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Nakase Y, Murakami H, Suma M, Nagano K, Wakuda A, Kitagawa T, Matsumoto T. Cdc48 and its co-factor Ufd1 extract CENP-A from centromeric chromatin and can induce chromosome elimination in the fission yeast Schizosaccharomyces pombe. Biol Open 2024; 13:bio060287. [PMID: 38526189 PMCID: PMC11033524 DOI: 10.1242/bio.060287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/14/2024] [Indexed: 03/26/2024] Open
Abstract
CENP-A determines the identity of the centromere. Because the position and size of the centromere and its number per chromosome must be maintained, the distribution of CENP-A is strictly regulated. In this study, we have aimed to understand mechanisms to regulate the distribution of CENP-A (Cnp1SP) in fission yeast. A mutant of the ufd1+ gene (ufd1-73) encoding a cofactor of Cdc48 ATPase is sensitive to Cnp1 expressed at a high level and allows mislocalization of Cnp1. The level of Cnp1 in centromeric chromatin is increased in the ufd1-73 mutant even when Cnp1 is expressed at a normal level. A preexisting mutant of the cdc48+ gene (cdc48-353) phenocopies the ufd1-73 mutant. We have also shown that Cdc48 and Ufd1 proteins interact physically with centromeric chromatin. Finally, Cdc48 ATPase with Ufd1 artificially recruited to the centromere of a mini-chromosome (Ch16) induce a loss of Cnp1 from Ch16, leading to an increased rate of chromosome loss. It appears that Cdc48 ATPase, together with its cofactor Ufd1 remove excess Cnp1 from chromatin, likely in a direct manner. This mechanism may play a role in centromere disassembly, a process to eliminate Cnp1 to inactivate the kinetochore function during development, differentiation, and stress response.
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Affiliation(s)
- Yukiko Nakase
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe cho, Sakyo ku, Kyoto 606-8501, Japan
| | - Hiroaki Murakami
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe cho, Sakyo ku, Kyoto 606-8501, Japan
| | - Michiko Suma
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe cho, Sakyo ku, Kyoto 606-8501, Japan
| | - Kaho Nagano
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe cho, Sakyo ku, Kyoto 606-8501, Japan
| | - Airi Wakuda
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe cho, Sakyo ku, Kyoto 606-8501, Japan
| | - Teppei Kitagawa
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe cho, Sakyo ku, Kyoto 606-8501, Japan
| | - Tomohiro Matsumoto
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe cho, Sakyo ku, Kyoto 606-8501, Japan
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Nguyen TQ, My Le LT, Kim DH, Ko KS, Lee HT, Kim Nguyen YT, Kim HS, Han BW, Kang W, Yang JK. Structural basis for the interaction between human Npl4 and Npl4-binding motif of human Ufd1. Structure 2022; 30:1530-1537.e3. [PMID: 36087575 DOI: 10.1016/j.str.2022.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/19/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022]
Abstract
The heterodimer of human ubiquitin fusion degradation 1 (hUfd1) and human nuclear protein localization 4 (hNpl4) is a major cofactor of human p97 adenosine triphosphatase (ATPase). The p97-Ufd1-Npl4 complex translocates the ubiquitin-conjugated proteins from the endoplasmic reticulum membrane to the cytoplasm. Ubiquitinated proteins are then degraded by the proteasome. The structures of Npl4 and Ufd1-Npl4 (UN) complex in Saccharomyces cerevisiae have been recently reported; however, the structures of hNpl4 and the human UN complex remain unknown. Here, we report the crystal structures of the human UN complex at a resolution of 2.7 Å and hNpl4 at a resolution of 3.0 Å. We also present atomic details and characterization of the human UN complex. Crystallographic studies and site-directed mutagenesis of the hUfd1 residues involved in the interaction with hNpl4 revealed the atomic details of the two proteins.
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Affiliation(s)
- Thang Quyet Nguyen
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Le Thi My Le
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Do Hyeon Kim
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Kyung Soo Ko
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Hee Taek Lee
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Yen Thi Kim Nguyen
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyoun Sook Kim
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Byung Woo Han
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Wonchull Kang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea; Department of Physics and Integrative Institute of Basic Science, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea; Department of Green Chemistry and Material Engineering, Soongsil University, Seoul 06798, Republic of Korea.
| | - Jin Kuk Yang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea.
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Vijayakumari D, Müller J, Hauf S. Cdc48 influence on separase levels is independent of mitosis and suggests translational sensitivity of separase. Cell Rep 2022; 38:110554. [PMID: 35320724 DOI: 10.1016/j.celrep.2022.110554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 01/21/2022] [Accepted: 03/02/2022] [Indexed: 11/23/2022] Open
Abstract
Cdc48 (p97/VCP) is a AAA-ATPase that can extract ubiquitinated proteins from their binding partners and can cooperate with the proteasome for their degradation. A fission yeast cdc48 mutant (cdc48-353) shows low levels of the cohesin protease, separase, and pronounced chromosome segregation defects in mitosis. Separase initiates chromosome segregation when its binding partner securin is ubiquitinated and degraded. The low separase levels in the cdc48-353 mutant have been attributed to a failure to extract ubiquitinated securin from separase, resulting in co-degradation of separase along with securin. If true, Cdc48 would be important in mitosis. In contrast, we show here that low separase levels in the cdc48-353 mutant are independent of mitosis. Moreover, we find no evidence of enhanced separase degradation in the mutant. Instead, we suggest that the cdc48-353 mutant uncovers specific requirements for separase translation. Our results highlight a need to better understand how this key mitotic enzyme is synthesized.
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Ji Z, Li H, Peterle D, Paulo JA, Ficarro SB, Wales TE, Marto JA, Gygi SP, Engen JR, Rapoport TA. Translocation of polyubiquitinated protein substrates by the hexameric Cdc48 ATPase. Mol Cell 2022; 82:570-584.e8. [PMID: 34951965 PMCID: PMC8818041 DOI: 10.1016/j.molcel.2021.11.033] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/30/2021] [Accepted: 11/24/2021] [Indexed: 02/05/2023]
Abstract
The hexameric Cdc48 ATPase (p97 or VCP in mammals) cooperates with its cofactor Ufd1/Npl4 to extract polyubiquitinated proteins from membranes or macromolecular complexes for degradation by the proteasome. Here, we clarify how the Cdc48 complex unfolds its substrates and translocates polypeptides with branchpoints. The Cdc48 complex recognizes primarily polyubiquitin chains rather than the attached substrate. Cdc48 and Ufd1/Npl4 cooperatively bind the polyubiquitin chain, resulting in the unfolding of one ubiquitin molecule (initiator). Next, the ATPase pulls on the initiator ubiquitin and moves all ubiquitin molecules linked to its C terminus through the central pore of the hexameric double ring, causing transient ubiquitin unfolding. When the ATPase reaches the isopeptide bond of the substrate, it can translocate and unfold both N- and C-terminal segments. Ubiquitins linked to the branchpoint of the initiator dissociate from Ufd1/Npl4 and move outside the central pore, resulting in the release of unfolded, polyubiquitinated substrate from Cdc48.
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Affiliation(s)
- Zhejian Ji
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.,Corresponding authors: Zhejian Ji and Tom Rapoport, Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA., and
| | - Hao Li
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Daniele Peterle
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Scott B. Ficarro
- Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA,Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jarrod A. Marto
- Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA,Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Tom A. Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.,Corresponding authors: Zhejian Ji and Tom Rapoport, Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA., and
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Blythe EE, Olson KC, Chau V, Deshaies RJ. 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:E4380-8. [PMID: 28512218 DOI: 10.1073/pnas.1706205114] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Neal S, Mak R, Bennett EJ, Hampton R. A Cdc48 "Retrochaperone" Function Is Required for the Solubility of Retrotranslocated, Integral Membrane Endoplasmic Reticulum-associated Degradation (ERAD-M) Substrates. J Biol Chem 2017; 292:3112-3128. [PMID: 28077573 DOI: 10.1074/jbc.m116.770610] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/10/2017] [Indexed: 12/22/2022] Open
Abstract
A surprising feature of endoplasmic reticulum (ER)-associated degradation (ERAD) is the movement, or retrotranslocation, of ubiquitinated substrates from the ER lumen or membrane to the cytosol where they are degraded by the 26S proteasome. Multispanning ER membrane proteins, called ERAD-M substrates, are retrotranslocated to the cytosol as full-length intermediates during ERAD, and we have investigated how they maintain substrate solubility. Using an in vivo assay, we show that retrotranslocated ERAD-M substrates are moved to the cytoplasm as part of the normal ERAD pathway, where they are part of a solely proteinaceous complex. Using proteomics and direct biochemical confirmation, we found that Cdc48 serves as a critical "retrochaperone" for these ERAD-M substrates. Cdc48 binding to retrotranslocated, ubiquitinated ERAD-M substrates is required for their solubility; removal of the polyubiquitin chains or competition for binding by addition of free polyubiquitin liberated Cdc48 from retrotranslocated proteins and rendered them insoluble. All components of the canonical Cdc48 complex Cdc48-Npl4-Ufd1 were present in solubilized ERAD-M substrates. This function of the complex was observed for both HRD and DOA pathway substrates. Thus, in addition to the long known ATP-dependent extraction of ERAD substrates during retrotranslocation, the Cdc48 complex is generally and critically needed for the solubility of retrotranslocated ERAD-M intermediates.
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Affiliation(s)
- Sonya Neal
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093
| | - Raymond Mak
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093
| | - Eric J Bennett
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093
| | - Randolph Hampton
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093.
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