1
|
Davies C, Hu RM, Kamitsuka PJ, Morais GN, de Gonzalez RS, Bustin KA, Matthews ML, Parsons WH. Activity-Based Protein Profiling of RHBDL4 Reveals Proteolysis of the Enzyme and a Distinct Inhibitor Profile. ACS Chem Biol 2024; 19:1674-1682. [PMID: 39041925 PMCID: PMC11334910 DOI: 10.1021/acschembio.4c00273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/19/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
Rhomboid proteases have fascinated scientists by virtue of their membrane-embedded active sites and proposed involvement in physiological and disease pathways. The human rhomboid protease RHBDL4 has generated particular interest due to its role in endoplasmic reticulum-associated protein degradation and upregulation in several cancers; however, chemical tools for studying this enzyme are currently lacking. Here, we describe the development of an activity-based protein profiling (ABPP) assay for RHBDL4. We have employed this assay to determine that human RHBDL4 undergoes proteolytic processing in cells to produce multiple active proteoforms with truncated C-termini. We have also used this assay to identify chemical scaffolds capable of inhibiting RHBDL4 activity and have observed distinct inhibitor preferences between RHBDL4 and a second human rhomboid protease PARL. Our work demonstrates the power of ABPP technology to characterize active forms of enzymes that might otherwise elude detection and the potential to achieve selective inhibition among the human rhomboid proteases.
Collapse
Affiliation(s)
- Cassondra
C. Davies
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Ren-Ming Hu
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Paul J. Kamitsuka
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Gabriel N. Morais
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | | | - Katelyn A. Bustin
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Megan L. Matthews
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - William H. Parsons
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| |
Collapse
|
2
|
Braxton JR, Southworth DR. Structural insights of the p97/VCP AAA+ ATPase: How adapter interactions coordinate diverse cellular functionality. J Biol Chem 2023; 299:105182. [PMID: 37611827 PMCID: PMC10641518 DOI: 10.1016/j.jbc.2023.105182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/05/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
p97/valosin-containing protein is an essential eukaryotic AAA+ ATPase with diverse functions including protein homeostasis, membrane remodeling, and chromatin regulation. Dysregulation of p97 function causes severe neurodegenerative disease and is associated with cancer, making this protein a significant therapeutic target. p97 extracts polypeptide substrates from macromolecular assemblies by hydrolysis-driven translocation through its central pore. Growing evidence indicates that this activity is highly coordinated by "adapter" partner proteins, of which more than 30 have been identified and are commonly described to facilitate translocation through substrate recruitment or modification. In so doing, these adapters enable critical p97-dependent functions such as extraction of misfolded proteins from the endoplasmic reticulum or mitochondria, and are likely the reason for the extreme functional diversity of p97 relative to other AAA+ translocases. Here, we review the known functions of adapter proteins and highlight recent structural and biochemical advances that have begun to reveal the diverse molecular bases for adapter-mediated regulation of p97 function. These studies suggest that the range of mechanisms by which p97 activity is controlled is vastly underexplored with significant advances possible for understanding p97 regulation by the most known adapters.
Collapse
Affiliation(s)
- Julian R Braxton
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, California, USA; Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California, USA
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California, USA.
| |
Collapse
|
3
|
Körner M, Meyer SR, Marincola G, Kern MJ, Grimm C, Schuelein-Voelk C, Fischer U, Hofmann K, Buchberger A. The FAM104 proteins VCF1/2 promote the nuclear localization of p97/VCP. eLife 2023; 12:e92409. [PMID: 37713320 PMCID: PMC10541173 DOI: 10.7554/elife.92409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 09/17/2023] Open
Abstract
The ATPase p97 (also known as VCP, Cdc48) has crucial functions in a variety of important cellular processes such as protein quality control, organellar homeostasis, and DNA damage repair, and its de-regulation is linked to neuromuscular diseases and cancer. p97 is tightly controlled by numerous regulatory cofactors, but the full range and function of the p97-cofactor network is unknown. Here, we identify the hitherto uncharacterized FAM104 proteins as a conserved family of p97 interactors. The two human family members VCP nuclear cofactor family member 1 and 2 (VCF1/2) bind p97 directly via a novel, alpha-helical motif and associate with p97-UFD1-NPL4 and p97-UBXN2B complexes in cells. VCF1/2 localize to the nucleus and promote the nuclear import of p97. Loss of VCF1/2 results in reduced nuclear p97 levels, slow growth, and hypersensitivity to chemical inhibition of p97 in the absence and presence of DNA damage, suggesting that FAM104 proteins are critical regulators of nuclear p97 functions.
Collapse
Affiliation(s)
- Maria Körner
- University of Würzburg, Biocenter, Chair of Biochemistry IWürzburgGermany
| | - Susanne R Meyer
- University of Würzburg, Biocenter, Chair of Biochemistry IWürzburgGermany
| | | | - Maximilian J Kern
- Department of Molecular Cell Biology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Clemens Grimm
- University of Würzburg, Biocenter, Chair of Biochemistry IWürzburgGermany
| | | | - Utz Fischer
- University of Würzburg, Biocenter, Chair of Biochemistry IWürzburgGermany
| | - Kay Hofmann
- Institute of Genetics, University of CologneCologneGermany
| | | |
Collapse
|
4
|
Hsiao JM, Penalva YCM, Wu HYL, Xiao B, Jansen G, Dejgaard K, Young JC, Munter LM. Putative Protein Interactome of the Rhomboid Protease RHBDL4. Biochemistry 2023; 62:1209-1218. [PMID: 36857408 DOI: 10.1021/acs.biochem.2c00680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The physiological functions of the rhomboid-related protein 4 (RHBDL4) are emerging, but their molecular details remain unclear. Because increased expression of RHBDL4 has been clinically linked to poorer outcomes in cancer patients, this association urgently demands a better understanding of RHBDL4. To elucidate the molecular interactions and pathways that RHBDL4 may be involved in, we conducted proximity-dependent biotin identification (BioID) assays. Our analyses corroborated several of the expected protein interactors such as the transitional endoplasmic reticulum (ER) ATPase VCP/p97 (TERA), but they also described novel putative interactors including IRS4, PGAM5, and GORS2. Using proximity-ligation assays, we validated VCP/p97, COPB, and VRK2 as proteins that are in proximity to RHBDL4. Overall, our results support the emerging functions of RHBDL4 in ER quality control and also point toward putative RHBDL4 functions in protein membrane insertion and membrane organization and trafficking.
Collapse
Affiliation(s)
| | - Ylauna Christine Mégane Penalva
- Department of Pharmacology & Therapeutics, McGill University, Montreal H3G 0B1, Québec, Canada
- Integrated Program in Neuroscience, McGill University, Montreal H3A 2B4, Québec, Canada
- Cell Information Systems Group, Bellini Life Sciences Complex, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Helen Yee-Li Wu
- Department of Pharmacology & Therapeutics, McGill University, Montreal H3G 0B1, Québec, Canada
- Cell Information Systems Group, Bellini Life Sciences Complex, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Bin Xiao
- Department of Pharmacology & Therapeutics, McGill University, Montreal H3G 0B1, Québec, Canada
- Cell Information Systems Group, Bellini Life Sciences Complex, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Gregor Jansen
- Department of Biochemistry, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Kurt Dejgaard
- Department of Biochemistry, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Jason C Young
- Department of Biochemistry, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Lisa Marie Munter
- Department of Pharmacology & Therapeutics, McGill University, Montreal H3G 0B1, Québec, Canada
- Cell Information Systems Group, Bellini Life Sciences Complex, McGill University, Montreal H3G 0B1, Québec, Canada
| |
Collapse
|
5
|
Bhaduri S, Scott NA, Neal SE. The Role of the Rhomboid Superfamily in ER Protein Quality Control: From Mechanisms and Functions to Diseases. Cold Spring Harb Perspect Biol 2023; 15:a041248. [PMID: 35940905 PMCID: PMC9899648 DOI: 10.1101/cshperspect.a041248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The endoplasmic reticulum (ER) is an essential organelle in eukaryotic cells and is a major site for protein folding, modification, and lipid synthesis. Perturbations within the ER, such as protein misfolding and high demand for protein folding, lead to dysregulation of the ER protein quality control network and ER stress. Recently, the rhomboid superfamily has emerged as a critical player in ER protein quality control because it has diverse cellular functions, including ER-associated degradation (ERAD), endosome Golgi-associated degradation (EGAD), and ER preemptive quality control (ERpQC). This breadth of function both illustrates the importance of the rhomboid superfamily in health and diseases and emphasizes the necessity of understanding their mechanisms of action. Because dysregulation of rhomboid proteins has been implicated in various diseases, such as neurological disorders and cancers, they represent promising potential therapeutic drug targets. This review provides a comprehensive account of the various roles of rhomboid proteins in the context of ER protein quality control and discusses their significance in health and disease.
Collapse
Affiliation(s)
- Satarupa Bhaduri
- School of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | - Nicola A Scott
- School of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | - Sonya E Neal
- School of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| |
Collapse
|
6
|
Rhomboid protease RHBDL4 promotes retrotranslocation of aggregation-prone proteins for degradation. Cell Rep 2022; 40:111175. [PMID: 35947953 PMCID: PMC9437926 DOI: 10.1016/j.celrep.2022.111175] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/02/2022] [Accepted: 07/18/2022] [Indexed: 11/22/2022] Open
Abstract
Protein degradation is fundamentally important to ensure cell homeostasis. In the endoplasmic reticulum (ER), the ER-associated degradation (ERAD) pathway targets incorrectly folded and unassembled proteins for turnover by the cytoplasmic proteasome. Previously, we showed that the rhomboid protease RHBDL4, together with p97, mediates membrane protein degradation. However, whether RHBDL4 acts in concert with additional ERAD components is unclear, and its full substrate spectrum remains to be defined. Here, we show that, in addition to membrane proteins, RHBDL4 cleaves aggregation-prone luminal ERAD substrates. Since mutations of the RHBDL4 rhomboid domain led to stabilization of substrates at the cytoplasmic side, we hypothesize that, analogous to the homolog ERAD factor derlin, RHBDL4 is directly involved in substrate retrotranslocation. RHBDL4's interaction with the erlin ERAD complex and reciprocal interaction of rhomboid substrates with erlins suggest that RHBDL4 and erlins form a complex that clips substrates and thereby rescues aggregation-prone peptides in the ER from aggregation.
Collapse
|
7
|
Kong KYE, Coelho JPL, Feige MJ, Khmelinskii A. Quality control of mislocalized and orphan proteins. Exp Cell Res 2021; 403:112617. [PMID: 33930402 DOI: 10.1016/j.yexcr.2021.112617] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/10/2021] [Accepted: 04/18/2021] [Indexed: 12/16/2022]
Abstract
A healthy and functional proteome is essential to cell physiology. However, this is constantly being challenged as most steps of protein metabolism are error-prone and changes in the physico-chemical environment can affect protein structure and function, thereby disrupting proteome homeostasis. Among a variety of potential mistakes, proteins can be targeted to incorrect compartments or subunits of protein complexes may fail to assemble properly with their partners, resulting in the formation of mislocalized and orphan proteins, respectively. Quality control systems are in place to handle these aberrant proteins, and to minimize their detrimental impact on cellular functions. Here, we discuss recent findings on quality control mechanisms handling mislocalized and orphan proteins. We highlight common principles involved in their recognition and summarize how accumulation of these aberrant molecules is associated with aging and disease.
Collapse
Affiliation(s)
| | - João P L Coelho
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Matthias J Feige
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | | |
Collapse
|
8
|
Ninagawa S, George G, Mori K. Mechanisms of productive folding and endoplasmic reticulum-associated degradation of glycoproteins and non-glycoproteins. Biochim Biophys Acta Gen Subj 2020; 1865:129812. [PMID: 33316349 DOI: 10.1016/j.bbagen.2020.129812] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND The quality of proteins destined for the secretory pathway is ensured by two distinct mechanisms in the endoplasmic reticulum (ER): productive folding of newly synthesized proteins, which is assisted by ER-localized molecular chaperones and in most cases also by disulfide bond formation and transfer of an oligosaccharide unit; and ER-associated degradation (ERAD), in which proteins unfolded or misfolded in the ER are recognized and processed for delivery to the ER membrane complex, retrotranslocated through the complex with simultaneous ubiquitination, extracted by AAA-ATPase to the cytosol, and finally degraded by the proteasome. SCOPE OF REVIEW We describe the mechanisms of productive folding and ERAD, with particular attention to glycoproteins versus non-glycoproteins, and to yeast versus mammalian systems. MAJOR CONCLUSION Molecular mechanisms of the productive folding of glycoproteins and non-glycoproteins mediated by molecular chaperones and protein disulfide isomerases are well conserved from yeast to mammals. Additionally, mammals have gained an oligosaccharide structure-dependent folding cycle for glycoproteins. The molecular mechanisms of ERAD are also well conserved from yeast to mammals, but redundant expression of yeast orthologues in mammals has been encountered, particularly for components involved in recognition and processing of glycoproteins and components of the ER membrane complex involved in retrotranslocation and simultaneous ubiquitination of glycoproteins and non-glycoproteins. This may reflect an evolutionary consequence of increasing quantity or quality needs toward mammals. GENERAL SIGNIFICANCE The introduction of innovative genome editing technology into analysis of the mechanisms of mammalian ERAD, as exemplified here, will provide new insights into the pathogenesis of various diseases.
Collapse
Affiliation(s)
- Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Ginto George
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kazutoshi Mori
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| |
Collapse
|
9
|
Kandel RR, Neal SE. The role of rhomboid superfamily members in protein homeostasis: Mechanistic insight and physiological implications. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118793. [PMID: 32645330 PMCID: PMC7434706 DOI: 10.1016/j.bbamcr.2020.118793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/30/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022]
Abstract
Cells are equipped with protein quality control pathways in order to maintain a healthy proteome; a process known as protein homeostasis. Dysfunction in protein homeostasis leads to the development of many diseases that are associated with proteinopathies. Recently, the rhomboid superfamily has attracted much attention concerning their involvement in protein homeostasis. While their functional role has become much clearer in the last few years, their systemic significance in mammals remains elusive. Here we delineate the current knowledge of rhomboids in protein quality control and how these functions are integrated at the organismal level.
Collapse
Affiliation(s)
- Rachel R Kandel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States of America
| | - Sonya E Neal
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States of America.
| |
Collapse
|
10
|
Abstract
p97 belongs to the functional diverse superfamily of AAA+ (ATPases Associated with diverse cellular Activities) ATPases and is characterized by an N-terminal regulatory domain and two stacked hexameric ATPase domains forming a central protein conducting channel. p97 is highly versatile and has key functions in maintaining protein homeostasis including protein quality control mechanisms like the ubiquitin proteasome system (UPS) and autophagy to disassemble polyubiquitylated proteins from chromatin, membranes, macromolecular protein complexes and aggregates which are either degraded by the proteasome or recycled. p97 can use energy derived from ATP hydrolysis to catalyze substrate unfolding and threading through its central channel. The function of p97 in a large variety of different cellular contexts is reflected by its simultaneous association with different cofactors, which are involved in substrate recognition and processing, thus leading to the formation of transient multi-protein complexes. Dysregulation in protein homeostasis and proteotoxic stress are often involved in the development of cancer and neurological diseases and targeting the UPS including p97 in cancer is a well-established pharmacological strategy. In this chapter we will describe structural and functional aspects of the p97 interactome in regulating diverse cellular processes and will discuss the role of p97 in targeted cancer therapy.
Collapse
|
11
|
Shi W, Ding R, Zhou PP, Fang Y, Wan R, Chen Y, Jin J. Coordinated Actions Between p97 and Cullin-RING Ubiquitin Ligases for Protein Degradation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1217:61-78. [PMID: 31898222 DOI: 10.1007/978-981-15-1025-0_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The cullin-RING ubiquitin ligases comprise the largest subfamily of ubiquitin ligases. They control ubiquitylation and degradation of a large number of protein substrates in eukaryotes. p97 is an ATPase domain-containing protein segregase. It plays essential roles in post-ubiquitylational events in the ubiquitin-proteasome pathway. Together with its cofactors, p97 collaborates with ubiquitin ligases to extract ubiquitylated substrates and deliver them to the proteasome for proteolysis. Here we review the structure, functions, and mechanisms of p97 in cellular protein degradation in coordination with its cofactors and the cullin-RING ubiquitin ligases.
Collapse
Affiliation(s)
- Wenbo Shi
- Life Science Institute, Zhejiang University, HangZhou, China
| | - Ran Ding
- Life Science Institute, Zhejiang University, HangZhou, China
| | - Pei Pei Zhou
- Life Science Institute, Zhejiang University, HangZhou, China
| | - Yuan Fang
- Life Science Institute, Zhejiang University, HangZhou, China
| | - Ruixi Wan
- Life Science Institute, Zhejiang University, HangZhou, China
| | - Yilin Chen
- Life Science Institute, Zhejiang University, HangZhou, China
| | - Jianping Jin
- Life Science Institute, Zhejiang University, HangZhou, China.
| |
Collapse
|
12
|
Ikeda KN, Freeman M. Spatial proteomics reveal that the protein phosphatase PTP1B interacts with and may modify tyrosine phosphorylation of the rhomboid protease RHBDL4. J Biol Chem 2019; 294:11486-11497. [PMID: 31177093 PMCID: PMC6663880 DOI: 10.1074/jbc.ra118.007074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 06/03/2019] [Indexed: 12/23/2022] Open
Abstract
Rhomboid-like proteins are evolutionarily conserved, ubiquitous polytopic membrane proteins, including the canonical rhomboid intramembrane serine proteases and also others that have lost protease activity during evolution. We still have much to learn about their cellular roles, and evidence suggests that some may have more than one function. For example, RHBDL4 (rhomboid-like protein 4) is an endoplasmic reticulum (ER)-resident protease that forms a ternary complex with ubiquitinated substrates and p97/VCP (valosin-containing protein), a major driver of ER-associated degradation (ERAD). RHBDL4 is required for ERAD of some substrates, such as the pre-T-cell receptor α chain (pTα) and has also been shown to cleave amyloid precursor protein to trigger its secretion. In another case, RHBDL4 enables the release of full-length transforming growth factor α in exosomes. Using the proximity proteomic method BioID, here we screened for proteins that interact with or are in close proximity to RHBDL4. Bioinformatics analyses revealed that BioID hits of RHBDL4 overlap with factors related to protein stress at the ER, including proteins that interact with p97/VCP. PTP1B (protein-tyrosine phosphatase nonreceptor type 1, also called PTPN1) was also identified as a potential proximity factor and interactor of RHBDL4. Analysis of RHBDL4 peptides highlighted the presence of tyrosine phosphorylation at the cytoplasmic RHBDL4 C terminus. Site-directed mutagenesis targeting these tyrosine residues revealed that their phosphorylation modifies binding of RHBDL4 to p97/VCP and Lys63-linked ubiquitinated proteins. Our work lays a critical foundation for future mechanistic studies of the roles of RHBDL4 in ERAD and other important cellular pathways.
Collapse
Affiliation(s)
- Kyojiro N Ikeda
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Matthew Freeman
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| |
Collapse
|
13
|
Lee JG, Youn HS, Kang JY, Park SY, Kidera A, Yoo YJ, Eom SH. Crystal structure of the Ube2K/E2-25K and K48-linked di-ubiquitin complex provides structural insight into the mechanism of K48-specific ubiquitin chain synthesis. Biochem Biophys Res Commun 2018; 506:102-107. [DOI: 10.1016/j.bbrc.2018.10.067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/10/2018] [Indexed: 02/08/2023]
|
14
|
Tang WK, Zhang T, Ye Y, Xia D. Structural basis for nucleotide-modulated p97 association with the ER membrane. Cell Discov 2017; 3:17045. [PMID: 29238611 PMCID: PMC5725882 DOI: 10.1038/celldisc.2017.45] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/01/2017] [Indexed: 01/26/2023] Open
Abstract
Association of the cytosolic AAA (ATPases associated with various cellular activities) protein p97 to membranes is essential for various cellular processes including endoplasmic reticulum (ER)-associated degradation. The p97 consists of two ATPase domains and an N domain that interacts with numerous cofactors. The N domain of p97 is known to undergo a large nucleotide-dependent conformation switch, but its physiological relevance is unclear. Here we show p97 is recruited to canine ER membranes predominantly by interacting with VCP-interacting membrane protein (VIMP), an ER-resident protein. We found that the recruitment is modulated through a nucleotide-dependent conformation switch of the N domain in wild-type p97, but this modulation is absent in pathogenic mutants. We demonstrate the molecular mechanism of the modulation by a series of structures of p97, VIMP and their complexes and suggest a physiological role of the nucleotide-dependent N domain conformation switch. The lack of modulation in pathogenic mutants is caused by changes in interactions between the N and D1 domain, as demonstrated by multiple intermediate positions adopted by N domains of mutant p97. Our findings suggest the nucleotide-modulated membrane association may also have a role in other p97-dependent processes.
Collapse
Affiliation(s)
- Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ting Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Disease, 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
| |
Collapse
|
15
|
Rao MV, Williams DR, Cocklin S, Loll PJ. Interaction between the AAA + ATPase p97 and its cofactor ataxin3 in health and disease: Nucleotide-induced conformational changes regulate cofactor binding. J Biol Chem 2017; 292:18392-18407. [PMID: 28939772 DOI: 10.1074/jbc.m117.806281] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/16/2017] [Indexed: 12/29/2022] Open
Abstract
p97 is an essential ATPase associated with various cellular activities (AAA+) that functions as a segregase in diverse cellular processes, including the maintenance of proteostasis. p97 interacts with different cofactors that target it to distinct pathways; an important example is the deubiquitinase ataxin3, which collaborates with p97 in endoplasmic reticulum-associated degradation. However, the molecular details of this interaction have been unclear. Here, we characterized the binding of ataxin3 to p97, showing that ataxin3 binds with low-micromolar affinity to both wild-type p97 and mutants linked to degenerative disorders known as multisystem proteinopathy 1 (MSP1); we further showed that the stoichiometry of binding is one ataxin3 molecule per p97 hexamer. We mapped the binding determinants on each protein, demonstrating that ataxin3's p97/VCP-binding motif interacts with the inter-lobe cleft in the N-domain of p97. We also probed the nucleotide dependence of this interaction, confirming that ataxin3 and p97 associate in the presence of ATP and in the absence of nucleotide, but not in the presence of ADP. Our experiments suggest that an ADP-driven downward movement of the p97 N-terminal domain dislodges ataxin3 by inducing a steric clash between the D1-domain and ataxin3's C terminus. In contrast, MSP1 mutants of p97 bind ataxin3 irrespective of their nucleotide state, indicating a failure by these mutants to translate ADP binding into a movement of the N-terminal domain. Our model provides a mechanistic explanation for how nucleotides regulate the p97-ataxin3 interaction and why atypical cofactor binding is observed with MSP1 mutants.
Collapse
Affiliation(s)
- Maya V Rao
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102 and
| | - Dewight R Williams
- the LeRoy Eyring Center for Solid State Science, Arizona State University, Tempe, Arizona 85287
| | - Simon Cocklin
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102 and
| | - Patrick J Loll
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102 and
| |
Collapse
|
16
|
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.
Collapse
|
17
|
Hänzelmann P, Schindelin H. The Interplay of Cofactor Interactions and Post-translational Modifications in the Regulation of the AAA+ ATPase p97. Front Mol Biosci 2017; 4:21. [PMID: 28451587 PMCID: PMC5389986 DOI: 10.3389/fmolb.2017.00021] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/24/2017] [Indexed: 12/18/2022] Open
Abstract
The hexameric type II AAA ATPase (ATPase associated with various activities) p97 (also referred to as VCP, Cdc48, and Ter94) is critically involved in a variety of cellular activities including pathways such as DNA replication and repair which both involve chromatin remodeling, and is a key player in various protein quality control pathways mediated by the ubiquitin proteasome system as well as autophagy. Correspondingly, p97 has been linked to various pathophysiological states including cancer, neurodegeneration, and premature aging. p97 encompasses an N-terminal domain, two highly conserved ATPase domains and an unstructured C-terminal tail. This enzyme hydrolyzes ATP and utilizes the resulting energy to extract or disassemble protein targets modified with ubiquitin from stable protein assemblies, chromatin and membranes. p97 participates in highly diverse cellular processes and hence its activity is tightly controlled. This is achieved by multiple regulatory cofactors, which either associate with the N-terminal domain or interact with the extreme C-terminus via distinct binding elements and target p97 to specific cellular pathways, sometimes requiring the simultaneous association with more than one cofactor. Most cofactors are recruited to p97 through conserved binding motifs/domains and assist in substrate recognition or processing by providing additional molecular properties. A tight control of p97 cofactor specificity and diversity as well as the assembly of higher-order p97-cofactor complexes is accomplished by various regulatory mechanisms, which include bipartite binding, binding site competition, changes in oligomeric assemblies, and nucleotide-induced conformational changes. Furthermore, post-translational modifications (PTMs) like acetylation, palmitoylation, phosphorylation, SUMOylation, and ubiquitylation of p97 have been reported which further modulate its diverse molecular activities. In this review, we will describe the molecular basis of p97-cofactor specificity/diversity and will discuss how PTMs can modulate p97-cofactor interactions and affect the physiological and patho-physiological functions of p97.
Collapse
Affiliation(s)
- Petra Hänzelmann
- Rudolf Virchow Center for Experimental Biomedicine, University of WürzburgWürzburg, Germany
| | - Hermann Schindelin
- Rudolf Virchow Center for Experimental Biomedicine, University of WürzburgWürzburg, Germany
| |
Collapse
|
18
|
Lim JJ, Lee Y, Yoon SY, Ly TT, Kang JY, Youn HS, An JY, Lee JG, Park KR, Kim TG, Yang JK, Jun Y, Eom SH. Structural insights into the interaction of human p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease. FEBS Lett 2016; 590:4402-4413. [PMID: 27714797 DOI: 10.1002/1873-3468.12447] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/13/2016] [Accepted: 09/20/2016] [Indexed: 11/08/2022]
Abstract
The interaction of the rhomboid pseudoprotease Derlin-1 and p97 is crucial for the retrotranslocation of polyubiquitinated substrates in the endoplasmic reticulum-associated degradation pathway. We report a 2.25 Å resolution structure of the p97 N-terminal domain (p97N) in complex with the Derlin-1 SHP motif. Remarkably, the SHP motif adopts a short, antiparallel β-strand that interacts with the β-sheet of p97N-a site distinct from that to which most p97 adaptor proteins bind. Mutational and biochemical analyses contributed to defining the specific interaction, demonstrating the importance of a highly conserved binding pocket on p97N and a signature motif on SHP. Our findings may also provide insights into the interactions between other SHP-containing proteins and p97N.
Collapse
Affiliation(s)
- Jia Jia Lim
- School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
| | - Youngjin Lee
- School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
| | - So Young Yoon
- School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea
| | - Tue Tu Ly
- School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
| | - Jung Youn Kang
- School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
| | - Hyung-Seop Youn
- School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
| | - Jun Yop An
- School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
| | - Jung-Gyu Lee
- School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
| | - Kyoung Ryoung Park
- School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
| | - Tae Gyun Kim
- School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
| | - Jin Kuk Yang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul, Korea
| | - Youngsoo Jun
- School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea
| | - Soo Hyun Eom
- School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea.,Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Korea
| |
Collapse
|