1
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Anand A, Gautam G, Srivastava G, Yadav S, Ramalingam K, Siddiqi MI, Goyal N. Molecular, structural, and functional characterization of delta subunit of T-complex protein-1 from Leishmania donovani. Infect Immun 2024:e0023424. [PMID: 39248465 DOI: 10.1128/iai.00234-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 06/11/2024] [Indexed: 09/10/2024] Open
Abstract
Chaperonins/Heat shock protein 60 are ubiquitous multimeric protein complexes that assist in the folding of partially and/or misfolded proteins using metabolic energy into their native stage. The eukaryotic group II chaperonin, also referred as T-complex protein-1 ring complex (TRiC)/T-complex protein-1 (TCP1)/chaperonin containing T-complex protein (CCT), contains 8-9 paralogous subunits, arranged in each of the two rings of hetero-oligomeric complex. In Leishmania, till date, only one subunit, LdTCP1γ, has been well studied. Here, we report the molecular, structural, and functional characterization of TCP1δ subunit of Leishmania donovani (LdTCP1δ), the causative agent of Indian kala-azar. LdTCP1δ gene exhibited only 27.9% identity with LdTCP1γ and clustered in a separate branch in the phylogenic tree of LdTCP1 subunits. The purified recombinant protein formed a high molecular weight complex (0.75 MDa), arranged into 16-mer assembly, and performed in vitro chaperonin activity as assayed by ATP-dependent luciferase folding. LdTCP1δ exhibits 1.8-fold upregulated expression in metabolically active, rapidly dividing log phase promastigotes. Over-expression of LdTCP1δ in promastigotes results in increased infectivity and rate of multiplication of intracellular amastigotes. The study thus establishes the existence of an individual functionally active homo-oligomeric complex of LdTCP1δ chaperonin with its role in parasite infectivity and multiplication.
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Affiliation(s)
- Apeksha Anand
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Gunjan Gautam
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - Gaurava Srivastava
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - Shailendra Yadav
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Karthik Ramalingam
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - Mohammad Imran Siddiqi
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - Neena Goyal
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
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2
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Lee SW, Baek WY, Park SW, Chung JM, Park JH, Kang HC, Jung JY, Suh CH. Anti-TCP1 Antibody Is a Potential Biomarker for Diagnosing Systemic Lupus Erythematosus. Int J Mol Sci 2024; 25:8612. [PMID: 39201300 PMCID: PMC11354590 DOI: 10.3390/ijms25168612] [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: 07/10/2024] [Revised: 07/26/2024] [Accepted: 08/01/2024] [Indexed: 09/02/2024] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic inflammatory disease caused by autoantibodies. Serum samples from patients with SLE (n = 10) were compared with those from normal controls (NCs, n = 5) using 21K protein chip analysis to identify a biomarker for SLE, revealing 63 SLE-specific autoantibodies. The anti-chaperonin-containing t-complex polypeptide-1 (TCP1) antibody exhibited higher expression in patients with SLE than in NCs. To validate the specificity of the anti-TCP1 antibody in SLE, dot blot analysis was conducted using sera from patients with SLE (n = 100), rheumatoid arthritis (RA; n = 25), Behçet's disease (BD; n = 28), and systemic sclerosis (SSc; n = 30) and NCs (n = 50). The results confirmed the detection of anti-TCP1 antibodies in 79 of 100 patients with SLE, with substantially elevated expression compared to both NCs and patients with other autoimmune diseases. We performed an enzyme-linked immunosorbent assay to determine the relative amounts of anti-TCP1 antibodies; markedly elevated anti-TCP1 antibody levels were detected in the sera of patients with SLE (50.1 ± 17.3 arbitrary unit (AU), n = 251) compared to those in NCs (33.9 ± 9.3 AU), RA (35 ± 8.7 AU), BD (37.5 ± 11.6 AU), and SSc (43 ± 11.9 AU). These data suggest that the anti-TCP1 antibody is a potential diagnostic biomarker for SLE.
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Affiliation(s)
- Sang-Won Lee
- Department of Rheumatology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; (S.-W.L.); (W.-Y.B.); (S.-W.P.); (J.-Y.J.)
| | - Wook-Young Baek
- Department of Rheumatology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; (S.-W.L.); (W.-Y.B.); (S.-W.P.); (J.-Y.J.)
| | - So-Won Park
- Department of Rheumatology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; (S.-W.L.); (W.-Y.B.); (S.-W.P.); (J.-Y.J.)
| | - Jee-Min Chung
- Department of Molecular Physiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; (J.-M.C.); (H.C.K.)
| | - Ji-Hyun Park
- Office of Biostatistics, Medical Research Collaborating Center, Ajou Research Institute for Innovative Medicine, Ajou University Medical Center, Suwon 16499, Republic of Korea;
- Department of Mathematics, Ajou University, Suwon 16499, Republic of Korea
| | - Ho Chul Kang
- Department of Molecular Physiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; (J.-M.C.); (H.C.K.)
| | - Ju-Yang Jung
- Department of Rheumatology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; (S.-W.L.); (W.-Y.B.); (S.-W.P.); (J.-Y.J.)
| | - Chang-Hee Suh
- Department of Rheumatology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; (S.-W.L.); (W.-Y.B.); (S.-W.P.); (J.-Y.J.)
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
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3
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Bhakta K, Roy M, Samanta S, Ghosh A. Functional diversity in archaeal Hsp60: a molecular mosaic of Group I and Group II chaperonin. FEBS J 2024. [PMID: 38923213 DOI: 10.1111/febs.17213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/23/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
External stress disrupts the balance of protein homeostasis, necessitating the involvement of heat shock proteins (Hsps) in restoring equilibrium and ensuring cellular survival. The thermoacidophilic crenarchaeon Sulfolobus acidocaldarius, lacks the conventional Hsp100, Hsp90, and Hsp70, relying solely on a single ATP-dependent Group II chaperonin, Hsp60, comprising three distinct subunits (α, β, and γ) to refold unfolded substrates and maintain protein homeostasis. Hsp60 forms three different complexes, namely Hsp60αβγ, Hsp60αβ, and Hsp60β, at temperatures of 60 °C, 75 °C, and 90 °C, respectively. This study delves into the intricacies of Hsp60 complexes in S. acidocaldarius, uncovering their ability to form oligomeric structures in the presence of ATP. The recognition of substrates by Hsp60 involves hydrophobic interactions, and the subsequent refolding process occurs in an ATP-dependent manner through charge-driven interactions. Furthermore, the Hsp60β homo-oligomeric complex can protect the archaeal and eukaryotic membrane from stress-induced damage. Hsp60 demonstrates nested cooperativity in ATP hydrolysis activity, where MWC-type cooperativity is nested within KNF-type cooperativity. Remarkably, during ATP hydrolysis, Hsp60β, and Hsp60αβ complexes exhibit a mosaic behavior, aligning with characteristics observed in both Group I and Group II chaperonins, adding a layer of complexity to their functionality.
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Affiliation(s)
- Koustav Bhakta
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Mousam Roy
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Shirsha Samanta
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Abhrajyoti Ghosh
- Department of Biological Sciences, Bose Institute, Kolkata, India
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4
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Gisdon FJ, Zunker M, Wolf JN, Prüfer K, Ackermann J, Welsch C, Koch I. Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes. Bioinformatics 2024; 40:btae112. [PMID: 38449296 PMCID: PMC11212496 DOI: 10.1093/bioinformatics/btae112] [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: 12/04/2023] [Revised: 02/07/2024] [Accepted: 03/05/2024] [Indexed: 03/08/2024] Open
Abstract
MOTIVATION The functional complexity of biochemical processes is strongly related to the interplay of proteins and their assembly into protein complexes. In recent years, the discovery and characterization of protein complexes have substantially progressed through advances in cryo-electron microscopy, proteomics, and computational structure prediction. This development results in a strong need for computational approaches to analyse the data of large protein complexes for structural and functional characterization. Here, we aim to provide a suitable approach, which processes the growing number of large protein complexes, to obtain biologically meaningful information on the hierarchical organization of the structures of protein complexes. RESULTS We modelled the quaternary structure of protein complexes as undirected, labelled graphs called complex graphs. In complex graphs, the vertices represent protein chains and the edges spatial chain-chain contacts. We hypothesized that clusters based on the complex graph correspond to functional biological modules. To compute the clusters, we applied the Leiden clustering algorithm. To evaluate our approach, we chose the human respiratory complex I, which has been extensively investigated and exhibits a known biological module structure experimentally validated. Additionally, we characterized a eukaryotic group II chaperonin TRiC/CCT and the head of the bacteriophage Φ29. The analysis of the protein complexes correlated with experimental findings and indicated known functional, biological modules. Using our approach enables not only to predict functional biological modules in large protein complexes with characteristic features but also to investigate the flexibility of specific regions and coformational changes. The predicted modules can aid in the planning and analysis of experiments. AVAILABILITY AND IMPLEMENTATION Jupyter notebooks to reproduce the examples are available on our public GitHub repository: https://github.com/MolBIFFM/PTGLtools/tree/main/PTGLmodulePrediction.
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Affiliation(s)
- Florian J Gisdon
- Goethe University Frankfurt, Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, 60325 Frankfurt am Main, Germany
| | - Mariella Zunker
- Goethe University Frankfurt, Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, 60325 Frankfurt am Main, Germany
| | - Jan Niclas Wolf
- Goethe University Frankfurt, Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, 60325 Frankfurt am Main, Germany
| | - Kai Prüfer
- Goethe University Frankfurt, Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, 60325 Frankfurt am Main, Germany
| | - Jörg Ackermann
- Goethe University Frankfurt, Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, 60325 Frankfurt am Main, Germany
| | - Christoph Welsch
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, 60590 Frankfurt am Main, Germany
| | - Ina Koch
- Goethe University Frankfurt, Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, 60325 Frankfurt am Main, Germany
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5
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Kim H, Park J, Roh SH. The structural basis of eukaryotic chaperonin TRiC/CCT: Action and folding. Mol Cells 2024; 47:100012. [PMID: 38280673 PMCID: PMC11004407 DOI: 10.1016/j.mocell.2024.100012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/29/2024] Open
Abstract
Accurate folding of proteins in living cells often requires the cooperative support of molecular chaperones. Eukaryotic group II chaperonin Tailless complex polypeptide 1-Ring Complex (TRiC) accomplishes this task by providing a folding chamber for the substrate that is regulated by an Adenosine triphosphate (ATP) hydrolysis-dependent cycle. Once delivered to and recognized by TRiC, the nascent substrate enters the folding chamber and undergoes folding and release in a stepwise manner. During the process, TRiC subunits and cochaperones such as prefoldin and phosducin-like proteins interact with the substrate to assist the overall folding process in a substrate-specific manner. Coevolution between the components is supposed to consult the binding specificity and ultimately expand the substrate repertoire assisted by the chaperone network. This review describes the TRiC chaperonin and the substrate folding process guided by the TRiC network in cooperation with cochaperones, specifically focusing on recent progress in structural analyses.
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Affiliation(s)
- Hyunmin Kim
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Junsun Park
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Soung-Hun Roh
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea.
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6
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Luo D, Gao X, Zhu X, Xu J, Gao P, Zou J, Fan Q, Xu Y, Liu T. Biomarker screening using integrated bioinformatics for the development of "normal-impaired glucose intolerance-type 2 diabetes mellitus". Sci Rep 2024; 14:4558. [PMID: 38402348 PMCID: PMC10894242 DOI: 10.1038/s41598-024-55199-y] [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: 07/22/2023] [Accepted: 02/21/2024] [Indexed: 02/26/2024] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a progressive disease. We utilized bioinformatics analysis and experimental research to identify biomarkers indicative of the progression of T2DM, aiming for early detection of the disease and timely clinical intervention. Integrating Mfuzz analysis with differential expression analysis, we identified 76 genes associated with the progression of T2DM, which were primarily enriched in signaling pathways such as apoptosis, p53 signaling, and necroptosis. Subsequently, using various analytical methods, including machine learning, we further narrowed down the hub genes to STK17A and CCT5. Based on the hub genes, we calculated the risk score for samples and interestingly found that the score correlated with multiple programmed cell death (PCD) pathways. Animal experiments revealed that the diabetes model exhibited higher levels of MDA and LDH, with lower expression of SOD, accompanied by islet cell apoptosis. In conclusion, our study suggests that during the progression of diabetes, STK17A and CCT5 may contribute to the advancement of the disease by regulating oxidative stress, programmed cell death pathways, and critical signaling pathways such as p53 and MAPK, thereby promoting the death of islet cells. This provides substantial evidence in support of further disease prevention and treatment strategies.
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Affiliation(s)
- Dongqiang Luo
- Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
| | - Xiaolu Gao
- Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
| | - Xianqiong Zhu
- Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
| | - Jiongbo Xu
- Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
| | - Pengfei Gao
- Yunkang School of Medicine and Health, Nanfang College Guangzhou, Guangzhou, 510000, China
| | - Jiayi Zou
- Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
| | - Qiaoming Fan
- Foshan Hospital of Traditional Chinese Medicine, Foshan, 528000, China
| | - Ying Xu
- Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
| | - Tian Liu
- Foshan Hospital of Traditional Chinese Medicine, Foshan, 528000, China.
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7
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Park J, Kim H, Gestaut D, Lim S, Opoku-Nsiah KA, Leitner A, Frydman J, Roh SH. A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle. Nat Commun 2024; 15:1007. [PMID: 38307855 PMCID: PMC10837153 DOI: 10.1038/s41467-024-45242-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin-like proteins (PhLPs) to facilitate folding of essential eukaryotic proteins. Using cryoEM and biochemical analyses, we determine the ATP-driven cycle of TRiC-PFD-PhLP2A interaction. PhLP2A binds to open apo-TRiC through polyvalent domain-specific contacts with its chamber's equatorial and apical regions. PhLP2A N-terminal H3-domain binding to subunits CCT3/4 apical domains displace PFD from TRiC. ATP-induced TRiC closure rearranges the contacts of PhLP2A domains within the closed chamber. In the presence of substrate, actin and PhLP2A segregate into opposing chambers, each binding to positively charged inner surface residues from CCT1/3/6/8. Notably, actin induces a conformational change in PhLP2A, causing its N-terminal helices to extend across the inter-ring interface to directly contact a hydrophobic groove in actin. Our findings reveal an ATP-driven PhLP2A structural rearrangement cycle within the TRiC chamber to facilitate folding.
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Affiliation(s)
- Junsun Park
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Hyunmin Kim
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Daniel Gestaut
- Dept of Biology and Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Seyeon Lim
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | | | - Alexander Leitner
- Institute of Molecular Systems Biology, Dept of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Judith Frydman
- Dept of Biology and Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - Soung-Hun Roh
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.
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8
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Wang S, Sass MI, Kwon Y, Ludlam WG, Smith TM, Carter EJ, Gladden NE, Riggi M, Iwasa JH, Willardson BM, Shen PS. Visualizing the chaperone-mediated folding trajectory of the G protein β5 β-propeller. Mol Cell 2023; 83:3852-3868.e6. [PMID: 37852256 PMCID: PMC10841713 DOI: 10.1016/j.molcel.2023.09.032] [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: 05/17/2023] [Revised: 08/24/2023] [Accepted: 09/26/2023] [Indexed: 10/20/2023]
Abstract
The Chaperonin Containing Tailless polypeptide 1 (CCT) complex is an essential protein folding machine with a diverse clientele of substrates, including many proteins with β-propeller domains. Here, we determine the structures of human CCT in complex with its accessory co-chaperone, phosducin-like protein 1 (PhLP1), in the process of folding Gβ5, a component of Regulator of G protein Signaling (RGS) complexes. Cryoelectron microscopy (cryo-EM) and image processing reveal an ensemble of distinct snapshots that represent the folding trajectory of Gβ5 from an unfolded molten globule to a fully folded β-propeller. These structures reveal the mechanism by which CCT directs Gβ5 folding through initiating specific intermolecular contacts that facilitate the sequential folding of individual β sheets until the propeller closes into its native structure. This work directly visualizes chaperone-mediated protein folding and establishes that CCT orchestrates folding by stabilizing intermediates through interactions with surface residues that permit the hydrophobic core to coalesce into its folded state.
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Affiliation(s)
- Shuxin Wang
- Department of Biochemistry, School of Medicine, University of Utah, 15 N. Medical Drive East, Salt Lake City, UT 84112, USA
| | - Mikaila I Sass
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - Yujin Kwon
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - W Grant Ludlam
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - Theresa M Smith
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - Ethan J Carter
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - Nathan E Gladden
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - Margot Riggi
- Department of Biochemistry, School of Medicine, University of Utah, 15 N. Medical Drive East, Salt Lake City, UT 84112, USA
| | - Janet H Iwasa
- Department of Biochemistry, School of Medicine, University of Utah, 15 N. Medical Drive East, Salt Lake City, UT 84112, USA
| | - Barry M Willardson
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA.
| | - Peter S Shen
- Department of Biochemistry, School of Medicine, University of Utah, 15 N. Medical Drive East, Salt Lake City, UT 84112, USA.
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9
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Araki K, Watanabe-Nakayama T, Sasaki D, Sasaki YC, Mio K. Molecular Dynamics Mappings of the CCT/TRiC Complex-Mediated Protein Folding Cycle Using Diffracted X-ray Tracking. Int J Mol Sci 2023; 24:14850. [PMID: 37834298 PMCID: PMC10573753 DOI: 10.3390/ijms241914850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
The CCT/TRiC complex is a type II chaperonin that undergoes ATP-driven conformational changes during its functional cycle. Structural studies have provided valuable insights into the mechanism of this process, but real-time dynamics analyses of mammalian type II chaperonins are still scarce. We used diffracted X-ray tracking (DXT) to investigate the intramolecular dynamics of the CCT complex. We focused on three surface-exposed loop regions of the CCT1 subunit: the loop regions of the equatorial domain (E domain), the E and intermediate domain (I domain) juncture near the ATP-binding region, and the apical domain (A domain). Our results showed that the CCT1 subunit predominantly displayed rotational motion, with larger mean square displacement (MSD) values for twist (χ) angles compared with tilt (θ) angles. Nucleotide binding had a significant impact on the dynamics. In the absence of nucleotides, the region between the E and I domain juncture could act as a pivotal axis, allowing for greater motion of the E domain and A domain. In the presence of nucleotides, the nucleotides could wedge into the ATP-binding region, weakening the role of the region between the E and I domain juncture as the rotational axis and causing the CCT complex to adopt a more compact structure. This led to less expanded MSD curves for the E domain and A domain compared with nucleotide-absent conditions. This change may help to stabilize the functional conformation during substrate binding. This study is the first to use DXT to probe the real-time molecular dynamics of mammalian type II chaperonins at the millisecond level. Our findings provide new insights into the complex dynamics of chaperonins and their role in the functional folding cycle.
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Affiliation(s)
- Kazutaka Araki
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan;
| | - Takahiro Watanabe-Nakayama
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan;
| | - Daisuke Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan (Y.C.S.)
| | - Yuji C. Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan (Y.C.S.)
| | - Kazuhiro Mio
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan;
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10
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Betancourt Moreira K, Collier MP, Leitner A, Li KH, Lachapel ILS, McCarthy F, Opoku-Nsiah KA, Morales-Polanco F, Barbosa N, Gestaut D, Samant RS, Roh SH, Frydman J. A hierarchical assembly pathway directs the unique subunit arrangement of TRiC/CCT. Mol Cell 2023; 83:3123-3139.e8. [PMID: 37625406 PMCID: PMC11209756 DOI: 10.1016/j.molcel.2023.07.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/07/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023]
Abstract
How the essential eukaryotic chaperonin TRiC/CCT assembles from eight distinct subunits into a unique double-ring architecture remains undefined. We show TRiC assembly involves a hierarchical pathway that segregates subunits with distinct functional properties until holocomplex (HC) completion. A stable, likely early intermediate arises from small oligomers containing CCT2, CCT4, CCT5, and CCT7, contiguous subunits that constitute the negatively charged hemisphere of the TRiC chamber, which has weak affinity for unfolded actin. The remaining subunits CCT8, CCT1, CCT3, and CCT6, which comprise the positively charged chamber hemisphere that binds unfolded actin more strongly, join the ring individually. Unincorporated late-assembling subunits are highly labile in cells, which prevents their accumulation and premature substrate binding. Recapitulation of assembly in a recombinant system demonstrates that the subunits in each hemisphere readily form stable, noncanonical TRiC-like HCs with aberrant functional properties. Thus, regulation of TRiC assembly along a biochemical axis disfavors the formation of stable alternative chaperonin complexes.
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Affiliation(s)
| | | | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Natália Barbosa
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Daniel Gestaut
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Rahul S Samant
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Soung-Hun Roh
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA.
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11
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Liu C, Jin M, Wang S, Han W, Zhao Q, Wang Y, Xu C, Diao L, Yin Y, Peng C, Bao L, Wang Y, Cong Y. Pathway and mechanism of tubulin folding mediated by TRiC/CCT along its ATPase cycle revealed using cryo-EM. Commun Biol 2023; 6:531. [PMID: 37193829 DOI: 10.1038/s42003-023-04915-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/04/2023] [Indexed: 05/18/2023] Open
Abstract
The eukaryotic chaperonin TRiC/CCT assists the folding of about 10% of cytosolic proteins through an ATP-driven conformational cycle, and the essential cytoskeleton protein tubulin is the obligate substrate of TRiC. Here, we present an ensemble of cryo-EM structures of endogenous human TRiC throughout its ATPase cycle, with three of them revealing endogenously engaged tubulin in different folding stages. The open-state TRiC-tubulin-S1 and -S2 maps show extra density corresponding to tubulin in the cis-ring chamber of TRiC. Our structural and XL-MS analyses suggest a gradual upward translocation and stabilization of tubulin within the TRiC chamber accompanying TRiC ring closure. In the closed TRiC-tubulin-S3 map, we capture a near-natively folded tubulin-with the tubulin engaging through its N and C domains mainly with the A and I domains of the CCT3/6/8 subunits through electrostatic and hydrophilic interactions. Moreover, we also show the potential role of TRiC C-terminal tails in substrate stabilization and folding. Our study delineates the pathway and molecular mechanism of TRiC-mediated folding of tubulin along the ATPase cycle of TRiC, and may also inform the design of therapeutic agents targeting TRiC-tubulin interactions.
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Affiliation(s)
- Caixuan Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Mingliang Jin
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Shutian Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wenyu Han
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Qiaoyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Cong Xu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lei Diao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, CAS, 201210, Shanghai, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, CAS, 201210, Shanghai, China
| | - Lan Bao
- University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yanxing Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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12
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Wang S, Sass MI, Kwon Y, Ludlam WG, Smith TM, Carter EJ, Gladden NE, Riggi M, Iwasa JH, Willardson BM, Shen PS. Visualizing the chaperone-mediated folding trajectory of the G protein β5 β-propeller. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539424. [PMID: 37205387 PMCID: PMC10187262 DOI: 10.1101/2023.05.04.539424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The cytosolic Chaperonin Containing Tailless polypeptide 1 (CCT) complex is an essential protein folding machine with a diverse clientele of substrates, including many proteins with β-propeller domains. Here, we determined structures of CCT in complex with its accessory co-chaperone, phosducin-like protein 1 (PhLP1), in the process of folding Gβ5, a component of Regulator of G protein Signaling (RGS) complexes. Cryo-EM and image processing revealed an ensemble of distinct snapshots that represent the folding trajectory of Gβ5 from an unfolded molten globule to a fully folded β-propeller. These structures reveal the mechanism by which CCT directs Gβ5 folding through initiating specific intermolecular contacts that facilitate the sequential folding of individual β-sheets until the propeller closes into its native structure. This work directly visualizes chaperone-mediated protein folding and establishes that CCT directs folding by stabilizing intermediates through interactions with surface residues that permit the hydrophobic core to coalesce into its folded state.
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Affiliation(s)
- Shuxin Wang
- Department of Biochemistry, 15 N. Medical Drive East, University of Utah, Salt Lake City, UT, 84112, USA
| | - Mikaila I. Sass
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - Yujin Kwon
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - W. Grant Ludlam
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - Theresa M. Smith
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - Ethan J. Carter
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - Nathan E. Gladden
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - Margot Riggi
- Department of Biochemistry, 15 N. Medical Drive East, University of Utah, Salt Lake City, UT, 84112, USA
| | - Janet H. Iwasa
- Department of Biochemistry, 15 N. Medical Drive East, University of Utah, Salt Lake City, UT, 84112, USA
| | - Barry M. Willardson
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - Peter S. Shen
- Department of Biochemistry, 15 N. Medical Drive East, University of Utah, Salt Lake City, UT, 84112, USA
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13
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Wang H, Zhang L, Liu B, Su J, Ni X. Role of CCT4/ErbB signaling in nephroblastoma: Implications for a biomarker of Wilms tumor. Medicine (Baltimore) 2023; 102:e33219. [PMID: 37058032 PMCID: PMC10101284 DOI: 10.1097/md.0000000000033219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/16/2023] [Indexed: 04/15/2023] Open
Abstract
Wilms tumor is a common abdominal malignant tumor in children. However, the molecular mechanism of Wilms tumor is unclear. GSE66405 and GSE197047 were obtained from the Gene Expression Omnibus database. To identify differentially expressed genes (DEGs) in Wilms tumor, the R package "limma" was used. Weighted gene co-expression network analysis was performed to identify the significant module. The list of DEGs was input into the Search Tool for the Retrieval of Interacting Genes database to construct a protein-protein interaction network for predicting core genes. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes analysis are computational methods for assessing gene function and biological pathways. The genome was analyzed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes and developed by gene set enrichment analysis. Comparative Toxicogenomics Database analysis was performed to find the diseases most related to the core genes. TargetScan was used to screen for miRNAs that regulate hub genes. A total of 925 DEGs were identified. The differently expressed genes were mainly enriched in the metabolic pathway, AMPK signaling pathway, ErbB signaling pathway, mRNA detection pathway, and folded protein binding. A total of 16 core genes (HNRNPK, PABPC1, HNRNPD, NCL, YBX1, EIF4G1, KHDRBS1, HNRNPAB, HSPA4, EEF2, HSP90AA1, EEF1A1, A TP5A1, SDHA, CCT4, CCT5) were obtained. chaperonin containing TCP-1 subunit 4 (CCT4) was downregulated in tumor tissue samples, which may have reverse regulatory significance for Wilms tumor. CCT4, HSP90AA1, NCL, PABPC1, and YBX1 were found to be associated with kidney disease, acute kidney injury, edema, tumor metastasis, transitional cell carcinoma, necrosis, and inflammation. The research found that the related miRNA of the CCT4 gene was hsamiR-7-5p. CCT4 might play an essential role in the occurrence and development of Wilms tumor, and they may participate in the occurrence and development of Wilms tumor through the ERBB signal pathway. CCT4 may be a promising biomarker of Wilms tumor.
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Affiliation(s)
- Haoyuan Wang
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Lei Zhang
- Department of Urology Surgery, Fuxing Hospital Affiliated to Capital Medical University, Xicheng District, Beijing, PR China
| | - Bin Liu
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Jianzhi Su
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Xiaochen Ni
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
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14
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Park J, Kim H, Gestaut D, Lim S, Leitner A, Frydman J, Roh SH. A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534239. [PMID: 37016670 PMCID: PMC10071816 DOI: 10.1101/2023.03.25.534239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin-like proteins (PhLPs) to facilitate the folding of essential eukaryotic proteins. Using cryoEM and biochemical analyses, we determine the ATP-driven cycle of TRiC-PFD-PhLP2A interaction. In the open TRiC state, PhLP2A binds to the chamber's equator while its N-terminal H3-domain binds to the apical domains of CCT3/4, thereby displacing PFD from TRiC. ATP-induced TRiC closure rearranges the contacts of PhLP2A domains within the closed chamber. In the presence of substrate, actin and PhLP2A segregate into opposing chambers, each binding to the positively charged inner surfaces formed by CCT1/3/6/8. Notably, actin induces a conformational change in PhLP2A, causing its N-terminal helices to extend across the inter-ring interface to directly contact a hydrophobic groove in actin. Our findings reveal an ATP-driven PhLP2A structural rearrangement cycle within the TRiC chamber to facilitate folding.
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Affiliation(s)
- Junsun Park
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Hyunmin Kim
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Daniel Gestaut
- Dept of Biology, Stanford University, Stanford, CA 94305, USA
| | - Seyeon Lim
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Dept of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Judith Frydman
- Dept of Biology, Stanford University, Stanford, CA 94305, USA
- Dept of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Soung-Hun Roh
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
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15
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Han W, Jin M, Liu C, Zhao Q, Wang S, Wang Y, Yin Y, Peng C, Wang Y, Cong Y. Structural basis of plp2-mediated cytoskeletal protein folding by TRiC/CCT. SCIENCE ADVANCES 2023; 9:eade1207. [PMID: 36921056 PMCID: PMC10017041 DOI: 10.1126/sciadv.ade1207] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
The cytoskeletal proteins tubulin and actin are the obligate substrates of TCP-1 ring complex/Chaperonin containing TCP-1 (TRiC/CCT), and their folding involves co-chaperone. Through cryo-electron microscopy analysis, we present a more complete picture of TRiC-assisted tubulin/actin folding along TRiC adenosine triphosphatase cycle, under the coordination of co-chaperone plp2. In the open S1/S2 states, plp2 and tubulin/actin engaged within opposite TRiC chambers. Notably, we captured an unprecedented TRiC-plp2-tubulin complex in the closed S3 state, engaged with a folded full-length β-tubulin and loaded with a guanosine triphosphate, and a plp2 occupying opposite rings. Another closed S4 state revealed an actin in the intermediate folding state and a plp2. Accompanying TRiC ring closure, plp2 translocation could coordinate substrate translocation on the CCT6 hemisphere, facilitating substrate stabilization and folding. Our findings reveal the folding mechanism of the major cytoskeletal proteins tubulin/actin under the coordination of the biogenesis machinery TRiC and plp2 and extend our understanding of the links between cytoskeletal proteostasis and related human diseases.
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Affiliation(s)
- Wenyu Han
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Jin
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Caixuan Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiaoyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shutian Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, CAS, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, CAS, Shanghai 201210, China
| | - Yanxing Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Gestaut D, Zhao Y, Park J, Ma B, Leitner A, Collier M, Pintilie G, Roh SH, Chiu W, Frydman J. Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT. Cell 2022; 185:4770-4787.e20. [PMID: 36493755 PMCID: PMC9735246 DOI: 10.1016/j.cell.2022.11.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 09/01/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022]
Abstract
The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of β-tubulin using human prefoldin and TRiC. We find unstructured β-tubulin is delivered by prefoldin to the open TRiC chamber followed by ATP-dependent chamber closure. Cryo-EM resolves four near-atomic-resolution structures containing progressively folded β-tubulin intermediates within the closed TRiC chamber, culminating in native tubulin. This substrate folding pathway appears closely guided by site-specific interactions with conserved regions in the TRiC chamber. Initial electrostatic interactions between the TRiC interior wall and both the folded tubulin N domain and its C-terminal E-hook tail establish the native substrate topology, thus enabling C-domain folding. Intrinsically disordered CCT C termini within the chamber promote subsequent folding of tubulin's core and middle domains and GTP-binding. Thus, TRiC's chamber provides chemical and topological directives that shape the folding landscape of its obligate substrates.
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Affiliation(s)
- Daniel Gestaut
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Yanyan Zhao
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Junsun Park
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Boxue Ma
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Dept of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Miranda Collier
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Grigore Pintilie
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Soung-Hun Roh
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea,Co-Corresponding authors: (lead contact), ,
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA,Co-Corresponding authors: (lead contact), ,
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305, USA,Department of Genetics, Stanford University, Stanford, CA 94305, USA,Co-Corresponding authors: (lead contact), ,
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17
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Smith TM, Willardson BM. Mechanistic insights into protein folding by the eukaryotic chaperonin complex CCT. Biochem Soc Trans 2022; 50:1403-1414. [PMID: 36196890 PMCID: PMC9704529 DOI: 10.1042/bst20220591] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022]
Abstract
The cytosolic chaperonin CCT is indispensable to eukaryotic life, folding the cytoskeletal proteins actin and tubulin along with an estimated 10% of the remaining proteome. However, it also participates in human diseases such as cancer and viral infections, rendering it valuable as a potential therapeutic target. CCT consists of two stacked rings, each comprised of eight homologous but distinct subunits, that assists the folding of a remarkable substrate clientele that exhibits both broad diversity and specificity. Much of the work in recent years has been aimed at understanding the mechanisms of CCT substrate recognition and folding. These studies have revealed new binding sites and mechanisms by which CCT uses its distinctive subunit arrangement to fold structurally unrelated substrates. Here, we review recent structural insights into CCT-substrate interactions and place them into the broader context of CCT function and its implications for human health.
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Affiliation(s)
- Theresa M. Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, U.S.A
| | - Barry M. Willardson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, U.S.A
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18
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Identification of sitagliptin binding proteins by affinity purification mass spectrometry. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1453-1463. [PMID: 36239351 PMCID: PMC9827809 DOI: 10.3724/abbs.2022142] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is recognized as a serious public health concern with increasing incidence. The dipeptidyl peptidase-4 (DPP-4) inhibitor sitagliptin has been used for the treatment of T2DM worldwide. Although sitagliptin has excellent therapeutic outcome, adverse effects are observed. In addition, previous studies have suggested that sitagliptin may have pleiotropic effects other than treating T2DM. These pieces of evidence point to the importance of further investigation of the molecular mechanisms of sitagliptin, starting from the identification of sitagliptin-binding proteins. In this study, by combining affinity purification mass spectrometry (AP-MS) and stable isotope labeling by amino acids in cell culture (SILAC), we discover seven high-confidence targets that can interact with sitagliptin. Surface plasmon resonance (SPR) assay confirms the binding of sitagliptin to three proteins, i. e., LYPLAL1, TCP1, and CCAR2, with binding affinities (K D) ranging from 50.1 μM to 1490 μM. Molecular docking followed by molecular dynamic (MD) simulation reveals hydrogen binding between sitagliptin and the catalytic triad of LYPLAL1, and also between sitagliptin and the P-loop of ATP-binding pocket of TCP1. Molecular mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis indicates that sitagliptin can stably bind to LYPLAL1 and TCP1 in active sites, which may have an impact on the functions of these proteins. SPR analysis validates the binding affinity of sitagliptin to TCP1 mutant D88A is ~10 times lower than that to the wild-type TCP1. Our findings provide insights into the sitagliptin-targets interplay and demonstrate the potential of sitagliptin in regulating gluconeogenesis and in anti-tumor drug development.
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19
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Ghozlan H, Cox A, Nierenberg D, King S, Khaled AR. The TRiCky Business of Protein Folding in Health and Disease. Front Cell Dev Biol 2022; 10:906530. [PMID: 35602608 PMCID: PMC9117761 DOI: 10.3389/fcell.2022.906530] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/20/2022] [Indexed: 01/03/2023] Open
Abstract
Maintenance of the cellular proteome or proteostasis is an essential process that when deregulated leads to diseases like neurological disorders and cancer. Central to proteostasis are the molecular chaperones that fold proteins into functional 3-dimensional (3D) shapes and prevent protein aggregation. Chaperonins, a family of chaperones found in all lineages of organisms, are efficient machines that fold proteins within central cavities. The eukaryotic Chaperonin Containing TCP1 (CCT), also known as Tailless complex polypeptide 1 (TCP-1) Ring Complex (TRiC), is a multi-subunit molecular complex that folds the obligate substrates, actin, and tubulin. But more than folding cytoskeletal proteins, CCT differs from most chaperones in its ability to fold proteins larger than its central folding chamber and in a sequential manner that enables it to tackle proteins with complex topologies or very large proteins and complexes. Unique features of CCT include an asymmetry of charges and ATP affinities across the eight subunits that form the hetero-oligomeric complex. Variable substrate binding capacities endow CCT with a plasticity that developed as the chaperonin evolved with eukaryotes and acquired functional capacity in the densely packed intracellular environment. Given the decades of discovery on the structure and function of CCT, much remains unknown such as the scope of its interactome. New findings on the role of CCT in disease, and potential for diagnostic and therapeutic uses, heighten the need to better understand the function of this essential molecular chaperone. Clues as to how CCT causes cancer or neurological disorders lie in the early studies of the chaperonin that form a foundational knowledgebase. In this review, we span the decades of CCT discoveries to provide critical context to the continued research on the diverse capacities in health and disease of this essential protein-folding complex.
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Affiliation(s)
- Heba Ghozlan
- Division of Cancer Research, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
- Department of Physiology and Biochemistry, Jordan University of Science and Technology, Irbid, Jordan
| | - Amanda Cox
- Division of Cancer Research, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Daniel Nierenberg
- Division of Cancer Research, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Stephen King
- Division of Neuroscience, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Annette R. Khaled
- Division of Cancer Research, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
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20
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Anticarin- β shows a promising anti-osteosarcoma effect by specifically inhibiting CCT4 to impair proteostasis. Acta Pharm Sin B 2022; 12:2268-2279. [PMID: 35646538 PMCID: PMC9136613 DOI: 10.1016/j.apsb.2021.12.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/04/2021] [Accepted: 11/30/2021] [Indexed: 12/29/2022] Open
Abstract
Unlike healthy, non-transformed cells, the proteostasis network of cancer cells is taxed to produce proteins involved in tumor development. Cancer cells have a higher dependency on molecular chaperones to maintain proteostasis. The chaperonin T-complex protein ring complex (TRiC) contains eight paralogous subunits (CCT1-8), and assists the folding of as many as 10% of cytosolic proteome. TRiC is essential for the progression of some cancers, but the roles of TRiC subunits in osteosarcoma remain to be explored. Here, we show that CCT4/TRiC is significantly correlated in human osteosarcoma, and plays a critical role in osteosarcoma cell survival. We identify a compound anticarin-β that can specifically bind to and inhibit CCT4. Anticarin-β shows higher selectivity in cancer cells than in normal cells. Mechanistically, anticarin-β potently impedes CCT4-mediated STAT3 maturation. Anticarin-β displays remarkable antitumor efficacy in orthotopic and patient-derived xenograft models of osteosarcoma. Collectively, our data uncover a key role of CCT4 in osteosarcoma, and propose a promising treatment strategy for osteosarcoma by disrupting CCT4 and proteostasis.
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21
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Roy M, Horovitz A. Partitioning the Hill coefficient into contributions from ligand-promoted conformational changes and subunit heterogeneity. Protein Sci 2022; 31:e4298. [PMID: 35481656 PMCID: PMC8994510 DOI: 10.1002/pro.4298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 11/05/2022]
Abstract
Heterooligomers that undergo ligand-promoted conformational changes are ubiquitous in nature and involved in many essential processes. Conformational switching often leads to positive cooperativity in ligand binding that is reflected in a Hill coefficient with a value greater than one. The subunits comprising heterooligomers can differ, however, in their affinity for the ligand. Such so-called site heterogeneity results in apparent negative cooperativity that is reflected by a Hill coefficient with a value less than one. Consequently, positive cooperativity due to the ligand-promoted allosteric switch can be masked, in cases of such heterooligomers, by apparent negative cooperativity owing to site heterogeneity. Here, we derived expressions for the Hill coefficient, in the case of a heterodimer, in which the contributions from the ligand-promoted allosteric switch and site heterogeneity are separated. Using these equations and simulations for higher order oligomers, we show under which conditions site heterogeneity can significantly mask the extent of observed positive cooperativity.
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Affiliation(s)
- Mousam Roy
- Department of Chemical and Structural BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Amnon Horovitz
- Department of Chemical and Structural BiologyWeizmann Institute of ScienceRehovotIsrael
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22
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Kelly JJ, Tranter D, Pardon E, Chi G, Kramer H, Happonen L, Knee KM, Janz JM, Steyaert J, Bulawa C, Paavilainen VO, Huiskonen JT, Yue WW. Snapshots of actin and tubulin folding inside the TRiC chaperonin. Nat Struct Mol Biol 2022; 29:420-429. [PMID: 35449234 PMCID: PMC9113939 DOI: 10.1038/s41594-022-00755-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 03/01/2022] [Indexed: 01/16/2023]
Abstract
The integrity of a cell's proteome depends on correct folding of polypeptides by chaperonins. The chaperonin TCP-1 ring complex (TRiC) acts as obligate folder for >10% of cytosolic proteins, including he cytoskeletal proteins actin and tubulin. Although its architecture and how it recognizes folding substrates are emerging from structural studies, the subsequent fate of substrates inside the TRiC chamber is not defined. We trapped endogenous human TRiC with substrates (actin, tubulin) and cochaperone (PhLP2A) at different folding stages, for structure determination by cryo-EM. The already-folded regions of client proteins are anchored at the chamber wall, positioning unstructured regions toward the central space to achieve their native fold. Substrates engage with different sections of the chamber during the folding cycle, coupled to TRiC open-and-close transitions. Further, the cochaperone PhLP2A modulates folding, acting as a molecular strut between substrate and TRiC chamber. Our structural snapshots piece together an emerging model of client protein folding within TRiC.
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Affiliation(s)
- John J Kelly
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Dale Tranter
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Kelly M Knee
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Jay M Janz
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Christine Bulawa
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Ville O Paavilainen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, UK.
| | - Wyatt W Yue
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, UK.
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23
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Schulz L, Sendker FL, Hochberg GKA. Non-adaptive complexity and biochemical function. Curr Opin Struct Biol 2022; 73:102339. [PMID: 35247750 DOI: 10.1016/j.sbi.2022.102339] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/06/2021] [Accepted: 01/24/2022] [Indexed: 11/25/2022]
Abstract
Intricate biochemical structures are usually thought to be useful, because natural selection preserves them from degradation by a constant hail of destructive mutations. Biochemists therefore often deliberately disrupt them to understand how complexity improves protein function or fitness. However, evolutionary theory suggests that even useless complexity that never improved fitness can become completely essential if a simple set of evolutionary conditions is fulfilled. We review evidence that stable protein complexes, protein-chaperone interactions, and complexes consisting of several paralogs all fulfill these conditions. This makes reverse genetics or destructive mutagenesis unsuitable for assigning functions to these kinds of complexity. Instead, we advocate that incorporating evolutionary approaches into biochemistry overcomes this difficulty and allows us to distinguish useless from useful biochemical complexity.
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Affiliation(s)
- Luca Schulz
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany. https://twitter.com/schulluc
| | - Franziska L Sendker
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany. https://twitter.com/SendkerFL
| | - Georg K A Hochberg
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany; Department of Chemistry, University of Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Hans-Meerwein-Straße 6, 35032 Marburg, Germany.
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24
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Structural and Kinetic Views of Molecular Chaperones in Multidomain Protein Folding. Int J Mol Sci 2022; 23:ijms23052485. [PMID: 35269628 PMCID: PMC8910466 DOI: 10.3390/ijms23052485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/10/2022] Open
Abstract
Despite recent developments in protein structure prediction, the process of the structure formation, folding, remains poorly understood. Notably, folding of multidomain proteins, which involves multiple steps of segmental folding, is one of the biggest questions in protein science. Multidomain protein folding often requires the assistance of molecular chaperones. Molecular chaperones promote or delay the folding of the client protein, but the detailed mechanisms are still unclear. This review summarizes the findings of biophysical and structural studies on the mechanism of multidomain protein folding mediated by molecular chaperones and explains how molecular chaperones recognize the client proteins and alter their folding properties. Furthermore, we introduce several recent studies that describe the concept of kinetics-activity relationships to explain the mechanism of functional diversity of molecular chaperones.
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25
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Transcriptome Comparison of Brain and Kidney Endothelial Cells in Homeostasis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5239255. [PMID: 35132377 PMCID: PMC8817106 DOI: 10.1155/2022/5239255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/12/2022] [Indexed: 11/17/2022]
Abstract
Endothelial cells are heterogeneous, stemming from multiple organs, but there is still little known about the connection between the brain and kidney endothelial cells, especially in homeostasis. In this study, scRNA-seq results were obtained to compare genetic profiles and biological features of tissue-specific endothelial cells. On this basis, seven endothelial cell subpopulations were identified, two of which were upregulated genes in pathways related to stroke and/or depression, as characterized by neuroinflammation. This study revealed the similarities and distinctions between brain and kidney endothelial cells, providing baseline information needed to fully understand the relationship between renal diseases and neuroinflammation, such as stroke and depression.
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26
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Horovitz A, Reingewertz TH, Cuéllar J, Valpuesta JM. Chaperonin Mechanisms: Multiple and (Mis)Understood? Annu Rev Biophys 2022; 51:115-133. [DOI: 10.1146/annurev-biophys-082521-113418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The chaperonins are ubiquitous and essential nanomachines that assist in protein folding in an ATP-driven manner. They consist of two back-to-back stacked oligomeric rings with cavities in which protein (un)folding can take place in a shielding environment. This review focuses on GroEL from Escherichia coli and the eukaryotic chaperonin-containing t-complex polypeptide 1, which differ considerably in their reaction mechanisms despite sharing a similar overall architecture. Although chaperonins feature in many current biochemistry textbooks after being studied intensively for more than three decades, key aspects of their reaction mechanisms remain under debate and are discussed in this review. In particular, it is unclear whether a universal reaction mechanism operates for all substrates and whether it is passive, i.e., aggregation is prevented but the folding pathway is unaltered, or active. It is also unclear how chaperonin clients are distinguished from nonclients and what are the precise roles of the cofactors with which chaperonins interact. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Amnon Horovitz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel; Amnon.H
| | - Tali Haviv Reingewertz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel; Amnon.H
| | - Jorge Cuéllar
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - José María Valpuesta
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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27
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Cuellar J, Vallin J, Svanström A, Maestro-López M, Teresa Bueno-Carrasco M, Grant Ludlam W, Willardson BM, Valpuesta JM, Grantham J. The molecular chaperone CCT sequesters gelsolin and protects it from cleavage by caspase-3. J Mol Biol 2021; 434:167399. [PMID: 34896365 DOI: 10.1016/j.jmb.2021.167399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/19/2021] [Accepted: 12/03/2021] [Indexed: 11/27/2022]
Abstract
The actin filament severing and capping protein gelsolin plays an important role in modulation of actin filament dynamics by influencing the number of actin filament ends. During apoptosis, gelsolin becomes constitutively active due to cleavage by caspase-3. In non-apoptotic cells gelsolin is activated by the binding of Ca2+. This activated form of gelsolin binds to, but is not a folding substrate of the molecular chaperone CCT/TRiC. Here we demonstrate that in vitro, gelsolin is protected from cleavage by caspase-3 in the presence of CCT. Cryoelectron microscopy and single particle 3D reconstruction of the CCT:gelsolin complex reveals that gelsolin is located in the interior of the chaperonin cavity, with a placement distinct from that of the obligate CCT folding substrates actin and tubulin. In cultured mouse melanoma B16F1 cells, gelsolin co-localises with CCT upon stimulation of actin dynamics at peripheral regions during lamellipodia formation. These data indicate that localised sequestration of gelsolin by CCT may provide spatial control of actin filament dynamics.
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Affiliation(s)
- Jorge Cuellar
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain.
| | - Josefine Vallin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 40530 Gothenburg, Sweden
| | - Andreas Svanström
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 40530 Gothenburg, Sweden
| | - Moisés Maestro-López
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | | | - W Grant Ludlam
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Barry M Willardson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - José M Valpuesta
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - Julie Grantham
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 40530 Gothenburg, Sweden.
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28
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Liu J, Huang L, Zhu Y, He Y, Zhang W, Lei T, Xuan J, Xiao B, Li L, Zhou Q, Sun Z. Exploring the Expression and Prognostic Value of the TCP1 Ring Complex in Hepatocellular Carcinoma and Overexpressing Its Subunit 5 Promotes HCC Tumorigenesis. Front Oncol 2021; 11:739660. [PMID: 34676169 PMCID: PMC8525800 DOI: 10.3389/fonc.2021.739660] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 09/08/2021] [Indexed: 01/20/2023] Open
Abstract
T-complex protein-1 ring complex (TRiC), also known as Chaperonin Containing T-complex protein-1 (CCT), is a multisubunit chaperonin required for the folding of nascent proteins. Mounting evidence suggests that TRiC also contributes to the development and progression of tumors, but there are limited studies on pathogenic functions in hepatocellular carcinoma (HCC). We comprehensively evaluated the expression pattern and biological functions of TRiC subunits using The Cancer Genome Atlas and The Human Protein Atlas. Expression levels of TRiC subunits TCP1, CCT2/3/4/5/6A/7/8 were significantly upregulated in HCC tissues at both transcript and protein levels, which predicted shorter overall survival (OS). Moreover, high mutation rates were found in several CCT subunits, and patients with altered CCT genes exhibited poorer clinical outcomes. Functional enrichment analysis showed that co-regulated genes were preferentially involved in 'protein folding' and 'microtubule-based process', while genes co-expressed with CCT subunits were primarily involved in 'ribosome' and 'spliceosome'. Knockout of CCT5 in a HCC cell line reduced while overexpression enhanced proliferation rate, cycle transition, migration, and invasion. In conclusion, these findings suggest that subunits of the TRiC may be potential biomarkers for the diagnosis of HCC and play an important role in the occurrence and development of HCC.
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Affiliation(s)
- Jiahui Liu
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Ling Huang
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Yi Zhu
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Yongyin He
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Weiyun Zhang
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Ting Lei
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Junfeng Xuan
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Bin Xiao
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China.,Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Linhai Li
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China.,Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Quan Zhou
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China.,Laboratory of Basic Medical Science, General Hospital of Southern Theater Command of PLA, Guangzhou, China
| | - Zhaohui Sun
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
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29
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CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin. Nat Commun 2021; 12:4754. [PMID: 34362932 PMCID: PMC8346469 DOI: 10.1038/s41467-021-25099-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/21/2021] [Indexed: 12/05/2022] Open
Abstract
Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here we use cryoEM to study ATP binding in the homo-oligomeric archaeal chaperonin from Methanococcus maripaludis (MmCpn), consisting of two stacked rings composed of eight identical subunits each. Using a series of image classification steps, we obtained different structural snapshots of individual chaperonins undergoing the nucleotide binding process. We identified nucleotide-bound and free states of individual subunits in each chaperonin, allowing us to determine the ATP occupancy state of each MmCpn particle. We observe distinctive tertiary and quaternary structures reflecting variations in nucleotide occupancy and subunit conformations in each chaperonin complex. Detailed analysis of the nucleotide distribution in each MmCpn complex indicates that individual ATP binding events occur in a statistically random manner for MmCpn, both within and across the rings. Our findings illustrate the power of cryoEM to characterize a biochemical property of multi-subunit ligand binding cooperativity at the individual particle level. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here, the authors employ an approach that uses cryo-EM single particle analysis to track the number and distribution of nucleotides bound to each subunit in the homo-oligomeric MmCpn archaeal chaperonin complex and observe that ATP binds in a statistically random manner to MmCpn both within a ring and across the rings, which shows that there is no cooperativity in ATP binding to archaeal group II chaperonins under the conditions used in this study.
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30
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Green AM, DeWeerd RA, O'Leary DR, Hansen AR, Hayer KE, Kulej K, Dineen AS, Szeto JH, Garcia BA, Weitzman MD. Interaction with the CCT chaperonin complex limits APOBEC3A cytidine deaminase cytotoxicity. EMBO Rep 2021; 22:e52145. [PMID: 34347354 DOI: 10.15252/embr.202052145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
The APOBEC3 cytidine deaminases are implicated as the cause of a prevalent somatic mutation pattern found in cancer genomes. The APOBEC3 enzymes act as viral restriction factors by mutating viral genomes. Mutation of the cellular genome is presumed to be an off-target activity of the enzymes, although the regulatory measures for APOBEC3 expression and activity remain undefined. It is therefore difficult to predict circumstances that enable APOBEC3 interaction with cellular DNA that leads to mutagenesis. The APOBEC3A (A3A) enzyme is the most potent deaminase of the family. Using proteomics, we evaluate protein interactors of A3A to identify potential regulators. We find that A3A interacts with the chaperonin-containing TCP-1 (CCT) complex, a cellular machine that assists in protein folding and function. Importantly, depletion of CCT results in A3A-induced DNA damage and cytotoxicity. Evaluation of cancer genomes demonstrates an enrichment of A3A mutational signatures in cancers with silencing mutations in CCT subunit genes. Together, these data suggest that the CCT complex interacts with A3A, and that disruption of CCT function results in increased A3A mutational activity.
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Affiliation(s)
- Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - David R O'Leary
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ava R Hansen
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Katharina E Hayer
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katarzyna Kulej
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ariel S Dineen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Julia H Szeto
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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31
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Collier MP, Moreira KB, Li KH, Chen YC, Itzhak D, Samant R, Leitner A, Burlingame A, Frydman J. Native mass spectrometry analyses of chaperonin complex TRiC/CCT reveal subunit N-terminal processing and re-association patterns. Sci Rep 2021; 11:13084. [PMID: 34158536 PMCID: PMC8219831 DOI: 10.1038/s41598-021-91086-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/05/2021] [Indexed: 11/14/2022] Open
Abstract
The eukaryotic chaperonin TRiC/CCT is a large ATP-dependent complex essential for cellular protein folding. Its subunit arrangement into two stacked eight-membered hetero-oligomeric rings is conserved from yeast to man. A recent breakthrough enables production of functional human TRiC (hTRiC) from insect cells. Here, we apply a suite of mass spectrometry techniques to characterize recombinant hTRiC. We find all subunits CCT1-8 are N-terminally processed by combinations of methionine excision and acetylation observed in native human TRiC. Dissociation by organic solvents yields primarily monomeric subunits with a small population of CCT dimers. Notably, some dimers feature non-canonical inter-subunit contacts absent in the initial hTRiC. This indicates individual CCT monomers can promiscuously re-assemble into dimers, and lack the information to assume the specific interface pairings in the holocomplex. CCT5 is consistently the most stable subunit and engages in the greatest number of non-canonical dimer pairings. These findings confirm physiologically relevant post-translational processing and function of recombinant hTRiC and offer quantitative insight into the relative stabilities of TRiC subunits and interfaces, a key step toward reconstructing its assembly mechanism. Our results also highlight the importance of assigning contacts identified by native mass spectrometry after solution dissociation as canonical or non-canonical when investigating multimeric assemblies.
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Affiliation(s)
| | | | - Kathy H Li
- Department of Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Yu-Chan Chen
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Rahul Samant
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Alma Burlingame
- Department of Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA.
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32
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Chaperonin point mutation enhances cadmium endurance in Saccharomyces cerevisiae. Biotechnol Lett 2021; 43:1735-1745. [PMID: 34047865 DOI: 10.1007/s10529-021-03151-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/25/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To study the effect of the mutation in conserved G412E in Cct7p subunit of CCT complex on its cellular fate. RESULTS TriC/CCT is a dynamic multimeric protein that assists in protein folding in an energy-dependent manner. A point mutation in the ATP binding pocket in the equatorial domain of the Cct7p subunit delays the doubling time. The cell size was twice the wild type, and the formation of protein aggregates suggests disturbed folding of the proteins. Upon growing in stressful conditions of arsenous acid and cadmium chloride, the mutant was lethal in As3+ but grew well in Cd2+ with 10.5 µg cadmium uptake mg-1 compared to the wild type. The increased expression of vacuole transporters YCF1 and BPT1 by ten-fold and two-fold in mutant indicates the metal transportation to the vacuole. CONCLUSION CCT complex was vulnerable to the mutation in G412E in the Cct7p subunit of protein folding molecular machinery. Interestingly, already stressed cells provided robustness against oxidative stress and cadmium sequestration in the vacuole.
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33
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Structural and functional dissection of reovirus capsid folding and assembly by the prefoldin-TRiC/CCT chaperone network. Proc Natl Acad Sci U S A 2021; 118:2018127118. [PMID: 33836586 PMCID: PMC7980406 DOI: 10.1073/pnas.2018127118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intracellular protein homeostasis is maintained by a network of chaperones that function to fold proteins into their native conformation. The eukaryotic TRiC chaperonin (TCP1-ring complex, also called CCT for cytosolic chaperonin containing TCP1) facilitates folding of a subset of proteins with folding constraints such as complex topologies. To better understand the mechanism of TRiC folding, we investigated the biogenesis of an obligate TRiC substrate, the reovirus σ3 capsid protein. We discovered that the σ3 protein interacts with a network of chaperones, including TRiC and prefoldin. Using a combination of cryoelectron microscopy, cross-linking mass spectrometry, and biochemical approaches, we establish functions for TRiC and prefoldin in folding σ3 and promoting its assembly into higher-order oligomers. These studies illuminate the molecular dynamics of σ3 folding and establish a biological function for TRiC in virus assembly. In addition, our findings provide structural and functional insight into the mechanism by which TRiC and prefoldin participate in the assembly of protein complexes.
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34
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Zhang Y, Krieger J, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I. State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 160:104-120. [PMID: 32866476 PMCID: PMC7914283 DOI: 10.1016/j.pbiomolbio.2020.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/25/2020] [Accepted: 08/16/2020] [Indexed: 12/17/2022]
Abstract
The eukaryotic chaperonin TRiC/CCT plays a major role in assisting the folding of many proteins through an ATP-driven allosteric cycle. Recent structures elucidated by cryo-electron microscopy provide a broad view of the conformations visited at various stages of the chaperonin cycle, including a sequential activation of its subunits in response to nucleotide binding. But we lack a thorough mechanistic understanding of the structure-based dynamics and communication properties that underlie the TRiC/CCT machinery. In this study, we present a computational methodology based on elastic network models adapted to cryo-EM density maps to gain a deeper understanding of the structure-encoded allosteric dynamics of this hexadecameric machine. We have analysed several structures of the chaperonin resolved in different states toward mapping its conformational landscape. Our study indicates that the overall architecture intrinsically favours cooperative movements that comply with the structural variabilities observed in experiments. Furthermore, the individual subunits CCT1-CCT8 exhibit state-dependent sequential events at different states of the allosteric cycle. For example, in the ATP-bound state, subunits CCT5 and CCT4 selectively initiate the lid closure motions favoured by the overall architecture; whereas in the apo form of the heteromer, the subunit CCT7 exhibits the highest predisposition to structural change. The changes then propagate through parallel fluxes of allosteric signals to neighbours on both rings. The predicted state-dependent mechanisms of sequential activation provide new insights into TRiC/CCT intra- and inter-ring signal transduction events.
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Affiliation(s)
- Yan Zhang
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | - James Krieger
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | - Karolina Mikulska-Ruminska
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | - Burak Kaynak
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | | | - José-María Carazo
- Centro Nacional de Biotecnología (CSIC), Darwin, 3, 28049, Madrid, Spain
| | - Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA.
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Devi S, Kim JJ, Singh AP, Kumar S, Dubey AK, Singh SK, Singh RS, Kumar V. Proteotoxicity: A Fatal Consequence of Environmental Pollutants-Induced Impairments in Protein Clearance Machinery. J Pers Med 2021; 11:69. [PMID: 33503824 PMCID: PMC7912547 DOI: 10.3390/jpm11020069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 02/08/2023] Open
Abstract
A tightly regulated protein quality control (PQC) system maintains a healthy balance between correctly folded and misfolded protein species. This PQC system work with the help of a complex network comprised of molecular chaperones and proteostasis. Any intruder, especially environmental pollutants, disrupt the PQC network and lead to PQCs disruption, thus generating damaged and infectious protein. These misfolded/unfolded proteins are linked to several diseases such as Parkinson's disease, Alzheimer's disease, Huntington's disease, and cataracts. Numerous studies on proteins misfolding and disruption of PQCs by environmental pollutants highlight the necessity of detailed knowledge. This review represents the PQCs network and environmental pollutants' impact on the PQC network, especially through the protein clearance system.
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Affiliation(s)
- Shweta Devi
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Lucknow 226001, India;
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea;
| | - Anand Prakash Singh
- Division of Cardiovascular Disease, The University of Alabama at Birmingham (UAB), 1720 2nd Ave South, Birmingham, AL 35294-1913, USA;
| | - Surendra Kumar
- Cytogenetics Lab, Department of Anatomy, All India Institute of Medical Sciences, New Delhi 110029, India;
| | | | | | - Ravi Shankar Singh
- Department of Biochemistry, Microbiology & Immunology, University of Saskatchewan, Room 4D40, Health Sciences Building, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Vijay Kumar
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea;
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Martin-Cofreces NB, Chichon FJ, Calvo E, Torralba D, Bustos-Moran E, Dosil SG, Rojas-Gomez A, Bonzon-Kulichenko E, Lopez JA, Otón J, Sorrentino A, Zabala JC, Vernos I, Vazquez J, Valpuesta JM, Sanchez-Madrid F. The chaperonin CCT controls T cell receptor-driven 3D configuration of centrioles. SCIENCE ADVANCES 2020; 6:eabb7242. [PMID: 33268369 PMCID: PMC7821906 DOI: 10.1126/sciadv.abb7242] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/19/2020] [Indexed: 05/17/2023]
Abstract
T lymphocyte activation requires the formation of immune synapses (IS) with antigen-presenting cells. The dynamics of membrane receptors, signaling scaffolds, microfilaments, and microtubules at the IS determine the potency of T cell activation and subsequent immune response. Here, we show that the cytosolic chaperonin CCT (chaperonin-containing TCP1) controls the changes in reciprocal orientation of the centrioles and polarization of the tubulin dynamics induced by T cell receptor in T lymphocytes forming an IS. CCT also controls the mitochondrial ultrastructure and the metabolic status of T cells, regulating the de novo synthesis of tubulin as well as posttranslational modifications (poly-glutamylation, acetylation, Δ1 and Δ2) of αβ-tubulin heterodimers, fine-tuning tubulin dynamics. These changes ultimately determine the function and organization of the centrioles, as shown by three-dimensional reconstruction of resting and stimulated primary T cells using cryo-soft x-ray tomography. Through this mechanism, CCT governs T cell activation and polarity.
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Affiliation(s)
- N B Martin-Cofreces
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain.
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
| | - F J Chichon
- Department of Macromolecular Structure, Computational Systems Biology Group, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - E Calvo
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
- Laboratory of Cardiovascular Proteomics. Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - D Torralba
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - E Bustos-Moran
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - S G Dosil
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - A Rojas-Gomez
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - E Bonzon-Kulichenko
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
- Laboratory of Cardiovascular Proteomics. Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - J A Lopez
- Laboratory of Cardiovascular Proteomics. Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - J Otón
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - A Sorrentino
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, Barcelona 08290, Spain
| | - J C Zabala
- Departament of Molecular Biology, Facultad de Medicina, Universidad de Cantabria, Santander, 39005 Spain
| | - I Vernos
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona 08003, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - J Vazquez
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
- Laboratory of Cardiovascular Proteomics. Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - J M Valpuesta
- Department of Macromolecular Structure, Computational Systems Biology Group, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain.
| | - F Sanchez-Madrid
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain.
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
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Abstract
This chronologue seeks to document the discovery and development of an understanding of oligomeric ring protein assemblies known as chaperonins that assist protein folding in the cell. It provides detail regarding genetic, physiologic, biochemical, and biophysical studies of these ATP-utilizing machines from both in vivo and in vitro observations. The chronologue is organized into various topics of physiology and mechanism, for each of which a chronologic order is generally followed. The text is liberally illustrated to provide firsthand inspection of the key pieces of experimental data that propelled this field. Because of the length and depth of this piece, the use of the outline as a guide for selected reading is encouraged, but it should also be of help in pursuing the text in direct order.
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The TRiC/CCT Chaperonin and Its Role in Uncontrolled Proliferation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1243:21-40. [PMID: 32297209 DOI: 10.1007/978-3-030-40204-4_2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The cell cycle is a sophisticated space-time regulated mechanism where a wide variety of protein modules and complexes associate functioning in a concerted manner to regulate and transfer the genetic material to daughter cells. CCT (chaperonin containing TCP-1, also known as TRiC) is a molecular machine that forms a high molecular weight complex (1000 KDa). CCT is emerging as a key molecule during mitosis due to its essential role in the folding of many important proteins involved in cell division (Cdh1, Plk1, p27, Cdc20, PP2a regulatory subunits, tubulin or actin) suggesting its involvement in uncontrolled proliferation. The assembly is formed by eight different subunits called CCTα, β, γ, δ, ε, ζ, η and θ in mammals corresponding to CCT1-8 in yeast. CCT/TRiC is organized in a unique intra- and inter-ring arrangement. The chaperonin monomers share a common domain structure including an equatorial domain, which contains all the inter-ring contacts, most of the intra-ring contacts and the ATP binding site, whose binding and hydrolysis triggers the conformational changes that take place during the functional cycle. All chaperonins display an open substrate-receptive conformation, where the unfolded protein is recognized and trapped, and a closed conformation where the substrate is isolated from the bulk of the intracellular environment. In this chapter we discuss the complex set of intra- and inter-ring allosteric signals during chaperonin function.
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An ensemble of cryo-EM structures of TRiC reveal its conformational landscape and subunit specificity. Proc Natl Acad Sci U S A 2019; 116:19513-19522. [PMID: 31492816 PMCID: PMC6765261 DOI: 10.1073/pnas.1903976116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The ATP-fueled TRiC/CCT acts in the folding of 10% cytosolic proteins. TRiC consists of 8 paralogous subunits, each of which plays special roles in TRiC assembly, allosteric cooperativity, and substrate folding. However, due to lack of a thorough picture of TRiC conformational landscape and atomic-resolution details, the underlying structural mechanisms of TRiC subunit specificity in nucleotide usage and substrate binding, and the allosteric transition during ring closure remain unclear. Here, through cryo-electron microscopy (cryo-EM) analysis, we captured a thorough picture of TRiC conformational landscape from open to closed states and its gradually enhanced allosteric coordination, including the N termini, in unprecedented structural detail. Our study also offers insights into the TRiC subunit specificities in nucleotide usage and ring closure. TRiC/CCT assists the folding of ∼10% of cytosolic proteins through an ATP-driven conformational cycle and is essential in maintaining protein homeostasis. Here, we determined an ensemble of cryo-electron microscopy (cryo-EM) structures of yeast TRiC at various nucleotide concentrations, with 4 open-state maps resolved at near-atomic resolutions, and a closed-state map at atomic resolution, revealing an extra layer of an unforeseen N-terminal allosteric network. We found that, during TRiC ring closure, the CCT7 subunit moves first, responding to nucleotide binding; CCT4 is the last to bind ATP, serving as an ATP sensor; and CCT8 remains ADP-bound and is hardly involved in the ATPase-cycle in our experimental conditions; overall, yeast TRiC consumes nucleotide in a 2-ring positively coordinated manner. Our results depict a thorough picture of the TRiC conformational landscape and its allosteric transitions from the open to closed states in more structural detail and offer insights into TRiC subunit specificity in ATP consumption and ring closure, and potentially in substrate processing.
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40
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Berger J, Berger S, Li M, Jacoby AS, Arner A, Bavi N, Stewart AG, Currie PD. In Vivo Function of the Chaperonin TRiC in α-Actin Folding during Sarcomere Assembly. Cell Rep 2019; 22:313-322. [PMID: 29320728 DOI: 10.1016/j.celrep.2017.12.069] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 09/11/2017] [Accepted: 12/19/2017] [Indexed: 12/14/2022] Open
Abstract
The TCP-1 ring complex (TRiC) is a multi-subunit group II chaperonin that assists nascent or misfolded proteins to attain their native conformation in an ATP-dependent manner. Functional studies in yeast have suggested that TRiC is an essential and generalized component of the protein-folding machinery of eukaryotic cells. However, TRiC's involvement in specific cellular processes within multicellular organisms is largely unknown because little validation of TRiC function exists in animals. Our in vivo analysis reveals a surprisingly specific role of TRiC in the biogenesis of skeletal muscle α-actin during sarcomere assembly in myofibers. TRiC acts at the sarcomere's Z-disk, where it is required for efficient assembly of actin thin filaments. Binding of ATP specifically by the TRiC subunit Cct5 is required for efficient actin folding in vivo. Furthermore, mutant α-actin isoforms that result in nemaline myopathy in patients obtain their pathogenic conformation via this function of TRiC.
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Affiliation(s)
- Joachim Berger
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Victoria Node, EMBL Australia, Clayton, VIC 3800, Australia.
| | - Silke Berger
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Victoria Node, EMBL Australia, Clayton, VIC 3800, Australia
| | - Mei Li
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Victoria Node, EMBL Australia, Clayton, VIC 3800, Australia; Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Arie S Jacoby
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Victoria Node, EMBL Australia, Clayton, VIC 3800, Australia
| | - Anders Arner
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Navid Bavi
- Department of Physiology, School of Medical Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Victoria Node, EMBL Australia, Clayton, VIC 3800, Australia.
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Structural and functional analysis of the role of the chaperonin CCT in mTOR complex assembly. Nat Commun 2019; 10:2865. [PMID: 31253771 PMCID: PMC6599039 DOI: 10.1038/s41467-019-10781-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/01/2019] [Indexed: 01/01/2023] Open
Abstract
The mechanistic target of rapamycin (mTOR) kinase forms two multi-protein signaling complexes, mTORC1 and mTORC2, which are master regulators of cell growth, metabolism, survival and autophagy. Two of the subunits of these complexes are mLST8 and Raptor, β-propeller proteins that stabilize the mTOR kinase and recruit substrates, respectively. Here we report that the eukaryotic chaperonin CCT plays a key role in mTORC assembly and signaling by folding both mLST8 and Raptor. A high resolution (4.0 Å) cryo-EM structure of the human mLST8-CCT intermediate isolated directly from cells shows mLST8 in a near-native state bound to CCT deep within the folding chamber between the two CCT rings, and interacting mainly with the disordered N- and C-termini of specific CCT subunits of both rings. These findings describe a unique function of CCT in mTORC assembly and a distinct binding site in CCT for mLST8, far from those found for similar β-propeller proteins. β-propeller domains are an important class of folding substrates for the eukaryotic cytosolic chaperonin CTT. Here the authors find that CTT contributes to the folding and assembly of two β-propeller proteins from mTOR complexes, mLST8 and Raptor, and determine the 4.0 Å cryoEM structure of a human mLST8-CCT intermediate that shows mLST8 in a near-native state.
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42
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Zhao Q, Zhang X, Sommer F, Ta N, Wang N, Schroda M, Cong Y, Liu C. Hetero-oligomeric CPN60 resembles highly symmetric group-I chaperonin structure revealed by Cryo-EM. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:798-812. [PMID: 30735603 DOI: 10.1111/tpj.14273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/07/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
The chloroplast chaperonin system is indispensable for the biogenesis of Rubisco, the key enzyme in photosynthesis. Using Chlamydomonas reinhardtii as a model system, we found that in vivo the chloroplast chaperonin consists of CPN60α, CPN60β1 and CPN60β2 and the co-chaperonin of the three subunits CPN20, CPN11 and CPN23. In Escherichia coli, CPN20 homo-oligomers and all possible other chloroplast co-chaperonin hetero-oligomers are functional, but only that consisting of CPN11/20/23-CPN60αβ1β2 can fully replace GroES/GroEL under stringent stress conditions. Endogenous CPN60 was purified and its stoichiometry was determined to be 6:2:6 for CPN60α:CPN60β1:CPN60β2. The cryo-EM structures of endogenous CPN60αβ1β2/ADP and CPN60αβ1β2/co-chaperonin/ADP were solved at resolutions of 4.06 and 3.82 Å, respectively. In both hetero-oligomeric complexes the chaperonin subunits within each ring are highly symmetric. Through hetero-oligomerization, the chloroplast co-chaperonin CPN11/20/23 forms seven GroES-like domains, which symmetrically interact with CPN60αβ1β2. Our structure also reveals an uneven distribution of roof-forming domains in the dome-shaped CPN11/20/23 co-chaperonin and potentially diversified surface properties in the folding cavity of the CPN60αβ1β2 chaperonin that might enable the chloroplast chaperonin system to assist in the folding of specific substrates.
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Affiliation(s)
- Qian Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiang Zhang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Frederik Sommer
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Na Ta
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Ning Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Erwin-Schroedinger Str. 70, 67663, Kaiserslautern, Germany
| | - Yao Cong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Cuimin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
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Ahn HK, Yoon JT, Choi I, Kim S, Lee HS, Pai HS. Functional characterization of chaperonin containing T-complex polypeptide-1 and its conserved and novel substrates in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2741-2757. [PMID: 30825377 PMCID: PMC6506772 DOI: 10.1093/jxb/erz099] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/21/2019] [Indexed: 05/31/2023]
Abstract
Chaperonin containing T-complex polypeptide-1 (CCT) is an evolutionarily conserved chaperonin multi-subunit complex that mediates protein folding in eukaryotes. It is essential for cell growth and survival in yeast and mammals, with diverse substrate proteins. However, only a few studies on plant CCT have been reported to date, due to the essentiality of CCT subunit genes and the large size of the complex. Here, we have investigated the structure and function of the Arabidopsis CCT complex in detail. The plant CCT consisted of eight subunits that assemble to form a high-molecular-mass protein complex, shown by diverse methods. CCT-deficient cells exhibited depletion of cortical microtubules, accompanied by a reduction in cellular α- and β-tubulin levels due to protein degradation. Cycloheximide-chase assays suggested that CCT is involved in the folding of tubulins in plants. Furthermore, CCT interacted with PPX1, the catalytic subunit of protein phosphatase 4, and may participate in the folding of PPX1 as its substrate. CCT also interacted with Tap46, a regulatory subunit of PP2A family phosphatases, but Tap46 appeared to function in PPX1 stabilization, rather than as a CCT substrate. Collectively, our findings reveal the essential functions of CCT chaperonin in plants and its conserved and novel substrates.
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Affiliation(s)
- Hee-Kyung Ahn
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Joong-Tak Yoon
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Ilyeong Choi
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Sumin Kim
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Ho-Seok Lee
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul, Korea
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44
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Gestaut D, Limatola A, Joachimiak L, Frydman J. The ATP-powered gymnastics of TRiC/CCT: an asymmetric protein folding machine with a symmetric origin story. Curr Opin Struct Biol 2019; 55:50-58. [PMID: 30978594 DOI: 10.1016/j.sbi.2019.03.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 03/04/2019] [Indexed: 10/27/2022]
Abstract
The eukaryotic chaperonin TRiC/CCT is a large hetero-oligomeric complex that plays an essential role assisting cellular protein folding and suppressing protein aggregation. It consists of two rings, and each composed of eight different subunits; non-native polypeptides bind and fold in an ATP-dependent manner within their central chamber. Here, we review recent advances in our understanding of TRiC structure and mechanism enabled by application of hybrid structural methods including the integration of cryo-electron microscopy with distance constraints from crosslinking mass spectrometry. These new insights are revealing how the different TRiC/CCT subunits create asymmetry in its ATP-driven conformational cycle and its interaction with non-native polypeptides, which ultimately underlie its unique ability to fold proteins that cannot be folded by other chaperones.
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Affiliation(s)
- Daniel Gestaut
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305-5430, USA
| | - Antonio Limatola
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305-5430, USA
| | - Lukasz Joachimiak
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305-5430, USA
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305-5430, USA.
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45
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Gestaut D, Roh SH, Ma B, Pintilie G, Joachimiak LA, Leitner A, Walzthoeni T, Aebersold R, Chiu W, Frydman J. The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis. Cell 2019; 177:751-765.e15. [PMID: 30955883 DOI: 10.1016/j.cell.2019.03.012] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 12/03/2018] [Accepted: 03/04/2019] [Indexed: 01/02/2023]
Abstract
Maintaining proteostasis in eukaryotic protein folding involves cooperation of distinct chaperone systems. To understand how the essential ring-shaped chaperonin TRiC/CCT cooperates with the chaperone prefoldin/GIMc (PFD), we integrate cryoelectron microscopy (cryo-EM), crosslinking-mass-spectrometry and biochemical and cellular approaches to elucidate the structural and functional interplay between TRiC/CCT and PFD. We find these hetero-oligomeric chaperones associate in a defined architecture, through a conserved interface of electrostatic contacts that serves as a pivot point for a TRiC-PFD conformational cycle. PFD alternates between an open "latched" conformation and a closed "engaged" conformation that aligns the PFD-TRiC substrate binding chambers. PFD can act after TRiC bound its substrates to enhance the rate and yield of the folding reaction, suppressing non-productive reaction cycles. Disrupting the TRiC-PFD interaction in vivo is strongly deleterious, leading to accumulation of amyloid aggregates. The supra-chaperone assembly formed by PFD and TRiC is essential to prevent toxic conformations and ensure effective cellular proteostasis.
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Affiliation(s)
- Daniel Gestaut
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Soung Hun Roh
- Department of Biological Science, Seoul National University, Seoul, South Korea
| | - Boxue Ma
- Baylor College of Medicine, Houston, TX 77030, USA
| | - Grigore Pintilie
- Department of Biological Science, Seoul National University, Seoul, South Korea
| | - Lukasz A Joachimiak
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, UTSouthwestern, North Campus, Dallas, TX 75390, USA
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Thomas Walzthoeni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland; PhD Program in Molecular Life Sciences, University of Zurich/ETH Zurich, 8057 Zurich, Switzerland; Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA.
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Vallin J, Grantham J. The role of the molecular chaperone CCT in protein folding and mediation of cytoskeleton-associated processes: implications for cancer cell biology. Cell Stress Chaperones 2019; 24:17-27. [PMID: 30506376 PMCID: PMC6363620 DOI: 10.1007/s12192-018-0949-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 11/02/2018] [Accepted: 11/09/2018] [Indexed: 11/21/2022] Open
Abstract
The chaperonin-containing tailless complex polypeptide 1 (CCT) is required in vivo for the folding of newly synthesized tubulin and actin proteins and is thus intrinsically connected to all cellular processes that rely on the microtubule and actin filament components of the cytoskeleton, both of which are highly regulated and dynamic assemblies. In addition to CCT acting as a protein folding oligomer, further modes of CCT action mediated either by the CCT oligomer itself or via CCT subunits in their monomeric forms can influence processes associated with assembled actin filaments and microtubules. Thus, there is an extended functional role for CCT with regard to its major folding substrates with a complex interplay between CCT as folding machine for tubulin/actin and as a modulator of processes involving the assembled cytoskeleton. As cell division, directed cell migration, and invasion are major drivers of cancer development and rely on the microtubule and actin filament components of the cytoskeleton, CCT activity is fundamentally linked to cancer. Furthermore, the CCT oligomer also folds proteins connected to cell cycle progression and interacts with several other proteins that are linked to cancer such as tumor-suppressor proteins and regulators of the cytoskeleton, while CCT monomer function can influence cell migration. Thus, understanding CCT activity is important for many aspects of cancer cell biology and may reveal new ways to target tumor growth and invasion.
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Affiliation(s)
- Josefine Vallin
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Julie Grantham
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden.
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Abstract
The eukaryotic group II chaperonin TRiC/CCT assists the folding of 10% of cytosolic proteins including many key structural and regulatory proteins. TRiC plays an essential role in maintaining protein homeostasis, and dysfunction of TRiC is closely related to human diseases including cancer and neurodegenerative diseases. TRiC consists of eight paralogous subunits, each of which plays a specific role in the assembly, allosteric cooperativity, and substrate recognition and folding of this complex macromolecular machine. TRiC-mediated substrate folding is regulated through its ATP-driven conformational changes. In recent years, progresses have been made on the structure, subunit arrangement, conformational cycle, and substrate folding of TRiC. Additionally, accumulating evidences also demonstrate the linkage between TRiC oligomer or monomer and diseases. In this review, we focus on the TRiC structure itself, TRiC assisted substrate folding, TRiC and disease, and the potential therapeutic application of TRiC in various diseases.
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Affiliation(s)
- Mingliang Jin
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Caixuan Liu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Wenyu Han
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yao Cong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China.
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48
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Fernández-Higuero JÁ, Betancor-Fernández I, Mesa-Torres N, Muga A, Salido E, Pey AL. Structural and functional insights on the roles of molecular chaperones in the mistargeting and aggregation phenotypes associated with primary hyperoxaluria type I. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:119-152. [PMID: 30635080 DOI: 10.1016/bs.apcsb.2018.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To carry out their biological function in cells, proteins must be folded and targeted to the appropriate subcellular location. These processes are controlled by a vast collection of interacting proteins collectively known as the protein homeostasis network, in which molecular chaperones play a prominent role. Protein homeostasis can be impaired by inherited mutations leading to genetic diseases. In this chapter, we focus on a particular disease, primary hyperoxaluria type 1 (PH1), in which disease-associated mutations exacerbate protein aggregation in the cell and mistarget the peroxisomal alanine:glyoxylate aminotransferase (AGT) protein to mitochondria, in part due to native state destabilization and enhanced interaction with Hsp60, 70 and 90 chaperone systems. After a general introduction of molecular chaperones and PH1, we review our current knowledge on the structural and energetic features of PH1-causing mutants that lead to these particular pathogenic mechanisms. From this perspective, and in the context of the key role of molecular chaperones in PH1 pathogenesis, we present and discuss current and future perspectives for pharmacological treatments for this disease.
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Affiliation(s)
- José Ángel Fernández-Higuero
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, ITB, University of La Laguna, Tenerife, Spain
| | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Arturo Muga
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, ITB, University of La Laguna, Tenerife, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain.
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49
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The structure and evolution of eukaryotic chaperonin-containing TCP-1 and its mechanism that folds actin into a protein spring. Biochem J 2018; 475:3009-3034. [DOI: 10.1042/bcj20170378] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/16/2018] [Accepted: 08/28/2018] [Indexed: 12/15/2022]
Abstract
Actin is folded to its native state in eukaryotic cytosol by the sequential allosteric mechanism of the chaperonin-containing TCP-1 (CCT). The CCT machine is a double-ring ATPase built from eight related subunits, CCT1–CCT8. Non-native actin interacts with specific subunits and is annealed slowly through sequential binding and hydrolysis of ATP around and across the ring system. CCT releases a folded but soft ATP-G-actin monomer which is trapped 80 kJ/mol uphill on the folding energy surface by its ATP-Mg2+/Ca2+ clasp. The energy landscape can be re-explored in the actin filament, F-actin, because ATP hydrolysis produces dehydrated and more compact ADP-actin monomers which, upon application of force and strain, are opened and closed like the elements of a spring. Actin-based myosin motor systems underpin a multitude of force generation processes in cells and muscles. We propose that the water surface of F-actin acts as a low-binding energy, directional waveguide which is recognized specifically by the myosin lever-arm domain before the system engages to form the tight-binding actomyosin complex. Such a water-mediated recognition process between actin and myosin would enable symmetry breaking through fast, low energy initial binding events. The origin of chaperonins and the subsequent emergence of the CCT–actin system in LECA (last eukaryotic common ancestor) point to the critical role of CCT in facilitating phagocytosis during early eukaryotic evolution and the transition from the bacterial world. The coupling of CCT-folding fluxes to the cell cycle, cell size control networks and cancer are discussed together with directions for further research.
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50
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Pathway of Actin Folding Directed by the Eukaryotic Chaperonin TRiC. Cell 2018; 174:1507-1521.e16. [PMID: 30100183 DOI: 10.1016/j.cell.2018.07.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/20/2018] [Accepted: 07/03/2018] [Indexed: 12/22/2022]
Abstract
The hetero-oligomeric chaperonin of eukarya, TRiC, is required to fold the cytoskeletal protein actin. The simpler bacterial chaperonin system, GroEL/GroES, is unable to mediate actin folding. Here, we use spectroscopic and structural techniques to determine how TRiC promotes the conformational progression of actin to the native state. We find that actin fails to fold spontaneously even in the absence of aggregation but populates a kinetically trapped, conformationally dynamic state. Binding of this frustrated intermediate to TRiC specifies an extended topology of actin with native-like secondary structure. In contrast, GroEL stabilizes bound actin in an unfolded state. ATP binding to TRiC effects an asymmetric conformational change in the chaperonin ring. This step induces the partial release of actin, priming it for folding upon complete release into the chaperonin cavity, mediated by ATP hydrolysis. Our results reveal how the unique features of TRiC direct the folding pathway of an obligate eukaryotic substrate.
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