1
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Arie M, Matzov D, Karmona R, Szenkier N, Stanhill A, Navon A. A non-symmetrical p97 conformation initiates a multistep recruitment of Ufd1/Npl4. iScience 2024; 27:110061. [PMID: 38947518 PMCID: PMC11214410 DOI: 10.1016/j.isci.2024.110061] [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: 02/18/2024] [Revised: 04/10/2024] [Accepted: 05/17/2024] [Indexed: 07/02/2024] Open
Abstract
In vitro experiments and cryo-EM structures of p97 and its cofactor, Ufd1/Npl4 (UN), elucidated substrate processing. Yet, the structural transitions and the related ATPase cycle upon UN binding remain unresolved. We captured two discrete conformations: One in which D1 protomers are ATP bound, while the D2 subunits are in the ADP state, presumably required for substrate engagement with the D2 pore; and a heterologous nucleotide state within the D1 ring in which only two NTDs are in the "up" ATP state that favors UN binding. Further analysis suggests that initially, UN binds p97's non-symmetrical conformation, this association promotes a structural transition upon which five NTDs shift to an "up" state and are poised to bind ATP. The UBXL domain of Npl4 was captured bound to an NTD in the ADP state, demonstrating a conformation that may provide directionality to incoming substrate and introduce the flexibility needed for substrate processing.
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Affiliation(s)
- Michal Arie
- Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Donna Matzov
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rotem Karmona
- Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Natalia Szenkier
- Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ariel Stanhill
- Department of Natural Sciences, The Open University of Israel, Raanana 4353701, Israel
| | - Ami Navon
- Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
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2
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Zhan J, Zeher A, Huang R, Tang WK, Jenkins LM, Xia D. Conformations of Bcs1L undergoing ATP hydrolysis suggest a concerted translocation mechanism for folded iron-sulfur protein substrate. Nat Commun 2024; 15:4655. [PMID: 38821922 PMCID: PMC11143374 DOI: 10.1038/s41467-024-49029-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/20/2024] [Indexed: 06/02/2024] Open
Abstract
The human AAA-ATPase Bcs1L translocates the fully assembled Rieske iron-sulfur protein (ISP) precursor across the mitochondrial inner membrane, enabling respiratory Complex III assembly. Exactly how the folded substrate is bound to and released from Bcs1L has been unclear, and there has been ongoing debate as to whether subunits of Bcs1L act in sequence or in unison hydrolyzing ATP when moving the protein cargo. Here, we captured Bcs1L conformations by cryo-EM during active ATP hydrolysis in the presence or absence of ISP substrate. In contrast to the threading mechanism widely employed by AAA proteins in substrate translocation, subunits of Bcs1L alternate uniformly between ATP and ADP conformations without detectable intermediates that have different, co-existing nucleotide states, indicating that the subunits act in concert. We further show that the ISP can be trapped by Bcs1 when its subunits are all in the ADP-bound state, which we propose to be released in the apo form.
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Affiliation(s)
- Jingyu Zhan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Allison Zeher
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- NIH Intramural Cryo-EM Consortium (NICE), Bethesda, MD, USA
| | - Rick Huang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- NIH Intramural Cryo-EM Consortium (NICE), Bethesda, MD, USA
| | - Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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3
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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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4
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Columbres RCA, Chin Y, Pratti S, Quinn C, Gonzalez-Cuyar LF, Weiss M, Quintero-Rivera F, Kimonis V. Novel Variants in the VCP Gene Causing Multisystem Proteinopathy 1. Genes (Basel) 2023; 14:genes14030676. [PMID: 36980948 PMCID: PMC10048343 DOI: 10.3390/genes14030676] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Valosin-containing protein (VCP) gene mutations have been associated with a rare autosomal dominant, adult-onset progressive disease known as multisystem proteinopathy 1 (MSP1), or inclusion body myopathy (IBM), Paget's disease of bone (PDB), frontotemporal dementia (FTD), (IBMPFD), and amyotrophic lateral sclerosis (ALS). We report the clinical and genetic analysis findings in five patients, three from the same family, with novel VCP gene variants: NM_007126.5 c.1106T>C (p.I369T), c.478G>A (p.A160T), and c.760A>T (p.I254F), associated with cardinal MSP1 manifestations including myopathy, PDB, and FTD. Our report adds to the spectrum of heterozygous pathogenic variants found in the VCP gene and the high degree of clinical heterogeneity. This case series prompts increased awareness and early consideration of MSP1 in the differential diagnosis of myopathies and/or PDB, dementia, or ALS to improve the diagnosis and early management of clinical symptoms.
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Affiliation(s)
- Rod Carlo Agram Columbres
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA 92697, USA
- College of Osteopathic Medicine, William Carey University, Hattiesburg, MS 39401, USA
| | - Yue Chin
- College of Osteopathic Medicine, William Carey University, Hattiesburg, MS 39401, USA
| | - Sanjana Pratti
- College of Osteopathic Medicine, William Carey University, Hattiesburg, MS 39401, USA
| | - Colin Quinn
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Luis F Gonzalez-Cuyar
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98104, USA
| | - Michael Weiss
- Department of Neurology, University of Washington, Seattle, WA 98195, USA
| | - Fabiola Quintero-Rivera
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA 92697, USA
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Virginia Kimonis
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA 92697, USA
- Department of Neurology, University of California, Irvine, CA 92697, USA
- Department of Pathology, University of California, Irvine, CA 92697, USA
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5
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Wang K, Chen L, Dai X, Ye Z, Zhou C, Zhang CJ, Feng Z. Synthesis and structure-activity relationships of N - (3 - (1H-imidazol-2-yl) phenyl) - 3-phenylpropionamide derivatives as a novel class of covalent inhibitors of p97/VCP ATPase. Eur J Med Chem 2023; 248:115094. [PMID: 36634454 DOI: 10.1016/j.ejmech.2023.115094] [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: 11/10/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
Noncovalent inhibitors of p97 have entered clinical studies. Compared with noncovalent inhibitors, covalent inhibitors have unique advantages in maintaining inhibitory effect and improving the resistance of the target. We previously employed the activity-based protein profiling to definitely identify p97 as the protein target of FL-18 that has a unique scaffold of benpropargylamide coupled with an imidazole. In this study, we report a thorough structure-activity-relationship study involving the new scaffold. A total of three rounds of optimization led to the discovery of the most potent covalent inhibitor of p97 to date. A chemical proteomics study indicated that the newly-synthesized compounds still targeted the C522 residue of p97 and retained selectivity among the complicated whole proteome. This study provides a suite of new covalent inhibitors of p97 to assist in its biological study and drug discovery.
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Affiliation(s)
- Ke Wang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Xiannongtan Street, Beijing, 100050, PR China
| | - Lianguo Chen
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, PR China
| | - Xinyan Dai
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Xiannongtan Street, Beijing, 100050, PR China
| | - Zi Ye
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Xiannongtan Street, Beijing, 100050, PR China; State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, PR China
| | - Chuan Zhou
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Xiannongtan Street, Beijing, 100050, PR China
| | - Chong-Jing Zhang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Xiannongtan Street, Beijing, 100050, PR China; State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, PR China.
| | - Zhiqiang Feng
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Xiannongtan Street, Beijing, 100050, PR China.
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6
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Tosar JP, Cayota A, Witwer K. Exomeres and Supermeres: monolithic or diverse? JOURNAL OF EXTRACELLULAR BIOLOGY 2022; 1:e45. [PMID: 36311878 PMCID: PMC9610496 DOI: 10.1002/jex2.45] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/31/2022] [Accepted: 05/09/2022] [Indexed: 01/11/2023]
Abstract
Extracellular vesicles (EVs), including exosomes and microvesicles, are far from being the only RNA-containing extracellular particles (EPs). Recently, new 35 nm-sized EPs were discovered by asymmetric-flow field-flow fractionation and termed "exomeres". Purification of exomeres was later performed by differential ultracentrifugation as well. More recently, the supernatant of the high-speed ultracentrifugation used to collect exomeres was further centrifuged to collect a new class of EP, termed "supermeres". Supermeres contain high quantities of extracellular RNA and are enriched in miR-1246. They are also replete in disease biomarkers and can induce metabolic and adaptive changes in recipient cells. Here, we reanalyzed proteomic and transcriptomic data obtained in this exciting study to obtain further insights into the molecular composition of exomeres and supermeres. We found that the top-ranking RNAs in supermeres correspond to the footprints of extracellular protein complexes. These complexes protect fragments of the small nuclear RNA U2 and the 28S rRNA from extracellular ribonucleases (exRNases). We suggest that intracellular nanoparticles such as the U2 ribonucleoprotein, ribosomes and LGALS3BP ring-like decamers are released into the extracellular space. These heterogeneous EPs might be further processed by exRNases and co-isolate by ultracentrifugation with other components of exomeres and supermeres. We look forward to continuing progress in defining exRNA carriers, bridging process definitions with molecular composition and function.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry UnitNuclear Research CenterSchool of ScienceUniversidad de la RepúblicaMontevideoUruguay
- Functional Genomics UnitInstitut Pasteur de MontevideoMontevideoUruguay
| | - Alfonso Cayota
- Functional Genomics UnitInstitut Pasteur de MontevideoMontevideoUruguay
- Department of MedicineUniversity HospitalUniversidad de la RepúblicaMontevideoUruguay
| | - Kenneth Witwer
- Department of Molecular and Comparative PathobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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7
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Yang L, Zhu M, Yang Y, Wang K, Che Y, Yang S, Wang J, Yu X, Li L, Wu S, Palme K, Li X. CDC48B facilitates the intercellular trafficking of SHORT-ROOT during radial patterning in roots. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:843-858. [PMID: 35088574 DOI: 10.1111/jipb.13231] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
CELL DIVISION CONTROL PROTEIN48 (CDC48) is essential for membrane fusion, protein degradation, and other cellular processes. Here, we revealed the crucial role of CDC48B in regulating periclinal cell division in roots by analyzing the recessive gen1 mutant. We identified the GEN1 gene through map-based cloning and verified that GEN1 encodes CDC48B. gen1 showed severely inhibited root growth, increased periclinal cell division in the endodermis, defective middle cortex (MC) formation, and altered ground tissue patterning in roots. Consistent with these phenotypes, CYCLIND 6;1(CYCD6;1), a periclinal cell division marker, was upregulated in gen1 compared to Col-0. The ratio of SHRpro :SHR-GFP fluorescence in pre-dividing nuclei versus the adjacent stele decreased by 33% in gen1, indicating that the trafficking of SHORT-ROOT (SHR) decreased in gen1 when endodermal cells started to divide. These findings suggest that the loss of function of CDC48B inhibits the intercellular trafficking of SHR from the stele to the endodermis, thereby decreasing SHR accumulation in the endodermis. These findings shed light on the crucial role of CDC48B in regulating periclinal cell division in roots.
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Affiliation(s)
- Lihui Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, Freiburg, D-79104, Germany
- Department of Genetics, Northwest Women's and Children's Hospital, Xi'an, 710061, China
| | - Mingyue Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Sino German Joint Research Center for Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Yi Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Sino German Joint Research Center for Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Ke Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Sino German Joint Research Center for Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Yulei Che
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Sino German Joint Research Center for Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Shurui Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Sino German Joint Research Center for Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Jinxiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510640, China
| | - Xin Yu
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Lixin Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Shuang Wu
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Klaus Palme
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, Freiburg, D-79104, Germany
- Sino German Joint Research Center for Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Xugang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Sino German Joint Research Center for Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
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8
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Cryo-EM structure of dodecamer human p97 in complex with NMS-873 reveals S 765-G 779 peptide plays critical role for D2 ring oligomerization. Biochem Biophys Res Commun 2022; 601:146-152. [PMID: 35247768 DOI: 10.1016/j.bbrc.2022.02.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 01/04/2023]
Abstract
The AAA + ATPase p97 is a well-known hexametric enzyme that is evolutionary conserved in eukaryotes. p97 contains an amino-terminal N domain, two tandem ATPase domains (D1 and D2 domain) and a C-terminal unstructured extensive tail, involved in many cellular processes and plays important biological functions, but the structural basis of p97 for its biological roles still remain unclear. Here we report the Cryo-EM structure of full-length human p97 dodecamer in 3.0 Å resolution, the structure was captured in ADP-bound form but only D1 ATPase sites were well occupied by nucleotide and D2 sites are empty, furthermore, 12 non-ATP-competitive inhibitors of NMS-873 bound in the interface between each p97 monomer. We also found that the C-terminal S765-G779 (765-'SRGFGSFRFPSGNQG'-779) peptide plays critical roles for the D2 ring oligomerization, biochemical and electron microscopy studies confirm that the S765-G779 peptide could induce the D2 ring itself to form the heptamer, this give new insights how p97 protomers assemble to the biological functional multimers.
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9
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Johnson SL, Libohova K, Blount JR, Sujkowski AL, Prifti MV, Tsou WL, Todi SV. Targeting the VCP-binding motif of ataxin-3 improves phenotypes in Drosophila models of Spinocerebellar Ataxia Type 3. Neurobiol Dis 2021; 160:105516. [PMID: 34563642 PMCID: PMC8693084 DOI: 10.1016/j.nbd.2021.105516] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/23/2021] [Accepted: 09/21/2021] [Indexed: 11/28/2022] Open
Abstract
Of the family of polyglutamine (polyQ) neurodegenerative diseases, Spinocerebellar Ataxia Type 3 (SCA3) is the most common. Like other polyQ diseases, SCA3 stems from abnormal expansions in the CAG triplet repeat of its disease gene resulting in elongated polyQ repeats within its protein, ataxin-3. Various ataxin-3 protein domains contribute to its toxicity, including the valosin-containing protein (VCP)-binding motif (VBM). We previously reported that VCP, a homo-hexameric protein, enhances pathogenic ataxin-3 aggregation and exacerbates its toxicity. These findings led us to explore the impact of targeting the SCA3 protein by utilizing a decoy protein comprising the N-terminus of VCP (N-VCP) that binds ataxin-3's VBM. The notion was that N-VCP would reduce binding of ataxin-3 to VCP, decreasing its aggregation and toxicity. We found that expression of N-VCP in Drosophila melanogaster models of SCA3 ameliorated various phenotypes, coincident with reduced ataxin-3 aggregation. This protective effect was specific to pathogenic ataxin-3 and depended on its VBM. Increasing the amount of N-VCP resulted in further phenotype improvement. Our work highlights the protective potential of targeting the VCP-ataxin-3 interaction in SCA3, a key finding in the search for therapeutic opportunities for this incurable disorder.
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Affiliation(s)
- Sean L Johnson
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jessica R Blount
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Alyson L Sujkowski
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Matthew V Prifti
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Department of Neurology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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10
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Roux B, Vaganay C, Vargas JD, Alexe G, Benaksas C, Pardieu B, Fenouille N, Ellegast JM, Malolepsza E, Ling F, Sodaro G, Ross L, Pikman Y, Conway AS, Tang Y, Wu T, Anderson DJ, Le Moigne R, Zhou HJ, Luciano F, Hartigan CR, Galinsky I, DeAngelo DJ, Stone RM, Auberger P, Schenone M, Carr SA, Guirouilh-Barbat J, Lopez B, Khaled M, Lage K, Hermine O, Hemann MT, Puissant A, Stegmaier K, Benajiba L. Targeting acute myeloid leukemia dependency on VCP-mediated DNA repair through a selective second-generation small-molecule inhibitor. Sci Transl Med 2021; 13:13/587/eabg1168. [PMID: 33790022 DOI: 10.1126/scitranslmed.abg1168] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/12/2021] [Indexed: 12/13/2022]
Abstract
The development and survival of cancer cells require adaptive mechanisms to stress. Such adaptations can confer intrinsic vulnerabilities, enabling the selective targeting of cancer cells. Through a pooled in vivo short hairpin RNA (shRNA) screen, we identified the adenosine triphosphatase associated with diverse cellular activities (AAA-ATPase) valosin-containing protein (VCP) as a top stress-related vulnerability in acute myeloid leukemia (AML). We established that AML was the most responsive disease to chemical inhibition of VCP across a panel of 16 cancer types. The sensitivity to VCP inhibition of human AML cell lines, primary patient samples, and syngeneic and xenograft mouse models of AML was validated using VCP-directed shRNAs, overexpression of a dominant-negative VCP mutant, and chemical inhibition. By combining mass spectrometry-based analysis of the VCP interactome and phospho-signaling studies, we determined that VCP is important for ataxia telangiectasia mutated (ATM) kinase activation and subsequent DNA repair through homologous recombination in AML. A second-generation VCP inhibitor, CB-5339, was then developed and characterized. Efficacy and safety of CB-5339 were validated in multiple AML models, including syngeneic and patient-derived xenograft murine models. We further demonstrated that combining DNA-damaging agents, such as anthracyclines, with CB-5339 treatment synergizes to impair leukemic growth in an MLL-AF9-driven AML murine model. These studies support the clinical testing of CB-5339 as a single agent or in combination with standard-of-care DNA-damaging chemotherapy for the treatment of AML.
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Affiliation(s)
- Blandine Roux
- Université de Paris, INSERM U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
| | - Camille Vaganay
- Université de Paris, INSERM U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
| | | | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Chaima Benaksas
- Université de Paris, INSERM U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
| | - Bryann Pardieu
- Université de Paris, INSERM U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
| | - Nina Fenouille
- Université de Paris, INSERM U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
| | - Jana M Ellegast
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Edyta Malolepsza
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Frank Ling
- Université de Paris, INSERM U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
| | - Gaetano Sodaro
- Université de Paris, INSERM U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
| | - Linda Ross
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Amy S Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | | - Tony Wu
- Cleave Therapeutics Inc., San Francisco, CA 94105, USA
| | | | | | - Han-Jie Zhou
- Cleave Therapeutics Inc., San Francisco, CA 94105, USA
| | | | - Christina R Hartigan
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Ilene Galinsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Patrick Auberger
- C3M, INSERM U1065, Team Cell Death, Differentiation, Inflammation and Cancer, 06204 Nice, France
| | - Monica Schenone
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Josée Guirouilh-Barbat
- Université de Paris, INSERM U1016 and CNRS UMR 8104, Institut Cochin, 75014 Paris, France
| | - Bernard Lopez
- Université de Paris, INSERM U1016 and CNRS UMR 8104, Institut Cochin, 75014 Paris, France
| | - Mehdi Khaled
- INSERM U1186, Gustave-Roussy Cancer Center, Université Paris-Saclay, 94805 Villejuif, France
| | - Kasper Lage
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Olivier Hermine
- Université de Paris, INSERM U1163 and CNRS 8254, Institut Imagine, Hôpital Necker, APHP, 75015 Paris, France
| | - Michael T Hemann
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Alexandre Puissant
- Université de Paris, INSERM U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France.
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA. .,Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Lina Benajiba
- Université de Paris, INSERM U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France.
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11
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Zhang G, Li S, Cheng KW, Chou TF. AAA ATPases as therapeutic targets: Structure, functions, and small-molecule inhibitors. Eur J Med Chem 2021; 219:113446. [PMID: 33873056 PMCID: PMC8165034 DOI: 10.1016/j.ejmech.2021.113446] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/21/2021] [Accepted: 03/30/2021] [Indexed: 01/07/2023]
Abstract
ATPases Associated with Diverse Cellular Activity (AAA ATPase) are essential enzymes found in all organisms. They are involved in various processes such as DNA replication, protein degradation, membrane fusion, microtubule serving, peroxisome biogenesis, signal transduction, and the regulation of gene expression. Due to the importance of AAA ATPases, several researchers identified and developed small-molecule inhibitors against these enzymes. We discuss six AAA ATPases that are potential drug targets and have well-developed inhibitors. We compare available structures that suggest significant differences of the ATP binding pockets among the AAA ATPases with or without ligand. The distances from ADP to the His20 in the His-Ser-His motif and the Arg finger (Arg353 or Arg378) in both RUVBL1/2 complex structures bound with or without ADP have significant differences, suggesting dramatically different interactions of the binding site with ADP. Taken together, the inhibitors of six well-studied AAA ATPases and their structural information suggest further development of specific AAA ATPase inhibitors due to difference in their structures. Future chemical biology coupled with proteomic approaches could be employed to develop variant specific, complex specific, and pathway specific inhibitors or activators for AAA ATPase proteins.
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Affiliation(s)
- Gang Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
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12
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Moon SL, Morisaki T, Stasevich TJ, Parker R. Coupling of translation quality control and mRNA targeting to stress granules. J Cell Biol 2021; 219:151851. [PMID: 32520986 PMCID: PMC7401812 DOI: 10.1083/jcb.202004120] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023] Open
Abstract
Stress granules are dynamic assemblies of proteins and nontranslating RNAs that form when translation is inhibited in response to diverse stresses. Defects in ubiquitin–proteasome system factors including valosin-containing protein (VCP) and the proteasome impact the kinetics of stress granule induction and dissolution as well as being implicated in neuropathogenesis. However, the impacts of dysregulated proteostasis on mRNA regulation and stress granules are not well understood. Using single mRNA imaging, we discovered ribosomes stall on some mRNAs during arsenite stress, and the release of transcripts from stalled ribosomes for their partitioning into stress granules requires the activities of VCP, components of the ribosome-associated quality control (RQC) complex, and the proteasome. This is an unexpected contribution of the RQC system in releasing mRNAs from translation under stress, thus identifying a new type of stress-activated RQC (saRQC) distinct from canonical RQC pathways in mRNA substrates, cellular context, and mRNA fate.
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Affiliation(s)
- Stephanie L Moon
- Department of Human Genetics, University of Michigan, Ann Arbor, MI.,Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI
| | - Tatsuya Morisaki
- Department of Biochemistry, Colorado State University, Fort Collins, CO
| | - Timothy J Stasevich
- Department of Biochemistry, Colorado State University, Fort Collins, CO.,World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO.,Howard Hughes Medical Institute, Chevy Chase, MD
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13
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Escobar-Henriques M, Anton V. Mitochondrial Surveillance by Cdc48/p97: MAD vs. Membrane Fusion. Int J Mol Sci 2020; 21:E6841. [PMID: 32961852 PMCID: PMC7555132 DOI: 10.3390/ijms21186841] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 11/16/2022] Open
Abstract
Cdc48/p97 is a ring-shaped, ATP-driven hexameric motor, essential for cellular viability. It specifically unfolds and extracts ubiquitylated proteins from membranes or protein complexes, mostly targeting them for proteolytic degradation by the proteasome. Cdc48/p97 is involved in a multitude of cellular processes, reaching from cell cycle regulation to signal transduction, also participating in growth or death decisions. The role of Cdc48/p97 in endoplasmic reticulum-associated degradation (ERAD), where it extracts proteins targeted for degradation from the ER membrane, has been extensively described. Here, we present the roles of Cdc48/p97 in mitochondrial regulation. We discuss mitochondrial quality control surveillance by Cdc48/p97 in mitochondrial-associated degradation (MAD), highlighting the potential pathologic significance thereof. Furthermore, we present the current knowledge of how Cdc48/p97 regulates mitofusin activity in outer membrane fusion and how this may impact on neurodegeneration.
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Affiliation(s)
- Mafalda Escobar-Henriques
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Straße 26, 50931 Cologne, Germany;
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14
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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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15
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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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16
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Banchenko S, Arumughan A, Petrović S, Schwefel D, Wanker EE, Roske Y, Heinemann U. Common Mode of Remodeling AAA ATPases p97/CDC48 by Their Disassembling Cofactors ASPL/PUX1. Structure 2019; 27:1830-1841.e3. [PMID: 31648844 DOI: 10.1016/j.str.2019.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/16/2019] [Accepted: 09/30/2019] [Indexed: 10/25/2022]
Abstract
The hexameric ring structure of the type II AAA+ ATPases is considered as stable and permanent. Recently, the UBX domain-containing cofactors Arabidopsis thaliana PUX1 and human alveolar soft part sarcoma locus (ASPL) were reported to bind and disassemble the cognate AAA+ ATPases AtCDC48 and human p97. Here, we present two crystal structures related to these complexes: a truncated AtCDC48 (AtCDC48-ND1) and a hybrid complex containing human p97-ND1 and the UBX domain of plant PUX1 (p97-ND1:PUX1-UBX). These structures reveal close similarity between the human and plant AAA+ ATPases, but also highlight differences between disassembling and non-disassembling AAA+ ATPase cofactors. Based on an AtCDC48 disassembly assay with PUX1 and known crystal structures of the p97-bound human cofactor ASPL, we propose a general ATPase disassembly model. Thus, our structural and biophysical investigations provide detailed insight into the mechanism of AAA+ ATPase disassembly by UBX domain cofactors and suggest a general mode of regulating the cellular activity of these molecular machines.
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Affiliation(s)
- Sofia Banchenko
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Anup Arumughan
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Saša Petrović
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - David Schwefel
- Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Erich E Wanker
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany
| | - Yvette Roske
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany.
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany.
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17
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Rycenga HB, Wolfe KB, Yeh ES, Long DT. Uncoupling of p97 ATPase activity has a dominant negative effect on protein extraction. Sci Rep 2019; 9:10329. [PMID: 31316150 PMCID: PMC6637110 DOI: 10.1038/s41598-019-46949-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 07/04/2019] [Indexed: 12/13/2022] Open
Abstract
p97 is a highly abundant, homohexameric AAA+ ATPase that performs a variety of essential cellular functions. Characterized as a ubiquitin-selective chaperone, p97 recognizes proteins conjugated to K48-linked polyubiquitin chains and promotes their removal from chromatin and other molecular complexes. Changes in p97 expression or activity are associated with the development of cancer and several related neurodegenerative disorders. Although pathogenic p97 mutations cluster in and around p97’s ATPase domains, mutant proteins display normal or elevated ATPase activity. Here, we show that one of the most common p97 mutations (R155C) retains ATPase activity, but is functionally defective. p97-R155C can be recruited to ubiquitinated substrates on chromatin, but is unable to promote substrate removal. As a result, p97-R155C acts as a dominant negative, blocking protein extraction by a similar mechanism to that observed when p97’s ATPase activity is inhibited or inactivated. However, unlike ATPase-deficient proteins, p97-R155C consumes excess ATP, which can hinder high-energy processes. Together, our results shed new insight into how pathogenic mutations in p97 alter its cellular function, with implications for understanding the etiology and treatment of p97-associated diseases.
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Affiliation(s)
- Halley B Rycenga
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Kelly B Wolfe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Elizabeth S Yeh
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - David T Long
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA.
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18
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Shi L, Zhang XB, Shi YF, Xu X, He Y, Shao G, Huang QN, Wu JL. OsCDC48/48E complex is required for plant survival in rice (Oryza sativa L.). PLANT MOLECULAR BIOLOGY 2019; 100:163-179. [PMID: 30937701 PMCID: PMC6513905 DOI: 10.1007/s11103-019-00851-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
We demonstrate that the C-terminus of OsCDC48 is essential for maintaining its full ATPase activity and OsCDC48/48E interaction is required to modulate cellular processes and plant survival in rice. Cell division cycle 48 (CDC48) belongs to the superfamily protein of ATPases associated with diverse cellular activities (AAA). We previously isolated a rice CDC48 mutant (psd128) displaying premature senescence and death phenotype. Here, we showed that OsCDC48 (Os03g0151800) interacted with OsCDC48E (Os10g0442600), a homologue of OsCDC48, to control plant survival in rice. OsCDC48E knockout plants exhibited similar behavior to psd128 with premature senescence and plant death. Removal of the C-terminus of OsCDC48 caused altered expression of cell cycle-related genes, changed the percentage of cells in G1 and G2/M phases, and abolished the interaction between OsCDC48 itself and between OsCDC48 and OsCDC48E, respectively. Furthermore, the truncated OsCDC48-PSD128 protein lacking the C-terminal 27 amino acid residues showed a decreased level of ATPase activity. Overexpression of OsCDC48-psd128 resulted in differential expression of AAA-ATPase associated genes leading to increased total ATPase activity, accumulation of reactive oxygen species and decreased plant tiller numbers while overexpression of OsCDC48 also resulted in differential expression of AAA-ATPase associated genes leading to increased total ATPase activity, but increased plant tiller numbers and grain yield, indicating its potential utilization for yield improvement. Our results demonstrated that the C-terminal region of OsCDC48 was essential for maintaining the full ATPase activity and OsCDC48/48E complex might function in form of heteromultimers to modulate cellular processes and plant survival in rice.
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Affiliation(s)
- Lei Shi
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiao-Bo Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Yong-Feng Shi
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Xia Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guosheng Shao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Qi-Na Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China.
| | - Jian-Li Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China.
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19
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Wei Y, Toth JI, Blanco GA, Bobkov AA, Petroski MD. Adapted ATPase domain communication overcomes the cytotoxicity of p97 inhibitors. J Biol Chem 2018; 293:20169-20180. [PMID: 30381397 DOI: 10.1074/jbc.ra118.004301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/10/2018] [Indexed: 12/15/2022] Open
Abstract
The AAA+ ATPase p97 regulates ubiquitin-dependent protein homeostasis and has been pursued as a cancer drug target. The ATP-competitive inhibitor CB-5083 and allosteric inhibitor NMS-873 are the most advanced p97 inhibitors described to date. Previous studies have reported that their cytotoxicity can be readily overcome and involves single p97 mutations in the linker between the D1 and D2 ATPase domains and within D2. We report here that the proline 472 to leucine (P472L) mutation, in the D1-D2 linker and identified in CB-5083-resistant cells, desensitizes p97 to both inhibitor classes. This mutation does not disrupt the distinct D2-binding sites of the inhibitors. Instead, P472L changes ATPase domain communication within the p97 hexamer. P472L enhances cooperative D2 ATP binding and hydrolysis. This mechanism alters the function of the D1-D2 linker in the control of D2 activity involving the ATP-bound state of D1. Although increased D2 activity is sufficient to desensitize the P472L mutant to NMS-873, the mutant's desensitization to CB-5083 also requires D1 ATPase domain function. Our study highlights the remarkable adaptability of p97 ATPase domain communication that enables escape from mechanistically distinct classes of cytotoxic p97 inhibitors.
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Affiliation(s)
- Yang Wei
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Julia I Toth
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Gabrielle A Blanco
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Andrey A Bobkov
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Matthew D Petroski
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037.
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20
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Enzymatic complexes across scales. Essays Biochem 2018; 62:501-514. [PMID: 30315098 PMCID: PMC6204551 DOI: 10.1042/ebc20180008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/12/2018] [Accepted: 09/13/2018] [Indexed: 02/07/2023]
Abstract
An unprecedented opportunity to integrate ~100 years of meticulous in vitro biomolecular research is currently provided in the light of recent advances in methods to visualize closer-to-native architectures of biomolecular machines, and metabolic enzymes in particular. Traditional views of enzymes, namely biomolecular machines, only partially explain their role, organization and kinetics in the cellular milieu. Enzymes self- or hetero-associate, form fibers, may bind to membranes or cytoskeletal elements, have regulatory roles, associate into higher order assemblies (metabolons) or even actively participate in phase-separated membraneless organelles, and all the above in a transient, temporal and spatial manner in response to environmental changes or structural/functional changes of their assemblies. Here, we focus on traditional and emerging concepts in cellular biochemistry and discuss new opportunities in bridging structural, molecular and cellular analyses for metabolic pathways, accumulated over the years, highlighting functional aspects of enzymatic complexes discussed across different levels of spatial resolution.
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21
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Portaro S, Cacciola A, Naro A, Milardi D, Morabito R, Corallo F, Marino S, Bramanti A, Mazzon E, Calabrò RS. A case report of recessive myotonia congenita and early onset cognitive impairment: Is it a causal or casual link? Medicine (Baltimore) 2018; 97:e10785. [PMID: 29851785 PMCID: PMC6392771 DOI: 10.1097/md.0000000000010785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE Myotonia congenita (MC) is a non-dystrophic myotonia inherited either in dominant (Thomsen) or recessive (Becker) form. MC is due to an abnormal functioning of skeletal muscle voltage-gated chloride channel (CLCN1), but the genotype/phenotype correlation remains unclear. PATIENT CONCERNS A 48-year-old man, from consanguineous parents, presented with a fixed muscle weakness, muscle atrophy, and a cognitive impairment. Notably, his brother presented the same mutation but with a different phenotype, mainly involving cognitive function. INTERVENTIONS The patient was submitted to cognitive assessment, needle electromyography, brain and muscle MRI, and genetic analysis. OUTCOMES The Milan Overall Dementia Assessment showed short-term memory, verbal fluency and verbal intelligence impairment. His genetic analysis showed a recessive splice-site mutation in the CLCN1 gene (IVS19+2T>A). Muscle MRI revealed a symmetric and bilateral fat infiltration of the tensor of fascia lata, gluteus medius, and gluteus maximus muscles, associated to mild atrophy. DIAGNOSIS Recessive myotonia congenita was diagnosed. LESSONS Further studies should establish if and to which extent the CLCN1 mutation is responsible for this c MC phenotype, taking into account a gene-gene and /or a gene-environment.
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22
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Al-Tahan S, Al-Obeidi E, Yoshioka H, Lakatos A, Weiss L, Grafe M, Palmio J, Wicklund M, Harati Y, Omizo M, Udd B, Kimonis V. Novel valosin-containing protein mutations associated with multisystem proteinopathy. Neuromuscul Disord 2018; 28:491-501. [PMID: 29754758 DOI: 10.1016/j.nmd.2018.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/28/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022]
Abstract
Over fifty missense mutations in the gene coding for valosin-containing protein (VCP) are associated with a unique autosomal dominant adult-onset progressive disease associated with combinations of proximo-distal inclusion body myopathy (IBM), Paget's disease of bone (PDB), frontotemporal dementia (FTD), and amyotrophic lateral sclerosis (ALS). We report the clinical, histological, and molecular findings in four new patients/families carrying novel VCP mutations: c.474 G > A (p.M158I); c.478 G > C (p.A160P); c.383G > C (p.G128A); and c.382G > T (p.G128C). Clinical features included myopathy, PDB, ALS and Parkinson's disease though frontotemporal dementia was not an associated feature in these families. One of the patients was noted to have severe manifestations of PDB and was suspected of having neoplasia. There were wide inter- and intra-familial variations making genotype-phenotype correlations difficult between the novel mutations and frequency or age of onset of IBM, PDB, FTD, ALS and Parkinson's disease. Increasing awareness of the full spectrum of clinical presentations will improve diagnosis of VCP-related diseases and thus proactively manage or prevent associated clinical features such as PDB.
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Affiliation(s)
- Sejad Al-Tahan
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA
| | - Ebaa Al-Obeidi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA
| | - Hiroshi Yoshioka
- Department of Radiological Sciences, University of California, Irvine, CA
| | - Anita Lakatos
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA
| | - Lan Weiss
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA
| | - Marjorie Grafe
- Department of Pathology, Oregon Health and Science University, Portland, OR
| | - Johanna Palmio
- Neuromuscular Research Center, Tampere University and University Hospital, Neurology, Tampere, Finland
| | - Matt Wicklund
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO
| | - Yadollah Harati
- Department of Neurology, Baylor College of Medicine, Houston, TX
| | | | - Bjarne Udd
- Neuromuscular Research Center, Tampere University and University Hospital, Neurology, Tampere, Finland; Folkhälsan Institute of Genetics and the Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland; Neurology Department, Vasa Central Hospital, Vasa, Finland
| | - Virginia Kimonis
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA.
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23
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VCP/p97-Mediated Unfolding as a Principle in Protein Homeostasis and Signaling. Mol Cell 2017; 69:182-194. [PMID: 29153394 DOI: 10.1016/j.molcel.2017.10.028] [Citation(s) in RCA: 262] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/06/2017] [Accepted: 10/20/2017] [Indexed: 01/14/2023]
Abstract
The AAA+-type ATPase p97 governs an ever-expanding number of cellular processes reaching from degradation of damaged proteins and organelles to key signaling events and chromatin regulation with thousands of client proteins. With its relevance for cellular homeostasis and genome stability, it is linked to muscular and neuronal degeneration and, conversely, constitutes an attractive anti-cancer drug target. Its molecular function is ATP-driven protein unfolding, which is directed by ubiquitin and assisted by a host of cofactor proteins. This activity underlies p97's diverse ability to pull proteins out of membranes, unfold proteins for proteasomal degradation, or segregate proteins from partners for downstream activity. Recent advances in structural analysis and biochemical reconstitution have underscored this notion, resolved detailed molecular motions within the p97 hexamer, and suggested substrate threading through the central channel of the p97 hexamer as the driving mechanism. We will discuss the mechanisms and open questions in the context of the diverse cellular activities.
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24
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The AAA+ ATPase p97, a cellular multitool. Biochem J 2017; 474:2953-2976. [PMID: 28819009 PMCID: PMC5559722 DOI: 10.1042/bcj20160783] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/17/2017] [Accepted: 07/21/2017] [Indexed: 12/17/2022]
Abstract
The AAA+ (ATPases associated with diverse cellular activities) ATPase p97 is essential to a wide range of cellular functions, including endoplasmic reticulum-associated degradation, membrane fusion, NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) activation and chromatin-associated processes, which are regulated by ubiquitination. p97 acts downstream from ubiquitin signaling events and utilizes the energy from ATP hydrolysis to extract its substrate proteins from cellular structures or multiprotein complexes. A multitude of p97 cofactors have evolved which are essential to p97 function. Ubiquitin-interacting domains and p97-binding domains combine to form bi-functional cofactors, whose complexes with p97 enable the enzyme to interact with a wide range of ubiquitinated substrates. A set of mutations in p97 have been shown to cause the multisystem proteinopathy inclusion body myopathy associated with Paget's disease of bone and frontotemporal dementia. In addition, p97 inhibition has been identified as a promising approach to provoke proteotoxic stress in tumors. In this review, we will describe the cellular processes governed by p97, how the cofactors interact with both p97 and its ubiquitinated substrates, p97 enzymology and the current status in developing p97 inhibitors for cancer therapy.
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25
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Schwerter DP, Grimm I, Platta HW, Erdmann R. ATP-driven processes of peroxisomal matrix protein import. Biol Chem 2017; 398:607-624. [PMID: 27977397 DOI: 10.1515/hsz-2016-0293] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/11/2016] [Indexed: 12/13/2022]
Abstract
In peroxisomal matrix protein import two processes directly depend on the binding and hydrolysis of ATP, both taking place at the late steps of the peroxisomal import cycle. First, ATP hydrolysis is required to initiate a ubiquitin-transfer cascade to modify the import (co-)receptors. These receptors display a dual localization in the cytosol and at the peroxisomal membrane, whereas only the membrane bound fraction receives the ubiquitin modification. The second ATP-dependent process of the import cycle is carried out by the two AAA+-proteins Pex1p and Pex6p. These ATPases form a heterohexameric complex, which is recruited to the peroxisomal import machinery by the membrane anchor protein Pex15p. The Pex1p/Pex6p complex recognizes the ubiquitinated import receptors, pulls them out of the membrane and releases them into the cytosol. There the deubiquitinated receptors are provided for further rounds of import. ATP binding and hydrolysis are required for Pex1p/Pex6p complex formation and receptor export. In this review, we summarize the current knowledge on the peroxisomal import cascade. In particular, we will focus on the ATP-dependent processes, which are so far best understood in the model organism Saccharomyces cerevisiae.
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Affiliation(s)
- Daniel P Schwerter
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
| | - Immanuel Grimm
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
| | - Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum
| | - Ralf Erdmann
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
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26
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Ye Y, Tang WK, Zhang T, Xia D. A Mighty "Protein Extractor" of the Cell: Structure and Function of the p97/CDC48 ATPase. Front Mol Biosci 2017; 4:39. [PMID: 28660197 PMCID: PMC5468458 DOI: 10.3389/fmolb.2017.00039] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/22/2017] [Indexed: 12/13/2022] Open
Abstract
p97/VCP (known as Cdc48 in S. cerevisiae or TER94 in Drosophila) is one of the most abundant cytosolic ATPases. It is highly conserved from archaebacteria to eukaryotes. In conjunction with a large number of cofactors and adaptors, it couples ATP hydrolysis to segregation of polypeptides from immobile cellular structures such as protein assemblies, membranes, ribosome, and chromatin. This often results in proteasomal degradation of extracted polypeptides. Given the diversity of p97 substrates, this "segregase" activity has profound influence on cellular physiology ranging from protein homeostasis to DNA lesion sensing, and mutations in p97 have been linked to several human diseases. Here we summarize our current understanding of the structure and function of this important cellular machinery and discuss the relevant clinical implications.
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Affiliation(s)
- Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, United States
| | - Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesda, MD, United States
| | - Ting Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, United States
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesda, MD, United States
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27
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Saffert P, Enenkel C, Wendler P. Structure and Function of p97 and Pex1/6 Type II AAA+ Complexes. Front Mol Biosci 2017; 4:33. [PMID: 28611990 PMCID: PMC5447069 DOI: 10.3389/fmolb.2017.00033] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/05/2017] [Indexed: 12/16/2022] Open
Abstract
Protein complexes of the Type II AAA+ (ATPases associated with diverse cellular activities) family are typically hexamers of 80–150 kDa protomers that harbor two AAA+ ATPase domains. They form double ring assemblies flanked by associated domains, which can be N-terminal, intercalated or C-terminal to the ATPase domains. Most prominent members of this family include NSF (N-ethyl-maleimide sensitive factor), p97/VCP (valosin-containing protein), the Pex1/Pex6 complex and Hsp104 in eukaryotes and ClpB in bacteria. Tremendous efforts have been undertaken to understand the conformational dynamics of protein remodeling type II AAA+ complexes. A uniform mode of action has not been derived from these works. This review focuses on p97/VCP and the Pex1/6 complex, which both structurally remodel ubiquitinated substrate proteins. P97/VCP plays a role in many processes, including ER- associated protein degradation, and the Pex1/Pex6 complex dislocates and recycles the transport receptor Pex5 from the peroxisomal membrane during peroxisomal protein import. We give an introduction into existing knowledge about the biochemical and cellular activities of the complexes before discussing structural information. We particularly emphasize recent electron microscopy structures of the two AAA+ complexes and summarize their structural differences.
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Affiliation(s)
- Paul Saffert
- Department of Biochemistry, Institute of Biochemistry and Biology, University of PotsdamPotsdam, Germany
| | - Cordula Enenkel
- Department of Biochemistry, University of TorontoToronto, ON, Canada
| | - Petra Wendler
- Department of Biochemistry, Institute of Biochemistry and Biology, University of PotsdamPotsdam, Germany
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28
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Ubiquitin- and ATP-dependent unfoldase activity of P97/VCP•NPLOC4•UFD1L is enhanced by a mutation that causes multisystem proteinopathy. Proc Natl Acad Sci U S A 2017; 114:E4380-E4388. [PMID: 28512218 DOI: 10.1073/pnas.1706205114] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
p97 is a "segregase" that plays a key role in numerous ubiquitin (Ub)-dependent pathways such as ER-associated degradation. It has been hypothesized that p97 extracts proteins from membranes or macromolecular complexes to enable their proteasomal degradation; however, the complex nature of p97 substrates has made it difficult to directly observe the fundamental basis for this activity. To address this issue, we developed a soluble p97 substrate-Ub-GFP modified with K48-linked ubiquitin chains-for in vitro p97 activity assays. We demonstrate that WT p97 can unfold proteins and that this activity is dependent on the p97 adaptor NPLOC4-UFD1L, ATP hydrolysis, and substrate ubiquitination, with branched chains providing maximal stimulation. Furthermore, we show that a p97 mutant that causes inclusion body myopathy, Paget's disease of bone, and frontotemporal dementia in humans unfolds substrate faster, suggesting that excess activity may underlie pathogenesis. This work overcomes a significant barrier in the study of p97 and will allow the future dissection of p97 mechanism at a level of detail previously unattainable.
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29
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Rosnoblet C, Bègue H, Blanchard C, Pichereaux C, Besson-Bard A, Aimé S, Wendehenne D. Functional characterization of the chaperon-like protein Cdc48 in cryptogein-induced immune response in tobacco. PLANT, CELL & ENVIRONMENT 2017; 40:491-508. [PMID: 26662183 DOI: 10.1111/pce.12686] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/20/2015] [Accepted: 11/27/2015] [Indexed: 05/06/2023]
Abstract
Cdc48, a molecular chaperone conserved in different kingdoms, is a member of the AAA+ family contributing to numerous processes in mammals including proteins quality control and degradation, vesicular trafficking, autophagy and immunity. The functions of Cdc48 plant orthologues are less understood. We previously reported that Cdc48 is regulated by S-nitrosylation in tobacco cells undergoing an immune response triggered by cryptogein, an elicitin produced by the oomycete Phytophthora cryptogea. Here, we inv estigated the function of NtCdc48 in cryptogein signalling and induced hypersensitive-like cell death. NtCdc48 was found to accumulate in elicited cells at both the protein and transcript levels. Interestingly, only a small proportion of the overall NtCdc48 population appeared to be S-nitrosylated. Using gel filtration in native conditions, we confirmed that NtCdc48 was present in its hexameric active form. An immunoprecipitation-based strategy following my mass spectrometry analysis led to the identification of about a hundred NtCdc48 partners and underlined its contribution in cellular processes including targeting of ubiquitylated proteins for proteasome-dependent degradation, subcellular trafficking and redox regulation. Finally, the analysis of cryptogein-induced events in NtCdc48-overexpressing cells highlighted a correlation between NtCdc48 expression and hypersensitive cell death. Altogether, this study identified NtCdc48 as a component of cryptogein signalling and plant immunity.
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Affiliation(s)
- Claire Rosnoblet
- Pôle Mécanisme et Gestion des Interactions Plantes-Microorganismes - ERL CNRS 6300, Université de Bourgogne Franche-Comté, UMR 1347 Agroécologie, 17 rue Sully, BP 86510, 21065, Dijon cédex, France
| | - Hervé Bègue
- Pôle Mécanisme et Gestion des Interactions Plantes-Microorganismes - ERL CNRS 6300, Université de Bourgogne Franche-Comté, UMR 1347 Agroécologie, 17 rue Sully, BP 86510, 21065, Dijon cédex, France
| | - Cécile Blanchard
- Pôle Mécanisme et Gestion des Interactions Plantes-Microorganismes - ERL CNRS 6300, Université de Bourgogne Franche-Comté, UMR 1347 Agroécologie, 17 rue Sully, BP 86510, 21065, Dijon cédex, France
| | - Carole Pichereaux
- Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversité, CNRS, 31326, Castanet-Tolosan, France
- Institut de Pharmacologie et de Biologie Structurale - CNRS, Université de Toulouse, 205 route de Narbonne,, 31077, Toulouse, France
| | - Angélique Besson-Bard
- Pôle Mécanisme et Gestion des Interactions Plantes-Microorganismes - ERL CNRS 6300, Université de Bourgogne Franche-Comté, UMR 1347 Agroécologie, 17 rue Sully, BP 86510, 21065, Dijon cédex, France
| | - Sébastien Aimé
- INRA, UMR 1347 Agroécologie, Pôle Mécanisme et Gestion des Interactions Plantes-Microorganismes - ERL CNRS 6300, 17 rue Sully, BP 86510, 21065, Dijon cédex, France
| | - David Wendehenne
- Pôle Mécanisme et Gestion des Interactions Plantes-Microorganismes - ERL CNRS 6300, Université de Bourgogne Franche-Comté, UMR 1347 Agroécologie, 17 rue Sully, BP 86510, 21065, Dijon cédex, France
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30
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Tang WK, Xia D. Mutations in the Human AAA + Chaperone p97 and Related Diseases. Front Mol Biosci 2016; 3:79. [PMID: 27990419 PMCID: PMC5131264 DOI: 10.3389/fmolb.2016.00079] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022] Open
Abstract
A number of neurodegenerative diseases have been linked to mutations in the human protein p97, an abundant cytosolic AAA+ (ATPase associated with various cellular activities) ATPase, that functions in a large number of cellular pathways. With the assistance of a variety of cofactors and adaptor proteins, p97 couples the energy of ATP hydrolysis to conformational changes that are necessary for its function. Disease-linked mutations, which are found at the interface between two main domains of p97, have been shown to alter the function of the protein, although the pathogenic mutations do not appear to alter the structure of individual subunit of p97 or the formation of the hexameric biological unit. While exactly how pathogenic mutations alter the cellular function of p97 remains unknown, functional, biochemical and structural differences between wild-type and pathogenic mutants of p97 are being identified. Here, we summarize recent progress in the study of p97 pathogenic mutants.
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Affiliation(s)
- Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
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31
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Arumughan A, Roske Y, Barth C, Forero LL, Bravo-Rodriguez K, Redel A, Kostova S, McShane E, Opitz R, Faelber K, Rau K, Mielke T, Daumke O, Selbach M, Sanchez-Garcia E, Rocks O, Panáková D, Heinemann U, Wanker EE. Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers. Nat Commun 2016; 7:13047. [PMID: 27762274 PMCID: PMC5080433 DOI: 10.1038/ncomms13047] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/29/2016] [Indexed: 12/13/2022] Open
Abstract
Interaction mapping is a powerful strategy to elucidate the biological function of protein assemblies and their regulators. Here, we report the generation of a quantitative interaction network, directly linking 14 human proteins to the AAA+ ATPase p97, an essential hexameric protein with multiple cellular functions. We show that the high-affinity interacting protein ASPL efficiently promotes p97 hexamer disassembly, resulting in the formation of stable p97:ASPL heterotetramers. High-resolution structural and biochemical studies indicate that an extended UBX domain (eUBX) in ASPL is critical for p97 hexamer disassembly and facilitates the assembly of p97:ASPL heterotetramers. This spontaneous process is accompanied by a reorientation of the D2 ATPase domain in p97 and a loss of its activity. Finally, we demonstrate that overproduction of ASPL disrupts p97 hexamer function in ERAD and that engineered eUBX polypeptides can induce cell death, providing a rationale for developing anti-cancer polypeptide inhibitors that may target p97 activity. The AAA+ ATPase p97 is an essential hexameric protein with multiple protein interaction partners and cellular functions. Here, the authors use interaction mapping to examine partner proteins of this large complex, and assess the effects of these proteins on the disassembly of the p97 complex.
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Affiliation(s)
- Anup Arumughan
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Carolin Barth
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Laura Lleras Forero
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Kenny Bravo-Rodriguez
- Max-Planck-Institute for Coal Research, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Alexandra Redel
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Simona Kostova
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Erik McShane
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Robert Opitz
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Katja Faelber
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Kirstin Rau
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Thorsten Mielke
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14194 Berlin, Germany
| | - Oliver Daumke
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Elsa Sanchez-Garcia
- Max-Planck-Institute for Coal Research, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Oliver Rocks
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Daniela Panáková
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Udo Heinemann
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Erich E Wanker
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
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32
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Bègue H, Jeandroz S, Blanchard C, Wendehenne D, Rosnoblet C. Structure and functions of the chaperone-like p97/CDC48 in plants. Biochim Biophys Acta Gen Subj 2016; 1861:3053-3060. [PMID: 27717811 DOI: 10.1016/j.bbagen.2016.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/29/2016] [Accepted: 10/01/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND The chaperone-like p97 is a member of the AAA+ ATPase enzyme family that contributes to numerous cellular activities. P97 has been broadly studied in mammals (VCP/p97) and yeasts (CDC48: Cell Division Cycle 48/p97) and numerous investigations highlighted that this protein is post-translationally regulated, is structured in homohexamer and interacts with partners and cofactors that direct it to distinct cellular signalization pathway including protein quality control and degradation, cell cycle regulation, genome stability, vesicular trafficking, autophagy and immunity. SCOPE OF REVIEW p97 is also conserved in plants (CDC48) but its functions are less understood. In the present review we intended to present the state of the art of the structure, regulation and functions of CDC48 in plants. MAJOR CONCLUSIONS Evidence accumulated underline that CDC48 plays a crucial role in development, cell cycle regulation and protein turnover in plants. Furthermore, its involvement in plant immunity has recently emerged and first interacting partners have been identified, shedding light on its putative cellular activities. GENERAL SIGNIFICANCE Identification of emerging functions of CDC48 in plants opens new roads of research in immunity and provides new insights into the mechanisms of protein quality control.
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Affiliation(s)
- Hervé Bègue
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Sylvain Jeandroz
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Cécile Blanchard
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - David Wendehenne
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Claire Rosnoblet
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France.
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33
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Na H, Song G. Predicting the functional motions of p97 using symmetric normal modes. Proteins 2016; 84:1823-1835. [PMID: 27653958 DOI: 10.1002/prot.25164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/09/2016] [Accepted: 09/15/2016] [Indexed: 01/01/2023]
Abstract
p97 is a protein complex of the AAA+ family. Although functions of p97 are well understood, the mechanism by which p97 performs its unfolding activities remains unclear. In this work, we present a novel way of applying normal mode analysis to study this six-fold symmetric molecular machine. By selecting normal modes that are axial symmetric and give the largest movements at D1 or D2 pore residues, we are able to predict the functional motions of p97, which are then validated by experimentally observed conformational changes. Our results shed light and provide new understandings on several key steps of the p97 functional process that were previously unclear or controversial, and thus are able to reconcile multiple previous findings. Specifically, our results reveal that (i) a venous valve-like mechanism is used at D2 pore to ensure a one-way exit-only traffic of substrates; (ii) D1 pore remains shut during the functional process; (iii) the "swing-up" motion of the N domain is closely coupled with the vertical motion of the D1 pore along the pore axis; (iv) because of the shut D1 pore and the one-way traffic at D2 pore, it is highly likely that substrates enter the chamber through the gaps at the D1/D2 interface. The limited chamber volume inside p97 suggests that a substrate may be pulling out from D2 while at the same time being pulling in at the interface; (v) lastly, p97 uses a series of actions that alternate between twisting and pulling to remove the substrate. Proteins 2016; 84:1823-1835. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hyuntae Na
- Department of Computer Science, Penn State Harrisburg, Middletown, Pennsylvania, 17057
| | - Guang Song
- Department of Computer Science, Iowa State University, Ames, Iowa, 50011.,Program of Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, 50011.,L. H. Baker Center for Bioinformatics and Biological Statistics Iowa State University, Ames, Iowa, 50011
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34
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Vekaria PH, Home T, Weir S, Schoenen FJ, Rao R. Targeting p97 to Disrupt Protein Homeostasis in Cancer. Front Oncol 2016; 6:181. [PMID: 27536557 PMCID: PMC4971439 DOI: 10.3389/fonc.2016.00181] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/22/2016] [Indexed: 12/11/2022] Open
Abstract
Cancer cells are addicted to numerous non-oncogenic traits that enable them to thrive. Proteotoxic stress is one such non-oncogenic trait that is experienced by all tumor cells owing to increased genomic abnormalities and the resulting synthesis and accumulation of non-stoichiometric amounts of cellular proteins. This imbalance in the amounts of proteins ultimately culminates in proteotoxic stress. p97, or valosin-containing protein (VCP), is an ATPase whose function is essential to restore protein homeostasis in the cells. Working in concert with the ubiquitin proteasome system, p97 promotes the retrotranslocation from cellular organelles and/or degradation of misfolded proteins. Consequently, p97 inhibition has emerged as a novel therapeutic target in cancer cells, especially those that have a highly secretory phenotype. This review summarizes our current understanding of the function of p97 in maintaining protein homeostasis and its inhibition with small molecule inhibitors as an emerging strategy to target cancer cells.
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Affiliation(s)
| | - Trisha Home
- Division of Hematologic Malignancies and Cellular Therapeutics, Kansas University Medical Center , Kansas City, KS , USA
| | - Scott Weir
- The University of Kansas Cancer Center, University of Kansas , Kansas City, KS , USA
| | - Frank J Schoenen
- Specialized Chemistry Center, University of Kansas , Lawrence, KS , USA
| | - Rekha Rao
- Division of Hematologic Malignancies and Cellular Therapeutics, Kansas University Medical Center , Kansas City, KS , USA
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Wang T, Xu W, Qin M, Yang Y, Bao P, Shen F, Zhang Z, Xu J. Pathogenic Mutations in the Valosin-containing Protein/p97(VCP) N-domain Inhibit the SUMOylation of VCP and Lead to Impaired Stress Response. J Biol Chem 2016; 291:14373-14384. [PMID: 27226613 DOI: 10.1074/jbc.m116.729343] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Indexed: 11/06/2022] Open
Abstract
Valosin-containing protein/p97(VCP) is a hexameric ATPase vital to protein degradation during endoplasmic reticulum stress. It regulates diverse cellular functions including autophagy, chromatin remodeling, and DNA repair. In addition, mutations in VCP cause inclusion body myopathy, Paget disease of the bone, and frontotemporal dementia (IBMPFD), as well as amyotrophic lateral sclerosis. Nevertheless, how the VCP activities were regulated and how the pathogenic mutations affect the function of VCP during stress are not unclear. Here we show that the small ubiquitin-like modifier (SUMO)-ylation of VCP is a normal stress response inhibited by the disease-causing mutations in the N-domain. Under oxidative and endoplasmic reticulum stress conditions, the SUMOylation of VCP facilitates the distribution of VCP to stress granules and nucleus, and promotes the VCP hexamer assembly. In contrast, pathogenic mutations in the VCP N-domain lead to reduced SUMOylation and weakened VCP hexamer formation upon stress. Defective SUMOylation of VCP also causes altered co-factor binding and attenuated endoplasmic reticulum-associated protein degradation. Furthermore, SUMO-defective VCP fails to protect against stress-induced toxicity in Drosophila Therefore, our results have revealed SUMOylation as a molecular signaling switch to regulate the distribution and functions of VCP during stress response, and suggest that deficiency in VCP SUMOylation caused by pathogenic mutations will render cells vulnerable to stress insults.
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Affiliation(s)
- Tao Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031
| | - Wangchao Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031,; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Meiling Qin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031
| | - Yi Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031,; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Puhua Bao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031
| | - Fuxiao Shen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031
| | - Zhenlin Zhang
- Department of Osteoporosis and Bone Diseases, Metabolic Bone Disease and Genetic Research Unit, Shanghai Jiao Tong University Affiliated People's No.6 Hospital, Shanghai 200233, China
| | - Jin Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031,.
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Lee TC, Kang M, Kim CH, Schultz PG, Chapman E, Deniz AA. Dual Unnatural Amino Acid Incorporation and Click-Chemistry Labeling to Enable Single-Molecule FRET Studies of p97 Folding. Chembiochem 2016; 17:981-4. [PMID: 27115850 DOI: 10.1002/cbic.201500695] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Indexed: 01/01/2023]
Abstract
Many cellular functions are critically dependent on the folding of complex multimeric proteins, such as p97, a hexameric multidomain AAA+ chaperone. Given the complex architecture of p97, single-molecule (sm) FRET would be a powerful tool for studying folding while avoiding ensemble averaging. However, dual site-specific labeling of such a large protein for smFRET is a significant challenge. Here, we address this issue by using bioorthogonal azide-alkyne chemistry to attach an smFRET dye pair to site-specifically incorporated unnatural amino acids, allowing us to generate p97 variants reporting on inter- or intradomain structural features. An initial proof-of-principle set of smFRET results demonstrated the strengths of this labeling method. Our results highlight this as a powerful tool for structural studies of p97 and other large protein machines.
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Affiliation(s)
- Taehyung C Lee
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Minjin Kang
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ, 85721, USA
| | - Chan Hyuk Kim
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter G Schultz
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Eli Chapman
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ, 85721, USA.
| | - Ashok A Deniz
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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Mountassif D, Fabre L, Zaid Y, Halawani D, Rouiller I. Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring. Biochem Biophys Res Commun 2015; 468:636-41. [PMID: 26549226 DOI: 10.1016/j.bbrc.2015.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/02/2015] [Indexed: 11/25/2022]
Abstract
Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring.
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Affiliation(s)
- Driss Mountassif
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada
| | - Lucien Fabre
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada
| | - Younes Zaid
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada; Current address: Laboratory of Thrombosis and Hemostasis, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Dalia Halawani
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada; Current address: Department of Cell Biology, Lerner Research Institute, 9500 Euclid Avenue NC10, Cleveland, OH 44195, USA
| | - Isabelle Rouiller
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada.
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Hiraishi N, Ishida YI, Nagahama M. AAA-ATPase NVL2 acts on MTR4-exosome complex to dissociate the nucleolar protein WDR74. Biochem Biophys Res Commun 2015; 467:534-40. [DOI: 10.1016/j.bbrc.2015.09.160] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 09/30/2015] [Indexed: 01/29/2023]
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NVL2, a nucleolar AAA-ATPase, is associated with the nuclear exosome and is involved in pre-rRNA processing. Biochem Biophys Res Commun 2015; 464:780-6. [PMID: 26166824 DOI: 10.1016/j.bbrc.2015.07.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 07/07/2015] [Indexed: 11/22/2022]
Abstract
Nuclear VCP-like 2 (NVL2) is a member of the chaperone-like AAA-ATPase family and is involved in the biosynthesis of 60S ribosomal subunits in mammalian cells. We previously showed the interaction of NVL2 with a DExD/H-box RNA helicase MTR4/DOB1, which is a known cofactor for an exoribonuclease complex, the exosome. This finding implicated NVL2 in RNA metabolic processes during ribosome biogenesis. In the present study, we found that a series of mutations within the ATPase domain of NVL2 causes a defect in pre-rRNA processing into mature 28S and 5.8S rRNAs. Co-immunoprecipitation analysis showed that NVL2 was associated with the nuclear exosome complex, which includes RRP6 as a nucleus-specific catalytic subunit. This interaction was prevented by depleting either MTR4 or RRP6, indicating their essential role in mediating this interaction with NVL2. Additionally, knockdown of MPP6, another cofactor for the nuclear exosome, also prevented the interaction by causing MTR4 to dissociate from the nuclear exosome. These results suggest that NVL2 is involved in pre-rRNA processing by associating with the nuclear exosome complex and that MPP6 is required for maintaining the integrity of this rRNA processing complex.
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Valosin-containing protein (VCP/p97) is capable of unfolding polyubiquitinated proteins through its ATPase domains. Biochem Biophys Res Commun 2015; 463:453-7. [PMID: 26043696 DOI: 10.1016/j.bbrc.2015.05.111] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 05/29/2015] [Indexed: 11/21/2022]
Abstract
Valosin-containing protein (VCP or p97) is required for the proteasomal degradation of polyubiquitinated proteins. However, the molecular mechanism for VCP to process the polyubiquitinated proteins remains unclear. Here, we show that VCP can unfold polyubiquitinated proteins. It preferably unfolds the pentaubiquitin-over monoubiquin-conjugated dihydrofolate reductase (Ub5-DHFR or Ub-DHFR) in a dose dependent manner. In addition, the unfolding activity of VCP does not depend on its ATPase activity, on the contrary, ATP and its non-hydrolysable analogs suppress the unfolding of Ub5-DHFR. The structural and functional analysis showed that either D1 or D2 domain of VCP is sufficient to carry out this unfolding activity. The structure of the substrates also affects its unfolding by VCP. VCP is unable to unfold Ub5-DHFR in a tight structure when it binds with methotrexate, a folate analog with high affinity to DHFR. Thus, these results support that VCP is capable of unfolding polyubiquitinated proteins and suggest that VCP may facilitate the proteasomal degradation of polyubiquitinated proteins through its unfolding activity.
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41
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Chapman E, Maksim N, de la Cruz F, La Clair JJ. Inhibitors of the AAA+ chaperone p97. Molecules 2015; 20:3027-49. [PMID: 25685910 PMCID: PMC4576884 DOI: 10.3390/molecules20023027] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/03/2015] [Indexed: 12/22/2022] Open
Abstract
It is remarkable that a pathway as ubiquitous as protein quality control can be targeted to treat cancer. Bortezomib, an inhibitor of the proteasome, was first approved by the US Food and Drug Administration (FDA) more than 10 years ago to treat refractory myeloma and later extended to lymphoma. Its use has increased the survival rate of myeloma patients by as much as three years. This success was followed with the recent accelerated approval of the natural product derived proteasome inhibitor carfilzomib (Kyprolis®), which is used to treat patients with bortezomib-resistant multiple myeloma. The success of these two drugs has validated protein quality control as a viable target to fight select cancers, but begs the question why are proteasome inhibitors limited to lymphoma and myeloma? More recently, these limitations have encouraged the search for additional targets within the protein quality control system that might offer heightened cancer cell specificity, enhanced clinical utility, a lower rate of resistance, reduced toxicity, and mitigated side effects. One promising target is p97, an ATPase associated with various cellular activities (AAA+) chaperone. p97 figures prominently in protein quality control as well as serving a variety of other cellular functions associated with cancer. More than a decade ago, it was determined that up-regulation of p97 in many forms of cancer correlates with a poor clinical outcome. Since these initial discoveries, a mechanistic explanation for this observation has been partially illuminated, but details are lacking. Understandably, given this clinical correlation, myriad roles within the cell, and its importance in protein quality control, p97 has emerged as a potential therapeutic target. This review provides an overview of efforts towards the discovery of small molecule inhibitors of p97, offering a synopsis of efforts that parallel the excellent reviews that currently exist on p97 structure, function, and physiology.
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Affiliation(s)
- Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721-0207, USA.
| | - Nick Maksim
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721-0207, USA.
| | - Fabian de la Cruz
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721-0207, USA.
| | - James J La Clair
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721-0207, USA.
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42
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Song C, Wang Q, Song C, Lockett SJ, Colburn NH, Li CCH, Wang JM, Rogers TJ. Nucleocytoplasmic shuttling of valosin-containing protein (VCP/p97) regulated by its N domain and C-terminal region. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1853:222-32. [PMID: 25447673 PMCID: PMC4254625 DOI: 10.1016/j.bbamcr.2014.10.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 10/01/2014] [Accepted: 10/21/2014] [Indexed: 12/25/2022]
Abstract
Valosin-containing protein (VCP or p97), a member of the AAA family (ATPases associated with diverse cellular activities), plays a key role in many important cellular activities. A genetic deficiency of VCP can cause inclusion body myopathy associated with Paget's disease of bone and frontotemporal dementia (IBMPFD). Previous studies showed that the VCP N domain is essential for the regulation of nuclear entry of VCP. Here we report that IBMPFD mutations, which are mainly located in the N domain, suppress the nuclear entry of VCP. Moreover, the peptide sequence G780AGPSQ in the C-terminal region regulates the retention of VCP in the nucleus. A mutant lacking this sequence can increase the nuclear distribution of IBMPFD VCP, suggesting that this sequence is a potential molecular target for correcting the deficient nucleocytoplasmic shuttling of IBMPFD VCP proteins.
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Affiliation(s)
- Changcheng Song
- Center for Inflammation, Translational and Clinical Lung Research, School of Medicine, Temple University, Philadelphia, PA 19140, USA.
| | - Qing Wang
- Graduate Center for Toxicology, University of Kentucky, Lexington, KY, USA
| | - Changzheng Song
- Erythrocrine Project of Translational Medicine, Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Stephen J Lockett
- Optical Microscopy and Analysis Laboratory, Advanced Technology Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Nancy H Colburn
- Laboratory of Cancer Prevention, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Chou-Chi H Li
- Laboratory of Cancer Prevention, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Basic Research Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Ji Ming Wang
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Thomas J Rogers
- Center for Inflammation, Translational and Clinical Lung Research, School of Medicine, Temple University, Philadelphia, PA 19140, USA
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43
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The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proc Natl Acad Sci U S A 2014; 111:16166-71. [PMID: 25344531 DOI: 10.1073/pnas.1418564111] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48A(NPL4) complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.
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Kang M, Wu T, Wijeratne EMK, Lau EC, Mason DJ, Mesa C, Tillotson J, Zhang DD, Gunatilaka AAL, La Clair JJ, Chapman E. Functional chromatography reveals three natural products that target the same protein with distinct mechanisms of action. Chembiochem 2014; 15:2125-31. [PMID: 25125376 PMCID: PMC4187115 DOI: 10.1002/cbic.201402258] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Indexed: 01/12/2023]
Abstract
Access to lead compounds with defined molecular targets continues to be a barrier to the translation of natural product resources. As a solution, we developed a system that uses discrete, recombinant proteins as the vehicles for natural product isolation. Here, we describe the use of this functional chromatographic method to identify natural products that bind to the AAA+ chaperone, p97, a promising cancer target. Application of this method to a panel of fungal and plant extracts identified rheoemodin, 1-hydroxydehydroherbarin, and phomapyrrolidone A as distinct p97 modulators. Excitingly, each of these molecules displayed a unique mechanism of p97 modulation. This discovery provides strong support for the application of functional chromatography to the discovery of protein modulators that would likely escape traditional high-throughput or phenotypic screening platforms.
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Affiliation(s)
- MinJin Kang
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - Tongde Wu
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - E. M. Kithsiri Wijeratne
- Southwest Center for Natural Products Research and Commercialization, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85706-6800, United States
| | - Eric C. Lau
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - Damian J. Mason
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - Celestina Mesa
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - Joseph Tillotson
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - Donna D. Zhang
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - A. A. Leslie Gunatilaka
- Southwest Center for Natural Products Research and Commercialization, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85706-6800, United States
| | - James J. La Clair
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA 92163-1052, United States
| | - Eli Chapman
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
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Chou TF, Bulfer SL, Weihl CC, Li K, Lis LG, Walters MA, Schoenen FJ, Lin HJ, Deshaies RJ, Arkin MR. Specific inhibition of p97/VCP ATPase and kinetic analysis demonstrate interaction between D1 and D2 ATPase domains. J Mol Biol 2014; 426:2886-99. [PMID: 24878061 PMCID: PMC4102644 DOI: 10.1016/j.jmb.2014.05.022] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 10/25/2022]
Abstract
The p97 AAA (ATPase associated with diverse cellular activities), also called VCP (valosin-containing protein), is an important therapeutic target for cancer and neurodegenerative diseases. p97 forms a hexamer composed of two AAA domains (D1 and D2) that form two stacked rings and an N-terminal domain that binds numerous cofactor proteins. The interplay between the three domains in p97 is complex, and a deeper biochemical understanding is needed in order to design selective p97 inhibitors as therapeutic agents. It is clear that the D2 ATPase domain hydrolyzes ATP in vitro, but whether D1 contributes to ATPase activity is controversial. Here, we use Walker A and B mutants to demonstrate that D1 is capable of hydrolyzing ATP and show for the first time that nucleotide binding in the D2 domain increases the catalytic efficiency (kcat/Km) of D1 ATP hydrolysis 280-fold, by increasing kcat 7-fold and decreasing Km about 40-fold. We further show that an ND1 construct lacking D2 but including the linker between D1 and D2 is catalytically active, resolving a conflict in the literature. Applying enzymatic observations to small-molecule inhibitors, we show that four p97 inhibitors (DBeQ, ML240, ML241, and NMS-873) have differential responses to Walker A and B mutations, to disease-causing IBMPFD mutations, and to the presence of the N domain binding cofactor protein p47. These differential effects provide the first evidence that p97 cofactors and disease mutations can alter p97 inhibitor potency and suggest the possibility of developing context-dependent inhibitors of p97.
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Affiliation(s)
- Tsui-Fen Chou
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA 90502, USA.
| | - Stacie L Bulfer
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, CA 94158, USA
| | - Conrad C Weihl
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kelin Li
- Specialized Chemistry Center, University of Kansas, Lawrence, KS 66047, USA
| | - Lev G Lis
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, USA
| | - Michael A Walters
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, USA
| | - Frank J Schoenen
- Specialized Chemistry Center, University of Kansas, Lawrence, KS 66047, USA
| | - Henry J Lin
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA 90502, USA
| | - Raymond J Deshaies
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, CA 94158, USA
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46
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Morito D, Nishikawa K, Hoseki J, Kitamura A, Kotani Y, Kiso K, Kinjo M, Fujiyoshi Y, Nagata K. Moyamoya disease-associated protein mysterin/RNF213 is a novel AAA+ ATPase, which dynamically changes its oligomeric state. Sci Rep 2014; 4:4442. [PMID: 24658080 PMCID: PMC3963067 DOI: 10.1038/srep04442] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 03/06/2014] [Indexed: 12/05/2022] Open
Abstract
Moyamoya disease is an idiopathic human cerebrovascular disorder that is characterized by progressive stenosis and abnormal collateral vessels. We recently identified mysterin/RNF213 as its first susceptibility gene, which encodes a 591-kDa protein containing enzymatically active P-loop ATPase and ubiquitin ligase domains and is involved in proper vascular development in zebrafish. Here we demonstrate that mysterin further contains two tandem AAA+ ATPase modules and forms huge ring-shaped oligomeric complex. AAA+ ATPases are known to generally mediate various biophysical and mechanical processes with the characteristic ring-shaped structure. Fluorescence correlation spectroscopy and biochemical evaluation suggested that mysterin dynamically changes its oligomeric forms through ATP/ADP binding and hydrolysis cycles. Thus, the moyamoya disease-associated gene product is a unique protein that functions as ubiquitin ligase and AAA+ ATPase, which possibly contributes to vascular development through mechanical processes in the cell.
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Affiliation(s)
- Daisuke Morito
- Laboratory of Molecular and Cellular Biology, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Kouki Nishikawa
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan
| | - Jun Hoseki
- 1] Research Unit for Physiological Chemistry, The Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, 606-8502, Japan [2] Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Akira Kitamura
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Yuri Kotani
- Laboratory of Molecular and Cellular Biology, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Kazumi Kiso
- Laboratory of Molecular and Cellular Biology, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Yoshinori Fujiyoshi
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan
| | - Kazuhiro Nagata
- Laboratory of Molecular and Cellular Biology, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
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47
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Kravats AN, Tonddast-Navaei S, Bucher RJ, Stan G. Asymmetric processing of a substrate protein in sequential allosteric cycles of AAA+ nanomachines. J Chem Phys 2013; 139:121921. [DOI: 10.1063/1.4817410] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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48
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Rodriguez-Ortiz CJ, Hoshino H, Cheng D, Liu-Yescevitz L, Blurton-Jones M, Wolozin B, LaFerla FM, Kitazawa M. Neuronal-specific overexpression of a mutant valosin-containing protein associated with IBMPFD promotes aberrant ubiquitin and TDP-43 accumulation and cognitive dysfunction in transgenic mice. THE AMERICAN JOURNAL OF PATHOLOGY 2013; 183:504-15. [PMID: 23747512 DOI: 10.1016/j.ajpath.2013.04.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/25/2013] [Accepted: 04/03/2013] [Indexed: 12/12/2022]
Abstract
Mutations in valosin-containing protein (VCP) cause a rare, autosomal dominant disease called inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia (IBMPFD). One-third of patients with IBMPFD develop frontotemporal dementia, characterized by an extensive neurodegeneration in the frontal and temporal lobes. Neuropathologic hallmarks include nuclear and cytosolic inclusions positive to ubiquitin and transactive response DNA-binding protein 43 (TDP-43) in neurons and glial activation in affected regions. However, the pathogenic mechanisms by which mutant VCP triggers neurodegeneration remain unknown. Herein, we generated a mouse model selectively overexpressing a human mutant VCP in neurons to study pathogenic mechanisms of mutant VCP-mediated neurodegeneration and cognitive impairment. The overexpression of VCPA232E mutation in forebrain regions produced significant progressive impairments of cognitive function, including deficits in spatial memory, object recognition, and fear conditioning. Although overexpressed or endogenous VCP did not seem to focally aggregate inside neurons, TDP-43 and ubiquitin accumulated with age in transgenic mouse brains. TDP-43 was also found to co-localize with stress granules in the cytosolic compartment. Together with the appearance of high-molecular-weight TDP-43 in cytosolic fractions, these findings demonstrate the mislocalization and accumulation of abnormal TDP-43 in the cytosol of transgenic mice, which likely lead to an increase in cellular stress and cognitive impairment. Taken together, these results highlight an important pathologic link between VCP and cognition.
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49
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Kappel L, Loibl M, Zisser G, Klein I, Fruhmann G, Gruber C, Unterweger S, Rechberger G, Pertschy B, Bergler H. Rlp24 activates the AAA-ATPase Drg1 to initiate cytoplasmic pre-60S maturation. ACTA ACUST UNITED AC 2013. [PMID: 23185031 PMCID: PMC3514788 DOI: 10.1083/jcb.201205021] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Formation of eukaryotic ribosomes is driven by energy-consuming enzymes. The AAA-ATPase Drg1 is essential for the release of several shuttling proteins from cytoplasmic pre-60S particles and the loading of late joining proteins. However, its exact role in ribosome biogenesis has been unknown. Here we show that the shuttling protein Rlp24 recruited Drg1 to pre-60S particles and stimulated its ATPase activity. ATP hydrolysis in the second AAA domain of Drg1 was required to release shuttling proteins. In vitro, Drg1 specifically and exclusively extracted Rlp24 from purified pre-60S particles. Rlp24 release required ATP and was promoted by the interaction of Drg1 with the nucleoporin Nup116. Subsequent ATP hydrolysis in the first AAA domain dissociated Drg1 from Rlp24, liberating both proteins for consecutive cycles of activity. Our results show that release of Rlp24 by Drg1 defines a key event in large subunit formation that is a prerequisite for progression of cytoplasmic pre-60S maturation.
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Affiliation(s)
- Lisa Kappel
- Institut für Molekulare Biowissenschaften, Karl-Franzens Universität Graz, A-8010 Graz, Austria
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50
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Erzurumlu Y, Kose FA, Gozen O, Gozuacik D, Toth EA, Ballar P. A unique IBMPFD-related P97/VCP mutation with differential binding pattern and subcellular localization. Int J Biochem Cell Biol 2013; 45:773-82. [PMID: 23333620 DOI: 10.1016/j.biocel.2013.01.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 11/30/2012] [Accepted: 01/08/2013] [Indexed: 12/12/2022]
Abstract
p97/VCP is a hexameric AAA type ATPase that functions in a variety of cellular processes such as endoplasmic reticulum associated degradation (ERAD), organelle biogenesis, autophagy and cell-cycle regulation. Inclusion body myopathy associated with Paget disease of the bone and frontotemporal dementia (IBMPFD) is an autosomal dominant disorder which has been attributed to mutations in p97/VCP. Several missense mutations affecting twelve different amino acids have been identified in IBMPFD patients and some of them were suggested to be involved in the observed pathology. Here, we analyzed the effect of all twelve p97/VCP variants on ERAD substrates and their cofactor binding abilities. While all mutants cause ERAD substrate accumulation, P137L mutant p97/VCP differs from other IBMPFD mutants by having a unique solubility profile and subcellular localization. Intriguingly, although almost all mutants exhibit enhanced p47 and Ufd1-Npl4 binding, the P137L mutation completely abolishes p97/VCP interactions with Ufd1, Npl4 and p47, while retaining its gp78 binding. While recombinant R155C mutant protein consistently interacts with both Ufd1 and VIM of gp78, P137L mutant protein lost binding ability to Ufd1 but not to VIM in vitro. The differential impairments in p97/VCP interactions with its functional partners and function should help our understanding of the molecular pathogenesis of IBMPFD.
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Affiliation(s)
- Yalcin Erzurumlu
- Ege University, Faculty of Pharmacy, Biochemistry Department, Izmir, Turkey
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