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Tee A, Jones RA, Dunlop EA, Champion J, Doubleday P, Claessens T, Jalali Z, Seifan S, Perry I, Giles P, Harrison O, Coull B, Houweling A, Pause A, Ballif B. Characterizing the tumor suppressor activity of FLCN in Birt-Hogg-Dubé syndrome through transcriptiomic and proteomic analysis. RESEARCH SQUARE 2024:rs.3.rs-4510670. [PMID: 38978568 PMCID: PMC11230511 DOI: 10.21203/rs.3.rs-4510670/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Birt-Hogg-Dubé (BHD) syndrome patients are uniquely susceptible to all renal tumour subtypes. The underlying mechanism of carcinogenesis is unclear. To study cancer development in BHD, we used human proximal kidney (HK2) cells and found that long-term folliculin (FLCN) knockdown was required to increase their tumorigenic potential, forming larger spheroids in non-adherent conditions. Transcriptomic and proteomic analysis uncovered links between FLCN, cell cycle control and the DNA damage response (DDR) machinery. HK2 cells lacking FLCN had an altered transcriptome profile with cell cycle control gene enrichment. G1/S cell cycle checkpoint signaling was compromised with heightened protein levels of cyclin D1 (CCND1) and hyperphosphorylation of retinoblastoma 1 (RB1). A FLCN interactome screen uncovered FLCN binding to DNA-dependent protein kinase (DNA-PK). This novel interaction was reversed in an irradiation-responsive manner. Knockdown of FLCN in HK2 cells caused a marked elevation of γH2AX and RB1 phosphorylation. Both CCND1 and RB1 phosphorylation remained raised during DNA damage, showing an association with defective cell cycle control with FLCN knockdown. Furthermore, Flcn-knockdown C. elegans were defective in cell cycle arrest by DNA damage. This work implicates that long-term FLCN loss and associated cell cycle defects in BHD patients could contribute to their increased risk of cancer.
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Que Y, Qiu Y, Ding Z, Zhang S, Wei R, Xia J, Lin Y. The role of molecular chaperone CCT/TRiC in translation elongation: A literature review. Heliyon 2024; 10:e29029. [PMID: 38596045 PMCID: PMC11002246 DOI: 10.1016/j.heliyon.2024.e29029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Protein synthesis from mRNA is an energy-intensive and strictly controlled biological process. Translation elongation is a well-coordinated and multifactorial step in translation that ensures the accurate and efficient addition of amino acids to a growing nascent-peptide chain encoded in the sequence of messenger RNA (mRNA). Which undergoes dynamic regulation due to cellular state and environmental determinants. An expanding body of research points to translational elongation as a crucial process that controls the translation of an mRNA through multiple feedback mechanisms. Molecular chaperones are key players in protein homeostasis to keep the balance between protein synthesis, folding, assembly, and degradation. Chaperonin-containing tailless complex polypeptide 1 (CCT) or tailless complex polypeptide 1 ring complex (TRiC) is an essential eukaryotic molecular chaperone that plays an essential role in assisting cellular protein folding and suppressing protein aggregation. In this review, we give an overview of the factors that influence translation elongation, focusing on different functions of molecular chaperones in translation elongation, including how they affect translation rates and post-translational modifications. We also provide an understanding of the mechanisms by which the molecular chaperone CCT plays multiple roles in the elongation phase of eukaryotic protein synthesis.
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Affiliation(s)
- Yueyue Que
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Yudan Qiu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Zheyu Ding
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Shanshan Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Rong Wei
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Jianing Xia
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Yingying Lin
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
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Minoia M, Quintana-Cordero J, Jetzinger K, Kotan IE, Turnbull KJ, Ciccarelli M, Masser AE, Liebers D, Gouarin E, Czech M, Hauryliuk V, Bukau B, Kramer G, Andréasson C. Chp1 is a dedicated chaperone at the ribosome that safeguards eEF1A biogenesis. Nat Commun 2024; 15:1382. [PMID: 38360885 PMCID: PMC10869706 DOI: 10.1038/s41467-024-45645-w] [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: 06/02/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Cotranslational protein folding depends on general chaperones that engage highly diverse nascent chains at the ribosomes. Here we discover a dedicated ribosome-associated chaperone, Chp1, that rewires the cotranslational folding machinery to assist in the challenging biogenesis of abundantly expressed eukaryotic translation elongation factor 1A (eEF1A). Our results indicate that during eEF1A synthesis, Chp1 is recruited to the ribosome with the help of the nascent polypeptide-associated complex (NAC), where it safeguards eEF1A biogenesis. Aberrant eEF1A production in the absence of Chp1 triggers instant proteolysis, widespread protein aggregation, activation of Hsf1 stress transcription and compromises cellular fitness. The expression of pathogenic eEF1A2 variants linked to epileptic-dyskinetic encephalopathy is protected by Chp1. Thus, eEF1A is a difficult-to-fold protein that necessitates a biogenesis pathway starting with dedicated folding factor Chp1 at the ribosome to protect the eukaryotic cell from proteostasis collapse.
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Affiliation(s)
- Melania Minoia
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Jany Quintana-Cordero
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Katharina Jetzinger
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ilgin Eser Kotan
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kathryn Jane Turnbull
- Department of Clinical Microbiology, Rigshospitalet, 2200, Copenhagen, Denmark
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Michela Ciccarelli
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Anna E Masser
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Dorina Liebers
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Eloïse Gouarin
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marius Czech
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Vasili Hauryliuk
- Science for Life Laboratory, Department of Experimental Medical Science, Lund University, Lund, Sweden
- University of Tartu, Institute of Technology, 50411, Tartu, Estonia
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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Zeng C, Han S, Pan Y, Huang Z, Zhang B, Zhang B. Revisiting the chaperonin T-complex protein-1 ring complex in human health and disease: A proteostasis modulator and beyond. Clin Transl Med 2024; 14:e1592. [PMID: 38363102 PMCID: PMC10870801 DOI: 10.1002/ctm2.1592] [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: 11/23/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Disrupted protein homeostasis (proteostasis) has been demonstrated to facilitate the progression of various diseases. The cytosolic T-complex protein-1 ring complex (TRiC/CCT) was discovered to be a critical player in orchestrating proteostasis by folding eukaryotic proteins, guiding intracellular localisation and suppressing protein aggregation. Intensive investigations of TRiC/CCT in different fields have improved the understanding of its role and molecular mechanism in multiple physiological and pathological processes. MAIN BODY In this review, we embark on a journey through the dynamic protein folding cycle of TRiC/CCT, unraveling the intricate mechanisms of its substrate selection, recognition, and intriguing folding and assembly processes. In addition to discussing the critical role of TRiC/CCT in maintaining proteostasis, we detail its involvement in cell cycle regulation, apoptosis, autophagy, metabolic control, adaptive immunity and signal transduction processes. Furthermore, we meticulously catalogue a compendium of TRiC-associated diseases, such as neuropathies, cardiovascular diseases and various malignancies. Specifically, we report the roles and molecular mechanisms of TRiC/CCT in regulating cancer formation and progression. Finally, we discuss unresolved issues in TRiC/CCT research, highlighting the efforts required for translation to clinical applications, such as diagnosis and treatment. CONCLUSION This review aims to provide a comprehensive view of TRiC/CCT for researchers to inspire further investigations and explorations of potential translational possibilities.
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Affiliation(s)
- Chenglong Zeng
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Clinical Medical Research Center of Hepatic Surgery at Hubei ProvinceWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreatic‐Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Shenqi Han
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Clinical Medical Research Center of Hepatic Surgery at Hubei ProvinceWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreatic‐Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Yonglong Pan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Clinical Medical Research Center of Hepatic Surgery at Hubei ProvinceWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreatic‐Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Zhao Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Clinical Medical Research Center of Hepatic Surgery at Hubei ProvinceWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreatic‐Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Binhao Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Clinical Medical Research Center of Hepatic Surgery at Hubei ProvinceWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreatic‐Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Clinical Medical Research Center of Hepatic Surgery at Hubei ProvinceWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreatic‐Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Organ Transplantation, Ministry of EducationWuhanChina
- Key Laboratory of Organ Transplantation, National Health CommissionWuhanChina
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical SciencesWuhanChina
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Meng X, Wang X, Zhu X, Zhang R, Zhang Z, Sun Y. Quantitative analysis of acetylation in peste des petits ruminants virus-infected Vero cells. Virol J 2023; 20:227. [PMID: 37817180 PMCID: PMC10563215 DOI: 10.1186/s12985-023-02200-1] [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: 05/06/2022] [Accepted: 10/04/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Peste des petits ruminants virus (PPRV) is a highly contagious pathogen that strongly influences the productivity of small ruminants worldwide. Acetylation is an important post-translational modification involved in regulation of multiple biological functions. However, the extent and function of acetylation in host cells during PPRV infection remains unknown. METHODS Dimethylation-labeling-based quantitative proteomic analysis of the acetylome of PPRV-infected Vero cells was performed. RESULTS In total, 1068 proteins with 2641 modification sites were detected in response to PPRV infection, of which 304 differentially acetylated proteins (DAcPs) with 410 acetylated sites were identified (fold change < 0.83 or > 1.2 and P < 0.05), including 109 up-regulated and 195 down-regulated proteins. Gene Ontology (GO) classification indicated that DAcPs were mostly located in the cytoplasm (43%) and participated in cellular and metabolic processes related to binding and catalytic activity. Functional enrichment indicated that the DAcPs were involved in the minichromosome maintenance complex, unfolded protein binding, helicase activity. Only protein processing in endoplasmic reticulum pathway was enriched. A protein-protein interaction (PPI) network of the identified proteins further indicated that a various chaperone and ribosome processes were modulated by acetylation. CONCLUSIONS To the best of our knowledge, this is the first study on acetylome in PPRV-infected host cell. Our findings establish an important baseline for future study on the roles of acetylation in the host response to PPRV replication and provide novel insights for understanding the molecular pathological mechanism of PPRV infection.
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Affiliation(s)
- Xuelian Meng
- State Key Laboratory for Animal Disease Control and Preventiony, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Yanchangpu, Chengguan District, Lanzhou, 730046, China.
| | - Xiangwei Wang
- State Key Laboratory for Animal Disease Control and Preventiony, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Yanchangpu, Chengguan District, Lanzhou, 730046, China
| | - Xueliang Zhu
- State Key Laboratory for Animal Disease Control and Preventiony, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Yanchangpu, Chengguan District, Lanzhou, 730046, China
| | - Rui Zhang
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, Sichuan, China
| | - Zhidong Zhang
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, Sichuan, China.
| | - Yuefeng Sun
- State Key Laboratory for Animal Disease Control and Preventiony, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Yanchangpu, Chengguan District, Lanzhou, 730046, China
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Linnert J, Knapp B, Güler BE, Boldt K, Ueffing M, Wolfrum U. Usher syndrome proteins ADGRV1 (USH2C) and CIB2 (USH1J) interact and share a common interactome containing TRiC/CCT-BBS chaperonins. Front Cell Dev Biol 2023; 11:1199069. [PMID: 37427378 PMCID: PMC10323441 DOI: 10.3389/fcell.2023.1199069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
The human Usher syndrome (USH) is the most common form of a sensory hereditary ciliopathy characterized by progressive vision and hearing loss. Mutations in the genes ADGRV1 and CIB2 have been associated with two distinct sub-types of USH, namely, USH2C and USH1J. The proteins encoded by the two genes belong to very distinct protein families: the adhesion G protein-coupled receptor ADGRV1 also known as the very large G protein-coupled receptor 1 (VLGR1) and the Ca2+- and integrin-binding protein 2 (CIB2), respectively. In the absence of tangible knowledge of the molecular function of ADGRV1 and CIB2, pathomechanisms underlying USH2C and USH1J are still unknown. Here, we aimed to enlighten the cellular functions of CIB2 and ADGRV1 by the identification of interacting proteins, a knowledge that is commonly indicative of cellular functions. Applying affinity proteomics by tandem affinity purification in combination with mass spectrometry, we identified novel potential binding partners of the CIB2 protein and compared these with the data set we previously obtained for ADGRV1. Surprisingly, the interactomes of both USH proteins showed a high degree of overlap indicating their integration in common networks, cellular pathways and functional modules which we confirmed by GO term analysis. Validation of protein interactions revealed that ADGRV1 and CIB2 mutually interact. In addition, we showed that the USH proteins also interact with the TRiC/CCT chaperonin complex and the Bardet Biedl syndrome (BBS) chaperonin-like proteins. Immunohistochemistry on retinal sections demonstrated the co-localization of the interacting partners at the photoreceptor cilia, supporting the role of USH proteins ADGRV1 and CIB2 in primary cilia function. The interconnection of protein networks involved in the pathogenesis of both syndromic retinal dystrophies BBS and USH suggest shared pathomechanisms for both syndromes on the molecular level.
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Affiliation(s)
- Joshua Linnert
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Barbara Knapp
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Baran E. Güler
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Karsten Boldt
- Institute for Ophthalmic Research, Eberhard Karls University of Tuebingen, Tubingen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Eberhard Karls University of Tuebingen, Tubingen, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
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Wilkinson MD, Ferreira JL, Beeby M, Baum J, Willison KR. The malaria parasite chaperonin containing TCP-1 (CCT) complex: Data integration with other CCT proteomes. Front Mol Biosci 2022; 9:1057232. [PMID: 36567946 PMCID: PMC9772883 DOI: 10.3389/fmolb.2022.1057232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
The multi-subunit chaperonin containing TCP-1 (CCT) is an essential molecular chaperone that functions in the folding of key cellular proteins. This paper reviews the interactome of the eukaryotic chaperonin CCT and its primary clients, the ubiquitous cytoskeletal proteins, actin and tubulin. CCT interacts with other nascent proteins, especially the WD40 propeller proteins, and also assists in the assembly of several protein complexes. A new proteomic dataset is presented for CCT purified from the human malarial parasite, P. falciparum (PfCCT). The CCT8 subunit gene was C-terminally FLAG-tagged using Selection Linked Integration (SLI) and CCT complexes were extracted from infected human erythrocyte cultures synchronized for maximum expression levels of CCT at the trophozoite stage of the parasite's asexual life cycle. We analyze the new PfCCT proteome and incorporate it into our existing model of the CCT system, supported by accumulated data from biochemical and cell biological experiments in many eukaryotic species. Together with measurements of CCT mRNA, CCT protein subunit copy number and the post-translational and chemical modifications of the CCT subunits themselves, a cumulative picture is emerging of an essential molecular chaperone system sitting at the heart of eukaryotic cell growth control and cell cycle regulation.
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Affiliation(s)
- Mark D. Wilkinson
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Josie L. Ferreira
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Jake Baum
- Department of Life Sciences, Imperial College London, London, United Kingdom,School of Biomedical Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Keith R. Willison
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom,*Correspondence: Keith R. Willison,
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Hassell D, Denney A, Singer E, Benson A, Roth A, Ceglowski J, Steingesser M, McMurray M. Chaperone Requirements for De Novo Folding of Saccharomyces cerevisiae Septins. Mol Biol Cell 2022; 33:ar111. [PMID: 35947497 DOI: 10.1091/mbc.e22-07-0262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Polymers of septin protein complexes play cytoskeletal roles in eukaryotic cells. The specific subunit composition within complexes controls functions and higher-order structural properties. All septins have globular GTPase domains. The other eukaryotic cytoskeletal NTPases strictly require assistance from molecular chaperones of the cytosol, particularly the cage-like chaperonins, to fold into oligomerization-competent conformations. We previously identified cytosolic chaperones that bind septins and influence the oligomerization ability of septins carrying mutations linked to human disease, but it was unknown to what extent wild-type septins require chaperone assistance for their native folding. Here we use a combination of in vivo and in vitro approaches to demonstrate chaperone requirements for de novo folding and complex assembly by budding yeast septins. Individually purified septins adopted non-native conformations and formed non-native homodimers. In chaperonin- or Hsp70-deficient cells, septins folded slower and were unable to assemble post-translationally into native complexes. One septin, Cdc12, was so dependent on co-translational chaperonin assistance that translation failed without it. Our findings point to distinct translation elongation rates for different septins as a possible mechanism to direct a stepwise, co-translational assembly pathway in which general cytosolic chaperones act as key intermediaries.
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Affiliation(s)
- Daniel Hassell
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Ashley Denney
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Emily Singer
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Aleyna Benson
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Andrew Roth
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Julia Ceglowski
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Marc Steingesser
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Michael McMurray
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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Feng L, Li H, Du Y, Zhang T, Zhu Y, Li Z, Zhao L, Wang X, Wang G, Zhou L, Jiang Z, Liu Z, Ou Z, Wen Y, Zhuo Y. Chaperonin-Containing TCP1 Subunit 5 Protects Against the Effect of Mer Receptor Tyrosine Kinase Knockdown in Retinal Pigment Epithelial Cells by Interacting With Filamentous Actin and Activating the LIM-Kinase 1/Cofilin Pathway. Front Med (Lausanne) 2022; 9:861371. [PMID: 35492354 PMCID: PMC9043132 DOI: 10.3389/fmed.2022.861371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
Retinitis pigmentosa (RP), characterized by the gradual loss of rod and cone photoreceptors that eventually leads to blindness, is the most common inherited retinal disorder, affecting more than 2.5 million people worldwide. However, the underlying pathogenesis of RP remains unclear and there is no effective cure for RP. Mutations in the Mer receptor tyrosine kinase (MERTK) gene induce the phagocytic dysfunction of retinal pigment epithelium (RPE) cells, leading to RP. Studies have indicated that filamentous actin (F-actin)—which is regulated by chaperonin-containing TCP1 subunit 5 (CCT5)—plays a vital role in phagocytosis in RPE cells. However, whether CCT5/F-actin signaling is involved in MERTK-associated RP remains largely unknown. In the present study, we specifically knocked down MERTK and CCT5 through siRNA transfection and examined the expression of CCT5 and F-actin in human primary RPE (HsRPE) cells. We found that MERTK downregulation inhibited cell proliferation, migration, and phagocytic function; significantly decreased the expression of F-actin; and disrupted the regular arrangement of F-actin. Importantly, our findings firstly indicate that CCT5 interacts with F-actin and is inhibited by MERTK siRNA in HsRPE cells. Upregulating CCT5 using CCT5-specific lentiviral vectors (CCT5-Le) rescued the cell proliferation, migration, and phagocytic function of HsRPE cells under the MERTK knockdown condition by increasing the expression of F-actin and restoring its regular arrangement via the LIMK1/cofilin, but not the SSH1/cofilin, pathway. In conclusion, CCT5 protects against the effect of MERTK knockdown in HsRPE cells and demonstrates the potential for effective treatment of MERTK-associated RP.
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Affiliation(s)
- Lujia Feng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
| | - Haichun Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
| | - Yong Du
- Guizhou Provincial People's Hospital, Guizhou University, Guiyang, China
| | - Ting Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
| | - Yingting Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
| | - Zhidong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
| | - Ling Zhao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
| | - Xing Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
| | - Gongpei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
| | - Linbin Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
| | - Zhaorong Jiang
- Ophthalmology Department of Zhuhai Integrated Traditional Chinese and Western Medicine Hospital, Zhuhai, China
| | - Zheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
| | - Zhancong Ou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
| | - Yuwen Wen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Sun Yat-sen University, Guangzhou, China
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10
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Wang S, Zhen L, Li X, Fu X, Li P, Zhang D. Search for Key Genes and Functional Pathways of Ulcerative Colitis to Colon Cancer Based on Bioinformatics. Front Oncol 2022; 12:857148. [PMID: 35372018 PMCID: PMC8965385 DOI: 10.3389/fonc.2022.857148] [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: 01/18/2022] [Accepted: 02/16/2022] [Indexed: 12/30/2022] Open
Abstract
Ulcerative colitis (UC) is a persistent and diffuse inflammatory disease of the intestine. It is widely prevalent in developed countries. Approximately 30% of patients with UC suffer from widespread and aggressive colitis and are at increased risk of colon cancer. In this study, the genetic features and potential molecular mechanisms shared between UC and colorectal cancer were investigated. The datasets from GEO and TCGA were analyzed to obtain differentially expressed genes, of which there were 116 overlapping genes. A module containing 15 genes was obtained using String and Cytoscape to analyze the module and identify hub genes. Weighted gene co-expression network analysis (WGCNA) was used to identify co-expression modules associated with UC and colon cancer, with 52 overlapping genes. Functional clustering of the two gene cohorts was performed using the Metascape online tool, with three significant functions or pathways associated with both gene cohorts. A total of 19 key genes were included, and CCT2 was identified after expression and survival analyses. CCT2 is highly expressed in colon cancer and lowly expressed in UC, and its low expression is associated with a poor prognostic ratio. This study reveals, for the first time, that CCT2 may be a promoter of UC transformation into colon cancer and identifies new gene candidates that could be used as biomarkers or potential therapeutic targets.
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Affiliation(s)
- Shengbao Wang
- Emergency Center, Gansu Emergency Medicine Clinical Research Center,Lanzhou University Second Hospital, Lanzhou, China
| | - Lingling Zhen
- Infectious Department, Lanzhou University Second Hospital, Lanzhou, China
| | - Xiaoli Li
- Digestive Department, Lanzhou University Second Hospital, Lanzhou, China
| | - Xu Fu
- Key Laboratory of Emergency Medicine, Lanzhou University Second Hospital, Lanzhou, China
| | - Peiwu Li
- Emergency Center, Gansu Emergency Medicine Clinical Research Center,Lanzhou University Second Hospital, Lanzhou, China
| | - Dekui Zhang
- Department of Gastroenterology, Key Laboratory of Digestive Diseases Lanzhou University Second Hospital, Lanzhou, China
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11
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Quantitative Proteomics Reveals the Role of Lysine 2-Hydroxyisobutyrylation Pathway Mediated by Tip60. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:4571319. [PMID: 35178156 PMCID: PMC8847014 DOI: 10.1155/2022/4571319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/12/2022] [Indexed: 11/17/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a new type of posttranslational modifications (PTMs) extensively reported on eukaryotic cell histones. It is evolutionarily conserved and participates in diverse important biological processes, such as transcription and cell metabolism. Recently, it has been demonstrated that Khib can be regulated by p300 and Tip60. Although the specific Khib substrates mediated by p300 have been revealed, how Tip60 regulates diverse cellular processes through the Khib pathway and the different roles between Tip60 and p300 in regulating Khib remain largely unknown, which prevents us from understanding how this modification executes its biological functions. In this study, we report the first Khib proteome mediated by Tip60. In total, 3502 unique Khib sites from 1050 proteins were identified. Among them, 536 Khib sites from 406 proteins were present only in Tip60 overexpressing cells and 13 Khib sites increased more than 2-fold in response to Tip60 overexpression, indicating that Tip60 significantly affected global Khib. Notably, only 5 of the 549 Tip60-targeted Khib sites overlapped with the 149 known Khib sites targeted by p300, indicating the different Khib substrate preferences of Tip60 and p300. In addition, the Khib substrates regulated by Tip60 are deeply involved in processes such as nucleic acid metabolism and translation, and some are associated with Parkinson’s and Prion diseases. In summary, our research reveals the Khib substrates targeted by Tip60, which elucidates the effect of Tip60 in regulating various cellular processes through the Khib pathway, and proposes novel views into the functional mechanism of Tip60.
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12
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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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13
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Novel Binding Partners for CCT and PhLP1 Suggest a Common Folding Mechanism for WD40 Proteins with a 7-Bladed Beta-Propeller Structure. Proteomes 2021; 9:proteomes9040040. [PMID: 34698247 PMCID: PMC8544692 DOI: 10.3390/proteomes9040040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/15/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022] Open
Abstract
This study investigates whether selected WD40 proteins with a 7-bladed β-propeller structure, similar to that of the β subunit of the G protein heterotrimer, interact with the cytosolic chaperonin CCT and its known binding partner, PhLP1. Previous studies have shown that CCT is required for the folding of the Gβ subunit and other WD40 proteins. The role of PhLP1 in the folding of Gβ has also been established, but it is unknown if PhLP1 assists in the folding of other Gβ-like proteins. The binding of three Gβ-like proteins, TBL2, MLST8 and CDC20, to CCT and PhLP1, was demonstrated in this study. Co-immunoprecipitation assays identified one novel binding partner for CCT and three new interactors for PhLP1. All three of the studied proteins interact with CCT and PhLP1, suggesting that these proteins may have a folding machinery in common with that of Gβ and that the well-established Gβ folding mechanism may have significantly broader biological implications than previously thought. These findings contribute to continuous efforts to determine common traits and unique differences in the folding mechanism of the WD40 β-propeller protein family, and the role PhLP1 has in this process.
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14
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Denney AS, Weems AD, McMurray MA. Selective functional inhibition of a tumor-derived p53 mutant by cytosolic chaperones identified using split-YFP in budding yeast. G3-GENES GENOMES GENETICS 2021; 11:6318398. [PMID: 34544131 PMCID: PMC8496213 DOI: 10.1093/g3journal/jkab230] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/17/2021] [Indexed: 11/25/2022]
Abstract
Life requires the oligomerization of individual proteins into higher-order assemblies. In order to form functional oligomers, monomers must adopt appropriate 3D structures. Molecular chaperones transiently bind nascent or misfolded proteins to promote proper folding. Single missense mutations frequently cause disease by perturbing folding despite chaperone engagement. A misfolded mutant capable of oligomerizing with wild-type proteins can dominantly poison oligomer function. We previously found evidence that human-disease-linked mutations in Saccharomyces cerevisiae septin proteins slow folding and attract chaperones, resulting in a kinetic delay in oligomerization that prevents the mutant from interfering with wild-type function. Here, we build upon our septin studies to develop a new approach for identifying chaperone interactions in living cells, and use it to expand our understanding of chaperone involvement, kinetic folding delays, and oligomerization in the recessive behavior of tumor-derived mutants of the tumor suppressor p53. We find evidence of increased binding of several cytosolic chaperones to a recessive, misfolding-prone mutant, p53(V272M). Similar to our septin results, chaperone overexpression inhibits the function of p53(V272M) with minimal effect on the wild type. Unlike mutant septins, p53(V272M) is not kinetically delayed under conditions in which it is functional. Instead, it interacts with wild-type p53 but this interaction is temperature sensitive. At high temperatures or upon chaperone overexpression, p53(V272M) is excluded from the nucleus and cannot function or perturb wild-type function. Hsp90 inhibition liberates mutant p53 to enter the nucleus. These findings provide new insights into the effects of missense mutations.
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Affiliation(s)
- Ashley S Denney
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Andrew D Weems
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael A McMurray
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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15
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Human ribosomal protein and proteasomal subunit suppress cct mutations and reduce alpha-synuclein toxicity in Saccharomyces cerevisiae. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Oftedal BE, Maio S, Handel AE, White MPJ, Howie D, Davis S, Prevot N, Rota IA, Deadman ME, Kessler BM, Fischer R, Trede NS, Sezgin E, Maizels RM, Holländer GA. The chaperonin CCT8 controls proteostasis essential for T cell maturation, selection, and function. Commun Biol 2021; 4:681. [PMID: 34083746 PMCID: PMC8175432 DOI: 10.1038/s42003-021-02203-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
T cells rely for their development and function on the correct folding and turnover of proteins generated in response to a broad range of molecular cues. In the absence of the eukaryotic type II chaperonin complex, CCT, T cell activation induced changes in the proteome are compromised including the formation of nuclear actin filaments and the formation of a normal cell stress response. Consequently, thymocyte maturation and selection, and T cell homeostatic maintenance and receptor-mediated activation are severely impaired. In the absence of CCT-controlled protein folding, Th2 polarization diverges from normal differentiation with paradoxical continued IFN-γ expression. As a result, CCT-deficient T cells fail to generate an efficient immune protection against helminths as they are unable to sustain a coordinated recruitment of the innate and adaptive immune systems. These findings thus demonstrate that normal T cell biology is critically dependent on CCT-controlled proteostasis and that its absence is incompatible with protective immunity.
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Affiliation(s)
- Bergithe E Oftedal
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Clinical Science, University of Bergen, Bergen, Norway, K.G. Jebsen Center for Autoimmune Disorders, Bergen, Norway
| | - Stefano Maio
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Adam E Handel
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Madeleine P J White
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Duncan Howie
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Simon Davis
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Nicolas Prevot
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ioanna A Rota
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Mary E Deadman
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Nikolaus S Trede
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Rick M Maizels
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Georg A Holländer
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
- Paediatric Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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17
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Martín-Cófreces NB, Valpuesta JM, Sánchez-Madrid F. Folding for the Immune Synapse: CCT Chaperonin and the Cytoskeleton. Front Cell Dev Biol 2021; 9:658460. [PMID: 33912568 PMCID: PMC8075050 DOI: 10.3389/fcell.2021.658460] [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: 01/25/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022] Open
Abstract
Lymphocytes rearrange their shape, membrane receptors and organelles during cognate contacts with antigen-presenting cells (APCs). Activation of T cells by APCs through pMHC-TCR/CD3 interaction (peptide-major histocompatibility complex-T cell receptor/CD3 complexes) involves different steps that lead to the reorganization of the cytoskeleton and organelles and, eventually, activation of nuclear factors allowing transcription and ultimately, replication and cell division. Both the positioning of the lymphocyte centrosome in close proximity to the APC and the nucleation of a dense microtubule network beneath the plasma membrane from the centrosome support the T cell's intracellular polarity. Signaling from the TCR is facilitated by this traffic, which constitutes an important pathway for regulation of T cell activation. The coordinated enrichment upon T cell stimulation of the chaperonin CCT (chaperonin-containing tailless complex polypeptide 1; also termed TRiC) and tubulins at the centrosome area support polarized tubulin polymerization and T cell activation. The proteasome is also enriched in the centrosome of activated T cells, providing a mechanism to balance local protein synthesis and degradation. CCT assists the folding of proteins coming from de novo synthesis, therefore favoring mRNA translation. The functional role of this chaperonin in regulating cytoskeletal composition and dynamics at the immune synapse is discussed.
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Affiliation(s)
- Noa Beatriz Martín-Cófreces
- Immunology Service, Hospital Universitario de la Princesa, Universidad Autonoma Madrid (UAM), Instituto Investigacion Sanitaria-Instituto Princesa (IIS-IP), Madrid, Spain.,Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | | | - Francisco Sánchez-Madrid
- Immunology Service, Hospital Universitario de la Princesa, Universidad Autonoma Madrid (UAM), Instituto Investigacion Sanitaria-Instituto Princesa (IIS-IP), Madrid, Spain.,Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
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18
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Horianopoulos LC, Kronstad JW. Chaperone Networks in Fungal Pathogens of Humans. J Fungi (Basel) 2021; 7:209. [PMID: 33809191 PMCID: PMC7998936 DOI: 10.3390/jof7030209] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 12/14/2022] Open
Abstract
The heat shock proteins (HSPs) function as chaperones to facilitate proper folding and modification of proteins and are of particular importance when organisms are subjected to unfavourable conditions. The human fungal pathogens are subjected to such conditions within the context of infection as they are exposed to human body temperature as well as the host immune response. Herein, the roles of the major classes of HSPs are briefly reviewed and their known contributions in human fungal pathogens are described with a focus on Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus. The Hsp90s and Hsp70s in human fungal pathogens broadly contribute to thermotolerance, morphological changes required for virulence, and tolerance to antifungal drugs. There are also examples of J domain co-chaperones and small HSPs influencing the elaboration of virulence factors in human fungal pathogens. However, there are diverse members in these groups of chaperones and there is still much to be uncovered about their contributions to pathogenesis. These HSPs do not act in isolation, but rather they form a network with one another. Interactions between chaperones define their specific roles and enhance their protein folding capabilities. Recent efforts to characterize these HSP networks in human fungal pathogens have revealed that there are unique interactions relevant to these pathogens, particularly under stress conditions. The chaperone networks in the fungal pathogens are also emerging as key coordinators of pathogenesis and antifungal drug tolerance, suggesting that their disruption is a promising strategy for the development of antifungal therapy.
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Affiliation(s)
| | - James W. Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
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19
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Lattmann E, Deng T, Hajnal A. To Divide or Invade: A Look Behind the Scenes of the Proliferation-Invasion Interplay in the Caenorhabditis elegans Anchor Cell. Front Cell Dev Biol 2021; 8:616051. [PMID: 33490081 PMCID: PMC7815685 DOI: 10.3389/fcell.2020.616051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Cell invasion is defined by the capability of cells to migrate across compartment boundaries established by basement membranes (BMs). The development of complex organs involves regulated cell growth and regrouping of different cell types, which are enabled by controlled cell proliferation and cell invasion. Moreover, when a malignant tumor takes control over the body, cancer cells evolve to become invasive, allowing them to spread to distant sites and form metastases. At the core of the switch between proliferation and invasion are changes in cellular morphology driven by remodeling of the cytoskeleton. Proliferative cells utilize their actomyosin network to assemble a contractile ring during cytokinesis, while invasive cells form actin-rich protrusions, called invadopodia that allow them to breach the BMs. Studies of developmental cell invasion as well as of malignant tumors revealed that cell invasion and proliferation are two mutually exclusive states. In particular, anchor cell (AC) invasion during Caenorhabditis elegans larval development is an excellent model to study the transition from cell proliferation to cell invasion under physiological conditions. This mini-review discusses recent insights from the C. elegans AC invasion model into how G1 cell-cycle arrest is coordinated with the activation of the signaling networks required for BM breaching. Many regulators of the proliferation-invasion network are conserved between C. elegans and mammals. Therefore, the worm may provide important clues to better understand cell invasion and metastasis formation in humans.
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Affiliation(s)
- Evelyn Lattmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ting Deng
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Molecular Life Science PhD Program, University and ETH Zurich, Zurich, Switzerland
| | - Alex Hajnal
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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20
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Tocci N, Weil T, Perenzoni D, Moretto M, Nürk N, Madriñán S, Ferrazza R, Guella G, Mattivi F. Potent Antifungal Properties of Dimeric Acylphloroglucinols from Hypericum mexicanum and Mechanism of Action of a Highly Active 3'Prenyl Uliginosin B. Metabolites 2020; 10:metabo10110459. [PMID: 33202828 PMCID: PMC7697946 DOI: 10.3390/metabo10110459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 02/02/2023] Open
Abstract
The success of antifungal therapies is often hindered by the limited number of available drugs. To close the gap in the antifungal pipeline, the search of novel leads is of primary importance, and here the exploration of neglected plants has great promise for the discovery of new principles. Through bioassay-guided isolation, uliginosin B and five new dimeric acylphloroglucinols (uliginosins C-D, and 3′prenyl uliginosins B-D), besides cembrenoids, have been isolated from the lipophilic extract of Hypericum mexicanum. Their structures were elucidated by a combination of Liquid Chromatography - Mass Spectrometry LC-MS and Nuclear Magnetic Resonance (NMR) measurements. The compounds showed strong anti-Candida activity, also against fluconazole-resistant strains, with fungal growth inhibition properties at concentrations ranging from 3 to 32 µM, and reduced or absent cytotoxicity against human cell lines. A chemogenomic screen of 3′prenyl uliginosin B revealed target genes that are important for cell cycle regulation and cytoskeleton assembly in fungi. Taken together, our study suggests dimeric acylphloroglucinols as potential candidates for the development of alternative antifungal therapies.
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Affiliation(s)
- Noemi Tocci
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige (TN), Italy; (N.T.); (T.W.); (D.P.); (M.M.)
| | - Tobias Weil
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige (TN), Italy; (N.T.); (T.W.); (D.P.); (M.M.)
| | - Daniele Perenzoni
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige (TN), Italy; (N.T.); (T.W.); (D.P.); (M.M.)
| | - Marco Moretto
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige (TN), Italy; (N.T.); (T.W.); (D.P.); (M.M.)
| | - Nicolai Nürk
- Department of Plant Systematics, BayCEER, University of Bayreuth, 95447 Bayreuth, Germany;
| | - Santiago Madriñán
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá 111711, Colombia;
- Jardín Botánico de Cartagena “Guillermo Piñeres”, Turbaco, Bolívar 131007, Colombia
| | - Ruggero Ferrazza
- Department of Physics, University of Trento, 38123 Trento, Italy;
| | - Graziano Guella
- Department of Physics, University of Trento, 38123 Trento, Italy;
- Correspondence: (G.G.); (F.M.)
| | - Fulvio Mattivi
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige (TN), Italy; (N.T.); (T.W.); (D.P.); (M.M.)
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38122 Trento, Italy
- Correspondence: (G.G.); (F.M.)
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21
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Scarpin MR, Leiboff S, Brunkard JO. Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation. eLife 2020; 9:e58795. [PMID: 33054972 PMCID: PMC7584452 DOI: 10.7554/elife.58795] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Target of rapamycin (TOR) is a protein kinase that coordinates eukaryotic metabolism. In mammals, TOR specifically promotes translation of ribosomal protein (RP) mRNAs when amino acids are available to support protein synthesis. The mechanisms controlling translation downstream from TOR remain contested, however, and are largely unexplored in plants. To define these mechanisms in plants, we globally profiled the plant TOR-regulated transcriptome, translatome, proteome, and phosphoproteome. We found that TOR regulates ribosome biogenesis in plants at multiple levels, but through mechanisms that do not directly depend on 5' oligopyrimidine tract motifs (5'TOPs) found in mammalian RP mRNAs. We then show that the TOR-LARP1-5'TOP signaling axis is conserved in plants and regulates expression of a core set of eukaryotic 5'TOP mRNAs, as well as new, plant-specific 5'TOP mRNAs. Our study illuminates ancestral roles of the TOR-LARP1-5'TOP metabolic regulatory network and provides evolutionary context for ongoing debates about the molecular function of LARP1.
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Affiliation(s)
- M Regina Scarpin
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
| | - Samuel Leiboff
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallisUnited States
| | - Jacob O Brunkard
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
- Laboratory of Genetics, University of Wisconsin—MadisonMadisonUnited States
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Zheng J, Lu T, Zhou C, Cai J, Zhang X, Liang J, Sui X, Chen X, Chen L, Sun Y, Zhang J, Chen W, Zhang Y, Yao J, Chen G, Yang Y. Extracellular Vesicles Derived from Human Umbilical Cord Mesenchymal Stem Cells Protect Liver Ischemia/Reperfusion Injury by Reducing CD154 Expression on CD4+ T Cells via CCT2. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903746. [PMID: 32999825 PMCID: PMC7509664 DOI: 10.1002/advs.201903746] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 07/14/2020] [Indexed: 05/07/2023]
Abstract
As a cause of postoperative complications and early hepatic failure after liver transplantation, liver ischemia/reperfusion injury (IRI) still has no effective treatment during clinical administration. Although the therapeutic potential of mesenchymal stem cells (MSCs) for liver IRI has been previously shown, the underlying mechanisms are not completely clear. It is accepted that MSC-derived extracellular vesicles (MSC-EVs) are newly uncovered messengers for intercellular communication. Herein, it is reported that umbilical cord-derived MSCs (UC-MSCs) improve liver IRI in mice through their secreted EVs. It is also visualized that UC-MSC-EVs mainly concentrate in liver after 6 h of reperfusion. Furthermore, UC-MSC-EVs are found to significantly modulate the membranous expression of CD154 of intrahepatic CD4+ T cells, which is an initiation of inflammatory response in liver and can aggravate liver IRI. Mechanistically, protein mass spectrum analysis is performed and it is revealed that Chaperonin containing TCP1 subunit 2 (CCT2) enriches in UC-MSC-EVs, which regulates the calcium channels to affect Ca2+ influx and suppress CD154 synthesis in CD4+ T cells. In conclusion, these results highlight the therapeutic potential of UC-MSC-EVs in attenuating liver IRI. This finding suggests that CCT2 from UC-MSC-EVs can modulate CD154 expression of intrahepatic CD4+ T cells during liver IRI through the Ca2+-calcineurin-NFAT1 signaling pathway.
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Affiliation(s)
- Jun Zheng
- Department of Hepatic Surgery and Liver Transplantation Center, Guangdong Key Laboratory of Liver Disease ResearchGuangdong Province Engineering Laboratory for Transplantation MedicineThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Tongyu Lu
- Department of Hepatic Surgery and Liver Transplantation Center, Guangdong Key Laboratory of Liver Disease ResearchGuangdong Province Engineering Laboratory for Transplantation MedicineThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Chaorong Zhou
- Department of Hepatic Surgery and Liver Transplantation CenterThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
- The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510630China
| | - Jianye Cai
- Department of Hepatic Surgery and Liver Transplantation Center, Guangdong Key Laboratory of Liver Disease ResearchGuangdong Province Engineering Laboratory for Transplantation MedicineThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Xiaomei Zhang
- Organ Transplantation Research Center of Guangdong ProvinceKey Laboratory of Liver Disease Biotherapy and Translational Medicine of Guangdong Higher Education InstitutesThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Jinliang Liang
- Organ Transplantation Research Center of Guangdong ProvinceKey Laboratory of Liver Disease Biotherapy and Translational Medicine of Guangdong Higher Education InstitutesThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Xin Sui
- Surgical ICUThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Xiaoyan Chen
- Biological Treatment CenterThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Liang Chen
- Department of Hepatic Surgery and Liver Transplantation Center, Guangdong Key Laboratory of Liver Disease ResearchGuangdong Province Engineering Laboratory for Transplantation MedicineThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Yao Sun
- Surgical ICUThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Jiebin Zhang
- Department of Hepatic Surgery and Liver Transplantation Center, Guangdong Key Laboratory of Liver Disease ResearchGuangdong Province Engineering Laboratory for Transplantation MedicineThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Wenjie Chen
- Biological Treatment CenterThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Yingcai Zhang
- Department of Hepatic Surgery and Liver Transplantation Center, Guangdong Key Laboratory of Liver Disease ResearchGuangdong Province Engineering Laboratory for Transplantation MedicineThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Jia Yao
- Department of Hepatic Surgery and Liver Transplantation Center, Guangdong Key Laboratory of Liver Disease ResearchGuangdong Province Engineering Laboratory for Transplantation MedicineThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Guihua Chen
- Department of Hepatic Surgery and Liver Transplantation Center, Guangdong Key Laboratory of Liver Disease ResearchGuangdong Province Engineering Laboratory for Transplantation MedicineThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
| | - Yang Yang
- Department of Hepatic Surgery and Liver Transplantation Center, Guangdong Key Laboratory of Liver Disease ResearchGuangdong Province Engineering Laboratory for Transplantation MedicineThe Third Affiliated Hospital of Sun Yat‐sen University600 Tianhe RoadGuangzhou510630China
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TCP1γ Subunit Is Indispensable for Growth and Infectivity of Leishmania donovani. Antimicrob Agents Chemother 2020; 64:AAC.00669-20. [PMID: 32457112 DOI: 10.1128/aac.00669-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/18/2020] [Indexed: 01/20/2023] Open
Abstract
T-complex protein-1 (TCP1) is a ubiquitous group II chaperonin and is known to fold various proteins, such as actin and tubulin. In Leishmania donovani, the γ subunit of TCP1 (LdTCP1γ) has been cloned and characterized. It forms a high-molecular-weight homo-oligomeric complex that performs ATP-dependent protein folding. In the present study, we evaluated the essentiality of the LdTCP1γ gene. Gene replacement studies indicated that LdTCP1γ is essential for parasite survival. The LdTCP1γ single-allele-replacement mutants exhibited slowed growth and decreased infectivity in mouse macrophages compared to the growth and infectivity of the wild-type parasites. Modulation of LdTCP1γ expression in promastigotes also modulated cell cycle progression. Suramin, an antitrypanosomal drug, not only inhibited the luciferase refolding activity of the recombinant LdTCP1γ (rLdTCP1γ) homo-oligomeric complex but also exhibited potential antileishmanial efficacy both in vitro and in vivo The interaction of suramin and LdTCP1γ was further validated by isothermal titration calorimetry. The study suggests LdTCP1γ as a potential drug target and also provides a framework for the development of a new class of drugs.
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TRiC/CCT Complex, a Binding Partner of NS1 Protein, Supports the Replication of Zika Virus in Both Mammalians and Mosquitoes. Viruses 2020; 12:v12050519. [PMID: 32397176 PMCID: PMC7290343 DOI: 10.3390/v12050519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/02/2020] [Accepted: 05/06/2020] [Indexed: 11/23/2022] Open
Abstract
Mosquito-borne Zika virus (ZIKV) can cause congenital microcephaly and Guillain–Barré syndrome, among other symptoms. Specific treatments and vaccines for ZIKV are not currently available. To further understand the host factors that support ZIKV replication, we used mass spectrometry to characterize mammalian proteins that associate with the ZIKV NS1 protein and identified the TRiC/CCT complex as an interacting partner. Furthermore, the suppression of CCT2, one of the critical components of the TRiC/CCT complex, inhibited ZIKV replication in both mammalian cells and mosquitoes. These results highlight an important role for the TRiC/CCT complex in ZIKV infection, suggesting that the TRiC/CCT complex may be a promising therapeutic target.
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25
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Muellner J, Schmidt KH. Yeast Genome Maintenance by the Multifunctional PIF1 DNA Helicase Family. Genes (Basel) 2020; 11:genes11020224. [PMID: 32093266 PMCID: PMC7073672 DOI: 10.3390/genes11020224] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/04/2022] Open
Abstract
The two PIF1 family helicases in Saccharomyces cerevisiae, Rrm3, and ScPif1, associate with thousands of sites throughout the genome where they perform overlapping and distinct roles in telomere length maintenance, replication through non-histone proteins and G4 structures, lagging strand replication, replication fork convergence, the repair of DNA double-strand break ends, and transposable element mobility. ScPif1 and its fission yeast homolog Pfh1 also localize to mitochondria where they protect mitochondrial genome integrity. In addition to yeast serving as a model system for the rapid functional evaluation of human Pif1 variants, yeast cells lacking Rrm3 have proven useful for elucidating the cellular response to replication fork pausing at endogenous sites. Here, we review the increasingly important cellular functions of the yeast PIF1 helicases in maintaining genome integrity, and highlight recent advances in our understanding of their roles in facilitating fork progression through replisome barriers, their functional interactions with DNA repair, and replication stress response pathways.
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Affiliation(s)
- Julius Muellner
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA;
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Kristina H. Schmidt
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA;
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Correspondence:
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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: 17] [Impact Index Per Article: 4.3] [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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27
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Caplan T, Polvi EJ, Xie JL, Buckhalter S, Leach MD, Robbins N, Cowen LE. Functional Genomic Screening Reveals Core Modulators of Echinocandin Stress Responses in Candida albicans. Cell Rep 2019; 23:2292-2298. [PMID: 29791841 DOI: 10.1016/j.celrep.2018.04.084] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/28/2018] [Accepted: 04/18/2018] [Indexed: 01/28/2023] Open
Abstract
Candida albicans is a leading cause of death due to fungal infection. Treatment of systemic candidiasis often relies on echinocandins, which disrupt cell wall synthesis. Resistance is readily acquired via mutations in the drug target gene, FKS1. Both basal tolerance and resistance to echinocandins require cellular stress responses. We performed a systematic analysis of 3,030 C. albicans mutants to define circuitry governing cellular responses to echinocandins. We identified 16 genes for which deletion or transcriptional repression enhanced echinocandin susceptibility, including components of the Pkc1-MAPK signaling cascade. We discovered that the molecular chaperone Hsp90 is required for the stability of Pkc1 and Bck1, establishing key mechanisms through which Hsp90 mediates echinocandin resistance. We also discovered that perturbation of the CCT chaperonin complex causes enhanced echinocandin sensitivity, altered cell wall architecture, and aberrant septin localization. Thus, we provide insights into the mechanisms by which cellular chaperones enable crucial responses to echinocandin-induced stress.
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Affiliation(s)
- Tavia Caplan
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Elizabeth J Polvi
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Jinglin L Xie
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Shoshana Buckhalter
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Michelle D Leach
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada; Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada.
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Gvozdenov Z, Kolhe J, Freeman BC. The Nuclear and DNA-Associated Molecular Chaperone Network. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a034009. [PMID: 30745291 PMCID: PMC6771373 DOI: 10.1101/cshperspect.a034009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Maintenance of a healthy and functional proteome in all cellular compartments is critical to cell and organismal homeostasis. Yet, our understanding of the proteostasis process within the nucleus is limited. Here, we discuss the identified roles of the major molecular chaperones Hsp90, Hsp70, and Hsp60 with client proteins working in diverse DNA-associated pathways. The unique challenges facing proteins in the nucleus are considered as well as the conserved features of the molecular chaperone system in facilitating DNA-linked processes. As nuclear protein inclusions are a common feature of protein-aggregation diseases (e.g., neurodegeneration), a better understanding of nuclear proteostasis is warranted.
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Affiliation(s)
- Zlata Gvozdenov
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801.,Department Chemie, Technische Universität München, Garching 85748, Germany
| | - Janhavi Kolhe
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801
| | - Brian C Freeman
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801
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29
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Dynamics of Non-Canonical Amino Acid-Labeled Intra- and Extracellular Proteins in the Developing Mouse. Cell Mol Bioeng 2019; 12:495-509. [PMID: 31719929 DOI: 10.1007/s12195-019-00592-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/17/2019] [Indexed: 12/24/2022] Open
Abstract
Introduction Mapping protein synthesis and turnover during development will provide insight into functional tissue assembly; however, quantitative in vivo characterization has been hindered by a lack of tools. To address this gap, we previously demonstrated murine embryos can be labeled with the non-canonical amino acid azidohomoalanine (Aha), which enables the enrichment and identification of newly synthesized proteins. Using this technique, we now show how protein turnover varies as a function of both time and cellular compartment during murine development. Methods Pregnant C57BL/6 mice were injected with Aha or PBS (control) at different embryonic time points. Aha-labeled proteins from homogenized E12.5 and E15.5 embryos were conjugated with diazo biotin-alkyne, bound to NeutrAvidin beads, selectively released, then processed for either SDS-PAGE or LC-MS/MS. For turnover studies, embryos were harvested 0-48 h after Aha injection at E12.5, separated into different cellular fractions based on solubility, and analyzed via western blotting. Results We developed an enhanced method for isolating Aha-labeled proteins from embryos that minimizes background signal from unlabeled proteins and avidin contamination. Approximately 50% of all identified proteins were found only in Aha samples. Comparing proteins present in both Aha and PBS samples, 90% were > 2-fold enriched in Aha-treated embryos. Furthermore, this method could resolve differences in the Aha-labeled proteome between developmental time points. Newly synthesized Aha-labeled proteins were observed by 3 h and peak labeling was around 6 h. Notably, extracellular matrix and cytoskeletal turnover appeared lower than the cytosolic fraction. Conclusions The methods developed in this work enable the identification and quantification of protein synthesis and turnover in different tissue fractions during development. This will provide insight into functional tissue assembly and ultimately inform the design of regenerative therapies that seek to promote growth and repair.
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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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31
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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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32
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Lu A, Disoma C, Zhou Y, Chen Z, Zhang L, Shen Y, Zhou M, Du A, Zheng R, Li S, Alsaadawe M, Li S, Li J, Wang W, Jiang T, Peng J, Xia Z. Protein interactome of the deamidase phosphoribosylformylglycinamidine synthetase (PFAS) by LC-MS/MS. Biochem Biophys Res Commun 2019; 513:746-752. [PMID: 30987822 DOI: 10.1016/j.bbrc.2019.04.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/04/2019] [Indexed: 12/27/2022]
Abstract
Phosphoribosylformylglycinamidine synthase (PFAS) is an essential enzyme in de novo synthesis of purine. Previously, PFAS has been reported to modulate RIG-I activation during viral infection via deamidation. In this study, we sought to identify potential substrates that PFAS can deamidate. Flag-PFAS was transfected into HEK-293T cells and PFAS associated proteins were purified with anti-Flag M2 magnetic beads. PFAS associated proteins were identified using mass spectrometry and were analyzed using bioinformatics tools including KEGG pathway analysis, gene ontology annotation, and protein interaction network analysis. A total of 441 proteins is suggested to potentially interact with PFAS. Of this number, 12 were previously identified and 429 are newly identified. The interactions of PFAS with CAD, CCT2, PRDX1, and PHGDH were confirmed by co-immunoprecipitation and western blotting. This study is first to report the interaction of PFAS with several proteins which play physiological roles in tumor development including CAD, CCT2, PRDX1, and PHGDH. Furthermore, we show here that PFAS is able to deamidate PHGDH, and induce other posttranslational modification into CAD, CCT2 and PRDX1. The present data provide insight on the biological function of PFAS. Further study to explore the role of these protein interactions in tumorigenesis and other diseases is recommended.
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Affiliation(s)
- Ai Lu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Cyrollah Disoma
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yuzheng Zhou
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zongpeng Chen
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Liming Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yilun Shen
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Mei Zhou
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Ashuai Du
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Rong Zheng
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Sijia Li
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Moyed Alsaadawe
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Shiqin Li
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jiada Li
- Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Weilan Wang
- School of Life Sciences and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Taijiao Jiang
- Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Suzhou Institute of Systems Medicine, Suzhou, China
| | - Jian Peng
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Zanxian Xia
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan, China.
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Willison KR. The substrate specificity of eukaryotic cytosolic chaperonin CCT. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0192. [PMID: 29735743 DOI: 10.1098/rstb.2017.0192] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2018] [Indexed: 12/22/2022] Open
Abstract
The cytosolic chaperonin CCT (chaperonin containing TCP-1) is an ATP-dependent double-ring protein machine mediating the folding of members of the eukaryotic cytoskeletal protein families. The actins and tubulins are obligate substrates of CCT because they are completely dependent on CCT activity to reach their native states. Genetic and proteomic analysis of the CCT interactome in the yeast Saccharomyces cerevisiae revealed a CCT network of approximately 300 genes and proteins involved in many fundamental biological processes. We classified network members into sets such as substrates, CCT cofactors and CCT-mediated assembly processes. Many members of the 7-bladed propeller family of proteins are commonly found tightly bound to CCT isolated from human and plant cells and yeasts. The anaphase promoting complex (APC/C) cofactor propellers, Cdh1p and Cdc20p, are also obligate substrates since they both require CCT for folding and functional activation. In vitro translation analysis in prokaryotic and eukaryotic cell extracts of a set of yeast propellers demonstrates their highly differential interactions with CCT and GroEL (another chaperonin). Individual propeller proteins have idiosyncratic interaction modes with CCT because they emerged independently with neo-functions many times throughout eukaryotic evolution. We present a toy model in which cytoskeletal protein biogenesis and folding flux through CCT couples cell growth and size control to time dependent cell cycle mechanisms.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Keith R Willison
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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34
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Chaperone Function of Hgh1 in the Biogenesis of Eukaryotic Elongation Factor 2. Mol Cell 2019; 74:88-100.e9. [DOI: 10.1016/j.molcel.2019.01.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/14/2018] [Accepted: 01/23/2019] [Indexed: 11/17/2022]
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Van Leene J, Han C, Gadeyne A, Eeckhout D, Matthijs C, Cannoot B, De Winne N, Persiau G, Van De Slijke E, Van de Cotte B, Stes E, Van Bel M, Storme V, Impens F, Gevaert K, Vandepoele K, De Smet I, De Jaeger G. Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase. NATURE PLANTS 2019; 5:316-327. [PMID: 30833711 DOI: 10.1038/s41477-019-0378-z] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/28/2019] [Indexed: 05/18/2023]
Abstract
The target of rapamycin (TOR) kinase is a conserved regulatory hub that translates environmental and nutritional information into permissive or restrictive growth decisions. Despite the increased appreciation of the essential role of the TOR complex in plants, no large-scale phosphoproteomics or interactomics studies have been performed to map TOR signalling events in plants. To fill this gap, we combined a systematic phosphoproteomics screen with a targeted protein complex analysis in the model plant Arabidopsis thaliana. Integration of the phosphoproteome and protein complex data on the one hand shows that both methods reveal complementary subspaces of the plant TOR signalling network, enabling proteome-wide discovery of both upstream and downstream network components. On the other hand, the overlap between both data sets reveals a set of candidate direct TOR substrates. The integrated network embeds both evolutionarily-conserved and plant-specific TOR signalling components, uncovering an intriguing complex interplay with protein synthesis. Overall, the network provides a rich data set to start addressing fundamental questions about how TOR controls key processes in plants, such as autophagy, auxin signalling, chloroplast development, lipid metabolism, nucleotide biosynthesis, protein translation or senescence.
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Affiliation(s)
- Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Chao Han
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan, China
| | - Astrid Gadeyne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Caroline Matthijs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Bernard Cannoot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Brigitte Van de Cotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Elisabeth Stes
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Veronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Francis Impens
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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Yusof NA, Kamaruddin S, Abu Bakar FD, Mahadi NM, Abdul Murad AM. Structural and functional insights into TRiC chaperonin from a psychrophilic yeast, Glaciozyma antarctica. Cell Stress Chaperones 2019; 24:351-368. [PMID: 30649671 PMCID: PMC6439030 DOI: 10.1007/s12192-019-00969-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/29/2022] Open
Abstract
Studies on TCP1-1 ring complex (TRiC) chaperonin have shown its indispensable role in folding cytosolic proteins in eukaryotes. In a psychrophilic organism, extreme cold temperature creates a low-energy environment that potentially causes protein denaturation with loss of activity. We hypothesized that TRiC may undergo evolution in terms of its structural molecular adaptation in order to facilitate protein folding in low-energy environment. To test this hypothesis, we isolated G. antarctica TRiC (GaTRiC) and found that the expression of GaTRiC mRNA in G. antarctica was consistently expressed at all temperatures indicating their importance in cell regulation. Moreover, we showed GaTRiC has the ability of a chaperonin whereby denatured luciferase can be folded to the functional stage in its presence. Structurally, three categories of residue substitutions were found in α, β, and δ subunits: (i) bulky/polar side chains to alanine or valine, (ii) charged residues to alanine, and (iii) isoleucine to valine that would be expected to increase intramolecular flexibility within the GaTRiC. The residue substitutions observed in the built structures possibly affect the hydrophobic, hydrogen bonds, and ionic and aromatic interactions which lead to an increase in structural flexibility. Our structural and functional analysis explains some possible structural features which may contribute to cold adaptation of the psychrophilic TRiC folding chamber.
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Affiliation(s)
- Nur Athirah Yusof
- Biotechnology Research Institute, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia.
| | - Shazilah Kamaruddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Nor Muhammad Mahadi
- Malaysia Genome Institute, Jalan Bangi, 43000, Kajang, Selangor Darul Ehsan, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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Young RM, Hawkins TA, Cavodeassi F, Stickney HL, Schwarz Q, Lawrence LM, Wierzbicki C, Cheng BYL, Luo J, Ambrosio EM, Klosner A, Sealy IM, Rowell J, Trivedi CA, Bianco IH, Allende ML, Busch-Nentwich EM, Gestri G, Wilson SW. Compensatory growth renders Tcf7l1a dispensable for eye formation despite its requirement in eye field specification. eLife 2019; 8:e40093. [PMID: 30777146 PMCID: PMC6380838 DOI: 10.7554/elife.40093] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/26/2019] [Indexed: 12/18/2022] Open
Abstract
The vertebrate eye originates from the eye field, a domain of cells specified by a small number of transcription factors. In this study, we show that Tcf7l1a is one such transcription factor that acts cell-autonomously to specify the eye field in zebrafish. Despite the much-reduced eye field in tcf7l1a mutants, these fish develop normal eyes revealing a striking ability of the eye to recover from a severe early phenotype. This robustness is not mediated through genetic compensation at neural plate stage; instead, the smaller optic vesicle of tcf7l1a mutants shows delayed neurogenesis and continues to grow until it achieves approximately normal size. Although the developing eye is robust to the lack of Tcf7l1a function, it is sensitised to the effects of additional mutations. In support of this, a forward genetic screen identified mutations in hesx1, cct5 and gdf6a, which give synthetically enhanced eye specification or growth phenotypes when in combination with the tcf7l1a mutation.
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Affiliation(s)
- Rodrigo M Young
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Thomas A Hawkins
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Florencia Cavodeassi
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Heather L Stickney
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Quenten Schwarz
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Lisa M Lawrence
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Claudia Wierzbicki
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Bowie YL Cheng
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Jingyuan Luo
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | | | - Allison Klosner
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Ian M Sealy
- Wellcome Sanger InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Department of MedicineUniversity of CambridgeCambridgeUnited Kingdom
| | - Jasmine Rowell
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Chintan A Trivedi
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Isaac H Bianco
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Miguel L Allende
- Center for Genome RegulationFacultad de Ciencias, Universidad de ChileSantiagoChile
| | - Elisabeth M Busch-Nentwich
- Wellcome Sanger InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Department of MedicineUniversity of CambridgeCambridgeUnited Kingdom
| | - Gaia Gestri
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
| | - Stephen W Wilson
- Department of Cell and Developmental BiologyUniversity College LondonLondonUnited Kingdom
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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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39
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Akhmetova KA, Chesnokov IN, Fedorova SA. [Functional Characterization of Septin Complexes]. Mol Biol (Mosk) 2018; 52:155-171. [PMID: 29695686 DOI: 10.7868/s0026898418020015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/27/2016] [Indexed: 12/28/2022]
Abstract
Septins belong to a family of conserved GTP-binding proteins found in majority of eukaryotic species except for higher plants. Septins form nonpolar complexes that further polymerize into filaments and associate with cell membranes, thus comprising newly acknowledged cytoskeletal system. Septins participate in a variety of cell processes and contribute to various pathophysiological states, including tumorigenesis and neurodegeneration. Here, we review the structural and functional properties of septins and the regulation of their dynamics with special emphasis on the role of septin filaments as a cytoskeletal system and its interaction with actin and microtubule cytoskeletons. We also discuss how septins compartmentalize the cell by forming local protein-anchoring scaffolds and by providing barriers for the lateral diffusion of the membrane proteins.
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Affiliation(s)
- K A Akhmetova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia.,University of Alabama at Birmingham, Birmingham, 35294 USA.,Novosibirsk National Research State University, Novosibirsk, 630090 Russia
| | - I N Chesnokov
- University of Alabama at Birmingham, Birmingham, 35294 USA
| | - S A Fedorova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia.,Novosibirsk National Research State University, Novosibirsk, 630090 Russia.,
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40
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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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41
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Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly. Sci Rep 2018; 8:13712. [PMID: 30209338 PMCID: PMC6135828 DOI: 10.1038/s41598-018-32009-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/24/2018] [Indexed: 01/27/2023] Open
Abstract
HDAC1 and HDAC2 are components of several corepressor complexes (NuRD, Sin3, CoREST and MiDAC) that regulate transcription by deacetylating histones resulting in a more compact chromatin environment. This limits access of transcriptional machinery to genes and silences transcription. While using an AP-MS approach to map HDAC1/2 protein interaction networks, we noticed that N-terminally tagged versions of HDAC1 and HDAC2 did not assemble into HDAC corepressor complexes as expected, but instead appeared to be stalled with components of the prefoldin-CCT chaperonin pathway. These N-terminally tagged HDACs were also catalytically inactive. In contrast to the N-terminally tagged HDACs, C-terminally tagged HDAC1 and HDAC2 captured complete histone deacetylase complexes and the purified proteins had deacetylation activity that could be inhibited by SAHA (Vorinostat), a Class I/II HDAC inhibitor. This tag-mediated reprogramming of the HDAC1/2 protein interaction network suggests a mechanism whereby HDAC1 is first loaded into the CCT complex by prefoldin to complete folding, and then assembled into active, functional HDAC complexes. Imaging revealed that the prefoldin subunit VBP1 colocalises with nuclear HDAC1, suggesting that delivery of HDAC1 to the CCT complex happens in the nucleus.
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42
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Rizzolo K, Houry WA. Multiple functionalities of molecular chaperones revealed through systematic mapping of their interaction networks. J Biol Chem 2018; 294:2142-2150. [PMID: 30194284 DOI: 10.1074/jbc.tm118.002805] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Chaperones are a highly interactive group of proteins that function globally in many cellular processes involved in maintaining protein homeostasis. Traditional biochemical assays typically do not provide a complete view of the intricate networks through which chaperones collaborate to promote proteostasis. Recent advances in high-throughput systematic analyses of chaperone interactions have uncovered that chaperones display a remarkable cooperativity in their interactions with numerous client proteins. This cooperativity has been found to be a fundamental aspect of a properly functioning cell. Aberrant formation or improper regulation of these interactions can easily lead to disease states. Herein, we provide an overview of the use of large-scale interaction assays, whether physical (protein-protein) or genetic (epistatic), to study chaperone interaction networks. Importantly, we discuss the ongoing need for such studies to determine the mechanisms by which protein homeostasis is controlled in the cell.
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Affiliation(s)
- Kamran Rizzolo
- From the Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 and
| | - Walid A Houry
- From the Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 and .,the Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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43
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Hodeify R, Nandakumar M, Own M, Courjaret RJ, Graumann J, Hubrack SZ, Machaca K. The CCT chaperonin is a novel regulator of Ca 2+ signaling through modulation of Orai1 trafficking. SCIENCE ADVANCES 2018; 4:eaau1935. [PMID: 30263962 PMCID: PMC6157965 DOI: 10.1126/sciadv.aau1935] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/14/2018] [Indexed: 05/23/2023]
Abstract
Store-operated Ca2+ entry (SOCE) encodes a range of cellular responses downstream of Ca2+ influx through the SOCE channel Orai1. Orai1 recycles at the plasma membrane (PM), with ~40% of the total Orai1 pool residing at the PM at steady state. The mechanisms regulating Orai1 recycling remain poorly understood. We map the domains in Orai1 that are required for its trafficking to and recycling at the PM. We further identify, using biochemical and proteomic approaches, the CCT [chaperonin-containing TCP-1 (T-complex protein 1)] chaperonin complex as a novel regulator of Orai1 recycling by primarily regulating Orai1 endocytosis. We show that Orai1 interacts with CCT through its intracellular loop and that inhibition of CCT-Orai1 interaction increases Orai1 PM residence. This increased residence is functionally significant as it results in prolonged Ca2+ signaling, early formation of STIM1-Orai1 puncta, and more rapid activation of NFAT (nuclear factor of activated T cells) downstream of SOCE. Therefore, the CCT chaperonin is a novel regulator of Orai1 trafficking and, as such, a modulator of Ca2+ signaling and effector activation kinetics.
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Affiliation(s)
- Rawad Hodeify
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Manjula Nandakumar
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Maryam Own
- Medical Program, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Raphael J. Courjaret
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Johannes Graumann
- Department of Biochemistry, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Satanay Z. Hubrack
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Khaled Machaca
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
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44
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Genetics and Expression Profile of the Tubulin Gene Superfamily in Breast Cancer Subtypes and Its Relation to Taxane Resistance. Cancers (Basel) 2018; 10:cancers10080274. [PMID: 30126203 PMCID: PMC6116153 DOI: 10.3390/cancers10080274] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 01/15/2023] Open
Abstract
Taxanes are a class of chemotherapeutic agents that inhibit cell division by disrupting the mitotic spindle through the stabilization of microtubules. Most breast cancer (BC) tumors show resistance against taxanes partially due to alterations in tubulin genes. In this project we investigated tubulin isoforms in BC to explore any correlation between tubulin alterations and taxane resistance. Genetic alteration and expression profiling of 28 tubulin isoforms in 6714 BC tumor samples from 4205 BC cases were analyzed. Protein-protein, drug-protein and alterations neighbor genes in tubulin pathways were examined in the tumor samples. To study correlation between promoter activity and expression of the tubulin isoforms in BC, we analyzed the ChIP-seq enrichment of active promoter histone mark H3K4me3 and mRNA expression profile of MCF-7, ZR-75-30, SKBR-3 and MDA-MB-231 cell lines. Potential correlation between tubulin alterations and taxane resistance, were investigated by studying the expression profile of taxane-sensitive and resistant BC tumors also the MDA-MB-231 cells acquired resistance to paclitaxel. All genomic data were obtained from public databases. Results showed that TUBD1 and TUBB3 were the most frequently amplified and deleted tubulin genes in the BC tumors respectively. The interaction analysis showed physical interactions of α-, β- and γ-tubulin isoforms with each other. The most of FDA-approved tubulin inhibitor drugs including taxanes target only β-tubulins. The analysis also revealed sex tubulin-interacting neighbor proteins including ENCCT3, NEK2, PFDN2, PTP4A3, SDCCAG8 and TBCE which were altered in at least 20% of the tumors. Three of them are tubulin-specific chaperons responsible for tubulin protein folding. Expression of tubulin genes in BC cell lines were correlated with H3K4me3 enrichment on their promoter chromatin. Analyzing expression profile of BC tumors and tumor-adjacent normal breast tissues showed upregulation of TUBA1A, TUBA1C, TUBB and TUBB3 and downregulation of TUBB2A, TUBB2B, TUBB6, TUBB7P pseudogene, and TUBGCP2 in the tumor tissues compared to the normal breast tissues. Analyzing taxane-sensitive versus taxane-resistant tumors revealed that expression of TUBB3 and TUBB6 was significantly downregulated in the taxane-resistant tumors. Our results suggest that downregulation of tumor βIII- and βV-tubulins is correlated with taxane resistance in BC. Based on our results, we conclude that aberrant protein folding of tubulins due to mutation and/or dysfunction of tubulin-specific chaperons may be potential mechanisms of taxane resistance. Thus, we propose studying the molecular pathology of tubulin mutations and folding in BC and their impacts on taxane resistance.
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45
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Genetics and Expression Profile of the Tubulin Gene Superfamily in Breast Cancer Subtypes and Its Relation to Taxane Resistance. Cancers (Basel) 2018. [DOI: 10.10.3390/cancers10080274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Taxanes are a class of chemotherapeutic agents that inhibit cell division by disrupting the mitotic spindle through the stabilization of microtubules. Most breast cancer (BC) tumors show resistance against taxanes partially due to alterations in tubulin genes. In this project we investigated tubulin isoforms in BC to explore any correlation between tubulin alterations and taxane resistance. Genetic alteration and expression profiling of 28 tubulin isoforms in 6714 BC tumor samples from 4205 BC cases were analyzed. Protein-protein, drug-protein and alterations neighbor genes in tubulin pathways were examined in the tumor samples. To study correlation between promoter activity and expression of the tubulin isoforms in BC, we analyzed the ChIP-seq enrichment of active promoter histone mark H3K4me3 and mRNA expression profile of MCF-7, ZR-75-30, SKBR-3 and MDA-MB-231 cell lines. Potential correlation between tubulin alterations and taxane resistance, were investigated by studying the expression profile of taxane-sensitive and resistant BC tumors also the MDA-MB-231 cells acquired resistance to paclitaxel. All genomic data were obtained from public databases. Results showed that TUBD1 and TUBB3 were the most frequently amplified and deleted tubulin genes in the BC tumors respectively. The interaction analysis showed physical interactions of α-, β- and γ-tubulin isoforms with each other. The most of FDA-approved tubulin inhibitor drugs including taxanes target only β-tubulins. The analysis also revealed sex tubulin-interacting neighbor proteins including ENCCT3, NEK2, PFDN2, PTP4A3, SDCCAG8 and TBCE which were altered in at least 20% of the tumors. Three of them are tubulin-specific chaperons responsible for tubulin protein folding. Expression of tubulin genes in BC cell lines were correlated with H3K4me3 enrichment on their promoter chromatin. Analyzing expression profile of BC tumors and tumor-adjacent normal breast tissues showed upregulation of TUBA1A, TUBA1C, TUBB and TUBB3 and downregulation of TUBB2A, TUBB2B, TUBB6, TUBB7P pseudogene, and TUBGCP2 in the tumor tissues compared to the normal breast tissues. Analyzing taxane-sensitive versus taxane-resistant tumors revealed that expression of TUBB3 and TUBB6 was significantly downregulated in the taxane-resistant tumors. Our results suggest that downregulation of tumor βIII- and βV-tubulins is correlated with taxane resistance in BC. Based on our results, we conclude that aberrant protein folding of tubulins due to mutation and/or dysfunction of tubulin-specific chaperons may be potential mechanisms of taxane resistance. Thus, we propose studying the molecular pathology of tubulin mutations and folding in BC and their impacts on taxane resistance.
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46
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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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Echbarthi M, Vallin J, Grantham J. Interactions between monomeric CCTδ and p150 Glued: A novel function for CCTδ at the cell periphery distinct from the protein folding activity of the molecular chaperone CCT. Exp Cell Res 2018; 370:137-149. [PMID: 29913154 DOI: 10.1016/j.yexcr.2018.06.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 01/08/2023]
Abstract
Chaperonin containing tailless complex polypeptide 1 (CCT) is a molecular chaperone consisting of eight distinct protein subunits, that when oligomeric is essential for the folding of newly synthesized tubulin and actin. In addition to folding, CCT activity includes functions of individual subunits in their monomeric form. For example, when CCTδ monomer levels are increased in cultured mammalian cells, numerous cell surface protrusions are formed from retraction fibres, indicating that an underlying function for the CCTδ monomer exists. Here, using a yeast two-hybrid screen we identify the dynactin complex component p150Glued as a binding partner for CCTδ and show by siRNA depletion that this interaction is required for the formation of CCTδ-induced cell surface protrusions. Intact microtubules are necessary for the formation of the protrusions, consistent with microtubule minus end transport driving the retraction fibre formation and depletion of either p150Glued or the dynactin complex-associated transmembrane protein dynAP prevents the previously observed localization of GFP-CCTδ to the plasma membrane. Wound healing assays reveal that CCTδ monomer levels influence directional cell migration and together our observations demonstrate that in addition to the folding activity of CCT in its oligomer form, a monomeric subunit is associated with events that involve the assembled cytoskeleton.
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Affiliation(s)
- Meriem Echbarthi
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Sweden
| | - Josefine Vallin
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Sweden
| | - Julie Grantham
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Sweden.
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Rizzolo K, Huen J, Kumar A, Phanse S, Vlasblom J, Kakihara Y, Zeineddine HA, Minic Z, Snider J, Wang W, Pons C, Seraphim TV, Boczek EE, Alberti S, Costanzo M, Myers CL, Stagljar I, Boone C, Babu M, Houry WA. Features of the Chaperone Cellular Network Revealed through Systematic Interaction Mapping. Cell Rep 2018; 20:2735-2748. [PMID: 28903051 DOI: 10.1016/j.celrep.2017.08.074] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/21/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022] Open
Abstract
A comprehensive view of molecular chaperone function in the cell was obtained through a systematic global integrative network approach based on physical (protein-protein) and genetic (gene-gene or epistatic) interaction mapping. This allowed us to decipher interactions involving all core chaperones (67) and cochaperones (15) of Saccharomyces cerevisiae. Our analysis revealed the presence of a large chaperone functional supercomplex, which we named the naturally joined (NAJ) chaperone complex, encompassing Hsp40, Hsp70, Hsp90, AAA+, CCT, and small Hsps. We further found that many chaperones interact with proteins that form foci or condensates under stress conditions. Using an in vitro reconstitution approach, we demonstrate condensate formation for the highly conserved AAA+ ATPases Rvb1 and Rvb2, which are part of the R2TP complex that interacts with Hsp90. This expanded view of the chaperone network in the cell clearly demonstrates the distinction between chaperones having broad versus narrow substrate specificities in protein homeostasis.
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Affiliation(s)
- Kamran Rizzolo
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Jennifer Huen
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Ashwani Kumar
- Department of Computer Science, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sadhna Phanse
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - James Vlasblom
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Yoshito Kakihara
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | | | - Zoran Minic
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Jamie Snider
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Wen Wang
- Department of Computer Science & Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA; Program in Bioinformatics and Computational Biology, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Edgar Erik Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Costanzo
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Chad L Myers
- Department of Computer Science & Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA; Program in Bioinformatics and Computational Biology, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - Igor Stagljar
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada.
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
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Bhatt JM, Enriquez AS, Wang J, Rojo HM, Molugu SK, Hildenbrand ZL, Bernal RA. Single-Ring Intermediates Are Essential for Some Chaperonins. Front Mol Biosci 2018; 5:42. [PMID: 29755985 PMCID: PMC5934643 DOI: 10.3389/fmolb.2018.00042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/13/2018] [Indexed: 11/20/2022] Open
Abstract
Chaperonins are macromolecular complexes found throughout all kingdoms of life that assist unfolded proteins reach a biologically active state. Historically, chaperonins have been classified into two groups based on sequence, subunit structure, and the requirement for a co-chaperonin. Here, we present a brief review of chaperonins that can form double- and single-ring conformational intermediates in their protein-folding catalytic pathway. To date, the bacteriophage encoded chaperonins ϕ-EL and OBP, human mitochondrial chaperonin and most recently, the bacterial groEL/ES systems, have been reported to form single-ring intermediates as part of their normal protein-folding activity. These double-ring chaperonins separate into single-ring intermediates that have the ability to independently fold a protein. We discuss the structural and functional features along with the biological relevance of single-ring intermediates in cellular protein folding. Of special interest are the ϕ-EL and OBP chaperonins which demonstrate features of both group I and II chaperonins in addition to their ability to function via single-ring intermediates.
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Affiliation(s)
- Jay M Bhatt
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Adrian S Enriquez
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Jinliang Wang
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Humberto M Rojo
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Sudheer K Molugu
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | | | - Ricardo A Bernal
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
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