discovered in plants. Here, we review key molecular components of the INMAD pathway and draw parallels between the yeast and plant system to discuss promising directions in the future study of the plant INMAD process.
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Affiliation(s)
- Enrico Calvanese
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
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22
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Song A, Wen AQ, Wen YE, Dzieciatkowska M, Kellems RE, Juneja HS, D'Alessandro A, Xia Y. p97 dysfunction underlies a loss of quality control of damaged membrane proteins and promotes oxidative stress and sickling in sickle cell disease. FASEB J 2022; 36:e22246. [PMID: 35405035 DOI: 10.1096/fj.202101500rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 11/11/2022]
Abstract
Sickling is the central pathogenic process of sickle cell disease (SCD), one of the most prevalent inherited hemolytic disorders. Having no easy access to antioxidants in the cytosol, elevated levels of reactive oxygen species (ROS) residing at the plasma membrane in sickle red blood cells (sRBCs) easily oxidize membrane proteins and thus contribute to sickling. Although the ubiquitin-proteasome system (UPS) is essential to rapidly clear ROS-damaged membrane proteins and maintain cellular homeostasis, the function and regulatory mechanism of the UPS for their clearance in sRBCs remains unidentified. Elevated levels of polyubiquitinated membrane-associated proteins in human sRBCs are reported here. High throughput and untargeted proteomic analyses of membrane proteins immunoprecipitated by ubiquitin antibodies detected elevated levels of ubiquitination of a series of proteins including cytoskeletal proteins, transporters, ROS-related proteins, and UPS machinery components in sRBCs. Polyubiquitination of membrane-associated catalase was increased in sRBCs, associated with decreased catalase activity and elevated ROS. Surprisingly, shuttling of p97 (ATP-dependent valosin-containing chaperone protein), a key component of the UPS to shuttle polyubiquitinated proteins from the membrane to cytosol for proteasomal degradation, was significantly impaired, resulting in significant accumulation of p97 along with polyubiquitinated proteins in the membrane of human sRBCs. Functionally, inhibition of p97 directly promoted accumulation of polyubiquitinated membrane-associated proteins, excessive ROS levels, and sickling in response to hypoxia. Overall, we revealed that p97 dysfunction underlies impaired UPS and contributes to oxidative stress in sRBCs.
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Affiliation(s)
- Anren Song
- Department of Biochemistry and Molecular Biology, the University of Texas McGovern Medical School, Houston, Texas, USA
| | - Alexander Q Wen
- Department of Biochemistry and Molecular Biology, the University of Texas McGovern Medical School, Houston, Texas, USA.,University of California at San Diego, La Jolla, California, USA
| | - Y Edward Wen
- Department of Biochemistry and Molecular Biology, the University of Texas McGovern Medical School, Houston, Texas, USA.,University of Texas Southwestern Medical School, Dallas, Texas, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Rodney E Kellems
- Department of Biochemistry and Molecular Biology, the University of Texas McGovern Medical School, Houston, Texas, USA.,Graduate Program in Biochemistry and Cell Biology, University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Harinder S Juneja
- Department of Internal Medicine, Divison of Hematology, the University of Texas McGovern Medical School, Houston, Texas, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Yang Xia
- Department of Biochemistry and Molecular Biology, the University of Texas McGovern Medical School, Houston, Texas, USA.,Graduate Program in Biochemistry and Cell Biology, University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
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23
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Sun X, Zhou N, Ma B, Wu W, Stoll S, Lai L, Qin G, Qiu H. Functional Inhibition of Valosin-Containing Protein Induces Cardiac Dilation and Dysfunction in a New Dominant-Negative Transgenic Mouse Model. Cells 2021; 10:2891. [PMID: 34831118 PMCID: PMC8616236 DOI: 10.3390/cells10112891] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/20/2022] Open
Abstract
Valosin-containing protein (VCP) was found to play a vital protective role against cardiac stresses. Genetic mutations of VCP are associated with human dilated cardiomyopathy. However, the essential role of VCP in the heart during the physiological condition remains unknown since the VCP knockout in mice is embryonically lethal. We generated a cardiac-specific dominant-negative VCP transgenic (DN-VCP TG) mouse to determine the effects of impaired VCP activity on the heart. Using echocardiography, we showed that cardiac-specific overexpression of DN-VCP induced a remarkable cardiac dilation and progressively declined cardiac function during the aging transition. Mechanistically, DN-VCP did not affect the endogenous VCP (EN-VCP) expression but significantly reduced cardiac ATPase activity in the DN-VCP TG mouse hearts, indicating a functional inhibition. DN-VCP significantly impaired the aging-related cytoplasmic/nuclear shuffling of EN-VCP and its co-factors in the heart tissues and interrupted the balance of the VCP-cofactors interaction between the activating co-factors, ubiquitin fusion degradation protein 1 (UFD-1)/nuclear protein localization protein 4 (NPL-4) complex, and its inhibiting co-factor P47, leading to the binding preference with the inhibitory co-factor, resulting in functional repression of VCP. This DN-VCP TG mouse provides a unique functional-inactivation model for investigating VCP in the heart in physiological and pathological conditions.
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Affiliation(s)
- Xiaonan Sun
- Center for Molecular and Translational Medicine, Institute of Biomedical Science, Georgia State University, Atlanta, GA 30303, USA; (X.S.); (B.M.); (W.W.); (L.L.)
| | - Ning Zhou
- Division of Physiology, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92318, USA; (N.Z.); (S.S.)
| | - Ben Ma
- Center for Molecular and Translational Medicine, Institute of Biomedical Science, Georgia State University, Atlanta, GA 30303, USA; (X.S.); (B.M.); (W.W.); (L.L.)
| | - Wenqian Wu
- Center for Molecular and Translational Medicine, Institute of Biomedical Science, Georgia State University, Atlanta, GA 30303, USA; (X.S.); (B.M.); (W.W.); (L.L.)
| | - Shaunrick Stoll
- Division of Physiology, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92318, USA; (N.Z.); (S.S.)
| | - Lo Lai
- Center for Molecular and Translational Medicine, Institute of Biomedical Science, Georgia State University, Atlanta, GA 30303, USA; (X.S.); (B.M.); (W.W.); (L.L.)
| | - Gangjian Qin
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Hongyu Qiu
- Center for Molecular and Translational Medicine, Institute of Biomedical Science, Georgia State University, Atlanta, GA 30303, USA; (X.S.); (B.M.); (W.W.); (L.L.)
- Division of Physiology, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92318, USA; (N.Z.); (S.S.)
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24
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Thery F, Martina L, Asselman C, Zhang Y, Vessely M, Repo H, Sedeyn K, Moschonas GD, Bredow C, Teo QW, Zhang J, Leandro K, Eggermont D, De Sutter D, Boucher K, Hochepied T, Festjens N, Callewaert N, Saelens X, Dermaut B, Knobeloch KP, Beling A, Sanyal S, Radoshevich L, Eyckerman S, Impens F. Ring finger protein 213 assembles into a sensor for ISGylated proteins with antimicrobial activity. Nat Commun 2021; 12:5772. [PMID: 34599178 PMCID: PMC8486878 DOI: 10.1038/s41467-021-26061-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/14/2021] [Indexed: 12/20/2022] Open
Abstract
ISG15 is an interferon-stimulated, ubiquitin-like protein that can conjugate to substrate proteins (ISGylation) to counteract microbial infection, but the underlying mechanisms remain elusive. Here, we use a virus-like particle trapping technology to identify ISG15-binding proteins and discover Ring Finger Protein 213 (RNF213) as an ISG15 interactor and cellular sensor of ISGylated proteins. RNF213 is a poorly characterized, interferon-induced megaprotein that is frequently mutated in Moyamoya disease, a rare cerebrovascular disorder. We report that interferon induces ISGylation and oligomerization of RNF213 on lipid droplets, where it acts as a sensor for ISGylated proteins. We show that RNF213 has broad antimicrobial activity in vitro and in vivo, counteracting infection with Listeria monocytogenes, herpes simplex virus 1, human respiratory syncytial virus and coxsackievirus B3, and we observe a striking co-localization of RNF213 with intracellular bacteria. Together, our findings provide molecular insights into the ISGylation pathway and reveal RNF213 as a key antimicrobial effector.
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Affiliation(s)
- Fabien Thery
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lia Martina
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Caroline Asselman
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Yifeng Zhang
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Madeleine Vessely
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Heidi Repo
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - George D Moschonas
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Clara Bredow
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Berlin, Germany
| | - Qi Wen Teo
- HKU-Pasteur Research Pole, School of Public Health, University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Jingshu Zhang
- HKU-Pasteur Research Pole, School of Public Health, University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kevin Leandro
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Denzel Eggermont
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Delphine De Sutter
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Katie Boucher
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, VIB, Ghent, Belgium
| | - Tino Hochepied
- VIB Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Nele Festjens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Nico Callewaert
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Bart Dermaut
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Antje Beling
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Berlin, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), partner side Berlin, Berlin, Germany
| | - Sumana Sanyal
- HKU-Pasteur Research Pole, School of Public Health, University of Hong Kong, Pok Fu Lam, Hong Kong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Lilliana Radoshevich
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- VIB Proteomics Core, VIB, Ghent, Belgium.
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25
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Conserved L464 in p97 D1-D2 linker is critical for p97 cofactor regulated ATPase activity. Biochem J 2021; 478:3185-3204. [PMID: 34405853 DOI: 10.1042/bcj20210288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 11/17/2022]
Abstract
p97 protein is a highly conserved, abundant, functionally diverse, structurally dynamic homohexameric AAA enzyme-containing N, D1, and D2 domains. A truncated p97 protein containing the N and D1 domains and the D1-D2 linker (ND1L) exhibits 79% of wild-type (WT) ATPase activity whereas the ND1 domain alone without the linker only has 2% of WT activity. To investigate the relationship between the D1-D2 linker and the D1 domain, we produced p97 ND1L mutants and demonstrated that this 22-residue linker region is essential for D1 ATPase activity. The conserved amino acid leucine 464 (L464) is critical for regulating D1 and D2 ATPase activity by p97 cofactors p37, p47, and Npl4-Ufd1 (NU). Changing leucine to alanine, proline, or glutamate increased the maximum rate of ATP turnover (kcat) of p47-regulated ATPase activities for these mutants, but not for WT. p37 and p47 increased the kcat of the proline substituted linker, suggesting that they induced linker conformations facilitating ATP hydrolysis. NU inhibited D1 ATPase activities of WT and mutant ND1L proteins, but activated D2 ATPase activity of full-length p97. To further understand the mutant mechanism, we used single-particle cryo-EM to visualize the full-length p97L464P and revealed the conformational change of the D1-D2 linker, resulting in a movement of the helix-turn-helix motif (543-569). Taken together with the biochemical and structural results we conclude that the linker helps maintain D1 in a competent conformation and relays the communication to/from the N-domain to the D1 and D2 ATPase domains, which are ∼50 Å away.
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26
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Geng T, Yang D, Lin T, Harrison AG, Wang B, Torrance B, Wang K, Wang Y, Yang L, Haynes L, Cheng G, Vella AT, Fikrig E, Wang P. An Essential Role of UBXN3B in B Lymphopoiesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34462748 DOI: 10.1101/2021.03.04.433919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Hematopoiesis is finely regulated to enable timely production of the right numbers and types of mature immune cells to maintain tissue homeostasis. Dysregulated hematopoiesis may compromise antiviral immunity and/or exacerbate immunopathogenesis. Herein, we report an essential role of UBXN3B in maintenance of hematopoietic homeostasis and restriction of immunopathogenesis during respiratory viral infection. Ubxn3b deficient ( Ubxn3b -/- ) mice are highly vulnerable to SARS-CoV-2 and influenza A infection, characterized by more severe lung immunopathology, lower virus-specific IgG, significantly fewer B cells, but more myeloid cells than Ubxn3b +/+ littermates. This aberrant immune compartmentalization is recapitulated in uninfected Ubxn3b -/- mice. Mechanistically, UBXN3B controls precursor B-I (pre-BI) transition to pre-BII and subsequent proliferation in a cell-intrinsic manner, by maintaining BLNK protein stability and pre-BCR signaling. These results reveal an essential role of UBXN3B for the early stage of B cell development.
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27
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Nandi P, Li S, Columbres RCA, Wang F, Williams DR, Poh YP, Chou TF, Chiu PL. Structural and Functional Analysis of Disease-Linked p97 ATPase Mutant Complexes. Int J Mol Sci 2021; 22:ijms22158079. [PMID: 34360842 PMCID: PMC8347982 DOI: 10.3390/ijms22158079] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 01/14/2023] Open
Abstract
IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase malfunction remains unclear. To understand how the mutation alters the ATPase regulation, we assembled a full-length p97R155H with its p47 cofactor and first visualized their structures using single-particle cryo-EM. More than one-third of the population was the dodecameric form. Nucleotide presence dissociates the dodecamer into two hexamers for its highly elevated function. The N-domains of the p97R155H mutant all show up configurations in ADP- or ATPγS-bound states. Our functional and structural analyses showed that the p47 binding is likely to impact the p97R155H ATPase activities via changing the conformations of arginine fingers. These functional and structural analyses underline the ATPase dysregulation with the miscommunication between the functional modules of the p97R155H.
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Affiliation(s)
- Purbasha Nandi
- Biodesign Center for Applied Structural Discovery, School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (R.C.A.C.); (F.W.); (Y.-P.P.)
| | - Rod Carlo A. Columbres
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (R.C.A.C.); (F.W.); (Y.-P.P.)
| | - Feng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (R.C.A.C.); (F.W.); (Y.-P.P.)
| | | | - Yu-Ping Poh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (R.C.A.C.); (F.W.); (Y.-P.P.)
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (R.C.A.C.); (F.W.); (Y.-P.P.)
- Correspondence: (T.-F.C.); (P.-L.C.)
| | - Po-Lin Chiu
- Biodesign Center for Applied Structural Discovery, School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA;
- Correspondence: (T.-F.C.); (P.-L.C.)
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28
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KARTAL B, ALİMOĞULLARI E, AKCAN G, ÇAYLI S, VERGİLİ MA. Immunohistochemical examination of p97/VCP expression in developing mouse pancreas and liver. JOURNAL OF HEALTH SCIENCES AND MEDICINE 2021. [DOI: 10.32322/jhsm.904567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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29
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Creekmore BC, Chang YW, Lee EB. The Cryo-EM Effect: Structural Biology of Neurodegenerative Disease Proteostasis Factors. J Neuropathol Exp Neurol 2021; 80:494-513. [PMID: 33860329 DOI: 10.1093/jnen/nlab029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neurodegenerative diseases are characterized by the accumulation of misfolded proteins. This protein aggregation suggests that abnormal proteostasis contributes to aging-related neurodegeneration. A better fundamental understanding of proteins that regulate proteostasis may provide insight into the pathophysiology of neurodegenerative disease and may perhaps reveal novel therapeutic opportunities. The 26S proteasome is the key effector of the ubiquitin-proteasome system responsible for degrading polyubiquitinated proteins. However, additional factors, such as valosin-containing protein (VCP/p97/Cdc48) and C9orf72, play a role in regulation and trafficking of substrates through the normal proteostasis systems of a cell. Nonhuman AAA+ ATPases, such as the disaggregase Hsp104, also provide insights into the biochemical processes that regulate protein aggregation. X-ray crystallography and cryo-electron microscopy (cryo-EM) structures not bound to substrate have provided meaningful information about the 26S proteasome, VCP, and Hsp104. However, recent cryo-EM structures bound to substrate have provided new information about the function and mechanism of these proteostasis factors. Cryo-EM and cryo-electron tomography data combined with biochemical data have also increased the understanding of C9orf72 and its role in maintaining proteostasis. These structural insights provide a foundation for understanding proteostasis mechanisms with near-atomic resolution upon which insights can be gleaned regarding the pathophysiology of neurodegenerative diseases.
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Affiliation(s)
- Benjamin C Creekmore
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yi-Wei Chang
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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30
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Wu R, Wei Z, Zhang L. Structural insight into mutations at 155 position of valosin containing protein (VCP) linked to inclusion body myopathy with Paget disease of bone and frontotemporal Dementia. Saudi J Biol Sci 2021; 28:2128-2138. [PMID: 33911929 PMCID: PMC8071901 DOI: 10.1016/j.sjbs.2021.02.048] [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: 11/19/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 10/31/2022] Open
Abstract
Mutations in Valosin-containing protein (VCP) have been implicated in the pathology linked to inclusion body myopathy, paget disease of bone and frontotemporal dementia (IBMPFD). VCP is an essential component of AAA-ATPase superfamily involved in various cellular functions. Advanced In-silico analysis was performed using prediction based servers to determine the most deleterious mutation. Molecular dynamics simulation was used to study the protein dynamics at atomic level. Molecular docking was used to study the effect of mutation on ATP/ADP transition in the kinase domain. This ATPase of 806 amino acids has four domains: N-terminal domain, C-terminal domain and two ATPase domains D1 and D2 and each of these domains have a distinct role in its functioning. The mutations in VCP protein are distributed among regions known as hotspots, one such hotspot is codon 155. Three missense mutations reported in this hotspot are R155C, R155H and R155P. Potentiality of the deleteriousness calculated using server based prediction models reveal R155C mutation to be the most deleterious. The atomic insight into the effect of mutation by molecular dynamics simulation revealed major conformational changes in R155C variants ATP binding site in D1 domain. The nucleotide-binding mode at the catalytic pocket of VCP and its three variants at codon 155 showed change in the structure, which affects the ATP-ADP transition kinetics in all the three variants.
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Affiliation(s)
- Rui Wu
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Zhijie Wei
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Li Zhang
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
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31
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Kaneko Y, Shimoda K, Ayala R, Goto Y, Panico S, Zhang X, Kondo H. p97 and p47 function in membrane tethering in cooperation with FTCD during mitotic Golgi reassembly. EMBO J 2021; 40:e105853. [PMID: 33555040 DOI: 10.15252/embj.2020105853] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/26/2020] [Accepted: 12/17/2020] [Indexed: 11/09/2022] Open
Abstract
p97ATPase-mediated membrane fusion is required for the biogenesis of the Golgi complex. p97 and its cofactor p47 function in soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor (SNARE) priming, but the tethering complex for p97/p47-mediated membrane fusion remains unknown. In this study, we identified formiminotransferase cyclodeaminase (FTCD) as a novel p47-binding protein. FTCD mainly localizes to the Golgi complex and binds to either p47 or p97 via its association with their polyglutamate motifs. FTCD functions in p97/p47-mediated Golgi reassembly at mitosis in vivo and in vitro via its binding to p47 and to p97. We also showed that FTCD, p47, and p97 form a big FTCD-p97/p47-FTCD tethering complex. In vivo tethering assay revealed that FTCD that was designed to localize to mitochondria caused mitochondria aggregation at mitosis by forming a complex with endogenous p97 and p47, which support a role for FTCD in tethering biological membranes in cooperation with the p97/p47 complex. Therefore, FTCD is thought to act as a tethering factor by forming the FTCD-p97/p47-FTCD complex in p97/p47-mediated Golgi membrane fusion.
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Affiliation(s)
- Yayoi Kaneko
- Department of Molecular Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kyohei Shimoda
- Department of Molecular Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Rafael Ayala
- Section of Structural Biology, Department of Infectious Diseases, Imperial College London, London, UK
| | - Yukina Goto
- Department of Molecular Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Silvia Panico
- Section of Structural Biology, Department of Infectious Diseases, Imperial College London, London, UK
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Infectious Diseases, Imperial College London, London, UK
| | - Hisao Kondo
- Department of Molecular Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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32
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Huang TN, Shih YT, Lin SC, Hsueh YP. Social behaviors and contextual memory of Vcp mutant mice are sensitive to nutrition and can be ameliorated by amino acid supplementation. iScience 2020; 24:101949. [PMID: 33437936 PMCID: PMC7786123 DOI: 10.1016/j.isci.2020.101949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/01/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023] Open
Abstract
Both genetic variations and nutritional deficiency are associated with autism spectrum disorders and other neurological disorders. However, it is less clear whether or how nutritional deficiency and genetic variations influence each other under pathogenic conditions. "Valosin-containing protein" (VCP, also known as p97) is associated with multiple neurological disorders and regulates dendritic spine formation by controlling endoplasmic reticulum formation and protein synthesis efficiency. Increased protein synthesis ameliorates the dendritic spine defects of Vcp-deficient neurons. Therefore, we investigated if Vcp-deficient mice are sensitive to nutritional conditions. Here, we show that social interaction and contextual memory of Vcp-deficient mice are indeed influenced by different dietary protein levels. Moreover, leucine supplementation ameliorates the behavioral deficits and dendritic spine density of Vcp-deficient mice, strengthening evidence for the role of protein synthesis in VCP function. Our study illustrates that genetic variation and nutrient factors cross-talk to influence neuronal and behavioral phenotypes.
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Affiliation(s)
- Tzyy-Nan Huang
- Institute of Molecular Biology, Academia Sinica, 128, Academia Road, Section 2, Taipei 11529, Taiwan, Republic of China
| | - Yu-Tzu Shih
- Institute of Molecular Biology, Academia Sinica, 128, Academia Road, Section 2, Taipei 11529, Taiwan, Republic of China
| | - Si-Cih Lin
- Institute of Molecular Biology, Academia Sinica, 128, Academia Road, Section 2, Taipei 11529, Taiwan, Republic of China
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, 128, Academia Road, Section 2, Taipei 11529, Taiwan, Republic of China
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33
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Talsness DM, Owings KG, Coelho E, Mercenne G, Pleinis JM, Partha R, Hope KA, Zuberi AR, Clark NL, Lutz CM, Rodan AR, Chow CY. A Drosophila screen identifies NKCC1 as a modifier of NGLY1 deficiency. eLife 2020; 9:57831. [PMID: 33315011 PMCID: PMC7758059 DOI: 10.7554/elife.57831] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 12/12/2020] [Indexed: 12/12/2022] Open
Abstract
N-Glycanase 1 (NGLY1) is a cytoplasmic deglycosylating enzyme. Loss-of-function mutations in the NGLY1 gene cause NGLY1 deficiency, which is characterized by developmental delay, seizures, and a lack of sweat and tears. To model the phenotypic variability observed among patients, we crossed a Drosophila model of NGLY1 deficiency onto a panel of genetically diverse strains. The resulting progeny showed a phenotypic spectrum from 0 to 100% lethality. Association analysis on the lethality phenotype, as well as an evolutionary rate covariation analysis, generated lists of modifying genes, providing insight into NGLY1 function and disease. The top association hit was Ncc69 (human NKCC1/2), a conserved ion transporter. Analyses in NGLY1-/- mouse cells demonstrated that NKCC1 has an altered average molecular weight and reduced function. The misregulation of this ion transporter may explain the observed defects in secretory epithelium function in NGLY1 deficiency patients.
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Affiliation(s)
- Dana M Talsness
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Katie G Owings
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Emily Coelho
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Gaelle Mercenne
- Department of Internal Medicine, Division of Nephrology and Hypertension, and Molecular Medicine Program, University of Utah, Salt Lake City, United States
| | - John M Pleinis
- Department of Internal Medicine, Division of Nephrology and Hypertension, and Molecular Medicine Program, University of Utah, Salt Lake City, United States
| | - Raghavendran Partha
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United States
| | - Kevin A Hope
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Aamir R Zuberi
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, United States
| | - Nathan L Clark
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Cathleen M Lutz
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, United States
| | - Aylin R Rodan
- Department of Internal Medicine, Division of Nephrology and Hypertension, and Molecular Medicine Program, University of Utah, Salt Lake City, United States.,Medical Service, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, United States
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
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White Spot Syndrome Virus Benefits from Endosomal Trafficking, Substantially Facilitated by a Valosin-Containing Protein, To Escape Autophagic Elimination and Propagate in the Crustacean Cherax quadricarinatus. J Virol 2020; 94:JVI.01570-20. [PMID: 32967962 DOI: 10.1128/jvi.01570-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/15/2020] [Indexed: 12/19/2022] Open
Abstract
As the most severely lethal viral pathogen for crustaceans in both brackish water and freshwater, white spot syndrome virus (WSSV) has a mechanism of infection that remains largely unknown, which profoundly limits the control of WSSV disease. By using a hematopoietic tissue (Hpt) stem cell culture from the red claw crayfish Cherax quadricarinatus suitable for WSSV propagation in vitro, the intracellular trafficking of live WSSV, in which the acidic-pH-dependent endosomal environment was a prerequisite for WSSV fusion, was determined for the first time via live-cell imaging. When the acidic pH within the endosome was alkalized by chemicals, the intracellular WSSV virions were detained in dysfunctional endosomes, resulting in appreciable blocking of the viral infection. Furthermore, disrupted valosin-containing protein (C. quadricarinatus VCP [CqVCP]) activity resulted in considerable aggregation of endocytic WSSV virions in the disordered endosomes, which subsequently recruited autophagosomes, likely by binding to CqGABARAP via CqVCP, to eliminate the aggregated virions within the dysfunctional endosomes. Importantly, both autophagic sorting and the degradation of intracellular WSSV virions were clearly enhanced in Hpt cells with increased autophagic activity, demonstrating that autophagy played a defensive role against WSSV infection. Intriguingly, most of the endocytic WSSV virions were directed to the endosomal delivery system facilitated by CqVCP activity so that they avoided autophagy degradation and successfully delivered the viral genome into Hpt cell nuclei, which was followed by the propagation of progeny virions. These findings will benefit anti-WSSV target design against the most severe viral disease currently affecting farmed crustaceans.IMPORTANCE White spot disease is currently the most devastating viral disease in farmed crustaceans, such as shrimp and crayfish, and has resulted in a severe ecological problem for both brackish water and freshwater aquaculture areas worldwide. Efficient antiviral control of WSSV disease is still lacking due to our limited knowledge of its pathogenesis. Importantly, research on the WSSV infection mechanism is also quite meaningful for the elucidation of viral pathogenesis and virus-host coevolution, as WSSV is one of the largest animal viruses, in terms of genome size, that infects only crustaceans. Here, we found that most of the endocytic WSSV virions were directed to the endosomal delivery system, strongly facilitated by CqVCP, so that they avoided autophagic degradation and successfully delivered the viral genome into the Hpt cell nucleus for propagation. Our data point to a virus-sorting model that might also explain the escape of other enveloped DNA viruses.
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Kracht M, van den Boom J, Seiler J, Kröning A, Kaschani F, Kaiser M, Meyer H. Protein Phosphatase-1 Complex Disassembly by p97 is Initiated through Multivalent Recognition of Catalytic and Regulatory Subunits by the p97 SEP-domain Adapters. J Mol Biol 2020; 432:6061-6074. [PMID: 33058883 DOI: 10.1016/j.jmb.2020.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 12/19/2022]
Abstract
The AAA-ATPase VCP/p97 cooperates with the SEP-domain adapters p37, UBXN2A and p47 in stripping inhibitor-3 (I3) from protein phosphatase-1 (PP1) for activation. In contrast to p97-mediated degradative processes, PP1 complex disassembly is ubiquitin-independent. It is therefore unclear how selective targeting is achieved. Using biochemical reconstitution and crosslink mass spectrometry, we show here that SEP-domain adapters use a multivalent substrate recognition strategy. An N-terminal sequence element predicted to form a helix, together with the SEP-domain, binds and engages the direct target I3 in the central pore of p97 for unfolding, while its partner PP1 is held by a linker between SHP box and UBX domain locked onto the peripheral N-domain of p97. Although the I3-binding element is functional in p47, p47 in vitro requires a transplant of the PP1-binding linker from p37 for activity stressing that both sites are essential to control specificity. Of note, unfolding is then governed by an inhibitory segment in the N-terminal region of p47, suggesting a regulatory function. Together, this study reveals how p97 adapters engage a protein complex for ubiquitin-independent disassembly while ensuring selectivity for one subunit.
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Affiliation(s)
- Matthias Kracht
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Johannes van den Boom
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jonas Seiler
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Alexander Kröning
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology and Analytics Core Facility, Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Markus Kaiser
- Chemical Biology and Analytics Core Facility, Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Hemmo Meyer
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany.
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36
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An intrinsically disordered motif regulates the interaction between the p47 adaptor and the p97 AAA+ ATPase. Proc Natl Acad Sci U S A 2020; 117:26226-26236. [PMID: 33028677 DOI: 10.1073/pnas.2013920117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
VCP/p97, an enzyme critical to proteostasis, is regulated through interactions with protein adaptors targeting it to specific cellular tasks. One such adaptor, p47, forms a complex with p97 to direct lipid membrane remodeling. Here, we use NMR and other biophysical methods to study the structural dynamics of p47 and p47-p97 complexes. Disordered regions in p47 are shown to be critical in directing intra-p47 and p47-p97 interactions via a pair of previously unidentified linear motifs. One of these, an SHP domain, regulates p47 binding to p97 in a manner that depends on the nucleotide state of p97. NMR and electron cryomicroscopy data have been used as restraints in molecular dynamics trajectories to develop structural ensembles for p47-p97 complexes in adenosine diphosphate (ADP)- and adenosine triphosphate (ATP)-bound conformations, highlighting differences in interactions in the two states. Our study establishes the importance of intrinsically disordered regions in p47 for the formation of functional p47-p97 complexes.
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37
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Garrison P, Bangs JD. p97 Inhibitor CB-5083 Blocks ERAD in Trypanosoma brucei. Mol Biochem Parasitol 2020; 239:111313. [PMID: 32735998 DOI: 10.1016/j.molbiopara.2020.111313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 11/26/2022]
Abstract
Misfolded proteins trapped in the endoplasmic reticulum (ER) are specifically recognized and retrotranslocated to the cytosol by the ER-Associated Degradation (ERAD) system and delivered to the proteasome for destruction. This process was recently described in Trypanosoma brucei (T. brucei) using the misfolded epitope tagged Transferrin Receptor subunits ESAG7:Ty and HA:ESAG6 (HA:E6). Critical to this work was the proteasomal inhibitor MG132. However, MG132 has off-target inhibitory effects on lysosomal Cathepsin L that could cause misinterpretation of turnover results. Here, we evaluate an orally bioavailable p97 inhibitor, CB-5083, for use in T. brucei. p97 is a ubiquitous protein involved in many cellular events including the membrane extraction step of ERAD. CB-5083 strongly inhibits turnover of HA:E6, with comparable protein recovery to MG132 treatment. Interestingly, little deglycosylated cytoplasmic species accumulates, though it normally emerges with MG132 treatment. This suggests that CB-5083 blocks ERAD upstream of the proteasome, as expected for inhibition of the trypanosomal p97 orthologue TbVCP. Under CB-5083 treatment, HA:E6 is also strongly membrane-associated, suggesting ER localization. Finally, we provide an experimental example where CB-5083 treatment offers clarity to the off-target effects of MG132 treatment.
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Affiliation(s)
- Paige Garrison
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY, 14203, USA
| | - James D Bangs
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY, 14203, USA.
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38
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Sukkaew A, Suksatu A, Roytrakul S, Smith DR, Ubol S. Proteomic analysis of CHIKV-infected human fibroblast-like synoviocytes: Identification of host factors potentially associated with CHIKV replication and cellular pathogenesis. Microbiol Immunol 2020; 64:445-457. [PMID: 32246487 DOI: 10.1111/1348-0421.12793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/21/2020] [Accepted: 03/26/2020] [Indexed: 01/02/2023]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne virus that causes arthralgic fever. Fibroblast-like synoviocytes play a key role in joint damage in inflammatory arthritides and can additionally serve as target cells for CHIKV infection. To gain a better understanding of CHIKV-induced arthralgia, the interaction between CHIKV and synoviocytes was investigated at the protein level. A gel-enhanced liquid chromatography-mass spectrometry (GeLC-MS/MS) approach was used to examine protein expression from primary human fibroblast-like synoviocytes (HFLS) infected with clinical isolates of CHIKV at 12 and 24 hr post infection. Our analysis identified 259 and 241 proteins of known function that were differentially expressed (>1.5 or <-1.5 fold change) following CHIKV infection at 12 and 24 hpi, respectively. These proteins are involved in cellular homeostasis, including cellular trafficking, cytoskeletal organization, immune response, metabolic process, and protein modification. Some of these proteins have previously been reported to participate in arthralgia/arthritis and the death of infected cells. Our results provide information on the CHIKV-induced modulation of cellular proteins of HFLS at an early stage of infection, as well as highlighting biological processes associated with CHIKV infection in the main target cells of the joint.
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Affiliation(s)
- Apamas Sukkaew
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Ampa Suksatu
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sittiruk Roytrakul
- Proteomics Research Laboratory, Genome Institute, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Duncan R Smith
- Center for Emerging and Neglected Infectious Diseases, Mahidol University, Bangkok, Thailand.,Institute of Molecular Bioscience, Mahidol University Salaya Campus, Nakorn Pathom, Thailand
| | - Sukathida Ubol
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Center for Emerging and Neglected Infectious Diseases, Mahidol University, Bangkok, Thailand
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39
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Sui X, Pan M, Li YM. Insights into the Design of p97-targeting Small Molecules from Structural Studies on p97 Functional Mechanism. Curr Med Chem 2020; 27:298-316. [PMID: 31584361 DOI: 10.2174/0929867326666191004162411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/24/2019] [Accepted: 08/27/2019] [Indexed: 12/14/2022]
Abstract
p97, also known as valosin-containing protein or CDC48, is a member of the AAA+ protein family that is highly conserved in eukaryotes. It binds to various cofactors in the body to perform its protein-unfolding function and participates in DNA repair, degradation of subcellular membrane proteins, and protein quality control pathways, among other processes. Its malfunction can lead to many diseases, such as inclusion body myopathy, associated with Paget's disease of bone and/or frontotemporal dementia, amyotrophic lateral sclerosis disease, and others. In recent years, many small-molecule inhibitors have been deployed against p97, including bis (diethyldithiocarbamate)- copper and CB-5083, which entered the first phase of clinical tests but failed. One bottleneck in the design of p97 drugs is that its molecular mechanism remains unclear. This paper summarizes recent studies on the molecular mechanisms of p97, which may lead to insight into how the next generation of small molecules targeting p97 can be designed.
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Affiliation(s)
- Xin Sui
- Department of Chemistry, Tsinghua University, Beijing 100086, China
| | - Man Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Yi-Ming Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
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40
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Abstract
p97 belongs to the functional diverse superfamily of AAA+ (ATPases Associated with diverse cellular Activities) ATPases and is characterized by an N-terminal regulatory domain and two stacked hexameric ATPase domains forming a central protein conducting channel. p97 is highly versatile and has key functions in maintaining protein homeostasis including protein quality control mechanisms like the ubiquitin proteasome system (UPS) and autophagy to disassemble polyubiquitylated proteins from chromatin, membranes, macromolecular protein complexes and aggregates which are either degraded by the proteasome or recycled. p97 can use energy derived from ATP hydrolysis to catalyze substrate unfolding and threading through its central channel. The function of p97 in a large variety of different cellular contexts is reflected by its simultaneous association with different cofactors, which are involved in substrate recognition and processing, thus leading to the formation of transient multi-protein complexes. Dysregulation in protein homeostasis and proteotoxic stress are often involved in the development of cancer and neurological diseases and targeting the UPS including p97 in cancer is a well-established pharmacological strategy. In this chapter we will describe structural and functional aspects of the p97 interactome in regulating diverse cellular processes and will discuss the role of p97 in targeted cancer therapy.
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41
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Figuerola-Conchas A, Saarbach J, Daguer JP, Cieren A, Barluenga S, Winssinger N, Gotta M. Small-Molecule Modulators of the ATPase VCP/p97 Affect Specific p97 Cellular Functions. ACS Chem Biol 2020; 15:243-253. [PMID: 31790201 DOI: 10.1021/acschembio.9b00832] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
VCP/p97 belongs to the AAA+ ATPase family and has an essential role in several cellular processes ranging from cell division to protein homeostasis. Compounds targeting p97 inhibit the main ATPase domain and cause cell death. Here, using PNA-encoded chemical libraries, we have identified two small molecules that target the regulatory domain of p97, comprising the N-terminal and the D1 ATPase domains, and do not cause cell death. One molecule, NW1028, inhibits the degradation of a p97-dependent reporter, whereas the other, NW1030, increases it. ATPase assays show that NW1028 and NW1030 do not affect the main catalytic domain of p97. Mapping of the binding site using a photoaffinity conjugate points to a cleft at the interface of the N-terminal and the D1 ATPase domains. We have therefore discovered two new compounds that bind to the regulatory domain of p97 and modulate specific p97 cellular functions. Using these compounds, we have revealed a role for p97 in the regulation of mitotic spindle orientation in HeLa cells.
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Affiliation(s)
- Ainoa Figuerola-Conchas
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Jacques Saarbach
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Adeline Cieren
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Nicolas Winssinger
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Monica Gotta
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
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42
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Stach L, Morgan RM, Makhlouf L, Douangamath A, von Delft F, Zhang X, Freemont PS. Crystal structure of the catalytic D2 domain of the AAA+ ATPase p97 reveals a putative helical split-washer-type mechanism for substrate unfolding. FEBS Lett 2019; 594:933-943. [PMID: 31701538 PMCID: PMC7154655 DOI: 10.1002/1873-3468.13667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/29/2019] [Accepted: 10/31/2019] [Indexed: 01/14/2023]
Abstract
Several pathologies have been associated with the AAA+ ATPase p97, an enzyme essential to protein homeostasis. Heterozygous polymorphisms in p97 have been shown to cause neurological disease, while elevated proteotoxic stress in tumours has made p97 an attractive cancer chemotherapy target. The cellular processes reliant on p97 are well described. High‐resolution structural models of its catalytic D2 domain, however, have proved elusive, as has the mechanism by which p97 converts the energy from ATP hydrolysis into mechanical force to unfold protein substrates. Here, we describe the high‐resolution structure of the p97 D2 ATPase domain. This crystal system constitutes a valuable tool for p97 inhibitor development and identifies a potentially druggable pocket in the D2 domain. In addition, its P61 symmetry suggests a mechanism for substrate unfolding by p97. Database The atomic coordinates and structure factors have been deposited in the PDB database under the accession numbers http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6G2V, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6G2W, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6G2X, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6G2Y, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6G2Z and http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6G30.
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Affiliation(s)
- Lasse Stach
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, UK
| | - Rhodri Marc Morgan
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, UK
| | - Linda Makhlouf
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, UK
| | - Alice Douangamath
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, UK
| | - Frank von Delft
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, UK.,Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, UK.,Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Xiaodong Zhang
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, UK
| | - Paul S Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, UK
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43
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Brody MJ, Vanhoutte D, Bakshi CV, Liu R, Correll RN, Sargent MA, Molkentin JD. Disruption of valosin-containing protein activity causes cardiomyopathy and reveals pleiotropic functions in cardiac homeostasis. J Biol Chem 2019; 294:8918-8929. [PMID: 31006653 DOI: 10.1074/jbc.ra119.007585] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/08/2019] [Indexed: 01/14/2023] Open
Abstract
Valosin-containing protein (VCP), also known as p97, is an ATPase with diverse cellular functions, although the most highly characterized is targeting of misfolded or aggregated proteins to degradation pathways, including the endoplasmic reticulum-associated degradation (ERAD) pathway. However, how VCP functions in the heart has not been carefully examined despite the fact that human mutations in VCP cause Paget disease of bone and frontotemporal dementia, an autosomal dominant multisystem proteinopathy that includes disease in the heart, skeletal muscle, brain, and bone. Here we generated heart-specific transgenic mice overexpressing WT VCP or a VCPK524A mutant with deficient ATPase activity. Transgenic mice overexpressing WT VCP exhibit normal cardiac structure and function, whereas mutant VCP-overexpressing mice develop cardiomyopathy. Mechanistically, mutant VCP-overexpressing hearts up-regulate ERAD complex components and have elevated levels of ubiquitinated proteins prior to manifestation of cardiomyopathy, suggesting dysregulation of ERAD and inefficient clearance of proteins targeted for proteasomal degradation. The hearts of mutant VCP transgenic mice also exhibit profound defects in cardiomyocyte nuclear morphology with increased nuclear envelope proteins and nuclear lamins. Proteomics revealed overwhelming interactions of endogenous VCP with ribosomal, ribosome-associated, and RNA-binding proteins in the heart, and impairment of cardiac VCP activity resulted in aggregation of large ribosomal subunit proteins. These data identify multifactorial functions and diverse mechanisms whereby VCP regulates cardiomyocyte protein and RNA quality control that are critical for cardiac homeostasis, suggesting how human VCP mutations negatively affect the heart.
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Affiliation(s)
- Matthew J Brody
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039
| | - Davy Vanhoutte
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039
| | - Chinmay V Bakshi
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039
| | - Ruije Liu
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039.,the Department of Biomedical Sciences, Grand Valley State University, Allendale, Michigan 49401, and
| | - Robert N Correll
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039.,the Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487-0344
| | - Michelle A Sargent
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039
| | - Jeffery D Molkentin
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039, .,the Howard Hughes Medical Institute, Cincinnati, Ohio 45229-3039
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44
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Non-Proteasomal UbL-UbA Family of Proteins in Neurodegeneration. Int J Mol Sci 2019; 20:ijms20081893. [PMID: 30999567 PMCID: PMC6514573 DOI: 10.3390/ijms20081893] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022] Open
Abstract
Ubiquitin-like/ubiquitin-associated proteins (UbL-UbA) are a well-studied family of non-proteasomal ubiquitin receptors that are evolutionarily conserved across species. Members of this non-homogenous family facilitate and support proteasomal activity by promoting different effects on proteostasis but exhibit diverse extra-proteasomal activities. Dysfunctional UbL-UbA proteins render cells, particularly neurons, more susceptible to stressors or aging and may cause earlier neurodegeneration. In this review, we summarized the properties and functions of UbL-UbA family members identified to date, with an emphasis on new findings obtained using Drosophila models showing a direct or indirect role in some neurodegenerative diseases.
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45
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Sarkar B, Nishikata I, Nakahata S, Ichikawa T, Shiraga T, Saha HR, Fujii M, Tanaka Y, Shimoda K, Morishita K. Degradation of p47 by autophagy contributes to CADM1 overexpression in ATLL cells through the activation of NF-κB. Sci Rep 2019; 9:3491. [PMID: 30837480 PMCID: PMC6400899 DOI: 10.1038/s41598-019-39424-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/25/2018] [Indexed: 12/20/2022] Open
Abstract
Cell adhesion molecule 1 (CADM1), a member of the immunoglobulin superfamily, is identified as a novel cell surface marker for human T-cell leukemia virus (HTLV-1)-infected T cells. Adult T-cell leukemia/lymphoma (ATLL) is developed in HTLV-1-infected T-cells after a long infection period. To examine the mechanism of CADM1 overexpression in ATLL, we first identified that CADM1 is transcriptionally up-regulated by a transcriptional enhancer element through NF-κB signaling pathway. In HTLV-1-infected T-cells, CADM1 expression is dependent on HTLV-1/Tax through activation of canonical and non-canonical NF-κB; however, in ATLL cells with frequent loss of Tax expression, the activation of canonical NF-κB only enhances the CADM1 expression. Along with active mutations in signaling molecules under T-cell recepor (TCR) signaling, degradation of p47, a negative regulator of NF-κB, was essential for activation of canonical NF-κB through stabilization of NEMO (NF-κB essential modulator). The mechanism of p47 degradation is primarily dependent on activation of lysosomal-autophagy and the autophagy is activated in most of the HTLV-infected and ATLL cells, suggesting that the p47 degradation may be a first key molecular event during HTLV-1 infection to T-cells as a connector of two important signaling pathways, NF-κB and autophagy.
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Affiliation(s)
- Bidhan Sarkar
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Ichiro Nishikata
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Shingo Nakahata
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Tomonaga Ichikawa
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Toshiyuki Shiraga
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.,Department of Foods and Human Nutrition, Faculty of Human Life Sciences, Notre Dame Seishin University, Okayama, Japan
| | - Hasi Rani Saha
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Masahiro Fujii
- Division of Virology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yuetsu Tanaka
- Department of Immunology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kazuya Shimoda
- Division of Gastroenterology and Hematology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Kazuhiro Morishita
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
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46
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Li Y, Liu T, Zhang J. The ATPase TER94 regulates Notch signaling during Drosophila wing development. Biol Open 2019; 8:bio.038984. [PMID: 30530809 PMCID: PMC6361195 DOI: 10.1242/bio.038984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The evolutionarily conserved Notch signaling pathway plays crucial roles in various developmental contexts. Multiple mechanisms are involved in the regulation of Notch pathway activity. Identified through a genetic mosaic screen, we show that the ATPase TER94 acts as a positive regulator of Notch signaling during Drosophila wing development. Depletion of TER94 causes marginal notches in the adult wing and the reduction of Notch target genes wingless and cut during wing margin formation. We provide evidence that TER94 is likely required for proper Notch protein localization and activation. Furthermore, we show that knockdown of the TER94 adaptor p47 leads to similar Notch signaling defects. Although the TER94 complex is implicated in various cellular processes, its role in the regulation of Notch pathways was previously uncharacterized. Our study demonstrates that TER94 positively regulates Notch signaling and thus reveals a novel role of TER94 in development. This article has an associated First Person interview with the first author of the paper. Summary: Our study demonstrates that the ATPase TER94 and the p47 adaptor positively regulate Notch signaling during Drosophila wing development, thus establishing a functional interaction between TER94 and Notch signaling activity.
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Affiliation(s)
- Yunlong Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100094 Beijing, China
| | - Tong Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100094 Beijing, China
| | - Junzheng Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100094 Beijing, China
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47
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Abstract
The Golgi apparatus is a central intracellular membrane-bound organelle with key functions in trafficking, processing, and sorting of newly synthesized membrane and secretory proteins and lipids. To best perform these functions, Golgi membranes form a unique stacked structure. The Golgi structure is dynamic but tightly regulated; it undergoes rapid disassembly and reassembly during the cell cycle of mammalian cells and is disrupted under certain stress and pathological conditions. In the past decade, significant amount of effort has been made to reveal the molecular mechanisms that regulate the Golgi membrane architecture and function. Here we review the major discoveries in the mechanisms of Golgi structure formation, regulation, and alteration in relation to its functions in physiological and pathological conditions to further our understanding of Golgi structure and function in health and diseases.
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Affiliation(s)
- Jie Li
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Erpan Ahat
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
- Department of Neurology, University of Michigan School of Medicine, Ann Arbor, MI, USA.
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48
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p47 licenses activation of the immune deficiency pathway in the tick Ixodes scapularis. Proc Natl Acad Sci U S A 2018; 116:205-210. [PMID: 30559180 DOI: 10.1073/pnas.1808905116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The E3 ubiquitin ligase X-linked inhibitor of apoptosis (XIAP) acts as a molecular rheostat for the immune deficiency (IMD) pathway of the tick Ixodes scapularis How XIAP activates the IMD pathway in response to microbial infection remains ill defined. Here, we identified the XIAP enzymatic substrate p47 as a positive regulator of the I. scapularis IMD network. XIAP polyubiquitylates p47 in a lysine 63-dependent manner and interacts with the p47 ubiquitin-like (UBX) module. p47 also binds to Kenny (IKKγ/NEMO), the regulatory subunit of the inhibitor of nuclear factor (NF)- κB kinase complex. Replacement of the amino acid lysine to arginine within the p47 linker region completely abrogated molecular interactions with Kenny. Furthermore, mitigation of p47 transcription levels through RNA interference in I. scapularis limited Kenny accumulation, reduced phosphorylation of IKKβ (IRD5), and impaired cleavage of the NF-κB molecule Relish. Accordingly, disruption of p47 expression increased microbial colonization by the Lyme disease spirochete Borrelia burgdorferi and the rickettsial agent Anaplasma phagocytophilum Collectively, we highlight the importance of ticks for the elucidation of paradigms in arthropod immunology. Manipulating immune signaling cascades within I. scapularis may lead to innovative approaches to reducing the burden of tick-borne diseases.
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Wang KZQ, Steer E, Otero PA, Bateman NW, Cheng MH, Scott AL, Wu C, Bahar I, Shih YT, Hsueh YP, Chu CT. PINK1 Interacts with VCP/p97 and Activates PKA to Promote NSFL1C/p47 Phosphorylation and Dendritic Arborization in Neurons. eNeuro 2018; 5:ENEURO.0466-18.2018. [PMID: 30783609 PMCID: PMC6377406 DOI: 10.1523/eneuro.0466-18.2018] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 01/06/2023] Open
Abstract
While PTEN-induced kinase 1 (PINK1) is well characterized for its role in mitochondrial homeostasis, much less is known concerning its ability to prevent synaptodendritic degeneration. Using unbiased proteomic methods, we identified valosin-containing protein (VCP) as a major PINK1-interacting protein. RNAi studies demonstrate that both VCP and its cofactor NSFL1C/p47 are necessary for the ability of PINK1 to increase dendritic complexity. Moreover, PINK1 regulates phosphorylation of p47, but not the VCP co-factor UFD1. Although neither VCP nor p47 interact directly with PKA, we found that PINK1 binds and phosphorylates the catalytic subunit of PKA at T197 [PKAcat(pT197)], a site known to activate the PKA holoenzyme. PKA in turn phosphorylates p47 at a novel site (S176) to regulate dendritic complexity. Given that PINK1 physically interacts with both the PKA holoenzyme and the VCP-p47 complex to promote dendritic arborization, we propose that PINK1 scaffolds a novel PINK1-VCP-PKA-p47 signaling pathway to orchestrate dendritogenesis in neurons. These findings highlight an important mechanism by which proteins genetically implicated in Parkinson's disease (PD; PINK1) and frontotemporal dementia (FTD; VCP) interact to support the health and maintenance of neuronal arbors.
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Affiliation(s)
- Kent Z. Q. Wang
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Erin Steer
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - P. Anthony Otero
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Nicholas W. Bateman
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Ana Ligia Scott
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Christine Wu
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Ivet Bahar
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Yu-Tzu Shih
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan 11529
| | - Yi-Ping Hsueh
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan 11529
| | - Charleen T. Chu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
- Pittsburgh Institute for Neurodegenerative Diseases, McGowan Institute for Regenerative Medicine, Center for Protein Conformational Diseases and Center for Neuroscience at the University of Pittsburgh, Pittsburgh, PA 15213
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Ubiquitin-Independent Disassembly by a p97 AAA-ATPase Complex Drives PP1 Holoenzyme Formation. Mol Cell 2018; 72:766-777.e6. [PMID: 30344098 DOI: 10.1016/j.molcel.2018.09.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/15/2018] [Accepted: 09/13/2018] [Indexed: 12/12/2022]
Abstract
The functional diversity of protein phosphatase-1 (PP1), with its countless substrates, relies on the ordered assembly of alternative PP1 holoenzymes. Here, we show that newly synthesized PP1 is first held by its partners SDS22 and inhibitor-3 (I3) in an inactive complex, which needs to be disassembled by the p97 AAA-ATPase to promote exchange to substrate specifiers. Unlike p97-mediated degradative processes that require the Ufd1-Npl4 ubiquitin adapters, p97 is targeted to PP1 by p37 and related adapter proteins. Reconstitution with purified components revealed direct interaction of the p37 SEP domain with I3 without the need for ubiquitination, and ATP-driven pulling of I3 into the central channel of the p97 hexamer, which triggers dissociation of I3 and SDS22. Thus, we establish regulatory ubiquitin-independent protein complex disassembly as part of the functional arsenal of p97 and define an unanticipated essential step in PP1 biogenesis that illustrates the molecular challenges of ordered subunit exchange.
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