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Hofstad M, Woods A, Parra K, Sychev ZE, Mazzagatti A, Yu L, Gilbreath C, Ly P, Drake JM, Kittler R. Dual inhibition of ATR and DNA-PKcs radiosensitizes ATM-mutant prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602941. [PMID: 39026771 PMCID: PMC11257504 DOI: 10.1101/2024.07.10.602941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
In advanced castration resistant prostate cancer (CRPC), mutations in the DNA damage response (DDR) gene ataxia telangiectasia mutated ( ATM ) are common. While poly(ADP-ribose) polymerase inhibitors are approved in this context, their clinical efficacy remains limited. Thus, there is a compelling need to identify alternative therapeutic avenues for ATM mutant prostate cancer patients. Here, we generated matched ATM-proficient and ATM-deficient CRPC lines to elucidate the impact of ATM loss on DDR in response to DNA damage via irradiation. Through unbiased phosphoproteomic screening, we unveiled that ATM-deficient CRPC lines maintain dependence on downstream ATM targets through activation of ATR and DNA-PKcs kinases. Dual inhibition of ATR and DNA-PKcs effectively inhibited downstream γH2AX foci formation in response to irradiation and radiosensitized ATM-deficient lines to a greater extent than either ATM-proficient controls or single drug treatment. Further, dual inhibition abrogated residual downstream ATM pathway signaling and impaired replication fork dynamics. To circumvent potential toxicity, we leveraged the RUVBL1/2 ATPase inhibitor Compound B, which leads to the degradation of both ATR and DNA-PKcs kinases. Compound B effectively radiosensitized ATM-deficient CRPC in vitro and in vivo , and impacted replication fork dynamics. Overall, dual targeting of both ATR and DNA-PKcs is necessary to block DDR in ATM-deficient CRPC, and Compound B could be utilized as a novel therapy in combination with irradiation in these patients.
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Serra-Bardenys G, Blanco E, Escudero-Iriarte C, Serra-Camprubí Q, Querol J, Pascual-Reguant L, Morancho B, Escorihuela M, Tissera NS, Sabé A, Martín L, Segura-Bayona S, Verde G, Aiese Cigliano R, Millanes-Romero A, Jerónimo C, Cebrià-Costa JP, Nuciforo P, Simonetti S, Viaplana C, Dienstmann R, Oliveira M, Peg V, Stracker TH, Arribas J, Canals F, Villanueva J, Di Croce L, García de Herreros A, Tian TV, Peiró S. LOXL2-mediated chromatin compaction is required to maintain the oncogenic properties of triple-negative breast cancer cells. FEBS J 2024; 291:2423-2448. [PMID: 38451841 DOI: 10.1111/febs.17112] [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: 06/01/2023] [Revised: 01/02/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Oxidation of histone H3 at lysine 4 (H3K4ox) is catalyzed by lysyl oxidase homolog 2 (LOXL2). This histone modification is enriched in heterochromatin in triple-negative breast cancer (TNBC) cells and has been linked to the maintenance of compacted chromatin. However, the molecular mechanism underlying this maintenance is still unknown. Here, we show that LOXL2 interacts with RuvB-Like 1 (RUVBL1), RuvB-Like 2 (RUVBL2), Actin-like protein 6A (ACTL6A), and DNA methyltransferase 1associated protein 1 (DMAP1), a complex involved in the incorporation of the histone variant H2A.Z. Our experiments indicate that this interaction and the active form of RUVBL2 are required to maintain LOXL2-dependent chromatin compaction. Genome-wide experiments showed that H2A.Z, RUVBL2, and H3K4ox colocalize in heterochromatin regions. In the absence of LOXL2 or RUVBL2, global levels of the heterochromatin histone mark H3K9me3 were strongly reduced, and the ATAC-seq signal in the H3K9me3 regions was increased. Finally, we observed that the interplay between these series of events is required to maintain H3K4ox-enriched heterochromatin regions, which in turn is key for maintaining the oncogenic properties of the TNBC cell line tested (MDA-MB-231).
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Affiliation(s)
- Gemma Serra-Bardenys
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Institut Bonanova FP Sanitaria, Consorci Mar Parc de Salut de Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Laura Pascual-Reguant
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | | | - Anna Sabé
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Luna Martín
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Gaetano Verde
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Alba Millanes-Romero
- Institute for Research in Biomedicine (IRB Barcelona) and Barcelona Institute of Science and Technology, Spain
| | - Celia Jerónimo
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institut de Recherches Cliniques de Montréal, Canada
| | | | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sara Simonetti
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | | | - Mafalda Oliveira
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Vicente Peg
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Travis H Stracker
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Joaquín Arribas
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Francesc Canals
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Antonio García de Herreros
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tian V Tian
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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Warnock JL, Ball JA, Najmi SM, Henes M, Vazquez A, Koshnevis S, Wieden HJ, Conn GL, Ghalei H. Differential roles of putative arginine fingers of AAA + ATPases Rvb1 and Rvb2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593962. [PMID: 38798342 PMCID: PMC11118528 DOI: 10.1101/2024.05.13.593962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The evolutionarily conserved AAA+ ATPases Rvb1 and Rvb2 proteins form a heteromeric complex (Rvb1/2) required for assembly or remodeling of macromolecular complexes in essential cellular processes ranging from chromatin remodeling to ribosome biogenesis. Rvb1 and Rvb2 have a high degree of sequence and structural similarity, and both contain the classical features of ATPases of their clade, including an N-terminal AAA+ subdomain with the Walker A motif, an insertion domain that typically interacts with various binding partners, and a C-terminal AAA+ subdomain containing a Walker B motif, the Sensor I and II motifs, and an arginine finger. In this study, we find that despite the high degree of structural similarity, Rvb1 and Rvb2 have distinct active sites that impact their activities and regulation within the Rvb1/2 complex. Using a combination of biochemical and genetic approaches, we show that replacing the homologous arginine fingers of Rvb1 and Rvb2 with different amino acids not only has distinct effects on the catalytic activity of the complex, but also impacts cell growth, and the Rvb1/2 interactions with binding partners. Using molecular dynamics simulations, we find that changes near the active site of Rvb1 and Rvb2 cause long-range effects on the protein dynamics in the insertion domain, suggesting a molecular basis for how enzymatic activity within the catalytic site of ATP hydrolysis can be relayed to other domains of the Rvb1/2 complex to modulate its function. Further, we show the impact that the arginine finger variants have on snoRNP biogenesis and validate the findings from molecular dynamics simulations using a targeted genetic screen. Together, our results reveal new aspects of the regulation of the Rvb1/2 complex by identifying a relay of long-range molecular communication from the ATPase active site of the complex to the binding site of cofactors. Most importantly, our findings suggest that despite high similarity and cooperation within the same protein complex, the two proteins have evolved with unique properties critical for the regulation and function of the Rvb1/2 complex.
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Affiliation(s)
- Jennifer L. Warnock
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Jacob A. Ball
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Saman M. Najmi
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Mina Henes
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
- Graduate Program in Biochemistry, Cell & Developmental Biology (BCDB), Emory University, Atlanta, Georgia, USA
- Medical Scientist Training Program, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Amanda Vazquez
- Department of Microbiology, Faculty of Science, University of Manitoba, Manitoba, Canada
| | - Sohail Koshnevis
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Hans-Joachim Wieden
- Department of Microbiology, Faculty of Science, University of Manitoba, Manitoba, Canada
| | - Graeme L. Conn
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Homa Ghalei
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
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Zhang XY, Liu Y, Rong Q, Qi MY, Guo H. RUVBL1 accelerates tongue squamous cell carcinoma by mediating CRaf/MEK/ERK pathway. iScience 2024; 27:109434. [PMID: 38523780 PMCID: PMC10960137 DOI: 10.1016/j.isci.2024.109434] [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: 10/07/2023] [Revised: 12/15/2023] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
RAF/MEK/ERK pathway is frequently activated in tumor. Therefore, this study will investigate the function of RUVBL1 (RAF-binding protein) in tongue squamous cell carcinoma (TSCC). Bioinformatics was performed to identify differentially expressed mRNAs (DE-mRNAs) in TCGA-oral squamous cell carcinoma, GSE13601, and GSE34105 datasets. A total of 672 shared DE-mRNAs were identified in three datasets, and they are regulating metastasis and angiogenesis. Patients with RUVBL1 low expression had high overall survival. Overexpressing RUVBL1 enhanced the viability, wound healing percentage, invasion, sphere formation, angiogenesis, and resistance to cisplatin and 5-fluorouracil in CAL-27 and SCC-4 cells, and the opposite results were obtained by knocking down RUVBL1. Moreover, overexpression of RUVBL1 bolstered tumor growth in vivo. Strikingly, RUVBL1 diminished the phosphorylation of CRAF Ser259, which led to activation of the MEK/ERK pathway. In conclusion, RUVBL1 contributes to the malignant biological behavior of TSCC via activating the CRAF/MEK/ERK pathway. This provides molecular mechanisms and perspectives for targeted therapy of the CRAF/MEK/ERK pathway.
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Affiliation(s)
- Xin-yu Zhang
- The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan Province 650032, China
| | - Yang Liu
- Kunming University of Science and Technology, Kunming, Yunnan Province 650500, China
| | - Qiong Rong
- The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan Province 650032, China
| | - Ming-yue Qi
- Kunming University of Science and Technology, Kunming, Yunnan Province 650500, China
| | - Hui Guo
- The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan Province 650032, China
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Tian J, Wen M, Gao P, Feng M, Wei G. RUVBL1 ubiquitination by DTL promotes RUVBL1/2-β-catenin-mediated transcriptional regulation of NHEJ pathway and enhances radiation resistance in breast cancer. Cell Death Dis 2024; 15:259. [PMID: 38609375 PMCID: PMC11015013 DOI: 10.1038/s41419-024-06651-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 02/04/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024]
Abstract
Radiotherapy effectiveness in breast cancer is limited by radioresistance. Nevertheless, the mechanisms behind radioresistance are not yet fully understood. RUVBL1 and RUVBL2, referred to as RUVBL1/2, are crucial AAA+ ATPases that act as co-chaperones and are connected to cancer. Our research revealed that RUVBL1, also known as pontin/TIP49, is excessively expressed in MMTV-PyMT mouse models undergoing radiotherapy, which is considered a murine spontaneous breast-tumor model. Our findings suggest that RUVBL1 enhances DNA damage repair and radioresistance in breast cancer cells both in vitro and in vivo. Mechanistically, we discovered that DTL, also known as CDT2 or DCAF2, which is a substrate adapter protein of CRL4, promotes the ubiquitination of RUVBL1 and facilitates its binding to RUVBL2 and transcription cofactor β-catenin. This interaction, in turn, attenuates its binding to acetyltransferase Tat-interacting protein 60 (TIP60), a comodulator of nuclear receptors. Subsequently, ubiquitinated RUVBL1 promotes the transcriptional regulation of RUVBL1/2-β-catenin on genes associated with the non-homologous end-joining (NHEJ) repair pathway. This process also attenuates TIP60-mediated H4K16 acetylation and the homologous recombination (HR) repair process. Expanding upon the prior study's discoveries, we exhibited that the ubiquitination of RUVBL1 by DTL advances the interosculation of RUVBL1/2-β-catenin. And, it then regulates the transcription of NHEJ repair pathway protein. Resulting in an elevated resistance of breast cancer cells to radiation therapy. From the aforementioned, it is evident that targeting DTL-RUVBL1/2-β-catenin provides a potential radiosensitization approach when treating breast cancer.
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Affiliation(s)
- Jie Tian
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Mingxin Wen
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Human Anatomy, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Peng Gao
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences and Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Maoxiao Feng
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.
| | - Guangwei Wei
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
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Mao YQ, Seraphim TV, Wan Y, Wu R, Coyaud E, Bin Munim M, Mollica A, Laurent E, Babu M, Mennella V, Raught B, Houry WA. DPCD is a regulator of R2TP in ciliogenesis initiation through Akt signaling. Cell Rep 2024; 43:113713. [PMID: 38306274 DOI: 10.1016/j.celrep.2024.113713] [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: 02/23/2023] [Revised: 10/31/2023] [Accepted: 01/12/2024] [Indexed: 02/04/2024] Open
Abstract
R2TP is a chaperone complex consisting of the AAA+ ATPases RUVBL1 and RUVBL2, as well as RPAP3 and PIH1D1 proteins. R2TP is responsible for the assembly of macromolecular complexes mainly acting through different adaptors. Using proximity-labeling mass spectrometry, we identified deleted in primary ciliary dyskinesia (DPCD) as an adaptor of R2TP. Here, we demonstrate that R2TP-DPCD influences ciliogenesis initiation through a unique mechanism by interaction with Akt kinase to regulate its phosphorylation levels rather than its stability. We further show that DPCD is a heart-shaped monomeric protein with two domains. A highly conserved region in the cysteine- and histidine-rich domains-containing proteins and SGT1 (CS) domain of DPCD interacts with the RUVBL2 DII domain with high affinity to form a stable R2TP-DPCD complex both in cellulo and in vitro. Considering that DPCD is one among several CS-domain-containing proteins found to associate with RUVBL1/2, we propose that RUVBL1/2 are CS-domain-binding proteins that regulate complex assembly and downstream signaling.
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Affiliation(s)
- Yu-Qian Mao
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Yimei Wan
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Ruikai Wu
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Muhammad Bin Munim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Antonio Mollica
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Estelle Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Vito Mennella
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; MRC Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QR, UK; Department of Pathology, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QP, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, 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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Pinard M, Moursli A, Coulombe B. Drugs targeting the particle for arrangement of quaternary structure (PAQosome) and protein complex assembly. Expert Opin Drug Discov 2024; 19:57-71. [PMID: 37840283 DOI: 10.1080/17460441.2023.2267974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023]
Abstract
INTRODUCTION The PAQosome is a 12-subunit complex that acts as a co-factor of the molecular chaperones HSP90 and HSP70. This co-chaperone has been shown to participate in assembly and maturation of several protein complexes, including nuclear RNA polymerases, RNA processing factors, the ribosome, PIKKs, and others. Subunits of the PAQosome, adaptors, and clients have been reported to be involved in various diseases, making them interesting targets for drug discovery. AREA COVERED In this review, the authors cover the detailed mechanisms of PAQosome and chaperone function. Specifically, the authors summarize the status of the PAQosome and some related chaperones and co-chaperones as candidate targets for drug discovery. Indeed, a number of compounds are currently being tested for the development of treatments against diseases, such as cancers and neurodegenerative conditions. EXPERT OPINION Searching for new drugs targeting the PAQosome requires a better understanding of PAQosome subunit interactions and the discovery of new interaction partners. Thus, PAQosome subunit crystallization is an important experiment to initiate virtual screening against new target and the development of in silico tools such as AlphaFold-multimer could accelerate the search for new interaction partner and determine more rapidly the interaction pocket needed for virtual drug screening.
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Affiliation(s)
- Maxime Pinard
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
| | - Asmae Moursli
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
| | - Benoit Coulombe
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
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López-Perrote A, Serna M, Llorca O. Maturation and Assembly of mTOR Complexes by the HSP90-R2TP-TTT Chaperone System: Molecular Insights and Mechanisms. Subcell Biochem 2024; 104:459-483. [PMID: 38963496 DOI: 10.1007/978-3-031-58843-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The mechanistic target of rapamycin (mTOR) is a master regulator of cell growth and metabolism, integrating environmental signals to regulate anabolic and catabolic processes, regulating lipid synthesis, growth factor-induced cell proliferation, cell survival, and migration. These activities are performed as part of two distinct complexes, mTORC1 and mTORC2, each with specific roles. mTORC1 and mTORC2 are elaborated dimeric structures formed by the interaction of mTOR with specific partners. mTOR functions only as part of these large complexes, but their assembly and activation require a dedicated and sophisticated chaperone system. mTOR folding and assembly are temporarily separated with the TELO2-TTI1-TTI2 (TTT) complex assisting the cotranslational folding of mTOR into a native conformation. Matured mTOR is then transferred to the R2TP complex for assembly of active mTORC1 and mTORC2 complexes. R2TP works in concert with the HSP90 chaperone to promote the incorporation of additional subunits to mTOR and dimerization. This review summarizes our current knowledge on how the HSP90-R2TP-TTT chaperone system facilitates the maturation and assembly of active mTORC1 and mTORC2 complexes, discussing interactions, structures, and mechanisms.
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Affiliation(s)
- Andrés López-Perrote
- Spanish National Cancer Research Centre (CNIO), Structural Biology Programme, Melchor Fernández Almagro 3, Madrid, Spain.
| | - Marina Serna
- Spanish National Cancer Research Centre (CNIO), Structural Biology Programme, Melchor Fernández Almagro 3, Madrid, Spain
| | - Oscar Llorca
- Spanish National Cancer Research Centre (CNIO), Structural Biology Programme, Melchor Fernández Almagro 3, Madrid, Spain.
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Monaghan L, Longman D, Cáceres JF. Translation-coupled mRNA quality control mechanisms. EMBO J 2023; 42:e114378. [PMID: 37605642 PMCID: PMC10548175 DOI: 10.15252/embj.2023114378] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/23/2023] Open
Abstract
mRNA surveillance pathways are essential for accurate gene expression and to maintain translation homeostasis, ensuring the production of fully functional proteins. Future insights into mRNA quality control pathways will enable us to understand how cellular mRNA levels are controlled, how defective or unwanted mRNAs can be eliminated, and how dysregulation of these can contribute to human disease. Here we review translation-coupled mRNA quality control mechanisms, including the non-stop and no-go mRNA decay pathways, describing their mechanisms, shared trans-acting factors, and differences. We also describe advances in our understanding of the nonsense-mediated mRNA decay (NMD) pathway, highlighting recent mechanistic findings, the discovery of novel factors, as well as the role of NMD in cellular physiology and its impact on human disease.
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Affiliation(s)
- Laura Monaghan
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Dasa Longman
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
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Li M, Yang L, Chan AKN, Pokharel SP, Liu Q, Mattson N, Xu X, Chang W, Miyashita K, Singh P, Zhang L, Li M, Wu J, Wang J, Chen B, Chan LN, Lee J, Zhang XH, Rosen ST, Müschen M, Qi J, Chen J, Hiom K, Bishop AJR, Chen C. Epigenetic Control of Translation Checkpoint and Tumor Progression via RUVBL1-EEF1A1 Axis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206584. [PMID: 37075745 PMCID: PMC10265057 DOI: 10.1002/advs.202206584] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/23/2023] [Indexed: 05/03/2023]
Abstract
Epigenetic dysregulation is reported in multiple cancers including Ewing sarcoma (EwS). However, the epigenetic networks underlying the maintenance of oncogenic signaling and therapeutic response remain unclear. Using a series of epigenetics- and complex-focused CRISPR screens, RUVBL1, the ATPase component of NuA4 histone acetyltransferase complex, is identified to be essential for EwS tumor progression. Suppression of RUVBL1 leads to attenuated tumor growth, loss of histone H4 acetylation, and ablated MYC signaling. Mechanistically, RUVBL1 controls MYC chromatin binding and modulates the MYC-driven EEF1A1 expression and thus protein synthesis. High-density CRISPR gene body scan pinpoints the critical MYC interacting residue in RUVBL1. Finally, this study reveals the synergism between RUVBL1 suppression and pharmacological inhibition of MYC in EwS xenografts and patient-derived samples. These results indicate that the dynamic interplay between chromatin remodelers, oncogenic transcription factors, and protein translation machinery can provide novel opportunities for combination cancer therapy.
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Affiliation(s)
- Mingli Li
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Lu Yang
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Anthony K. N. Chan
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Sheela Pangeni Pokharel
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Qiao Liu
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Nicole Mattson
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Xiaobao Xu
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Wen‐Han Chang
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Kazuya Miyashita
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Priyanka Singh
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Leisi Zhang
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Maggie Li
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Jun Wu
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Jinhui Wang
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Bryan Chen
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Lai N. Chan
- Center of Molecular and Cellular OncologyYale Cancer CenterYale School of MedicineNew HavenCT06510USA
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOH44195USA
| | - Jaewoong Lee
- Center of Molecular and Cellular OncologyYale Cancer CenterYale School of MedicineNew HavenCT06510USA
- School of Biosystems and Biomedical SciencesCollege of Health ScienceKorea UniversitySeoul02841South Korea
- Interdisciplinary Program in Precision Public HealthKorea UniversitySeoul02841South Korea
| | | | | | - Markus Müschen
- Center of Molecular and Cellular OncologyYale Cancer CenterYale School of MedicineNew HavenCT06510USA
| | - Jun Qi
- Department of Cancer BiologyDana‐Farber Cancer InstituteHarvard Medical SchoolBostonMA02215USA
| | - Jianjun Chen
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Kevin Hiom
- Division of Cellular MedicineSchool of MedicineUniversity of DundeeNethergateDundeeDD1 4HNUK
| | - Alexander J. R. Bishop
- Department of Cellular Systems and AnatomyUniversity of Texas Health Science Center at San AntonioSan AntonioTX78229USA
- Greehey Children's Cancer Research InstituteUniversity of Texas Health Science Center at San AntonioSan AntonioTX78229USA
| | - Chun‐Wei Chen
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
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11
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McCann JJ, Fleenor DE, Chen J, Lai CH, Bass TE, Kastan MB. Participation of ATM, SMG1, and DDX5 in a DNA Damage-Induced Alternative Splicing Pathway. Radiat Res 2023; 199:406-421. [PMID: 36921295 PMCID: PMC10162594 DOI: 10.1667/rade-22-00219.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/03/2023] [Indexed: 03/17/2023]
Abstract
Altered cellular responses to DNA damage can contribute to cancer development, progression, and therapeutic resistance. Mutations in key DNA damage response factors occur across many cancer types, and the DNA damage-responsive gene, TP53, is frequently mutated in a high percentage of cancers. We recently reported that an alternative splicing pathway induced by DNA damage regulates alternative splicing of TP53 RNA and further modulates cellular stress responses. Through damage-induced inhibition of the SMG1 kinase, TP53 pre-mRNA is alternatively spliced to generate TP53b mRNA and p53b protein is required for optimal induction of cellular senescence after ionizing radiation-induced DNA damage. Herein, we confirmed and extended these observations by demonstrating that the ATM protein kinase is required for repression of SMG1 kinase activity after ionizing radiation. We found that the RNA helicase and splicing factor, DDX5, interacts with SMG1, is required for alternative splicing of TP53 pre-mRNA to TP53b and TP53c mRNAs after DNA damage, and contributes to radiation-induced cellular senescence. Interestingly, the role of SMG1 in alternative splicing of p53 appears to be distinguishable from its role in regulating nonsense-mediated RNA decay. Thus, ATM, SMG1, and DDX5 participate in a DNA damage-induced alternative splicing pathway that regulates TP53 splicing and modulates radiation-induced cellular senescence.
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Affiliation(s)
- Jennifer J. McCann
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Donald E. Fleenor
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Jing Chen
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Chun-Hsiang Lai
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Thomas E. Bass
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Michael B. Kastan
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
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12
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Araveti PB, Kar PP, Kuriakose A, Sanju A, Kumar KA, Srivastava A. Identification of a Novel Interaction between Theileria Prohibitin ( TaPHB-1) and Bovine RuvB-Like AAA ATPase 1. Microbiol Spectr 2023; 11:e0250222. [PMID: 36651733 PMCID: PMC9927103 DOI: 10.1128/spectrum.02502-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Theileriosis is a tick-borne disease caused by Theileria annulata, an intracellular parasite that belongs to the phylum Apicomplexa. The infective forms of the parasite to cattle are sporozoites that are introduced into the host when the infected ticks take a blood meal. The sporozoites selectively invade bovine B cells, macrophages, or monocytes, leading to their cellular transformation. The parasite factors involved in the host cell transformation are not well explored. In pursuit of this, we revisited the probable secretome of the parasite and, following a stringent downscaling criterion, have identified Theileria prohibitin (TaPHB-1) as one of factors secreted into the host cells. Interestingly, in infected cells, TaPHB-1 localized both on the parasite surface and in the host cytoplasm, and independent approaches such as coimmunoprecipitation, yeast two-hybrid screening (Y2H), and liquid chromatography-tandem mass spectrometry (LC-MS/MS) confirmed RuvB-like AAA ATPase 1 (RUVBL-1) as one of its interacting partners. Further, the T. annulata infection does not affect the localization of bovine prohibitin. Mitigating the expression of bovine RUVBL-1 precluded the translocation of TaPHB-1 in the host cell cytoplasm without affecting the host cell viability. Taken together, we report for the first time a unique interaction of TaPHB-1 with bovine RUVBL-1 that is likely needed to cause cancer-like hallmarks during theileriosis. IMPORTANCE Theileria annulata is an apicomplexan parasite that causes tropical theileriosis in cattle. It is the only eukaryotic pathogen able to cause cellular transformation of host cells yielding a cancer-like phenotype. The parasite factors responsible for the transformation of the host cell are largely unknown. This study demonstrates for the first time the partial role of Theileria prohibitin (TaPHB-1) in maintaining the transformed state of the host cell and its interaction with RuvB-like AAA ATPase 1 (RUVBL-1) in a T. annulata-infected bovine cell line. Interestingly, the knockdown of bovine RUVBL-1 rendered the parasites metabolically inactive, implying that the identified interaction is critical for parasite survival. This study contributes to our understanding the Theileria-host interactions and offers scope for novel therapeutic interventions to control theileriosis.
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Affiliation(s)
- Prasanna Babu Araveti
- National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
- Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad, Haryana, India
| | - Prajna Parimita Kar
- National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
- Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad, Haryana, India
| | - Akshay Kuriakose
- National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
| | - Achintya Sanju
- National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
| | - Kota Arun Kumar
- Department of Animal Biology, School of Life Science, University of Hyderabad, Hyderabad, Telangana, India
| | - Anand Srivastava
- National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
- Regional Centre for Biotechnology (RCB), Faridabad, Haryana, India
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13
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Pinard M, Dastpeyman S, Poitras C, Bernard G, Gauthier MS, Coulombe B. Riluzole partially restores RNA polymerase III complex assembly in cells expressing the leukodystrophy-causative variant POLR3B R103H. Mol Brain 2022; 15:98. [PMID: 36451185 PMCID: PMC9710144 DOI: 10.1186/s13041-022-00974-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/16/2022] [Indexed: 12/12/2022] Open
Abstract
The mechanism of assembly of RNA polymerase III (Pol III), the 17-subunit enzyme that synthesizes tRNAs, 5 S rRNA, and other small-nuclear (sn) RNAs in eukaryotes, is not clearly understood. The recent discovery of the HSP90 co-chaperone PAQosome (Particle for Arrangement of Quaternary structure) revealed a function for this machinery in the biogenesis of nuclear RNA polymerases. However, the connection between Pol III subunits and the PAQosome during the assembly process remains unexplored. Here, we report the development of a mass spectrometry-based assay that allows the characterization of Pol III assembly. This assay was used to dissect the stages of Pol III assembly, to start defining the function of the PAQosome in this process, to dissect the assembly defects driven by the leukodystrophy-causative R103H substitution in POLR3B, and to discover that riluzole, an FDA-approved drug for alleviation of ALS symptoms, partly corrects these assembly defects. Together, these results shed new light on the mechanism and regulation of human nuclear Pol III biogenesis.
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Affiliation(s)
- Maxime Pinard
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada
| | - Samaneh Dastpeyman
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada
| | - Christian Poitras
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada
| | - Geneviève Bernard
- grid.63984.300000 0000 9064 4811Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Neurology and Neurosurgery, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Pediatrics, McGill University, Montreal, Canada ,grid.63984.300000 0000 9064 4811Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, Canada
| | - Marie-Soleil Gauthier
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada
| | - Benoit Coulombe
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada ,grid.14848.310000 0001 2292 3357Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec Canada
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14
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Nagel M, Noss M, Xu J, Horn N, Ueffing M, Boldt K, Schuele R. The kinesin motor KIF1C is a putative transporter of the exon junction complex in neuronal cells. RNA (NEW YORK, N.Y.) 2022; 29:rna.079426.122. [PMID: 36316088 PMCID: PMC9808568 DOI: 10.1261/rna.079426.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Neurons critically depend on regulated RNA localization and tight control of spatio-temporal gene expression to maintain their morphological and functional integrity. Mutations in the kinesin motor protein gene KIF1C cause Hereditary Spastic Paraplegia, an autosomal recessive disease leading to predominant degeneration of the long axons of central motoneurons. In this study we aimed to gain insight into the molecular function of KIF1C and understand how KIF1C dysfunction contributes to motoneuron degeneration. We used affinity proteomics in neuronally differentiated neuroblastoma cells (SH-SY5Y) to identify the protein complex associated with KIF1C in neuronal cells; candidate interactions were then validated by immunoprecipitation and mislocalization of putative KIF1C cargoes was studied by immunostainings. We found KIF1C to interact with all core components of the exon junction complex (EJC); expression of mutant KIF1C in neuronal cells leads to loss of the typical localization distally in neurites. Instead, EJC core components accumulate in the pericentrosomal region, here co-localizing with mutant KIF1C. These findings suggest KIF1C as a neuronal transporter of the EJC. Interestingly, the binding of KIF1C to the EJC is RNA-mediated, as treatment with RNAse prior to immunoprecipitation almost completely abolishes the interaction. Silica-based solid-phase extraction of UV-crosslinked RNA-protein complexes furthermore supports direct interaction of KIF1C with RNA, as recently also demonstrated for kinesin heavy chain. Taken together, our findings are consistent with a model where KIF1C transports mRNA in an EJC-bound and therefore transcriptionally silenced state along neurites, thus providing the missing link between the EJC and mRNA localization in neurons.
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Affiliation(s)
- Maike Nagel
- German Center for Neurodegenerative Diseases, Tuebingen; Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tuebingen; Graduate School of Cellular and Molecular Neuroscience
| | - Marvin Noss
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tuebingen
| | - Jishu Xu
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tuebingen; Institute of Medical Genetics and Applied Genomics, University of Tuebingen; Graduate School
| | - Nicola Horn
- Institute for Ophthalmic Research, University of Tuebingen
| | - Marius Ueffing
- Institute of Ophthalmic Research, University of Tuebingen
| | - Karsten Boldt
- Institute of Ophthalmic Research, University of Tuebingen
| | - Rebecca Schuele
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tuebingen; German Center for Neurodegenerative Diseases, Tuebingen
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15
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Wang H, Li B, Zuo L, Wang B, Yan Y, Tian K, Zhou R, Wang C, Chen X, Jiang Y, Zheng H, Qin F, Zhang B, Yu Y, Liu CP, Xu Y, Gao J, Qi Z, Deng W, Ji X. The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors. Nat Commun 2022; 13:5703. [PMID: 36171202 PMCID: PMC9519968 DOI: 10.1038/s41467-022-33433-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/16/2022] [Indexed: 11/10/2022] Open
Abstract
RNA polymerase II (Pol II) apparatuses are compartmentalized into transcriptional clusters. Whether protein factors control these clusters remains unknown. In this study, we find that the ATPase-associated with diverse cellular activities (AAA + ) ATPase RUVBL2 co-occupies promoters with Pol II and various transcription factors. RUVBL2 interacts with unphosphorylated Pol II in chromatin to promote RPB1 carboxy-terminal domain (CTD) clustering and transcription initiation. Rapid depletion of RUVBL2 leads to a decrease in the number of Pol II clusters and inhibits nascent RNA synthesis, and tethering RUVBL2 to an active promoter enhances Pol II clustering at the promoter. We also identify target genes that are directly linked to the RUVBL2-Pol II axis. Many of these genes are hallmarks of cancers and encode proteins with diverse cellular functions. Our results demonstrate an emerging activity for RUVBL2 in regulating Pol II cluster formation in the nucleus. RNA polymerase II (Pol II) transcription factories play a central role in gene expression and 3D chromatin organization. Here, the authors demonstrate that RUVBL2 directly regulates Pol II clustering at active gene promoters.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.,Department of Pathogenic Biology, Chengdu Medical College, Chengdu, 610500, China
| | - Boyuan Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Linyu Zuo
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Bo Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences (CLS), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yan Yan
- Institute for TCM-X; MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist (Beijing National Research Center for Information Science and Technology); Department of Automation, Tsinghua University, Beijing, 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Rong Zhou
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Fangfei Qin
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Bin Zhang
- Departments of Pathology and Laboratory Medicine, and Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA
| | - Yang Yu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chao-Pei Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Juntao Gao
- Institute for TCM-X; MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist (Beijing National Research Center for Information Science and Technology); Department of Automation, Tsinghua University, Beijing, 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Zhi Qi
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Wulan Deng
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences (CLS), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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16
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The Role of Hsp90-R2TP in Macromolecular Complex Assembly and Stabilization. Biomolecules 2022; 12:biom12081045. [PMID: 36008939 PMCID: PMC9406135 DOI: 10.3390/biom12081045] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 01/27/2023] Open
Abstract
Hsp90 is a ubiquitous molecular chaperone involved in many cell signaling pathways, and its interactions with specific chaperones and cochaperones determines which client proteins to fold. Hsp90 has been shown to be involved in the promotion and maintenance of proper protein complex assembly either alone or in association with other chaperones such as the R2TP chaperone complex. Hsp90-R2TP acts through several mechanisms, such as by controlling the transcription of protein complex subunits, stabilizing protein subcomplexes before their incorporation into the entire complex, and by recruiting adaptors that facilitate complex assembly. Despite its many roles in protein complex assembly, detailed mechanisms of how Hsp90-R2TP assembles protein complexes have yet to be determined, with most findings restricted to proteomic analyses and in vitro interactions. This review will discuss our current understanding of the function of Hsp90-R2TP in the assembly, stabilization, and activity of the following seven classes of protein complexes: L7Ae snoRNPs, spliceosome snRNPs, RNA polymerases, PIKKs, MRN, TSC, and axonemal dynein arms.
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17
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Cheung CY, Huang TT, Chow N, Zhang S, Zhao Y, Chau MP, Chan WC, Wong CCL, Boassa D, Phan S, Ellisman MH, Yates JR, Xu S, Yu Z, Zhang Y, Zhang R, Ng LL, Ko BCB. Unconventional tonicity-regulated nuclear trafficking of NFAT5 mediated by KPNB1, XPOT and RUVBL2. J Cell Sci 2022; 135:275560. [PMID: 35635291 PMCID: PMC9377714 DOI: 10.1242/jcs.259280] [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: 08/18/2021] [Accepted: 05/20/2022] [Indexed: 11/20/2022] Open
Abstract
NFAT5 is the only known mammalian tonicity-responsive transcription factor with essential role in cellular adaptation to hypertonic stress. It is also implicated in diverse physiological and pathological processes. NFAT5 activity is tightly regulated by extracellular tonicity, but the underlying mechanisms remain elusive. We demonstrated that NFAT5 enters the nucleus via the nuclear pore complex. We found that NFAT5 utilizes a unique nuclear localization signal (NFAT5-NLS) for nuclear import. siRNA screening revealed that only karyopherin β1 (KPNB1), but not karyopherin alpha, is responsible for the nuclear import of NFAT5 via direct interaction with the NFAT5-NLS. Proteomics analysis and siRNA screening further revealed that nuclear export of NFAT5 under hypotonicity is driven by Exportin-T, where the process requires RuvB-Like AAA type ATPase 2 (RUVBL2) as an indispensable chaperone. Our findings have identified an unconventional tonicity-dependent nucleocytoplasmic trafficking pathway for NFAT5, a critical step in orchestrating rapid cellular adaptation to change in extracellular tonicity. These findings offer an opportunity for the development of novel NFAT5 targeting strategies that are potentially useful for the treatment of diseases associated with NFAT5 dysregulation.
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Affiliation(s)
- Chris Y Cheung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ting-Ting Huang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ning Chow
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Shuqi Zhang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yanxiang Zhao
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Mary P Chau
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Wing Cheung Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Catherine C L Wong
- Center for Precision Medicine Muti-Omics Research, Health Science Center, Peking University, China Clinical Laboratory Department, The Cancer Hospital of the University of Chinese Academy of Sciences, Beijing, China
| | - Daniela Boassa
- Department of Neurosciences, University of California, San Diego, USA.,Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Sebastien Phan
- Department of Neurosciences, University of California, San Diego, USA.,Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Mark H Ellisman
- Department of Neurosciences, University of California, San Diego, USA.,Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - SongXiao Xu
- The Clinical Laboratory Department, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Zicheng Yu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yajing Zhang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Rui Zhang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ling Ling Ng
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ben C B Ko
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
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18
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Zhang G, Wang F, Li S, Cheng KW, Zhu Y, Huo R, Abdukirim E, Kang G, Chou TF. Discovery of small-molecule inhibitors of RUVBL1/2 ATPase. Bioorg Med Chem 2022; 62:116726. [PMID: 35364523 PMCID: PMC9034851 DOI: 10.1016/j.bmc.2022.116726] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/07/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]
Abstract
RUVBL1 and RUVBL2 are highly conserved AAA ATPases (ATPases Associated with various cellular Activities) and highly relevant to the progression of cancer, which makes them attractive targets for novel therapeutic anticancer drugs. In this work, docking-based virtual screening was performed to identify compounds with activity against the RUVBL1/2 complex. Seven compounds showed inhibitory activity against the complex in both enzymatic and cellular assays. A series of pyrazolo[1,5-a]pyrimidine-3-carboxamide analogs were synthesized based on the scaffold of compound 15 with inhibitory activity and good potential for structural manipulation. Analysis of the structure-activity relationship identified the benzyl group on R2 and aromatic ring-substituted piperazinyl on R4 as essential for inhibitory activity against the RUVBL1/2 complex. Of these, compound 18, which has IC50 values of 6.0 ± 0.6 μM and 7.7 ± 0.9 μM against RUVBL1/2 complex and RUVBL1 respectively, showed the most potent inhibition in cell lines A549, H1795, HCT116, and MDA-MB-231 with IC50 values of 15 ± 1.2 μM, 15 ± 1.8 μM, 11 ± 1.0 μM, and 8.9 ± 0.9 μM respectively. A docking study of the compound was performed to predict the binding mode of pyrazolo[1,5-a]pyrimidine-3-carboxamides. Furthermore, mass spectrometry-based proteomic analysis was employed to explore cellular proteins dysregulated by treatment with compounds 16, 18, and 19. Together, the data from these analyses suggest that that compound 18 could serve as a starting point for structural modifications in order to improve potency, selectivity, and pharmacokinetic parameters of potential therapeutic molecules.
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Affiliation(s)
- Gang Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States.
| | - Feng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Yingying Zhu
- School of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, China
| | - Ran Huo
- School of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, China
| | - Elyar Abdukirim
- School of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, China
| | - Guifeng Kang
- School of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, China.
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, United States.
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19
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Marques AR, Santos JX, Martiniano H, Vilela J, Rasga C, Romão L, Vicente AM. Gene Variants Involved in Nonsense-Mediated mRNA Decay Suggest a Role in Autism Spectrum Disorder. Biomedicines 2022; 10:biomedicines10030665. [PMID: 35327467 PMCID: PMC8945030 DOI: 10.3390/biomedicines10030665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a heterogeneous neurodevelopmental condition with unclear etiology. Many genes have been associated with ASD risk, but the underlying mechanisms are still poorly understood. An important post-transcriptional regulatory mechanism that plays an essential role during neurodevelopment, the Nonsense-Mediated mRNA Decay (NMD) pathway, may contribute to ASD risk. In this study, we gathered a list of 46 NMD factors and regulators and investigated the role of genetic variants in these genes in ASD. By conducting a comprehensive search for Single Nucleotide Variants (SNVs) in NMD genes using Whole Exome Sequencing data from 1828 ASD patients, we identified 270 SNVs predicted to be damaging in 28.7% of the population. We also analyzed Copy Number Variants (CNVs) from two cohorts of ASD patients (N = 3570) and discovered 38 CNVs in 1% of cases. Importantly, we discovered 136 genetic variants (125 SNVs and 11 CNVs) in 258 ASD patients that were located within protein domains required for NMD. These gene variants are classified as damaging using in silico prediction tools, and therefore may interfere with proper NMD function in ASD. The discovery of NMD genes as candidates for ASD in large patient genomic datasets provides evidence supporting the involvement of the NMD pathway in ASD pathophysiology.
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Affiliation(s)
- Ana Rita Marques
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - João Xavier Santos
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - Hugo Martiniano
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - Joana Vilela
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - Célia Rasga
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - Luísa Romão
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal
| | - Astrid Moura Vicente
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
- Correspondence:
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20
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Detilleux D, Raynaud P, Pradet-Balade B, Helmlinger D. The TRRAP transcription cofactor represses interferon-stimulated genes in colorectal cancer cells. eLife 2022; 11:69705. [PMID: 35244540 PMCID: PMC8926402 DOI: 10.7554/elife.69705] [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: 04/23/2021] [Accepted: 03/03/2022] [Indexed: 11/30/2022] Open
Abstract
Transcription is essential for cells to respond to signaling cues and involves factors with multiple distinct activities. One such factor, TRRAP, functions as part of two large complexes, SAGA and TIP60, which have crucial roles during transcription activation. Structurally, TRRAP belongs to the phosphoinositide 3 kinase-related kinases (PIKK) family but is the only member classified as a pseudokinase. Recent studies established that a dedicated HSP90 co-chaperone, the triple T (TTT) complex, is essential for PIKK stabilization and activity. Here, using endogenous auxin-inducible degron alleles, we show that the TTT subunit TELO2 promotes TRRAP assembly into SAGA and TIP60 in human colorectal cancer cells (CRCs). Transcriptomic analysis revealed that TELO2 contributes to TRRAP regulatory roles in CRC cells, most notably of MYC target genes. Surprisingly, TELO2 and TRRAP depletion also induced the expression of type I interferon genes. Using a combination of nascent RNA, antibody-targeted chromatin profiling (CUT&RUN), ChIP, and kinetic analyses, we propose a model by which TRRAP directly represses the transcription of IRF9, which encodes a master regulator of interferon-stimulated genes. We have therefore uncovered an unexpected transcriptional repressor role for TRRAP, which we propose contributes to its tumorigenic activity.
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Affiliation(s)
| | - Peggy Raynaud
- CRBM, University of Montpellier, CNRS, Montpellier, France
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21
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Structure of the Human TELO2-TTI1-TTI2 Complex. J Mol Biol 2021; 434:167370. [PMID: 34838521 DOI: 10.1016/j.jmb.2021.167370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 11/21/2022]
Abstract
Phosphatidylinositol 3-kinase-related protein kinases (PIKKs) play critical roles in various metabolic pathways related to cell proliferation and survival. The TELO2-TTI1-TTI2 (TTT) complex has been proposed to recognize newly synthesized PIKKs and to deliver them to the R2TP complex (RUVBL1-RUVBL2-RPAP3-PIH1D1) and the heat shock protein 90 chaperone, thereby supporting their folding and assembly. Here, we determined the cryo-EM structure of the TTT complex at an average resolution of 4.2 Å. We describe the full-length structures of TTI1 and TELO2, and a partial structure of TTI2. All three proteins form elongated helical repeat structures. TTI1 provides a platform on which TELO2 and TTI2 bind to its central region and C-terminal end, respectively. The TELO2 C-terminal domain (CTD) is required for the interaction with TTI1 and recruitment of Ataxia-telangiectasia mutated (ATM). The N- and C-terminal segments of TTI1 recognize the FRAP-ATM-TRRAP (FAT) domain and the N-terminal HEAT repeats of ATM, respectively. The TELO2 CTD and TTI1 N- and C-terminal segments are required for cell survival in response to ionizing radiation.
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22
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Zhang G, Li S, Cheng KW, Chou TF. AAA ATPases as therapeutic targets: Structure, functions, and small-molecule inhibitors. Eur J Med Chem 2021; 219:113446. [PMID: 33873056 PMCID: PMC8165034 DOI: 10.1016/j.ejmech.2021.113446] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/21/2021] [Accepted: 03/30/2021] [Indexed: 01/07/2023]
Abstract
ATPases Associated with Diverse Cellular Activity (AAA ATPase) are essential enzymes found in all organisms. They are involved in various processes such as DNA replication, protein degradation, membrane fusion, microtubule serving, peroxisome biogenesis, signal transduction, and the regulation of gene expression. Due to the importance of AAA ATPases, several researchers identified and developed small-molecule inhibitors against these enzymes. We discuss six AAA ATPases that are potential drug targets and have well-developed inhibitors. We compare available structures that suggest significant differences of the ATP binding pockets among the AAA ATPases with or without ligand. The distances from ADP to the His20 in the His-Ser-His motif and the Arg finger (Arg353 or Arg378) in both RUVBL1/2 complex structures bound with or without ADP have significant differences, suggesting dramatically different interactions of the binding site with ADP. Taken together, the inhibitors of six well-studied AAA ATPases and their structural information suggest further development of specific AAA ATPase inhibitors due to difference in their structures. Future chemical biology coupled with proteomic approaches could be employed to develop variant specific, complex specific, and pathway specific inhibitors or activators for AAA ATPase proteins.
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Affiliation(s)
- Gang Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
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23
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Payán-Bravo L, Fontalva S, Peñate X, Cases I, Guerrero-Martínez J, Pareja-Sánchez Y, Odriozola-Gil Y, Lara E, Jimeno-González S, Suñé C, Muñoz-Centeno M, Reyes J, Chávez S. Human prefoldin modulates co-transcriptional pre-mRNA splicing. Nucleic Acids Res 2021; 49:6267-6280. [PMID: 34096575 PMCID: PMC8216451 DOI: 10.1093/nar/gkab446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 11/14/2022] Open
Abstract
Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the human genome. Severe pre-mRNA splicing defects were also detected, particularly after serum stimulation. We found impairment of co-transcriptional splicing during transcription elongation, which explains why the induction of long genes with a high number of introns was affected the most. We detected genome-wide prefoldin binding to transcribed genes and found that it correlated with the negative impact of prefoldin depletion on gene expression. Lack of prefoldin caused global decrease in Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain. It also reduced the recruitment of the CTD kinase CDK9 to transcribed genes, and the association of splicing factors PRP19 and U2AF65 to chromatin, which is known to depend on CTD phosphorylation. Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.
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Affiliation(s)
- Laura Payán-Bravo
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Sara Fontalva
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Xenia Peñate
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Ildefonso Cases
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - José Antonio Guerrero-Martínez
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Yerma Pareja-Sánchez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Yosu Odriozola-Gil
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Esther Lara
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Silvia Jimeno-González
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Carles Suñé
- Department of Molecular Biology, Institute of Parasitology and Biomedicine “López Neyra” IPBLN-CSIC, PTS, Granada, Spain
| | - Mari Cruz Muñoz-Centeno
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - José C Reyes
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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24
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Zhang R, Cheung CY, Seo SU, Liu H, Pardeshi L, Wong KH, Chow LMC, Chau MP, Wang Y, Lee AR, Kwon WY, Chen S, Chan BKW, Wong K, Choy RKW, Ko BCB. RUVBL1/2 Complex Regulates Pro-Inflammatory Responses in Macrophages via Regulating Histone H3K4 Trimethylation. Front Immunol 2021; 12:679184. [PMID: 34276666 PMCID: PMC8282052 DOI: 10.3389/fimmu.2021.679184] [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: 03/11/2021] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
Macrophages play an important role in the host defense mechanism. In response to infection, macrophages activate a genetic program of pro-inflammatory response to kill any invading pathogen, and initiate an adaptive immune response. We have identified RUVBL2 - an ATP-binding protein belonging to the AAA+ (ATPase associated with diverse cellular activities) superfamily of ATPases - as a novel regulator in pro-inflammatory response of macrophages. Gene knockdown of Ruvbl2, or pharmacological inhibition of RUVBL1/2 activity, compromises type-2 nitric oxide synthase (Nos2) gene expression, nitric oxide production and anti-bacterial activity of mouse macrophages in response to lipopolysaccharides (LPS). RUVBL1/2 inhibitor similarly inhibits pro-inflammatory response in human monocytes, suggesting functional conservation of RUVBL1/2 in humans. Transcriptome analysis further revealed that major LPS-induced pro-inflammatory pathways in macrophages are regulated in a RUVBL1/2-dependent manner. Furthermore, RUVBL1/2 inhibition significantly reduced the level of histone H3K4me3 at the promoter region of Nos2 and Il6, two prototypical pro-inflammatory genes, and diminished the recruitment of NF-kappaB to the corresponding enhancers. Our study reveals RUVBL1/2 as an integral component of macrophage pro-inflammatory responses through epigenetic regulations, and the therapeutic potentials of RUVBL1/2 inhibitors in the treatment of diseases caused by aberrant activation of pro-inflammatory pathways.
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Affiliation(s)
- Rui Zhang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Chris Y Cheung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Sang-Uk Seo
- Department of Microbiology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hang Liu
- The University Research Facility in Chemical and Environmental Analysis, The Hong Kong Polytechnic University, Hong Kong, China
| | - Lakhansing Pardeshi
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau.,Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau.,Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau
| | - Larry M C Chow
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Mary P Chau
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yixiang Wang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ah Ra Lee
- Department of Microbiology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Woon Yong Kwon
- Department of Emergency Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, The City University of Hong Kong, Hong Kong, China
| | - Bill Kwan-Wai Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Kenneth Wong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Richard K W Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ben C B Ko
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
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25
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Wang R, Li X, Sun C, Yu L, Hua D, Shi C, Wang Q, Rao C, Luo W, Jiang Z, Zhou X, Yu S. The ATPase Pontin is a key cell cycle regulator by amplifying E2F1 transcription response in glioma. Cell Death Dis 2021; 12:141. [PMID: 33542204 PMCID: PMC7862657 DOI: 10.1038/s41419-021-03421-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 01/20/2023]
Abstract
Pontin (RUVBL1) is a highly conserved ATPase of the AAA + (ATPases Associated with various cellular Activities) superfamily and is implicated in various biological processes crucial for oncogenesis. Its overexpression is observed in multiple human cancers, whereas the relevance of Pontin to gliomagenesis remains obscure. To gain insights into Pontin involvement in glioma, we performed bioinformatics analyses of Pontin co-expressed genes, Pontin-affected genes, and carried out experimental studies. The results verified that Pontin was upregulated in gliomas. Its higher levels might predict the worse prognosis of glioma patients. The Pontin co-expressed genes were functionally enriched in cell cycle progression and RNA processing. In the nucleus, Pontin promoted cell growth via facilitating cell cycle progression. Using RNA-seq, we found that Pontin knockdown resulted in altered expression of multiple genes, among which the E2F1 targets accounted for a large proportion. Mechanistic studies found that Pontin interacted with E2F1 and markedly amplified the E2F1 transcription response in an ATPase domain-dependent manner. By analyzing the RNA-seq data, we also found that Pontin could impact on the alternative splicing (AS). Both differential expressed genes and AS events affected by Pontin were associated with cell cycle regulation. Taken together, our findings provide novel insights of the importance of Pontin in gliomagenesis by regulating cell cycle and AS, and shed light on the possible application of Pontin as an antineoplastic target in glioma.
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Affiliation(s)
- Run Wang
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Xuebing Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Cuiyun Sun
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Lin Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences of Tianjin Medical University, Tianjin, China
| | - Dan Hua
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Cuijuan Shi
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Qian Wang
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Chun Rao
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Wenjun Luo
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Zhendong Jiang
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Xuexia Zhou
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China. .,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China. .,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China.
| | - Shizhu Yu
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China. .,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China. .,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China.
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Guo Y, Tocchini C, Ciosk R. CLK-2/TEL2 is a conserved component of the nonsense-mediated mRNA decay pathway. PLoS One 2021; 16:e0244505. [PMID: 33444416 PMCID: PMC7808604 DOI: 10.1371/journal.pone.0244505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) controls eukaryotic mRNA quality, inducing the degradation of faulty transcripts. Key players in the NMD pathway were originally identified, through genetics, in Caenorhabditis elegans as smg (suppressor with morphological effect on genitalia) genes. Using forward genetics and fluorescence-based NMD reporters, we reexamined the genetic landscape underlying NMD. Employing a novel strategy for mapping sterile mutations, Het-Map, we identified clk-2, a conserved gene previously implicated in DNA damage signaling, as a player in the nematode NMD. We find that CLK-2 is expressed predominantly in the germline, highlighting the importance of auxiliary factors in tissue-specific mRNA decay. Importantly, the human counterpart of CLK-2/TEL2, TELO2, has been also implicated in the NMD, suggesting a conserved role of CLK-2/TEL2 proteins in mRNA surveillance. Recently, variants of TELO2 have been linked to an intellectual disability disorder, the You-Hoover-Fong syndrome, which could be related to its function in the NMD.
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Affiliation(s)
- Yanwu Guo
- Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Rafal Ciosk
- Department of Biosciences, University of Oslo, Oslo, Norway
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- * E-mail:
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27
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López-Perrote A, Hug N, González-Corpas A, Rodríguez CF, Serna M, García-Martín C, Boskovic J, Fernandez-Leiro R, Caceres JF, Llorca O. Regulation of RUVBL1-RUVBL2 AAA-ATPases by the nonsense-mediated mRNA decay factor DHX34, as evidenced by Cryo-EM. eLife 2020; 9:63042. [PMID: 33205750 PMCID: PMC7707835 DOI: 10.7554/elife.63042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/12/2020] [Indexed: 11/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades aberrant mRNAs and also regulates the expression of a wide range of physiological transcripts. RUVBL1 and RUVBL2 AAA-ATPases form an hetero-hexameric ring that is part of several macromolecular complexes such as INO80, SWR1, and R2TP. Interestingly, RUVBL1-RUVBL2 ATPase activity is required for NMD activation by an unknown mechanism. Here, we show that DHX34, an RNA helicase regulating NMD initiation, directly interacts with RUVBL1-RUVBL2 in vitro and in cells. Cryo-EM reveals that DHX34 induces extensive changes in the N-termini of every RUVBL2 subunit in the complex, stabilizing a conformation that does not bind nucleotide and thereby down-regulates ATP hydrolysis of the complex. Using ATPase-deficient mutants, we find that DHX34 acts exclusively on the RUVBL2 subunits. We propose a model, where DHX34 acts to couple RUVBL1-RUVBL2 ATPase activity to the assembly of factors required to initiate the NMD response.
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Affiliation(s)
- Andres López-Perrote
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Nele Hug
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburghx, Edinburgh, United Kingdom
| | - Ana González-Corpas
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Carlos F Rodríguez
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marina Serna
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Carmen García-Martín
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jasminka Boskovic
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Rafael Fernandez-Leiro
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Javier F Caceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburghx, Edinburgh, United Kingdom
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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28
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Unraveling the multifaceted nature of the nuclear function of mTOR. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118907. [PMID: 33189783 DOI: 10.1016/j.bbamcr.2020.118907] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/02/2020] [Accepted: 11/08/2020] [Indexed: 01/25/2023]
Abstract
Positioned at the axis between the cell and its environment, mTOR directs a wide range of cellular activity in response to nutrients, growth factors, and stress. Our understanding of the role of mTOR is evolving beyond the spatial confines of the cytosol, and its role in the nucleus becoming ever more apparent. In this review, we will address various studies that explore the role of nuclear mTOR (nmTOR) in specific cellular programs and how these pathways influence one another. To understand the emerging roles of nuclear mTOR, we discuss data and propose plausible mechanisms to offer novel ideas, hypotheses, and future research directions.
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Dauden MI, López-Perrote A, Llorca O. RUVBL1-RUVBL2 AAA-ATPase: a versatile scaffold for multiple complexes and functions. Curr Opin Struct Biol 2020; 67:78-85. [PMID: 33129013 DOI: 10.1016/j.sbi.2020.08.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/20/2022]
Abstract
RUVBL1 and RUVBL2 are two highly conserved AAA+ ATPases that form a hetero-hexameric complex that participates in a wide range of unrelated cellular processes, including chromatin remodeling, Fanconi Anemia (FA), nonsense-mediated mRNA decay (NMD), and assembly and maturation of several large macromolecular complexes such as RNA polymerases, the box C/D small nucleolar ribonucleoprotein (snoRNP) and mTOR complexes. How the RUVBL1-RUVBL2 complex works in such a variety of processes, sometimes antagonistic, has been obscure for a long time. Recent cryo-electron microscopy (cryo-EM) studies have started to reveal how RUVBL1-RUVBL2 forms a scaffold for complex protein-protein interactions and how the structure and ATPase activity of RUVBL1-RUVBL2 can be affected and regulated by the interaction with clients.
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Affiliation(s)
- Maria I Dauden
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain
| | - Andrés López-Perrote
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain.
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30
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Tafur L, Kefauver J, Loewith R. Structural Insights into TOR Signaling. Genes (Basel) 2020; 11:E885. [PMID: 32759652 PMCID: PMC7464330 DOI: 10.3390/genes11080885] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 12/31/2022] Open
Abstract
The Target of Rapamycin (TOR) is a highly conserved serine/threonine protein kinase that performs essential roles in the control of cellular growth and metabolism. TOR acts in two distinct multiprotein complexes, TORC1 and TORC2 (mTORC1 and mTORC2 in humans), which maintain different aspects of cellular homeostasis and orchestrate the cellular responses to diverse environmental challenges. Interest in understanding TOR signaling is further motivated by observations that link aberrant TOR signaling to a variety of diseases, ranging from epilepsy to cancer. In the last few years, driven in large part by recent advances in cryo-electron microscopy, there has been an explosion of available structures of (m)TORC1 and its regulators, as well as several (m)TORC2 structures, derived from both yeast and mammals. In this review, we highlight and summarize the main findings from these reports and discuss both the fascinating and unexpected molecular biology revealed and how this knowledge will potentially contribute to new therapeutic strategies to manipulate signaling through these clinically relevant pathways.
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Affiliation(s)
- Lucas Tafur
- Department of Molecular Biology, University of Geneva, 30 quai Ernest-Ansermet, CH1211 Geneva, Switzerland; (L.T.); (J.K.)
| | - Jennifer Kefauver
- Department of Molecular Biology, University of Geneva, 30 quai Ernest-Ansermet, CH1211 Geneva, Switzerland; (L.T.); (J.K.)
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, 30 quai Ernest-Ansermet, CH1211 Geneva, Switzerland; (L.T.); (J.K.)
- Swiss National Centre for Competence in Research (NCCR) in Chemical Biology, University of Geneva, Sciences II, Room 3-308, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland
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31
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Shin SH, Lee JS, Zhang JM, Choi S, Boskovic ZV, Zhao R, Song M, Wang R, Tian J, Lee MH, Kim JH, Jeong M, Lee JH, Petukhov M, Lee SW, Kim SG, Zou L, Byun S. Synthetic lethality by targeting the RUVBL1/2-TTT complex in mTORC1-hyperactive cancer cells. SCIENCE ADVANCES 2020; 6:eaay9131. [PMID: 32789167 PMCID: PMC7399646 DOI: 10.1126/sciadv.aay9131] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 03/19/2020] [Indexed: 05/08/2023]
Abstract
Despite considerable efforts, mTOR inhibitors have produced limited success in the clinic. To define the vulnerabilities of mTORC1-addicted cancer cells and to find previously unknown therapeutic targets, we investigated the mechanism of piperlongumine, a small molecule identified in a chemical library screen to specifically target cancer cells with a hyperactive mTORC1 phenotype. Sensitivity to piperlongumine was dependent on its ability to suppress RUVBL1/2-TTT, a complex involved in chromatin remodeling and DNA repair. Cancer cells with high mTORC1 activity are subjected to higher levels of DNA damage stress via c-Myc and displayed an increased dependency on RUVBL1/2 for survival and counteracting genotoxic stress. Examination of clinical cancer tissues also demonstrated that high mTORC1 activity was accompanied by high RUVBL2 expression. Our findings reveal a previously unknown role for RUVBL1/2 in cell survival, where it acts as a functional chaperone to mitigate stress levels induced in the mTORC1-Myc-DNA damage axis.
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Affiliation(s)
- Seung Ho Shin
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
- Department of Food and Nutrition, Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ji Su Lee
- Division of Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Jia-Min Zhang
- Massachusetts General Hospital Cancer Center, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Sungbin Choi
- Division of Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Zarko V. Boskovic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Ran Zhao
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Mengqiu Song
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Rui Wang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Jie Tian
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Mee-Hyun Lee
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Jae Hwan Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Minju Jeong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jung Hyun Lee
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Michael Petukhov
- Petersburg Nuclear Physics Institute named after B.P. Konstantinov, NRC "Kurchatov Institute", Gatchina, Russia
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Sam W. Lee
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
- Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sang Gyun Kim
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Building 149 13th Street, Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Sanguine Byun
- Division of Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
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32
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Sulkowska A, Auber A, Sikorski PJ, Silhavy DN, Auth M, Sitkiewicz E, Jean V, Merret RM, Bousquet-Antonelli CC, Kufel J. RNA Helicases from the DEA(D/H)-Box Family Contribute to Plant NMD Efficiency. PLANT & CELL PHYSIOLOGY 2020; 61:144-157. [PMID: 31560399 DOI: 10.1093/pcp/pcz186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic RNA surveillance mechanism that degrades aberrant mRNAs comprising a premature translation termination codon. The adenosine triphosphate (ATP)-dependent RNA helicase up-frameshift 1 (UPF1) is a major NMD factor in all studied organisms; however, the complexity of this mechanism has not been fully characterized in plants. To identify plant NMD factors, we analyzed UPF1-interacting proteins using tandem affinity purification coupled to mass spectrometry. Canonical members of the NMD pathway were found along with numerous NMD candidate factors, including conserved DEA(D/H)-box RNA helicase homologs of human DDX3, DDX5 and DDX6, translation initiation factors, ribosomal proteins and transport factors. Our functional studies revealed that depletion of DDX3 helicases enhances the accumulation of NMD target reporter mRNAs but does not result in increased protein levels. In contrast, silencing of DDX6 group leads to decreased accumulation of the NMD substrate. The inhibitory effect of DDX6-like helicases on NMD was confirmed by transient overexpression of RH12 helicase. These results indicate that DDX3 and DDX6 helicases in plants have a direct and opposing contribution to NMD and act as functional NMD factors.
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Affiliation(s)
- Aleksandra Sulkowska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andor Auber
- Agricultural Biotechnology Institute, Szent-Gy�rgyi 4, H-2100 G�d�llő, Hungary
| | - Pawel J Sikorski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Dï Niel Silhavy
- Agricultural Biotechnology Institute, Szent-Gy�rgyi 4, H-2100 G�d�llő, Hungary
| | - Mariann Auth
- Agricultural Biotechnology Institute, Szent-Gy�rgyi 4, H-2100 G�d�llő, Hungary
| | - Ewa Sitkiewicz
- Proteomics Laboratory, Biophysics Department, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Viviane Jean
- UMR5096 LGDP, Universit� de Perpignan Via Domitia, UMR5096 LGDP58, Avenue Paul Alduy, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, Perpignan Cedex, France
| | - Rï My Merret
- UMR5096 LGDP, Universit� de Perpignan Via Domitia, UMR5096 LGDP58, Avenue Paul Alduy, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, Perpignan Cedex, France
| | - Cï Cile Bousquet-Antonelli
- UMR5096 LGDP, Universit� de Perpignan Via Domitia, UMR5096 LGDP58, Avenue Paul Alduy, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, Perpignan Cedex, France
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
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33
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Delom F, Mohtar MA, Hupp T, Fessart D. The anterior gradient-2 interactome. Am J Physiol Cell Physiol 2020; 318:C40-C47. [DOI: 10.1152/ajpcell.00532.2018] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The anterior gradient-2 (AGR2) is an endoplasmic reticulum (ER)-resident protein belonging to the protein disulfide isomerase family that mediates the formation of disulfide bonds and assists the protein quality control in the ER. In addition to its role in proteostasis, extracellular AGR2 is responsible for various cellular effects in many types of cancer, including cell proliferation, survival, and metastasis. Various OMICs approaches have been used to identify AGR2 binding partners and to investigate the functions of AGR2 in the ER and outside the cell. Emerging data showed that AGR2 exists not only as monomer, but it can also form homodimeric structure and thus interact with different partners, yielding different biological outcomes. In this review, we summarize the AGR2 “interactome” and discuss the pathological and physiological role of such AGR2 interactions.
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Affiliation(s)
- Frederic Delom
- University of Bordeaux, ACTION, Bordeaux, France
- Institut National de la Santé et de la Recherche Médicale, Bordeaux, France
- Institut Bergonié, Bordeaux, France
| | - M. Aiman Mohtar
- University Kebangsaan Malaysia, Medical Molecular Biology Institute (UMBI), The National University of Malaysia, Kuala Lumpur, Malaysia
| | - Ted Hupp
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland, United Kingdom
- University of Gdansk, International Centre for Cancer Vaccine Science, Gdansk, Poland
| | - Delphine Fessart
- University of Bordeaux, ACTION, Bordeaux, France
- Institut National de la Santé et de la Recherche Médicale, Bordeaux, France
- Institut Bergonié, Bordeaux, France
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34
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Yenerall P, Das AK, Wang S, Kollipara RK, Li LS, Villalobos P, Flaming J, Lin YF, Huffman K, Timmons BC, Gilbreath C, Sonavane R, Kinch LN, Rodriguez-Canales J, Moran C, Behrens C, Hirasawa M, Takata T, Murakami R, Iwanaga K, Chen BPC, Grishin NV, Raj GV, Wistuba II, Minna JD, Kittler R. RUVBL1/RUVBL2 ATPase Activity Drives PAQosome Maturation, DNA Replication and Radioresistance in Lung Cancer. Cell Chem Biol 2019; 27:105-121.e14. [PMID: 31883965 DOI: 10.1016/j.chembiol.2019.12.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/07/2019] [Accepted: 12/06/2019] [Indexed: 02/03/2023]
Abstract
RUVBL1 and RUVBL2 (collectively RUVBL1/2) are essential AAA+ ATPases that function as co-chaperones and have been implicated in cancer. Here we investigated the molecular and phenotypic role of RUVBL1/2 ATPase activity in non-small cell lung cancer (NSCLC). We find that RUVBL1/2 are overexpressed in NSCLC patient tumors, with high expression associated with poor survival. Utilizing a specific inhibitor of RUVBL1/2 ATPase activity, we show that RUVBL1/2 ATPase activity is necessary for the maturation or dissociation of the PAQosome, a large RUVBL1/2-dependent multiprotein complex. We also show that RUVBL1/2 have roles in DNA replication, as inhibition of its ATPase activity can cause S-phase arrest, which culminates in cancer cell death via replication catastrophe. While in vivo pharmacological inhibition of RUVBL1/2 results in modest antitumor activity, it synergizes with radiation in NSCLC, but not normal cells, an attractive property for future preclinical development.
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Affiliation(s)
- Paul Yenerall
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Amit K Das
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shan Wang
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rahul K Kollipara
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Long Shan Li
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pamela Villalobos
- Department of Translational Molecular Pathology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Josiah Flaming
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu-Fen Lin
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenneth Huffman
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brenda C Timmons
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Collin Gilbreath
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rajni Sonavane
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa N Kinch
- Howard Hughes Medical Institute and Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Cesar Moran
- Department of Pathology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Makoto Hirasawa
- Drug Metabolism & Pharmacokinetics Research Laboratories, Daiichi-Sankyo Co., Ltd., Tokyo 103-8426, Japan
| | - Takehiko Takata
- Oncology Medical Science Department, Medical Affairs, Daiichi-Sankyo Co., Ltd., Tokyo 103-8426, Japan
| | - Ryo Murakami
- Oncology Research Laboratories II, Daiichi-Sankyo Co., Ltd., Tokyo 103-8426, Japan
| | - Koichi Iwanaga
- Oncology Medical Science Department, Medical Affairs, Daiichi-Sankyo Co., Ltd., Tokyo 103-8426, Japan
| | - Benjamin P C Chen
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute and Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ganesh V Raj
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Ralf Kittler
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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35
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Mello T, Materozzi M, Zanieri F, Simeone I, Ceni E, Bereshchenko O, Polvani S, Tarocchi M, Marroncini G, Nerlov C, Guasti D, Bani D, Pinzani M, Galli A. Liver haploinsufficiency of RuvBL1 causes hepatic insulin resistance and enhances hepatocellular carcinoma progression. Int J Cancer 2019; 146:3410-3422. [PMID: 31721195 DOI: 10.1002/ijc.32787] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/22/2019] [Accepted: 10/28/2019] [Indexed: 12/29/2022]
Abstract
RuvBL1 is an AAA+ ATPase whose expression in hepatocellular carcinoma (HCC) correlates with a poor prognosis. In vitro models suggest that targeting RuvBL1 could be an effective strategy against HCC. However, the role of RuvBL1 in the onset and progression of HCC remains unknown. To address this question, we developed a RuvBL1hep+/- mouse model and evaluated the outcome of DEN-induced liver carcinogenesis up to 12 months of progression. We found that RuvBL1 haploinsufficiency initially delayed the onset of liver cancer, due to a reduced hepatocyte turnover in RuvBL1hep+/- mice. However, RuvBL1hep+/- mice eventually developed HCC nodules that, with aging, grew larger than in the control mice. Moreover, RuvBL1hep+/- mice developed hepatic insulin resistance and impaired glucose homeostasis. We could determine that RuvBL1 regulates insulin signaling through the Akt/mTOR pathway in liver physiology in vivo as well as in normal hepatocytic and HCC cells in vitro. Whole transcriptome analysis of mice livers confirmed the major role of RuvBL1 in the regulation of hepatic glucose metabolism. Finally, RuvBL1 expression was found significantly correlated to glucose metabolism and mTOR signaling by bioinformatic analysis of human HCC sample from the publicly available TGCA database. These data uncover a role of RuvBL1 at the intersection of liver metabolism, hepatocyte proliferation and HCC development, providing a molecular rationale for its overexpression in liver cancer.
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Affiliation(s)
- Tommaso Mello
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Maria Materozzi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Francesca Zanieri
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Irene Simeone
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Elisabetta Ceni
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | | | - Simone Polvani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Mirko Tarocchi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Giada Marroncini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Claus Nerlov
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Daniele Guasti
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Daniele Bani
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Massimo Pinzani
- UCL Institute for Liver and Digestive Health, London, United Kingdom
| | - Andrea Galli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
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36
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Plasmodium falciparum R2TP complex: driver of parasite Hsp90 function. Biophys Rev 2019; 11:1007-1015. [PMID: 31734827 DOI: 10.1007/s12551-019-00605-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/30/2019] [Indexed: 02/04/2023] Open
Abstract
Heat shock protein 90 (Hsp90) is essential for the development of the main malaria agent, Plasmodium falciparum. Inhibitors that target Hsp90 function are known to not only kill the parasite, but also reverse resistance of the parasite to traditional antimalarials such as chloroquine. For this reason, Hsp90 has been tagged as a promising antimalarial drug target. As a molecular chaperone, Hsp90 facilitates folding of proteins such as steroid hormone receptors and kinases implicated in cell cycle and development. Central to Hsp90 function is its regulation by several co-chaperones. Various co-chaperones interact with Hsp90 to modulate its co-operation with other molecular chaperones such as Hsp70 and to regulate its interaction with substrates. The role of Hsp90 in the development of malaria parasites continues to receive research attention, and several Hsp90 co-chaperones have been mapped out. Recently, focus has shifted to P. falciparum R2TP proteins, which are thought to couple Hsp90 to a diverse set of client proteins. R2TP proteins are generally known to form a complex with Hsp90, and this complex drives multiple cellular processes central to signal transduction and cell division. Given the central role that the R2TP complex may play, the current review highlights the structure-function features of Hsp90 relative to R2TPs of P. falciparum.
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Yan T, Liu F, Gao J, Lu H, Cai J, Zhao X, Sun Y. Multilevel regulation of RUVBL2 expression predicts poor prognosis in hepatocellular carcinoma. Cancer Cell Int 2019; 19:249. [PMID: 31572066 PMCID: PMC6764127 DOI: 10.1186/s12935-019-0974-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/23/2019] [Indexed: 12/24/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the second-most lethal cancer worldwide with a complex pathogenesis. RuvB-like 2 (RUVBL2) was previously found to contribute to hepatocarcinogenesis. However, its expression, regulation and clinical significance have not been systematically evaluated in a large number of clinical samples. Methods Here, we performed a comprehensive analysis of RUVBL2 based on multiple datasets from 371 liver cancer patients of The Cancer Genome Atlas (TCGA) and on immunohistochemical staining in 153 subjects. In addition, the aberrant signaling pathways caused by RUVBL2 overexpression were investigated. Results We demonstrated that promoter hypomethylation, copy number gain, MYC amplification and CTNNB1 mutation were all responsible for RUVBL2 overexpression in HCC. High levels of RUVBL2 mRNA were associated with shorter recurrence-free survival time (RFS) but not overall survival time (OS). Furthermore, RUVBL2 protein was overexpressed in the nucleus and cytoplasm of HCC samples. Univariate and multivariate survival analyses showed that strong nuclear and cytoplasmic staining of RUVBL2 independently predicted worse OS and RFS with a 2.03-fold and a 1.71-fold increase in the hazard ratio, respectively. High levels of RUVBL2 promoted carcinogenesis through the heat shock protein 90 (HSP90)-Cell Division Cycle 37 (CDC37), AKT serine/threonine kinase (AKT) and mitogen-activated protein kinase (ERK/MAPK) pathways. Conclusion The deregulation of RUVBL2 in HCC is influenced at the genomic, epigenetic and transcriptional levels. Our findings highlight the potential roles of RUVBL2 as a promising prognostic marker as well as a therapeutic target for HCC.
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Affiliation(s)
- Tao Yan
- 1Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100021 China
| | - Fang Liu
- 2State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021 China
| | - Jiajia Gao
- 2State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021 China
| | - Haizhen Lu
- 3Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100021 China
| | - Jianqiang Cai
- 4Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100021 China
| | - Xiaohang Zhao
- 2State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021 China
| | - Yulin Sun
- 2State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021 China
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Coufalova D, Remnant L, Hernychova L, Muller P, Healy A, Kannan S, Westwood N, Verma CS, Vojtesek B, Hupp TR, Houston DR. An inter-subunit protein-peptide interface that stabilizes the specific activity and oligomerization of the AAA+ chaperone Reptin. J Proteomics 2019; 199:89-101. [PMID: 30862565 DOI: 10.1016/j.jprot.2019.02.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/16/2019] [Accepted: 02/23/2019] [Indexed: 12/26/2022]
Abstract
Reptin is a member of the AAA+ superfamily whose members can exist in equilibrium between monomeric apo forms and ligand bound hexamers. Inter-subunit protein-protein interfaces that stabilize Reptin in its oligomeric state are not well-defined. A self-peptide binding assay identified a protein-peptide interface mapping to an inter-subunit "rim" of the hexamer bridged by Tyrosine-340. A Y340A mutation reduced ADP-dependent oligomer formation using a gel filtration assay, suggesting that Y340 forms a dominant oligomer stabilizing side chain. The monomeric ReptinY340A mutant protein exhibited increased activity to its partner protein AGR2 in an ELISA assay, further suggesting that hexamer formation can preclude certain protein interactions. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) demonstrated that the Y340A mutation attenuated deuterium suppression of Reptin in this motif in the presence of ligand. By contrast, the tyrosine motif of Reptin interacts with a shallower pocket in the hetero-oligomeric structure containing Pontin and HDX-MS revealed no obvious role of the Y340 side chain in stabilizing the Reptin-Pontin oligomer. Molecular dynamic simulations (MDS) rationalized how the Y340A mutation impacts upon a normally stabilizing inter-subunit amino acid contact. MDS also revealed how the D299N mutation can, by contrast, remove oligomer de-stabilizing contacts. These data suggest that the Reptin interactome can be regulated by a ligand dependent equilibrium between monomeric and hexameric forms through a hydrophobic inter-subunit protein-protein interaction motif bridged by Tyrosine-340. SIGNIFICANCE: Discovering dynamic protein-protein interactions is a fundamental aim of research in the life sciences. An emerging view of protein-protein interactions in higher eukaryotes is that they are driven by small linear polypeptide sequences; the linear motif. We report on the use of linear-peptide motif screens to discover a relatively high affinity peptide-protein interaction for the AAA+ and pro-oncogenic protein Reptin. This peptide interaction site was shown to form a 'hot-spot' protein-protein interaction site, and validated to be important for ligand-induced oligomerization of the Reptin protein. These biochemical data provide a foundation to understand how single point mutations in Reptin can impact on its oligomerization and protein-protein interaction landscape.
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Affiliation(s)
- Dominika Coufalova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Lucy Remnant
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland EH4 2XR, United Kingdom
| | - Lenka Hernychova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Petr Muller
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Alan Healy
- St Andrews University, St Andrews, Scotland, United Kingdom
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix 07-01 138671, Singapore
| | | | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix 07-01 138671, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore; Department of Biological Sciences, National University of Singapore, 14, Science Drive 4, 117543, Singapore
| | - Borek Vojtesek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Ted R Hupp
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland EH4 2XR, United Kingdom; University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Douglas R Houston
- University of Edinburgh, Institute of Quantitative Biology, Biochemistry and Biotechnology, Edinburgh, Scotland EH9 3BF, United Kingdom
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39
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Muñoz-Hernández H, Pal M, Rodríguez CF, Fernandez-Leiro R, Prodromou C, Pearl LH, Llorca O. Structural mechanism for regulation of the AAA-ATPases RUVBL1-RUVBL2 in the R2TP co-chaperone revealed by cryo-EM. SCIENCE ADVANCES 2019; 5:eaaw1616. [PMID: 31049401 PMCID: PMC6494491 DOI: 10.1126/sciadv.aaw1616] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 03/16/2019] [Indexed: 05/04/2023]
Abstract
The human R2TP complex (RUVBL1-RUVBL2-RPAP3-PIH1D1) is an HSP90 co-chaperone required for the maturation of several essential multiprotein complexes, including RNA polymerase II, small nucleolar ribonucleoproteins, and PIKK complexes such as mTORC1 and ATR-ATRIP. RUVBL1-RUVBL2 AAA-ATPases are also primary components of other essential complexes such as INO80 and Tip60 remodelers. Despite recent efforts, the molecular mechanisms regulating RUVBL1-RUVBL2 in these complexes remain elusive. Here, we report cryo-EM structures of R2TP and show how access to the nucleotide-binding site of RUVBL2 is coupled to binding of the client recruitment component of R2TP (PIH1D1) to its DII domain. This interaction induces conformational rearrangements that lead to the destabilization of an N-terminal segment of RUVBL2 that acts as a gatekeeper to nucleotide exchange. This mechanism couples protein-induced motions of the DII domains with accessibility of the nucleotide-binding site in RUVBL1-RUVBL2, and it is likely a general mechanism shared with other RUVBL1-RUVBL2-containing complexes.
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Affiliation(s)
- Hugo Muñoz-Hernández
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Mohinder Pal
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Carlos F. Rodríguez
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Rafael Fernandez-Leiro
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Chrisostomos Prodromou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Laurence H. Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid, Spain
- Corresponding author.
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40
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Identification of RUVBL1 and RUVBL2 as Novel Cellular Interactors of the Ebola Virus Nucleoprotein. Viruses 2019; 11:v11040372. [PMID: 31018511 PMCID: PMC6521077 DOI: 10.3390/v11040372] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/15/2019] [Accepted: 04/19/2019] [Indexed: 12/25/2022] Open
Abstract
Ebola virus (EBOV) is a filovirus that has become a global public health threat in recent years. EBOV is the causative agent of a severe, often fatal hemorrhagic fever. A productive viral infection relies on the successful recruitment of host factors for various stages of the viral life cycle. To date, several investigations have discovered specific host-pathogen interactions for various EBOV proteins. However, relatively little is known about the EBOV nucleoprotein (NP) with regard to host interactions. In the present study, we aimed to elucidate NP-host protein-protein interactions (PPIs). Affinity purification-mass spectrometry (AP-MS) was used to identify candidate NP cellular interactors. Candidate interactors RUVBL1 and RUVBL2, partner proteins belonging to the AAA+ (ATPases Associated with various cellular Activities) superfamily, were confirmed to interact with NP in co-immunoprecipitation (co-IP) and immunofluorescence (IF) experiments. Functional studies using a minigenome system revealed that the siRNA-mediated knockdown of RUVBL1 but not RUVBL2 moderately decreased EBOV minigenome activity. Super resolution structured illumination microscopy (SIM) was used to identify an association between NP and components of the R2TP complex, which includes RUVBL1, RUVBL2, RPAP3, and PIH1D1, suggesting a potential role for the R2TP complex in capsid formation. Moreover, the siRNA-mediated knockdown of RPAP3 and subsequent downregulation of PIH1D1 was shown to have no effect on minigenome activity, further suggesting a role in capsid formation. Overall, we identify RUVBL1 and RUVBL2 as novel interactors of EBOV NP and for the first time report EBOV NP recruitment of the R2TP complex, which may provide novel targets for broad-acting anti-EBOV therapeutics.
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Vangala JR, Radhakrishnan SK. Nrf1-mediated transcriptional regulation of the proteasome requires a functional TIP60 complex. J Biol Chem 2018; 294:2036-2045. [PMID: 30559296 DOI: 10.1074/jbc.ra118.006290] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/03/2018] [Indexed: 12/15/2022] Open
Abstract
Inhibition of the proteasome leads to proteotoxic stress, which is characterized by the buildup of ubiquitinated proteins that cannot be degraded properly. The transcription factor Nrf1 (also called NFE2L1) counteracts proteotoxic stress by inducing transcription of proteasome subunit genes, resulting in the restoration of proteasome activity. Further understanding of the Nrf1 pathway is therefore of interest in both neurodegeneration, where proteasome activity could be enhanced, and cancer, where suppression of this pathway could potentiate the cell-killing effect mediated by proteasome inhibitor drugs. Here, to identify novel regulators of Nrf1, we performed an RNAi screen in an engineered cell line, reporting on Nrf1 transcriptional activity. In addition to validating known regulators, we discovered that the AAA+ ATPase RUVBL1 is necessary for Nrf1's transcriptional activity. Given that RUVBL1 is part of different multisubunit complexes that play key roles in transcription, we dissected this phenomenon further and found that the TIP60 chromatin-regulatory complex is essential for Nrf1-dependent transcription of proteasome genes. Consistent with these observations, Nrf1, RUVBL1, and TIP60 proteins were co-recruited to the promoter regions of proteasome genes after proteasome inhibitor treatments. More importantly, depletion of RUVBL1 or TIP60 in various cancer cells sensitized them to cell death induced by proteasome inhibition. Overall, our study provides a framework for manipulating the TIP60-Nrf1 axis to alter proteasome function in various human diseases, including cancer.
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Affiliation(s)
- Janakiram R Vangala
- From the Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Senthil K Radhakrishnan
- From the Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298
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42
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Javary J, Allain-Courtois N, Saucisse N, Costet P, Heraud C, Benhamed F, Pierre R, Bure C, Pallares-Lupon N, Do Cruzeiro M, Postic C, Cota D, Dubus P, Rosenbaum J, Benhamouche-Trouillet S. Liver Reptin/RUVBL2 controls glucose and lipid metabolism with opposite actions on mTORC1 and mTORC2 signalling. Gut 2018; 67:2192-2203. [PMID: 29074727 DOI: 10.1136/gutjnl-2017-314208] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 09/08/2017] [Accepted: 09/26/2017] [Indexed: 01/07/2023]
Abstract
OBJECTIVE The AAA+ ATPase Reptin is overexpressed in hepatocellular carcinoma and preclinical studies indicate that it could be a relevant therapeutic target. However, its physiological and pathophysiological roles in vivo remain unknown. This study aimed to determine the role of Reptin in mammalian adult liver. DESIGN AND RESULTS We generated an inducible liver-specific Reptin knockout (RepinLKO ) mouse model. Following Reptin invalidation, mice displayed decreased body and fat mass, hypoglycaemia and hypolipidaemia. This was associated with decreased hepatic mTOR protein abundance. Further experiments in primary hepatocytes demonstrated that Reptin maintains mTOR protein level through its ATPase activity. Unexpectedly, loss or inhibition of Reptin induced an opposite effect on mTORC1 and mTORC2 signalling, with: (1) strong inhibition of hepatic mTORC1 activity, likely responsible for the reduction of hepatocytes cell size, for decreased de novo lipogenesis and cholesterol transcriptional programmes and (2) enhancement of mTORC2 activity associated with inhibition of the gluconeogenesis transcriptional programme and hepatic glucose production. Consequently, the role of hepatic Reptin in the pathogenesis of insulin resistance (IR) and non-alcoholic fatty liver disease consecutive to a high-fat diet was investigated. We found that Reptin deletion completely rescued pathological phenotypes associated with IR, including glucose intolerance, hyperglycaemia, hyperlipidaemia and hepatic steatosis. CONCLUSION We show here that the AAA +ATPase Reptin is a regulator of mTOR signalling in the liver and global glucido-lipidic homeostasis. Inhibition of hepatic Reptin expression or activity represents a new therapeutic perspective for metabolic syndrome.
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Affiliation(s)
- Joaquim Javary
- INSERM, Bordeaux Research in Translational Oncology, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - Nathalie Allain-Courtois
- INSERM, Bordeaux Research in Translational Oncology, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - Nicolas Saucisse
- Université de Bordeaux, Bordeaux, France.,Physiopathologie de la Plasticité Neuronale, INSERM, Neuro Centre Magendie, Bordeaux, France
| | | | - Capucine Heraud
- INSERM, Bordeaux Research in Translational Oncology, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - Fadila Benhamed
- INSERM, Institut Cochin, Paris, France.,Université Paris Descartes, Paris, France
| | - Rémi Pierre
- Université Paris Descartes, Paris, France.,Plate-forme de Recombinaison Homologue, Institut Cochin, INSERM, Paris, France
| | - Corinne Bure
- Université de Bordeaux, Bordeaux, France.,UMR , Chimie et Biologie des Membranes et des Nano objets, Bordeaux, France
| | - Nestor Pallares-Lupon
- INSERM, Bordeaux Research in Translational Oncology, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - Marcio Do Cruzeiro
- Université Paris Descartes, Paris, France.,Plate-forme de Recombinaison Homologue, Institut Cochin, INSERM, Paris, France
| | - Catherine Postic
- INSERM, Institut Cochin, Paris, France.,Université Paris Descartes, Paris, France
| | - Daniela Cota
- Université de Bordeaux, Bordeaux, France.,Physiopathologie de la Plasticité Neuronale, INSERM, Neuro Centre Magendie, Bordeaux, France
| | - Pierre Dubus
- INSERM, Bordeaux Research in Translational Oncology, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - Jean Rosenbaum
- INSERM, Bordeaux Research in Translational Oncology, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
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43
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Lynham J, Houry WA. The Multiple Functions of the PAQosome: An R2TP- and URI1 Prefoldin-Based Chaperone Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1106:37-72. [DOI: 10.1007/978-3-030-00737-9_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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44
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Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones. Cell Rep 2018; 19:2033-2044. [PMID: 28591576 DOI: 10.1016/j.celrep.2017.05.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 04/05/2017] [Accepted: 05/09/2017] [Indexed: 12/18/2022] Open
Abstract
The hexameric AAA+ ATPases Rvb1 and Rvb2 (Rvbs) are essential for diverse processes ranging from metabolic signaling to chromatin remodeling, but their functions are unknown. While originally thought to act as helicases, recent proposals suggest that Rvbs act as protein assembly chaperones. However, experimental evidence for chaperone-like behavior is lacking. Here, we identify a potent protein activator of the Rvbs, a domain in the Ino80 ATPase subunit of the INO80 chromatin-remodeling complex, termed Ino80INS. Ino80INS stimulates Rvbs' ATPase activity by 16-fold while concomitantly promoting their dodecamerization. Using mass spectrometry, cryo-EM, and integrative modeling, we find that Ino80INS binds asymmetrically along the dodecamerization interface, resulting in a conformationally flexible dodecamer that collapses into hexamers upon ATP addition. Our results demonstrate the chaperone-like potential of Rvb1/Rvb2 and suggest a model where binding of multiple clients such as Ino80 stimulates ATP-driven cycling between hexamers and dodecamers, providing iterative opportunities for correct subunit assembly.
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Affiliation(s)
- Coral Y Zhou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jonathan B Johnston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eugene Palovcak
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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Kumar R, Maurya R, Saran S. Introducing a simple model system for binding studies of known and novel inhibitors of AMPK: a therapeutic target for prostate cancer. J Biomol Struct Dyn 2018; 37:781-795. [PMID: 29447108 DOI: 10.1080/07391102.2018.1441069] [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: 02/07/2023]
Abstract
Prostate cancer (PC) is one of the leading cancers in men, raising a serious health issue worldwide. Due to lack of suitable biomarker, their inhibitors and the platform for testing those inhibitors result in poor prognosis of PC. AMP-activated protein kinase (AMPK) is a highly conserved protein kinase found in eukaryotes that is involved in growth and development, and also acts as a therapeutic target for PC. The aim of the present study is to identify novel potent inhibitors of AMPK and propose a simple cellular model system for understanding its biology. Structural modelling and MD simulations were performed to construct and refine the 3D models of Dictyostelium and human AMPK. Binding mechanisms of different drug compounds were studied by performing molecular docking, molecular dynamics and MM-PBSA methods. Two novel drugs were isolated having higher binding affinity over the known drugs and hydrophobic forces that played a key role during protein-ligand interactions. The study also explored the simple cellular model system for drug screening and understanding the biology of a therapeutic target by performing in vitro experiments.
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Affiliation(s)
- Rakesh Kumar
- a School of Life Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Ranjana Maurya
- a School of Life Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Shweta Saran
- a School of Life Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
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46
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Causier B, Li Z, De Smet R, Lloyd JPB, Van de Peer Y, Davies B. Conservation of Nonsense-Mediated mRNA Decay Complex Components Throughout Eukaryotic Evolution. Sci Rep 2017; 7:16692. [PMID: 29192227 PMCID: PMC5709506 DOI: 10.1038/s41598-017-16942-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/13/2017] [Indexed: 11/15/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is an essential eukaryotic process regulating transcript quality and abundance, and is involved in diverse processes including brain development and plant defenses. Although some of the NMD machinery is conserved between kingdoms, little is known about its evolution. Phosphorylation of the core NMD component UPF1 is critical for NMD and is regulated in mammals by the SURF complex (UPF1, SMG1 kinase, SMG8, SMG9 and eukaryotic release factors). However, since SMG1 is reportedly missing from the genomes of fungi and the plant Arabidopsis thaliana, it remains unclear how UPF1 is activated outside the metazoa. We used comparative genomics to determine the conservation of the NMD pathway across eukaryotic evolution. We show that SURF components are present in all major eukaryotic lineages, including fungi, suggesting that in addition to UPF1 and SMG1, SMG8 and SMG9 also existed in the last eukaryotic common ancestor, 1.8 billion years ago. However, despite the ancient origins of the SURF complex, we also found that SURF factors have been independently lost across the Eukarya, pointing to genetic buffering within the essential NMD pathway. We infer an ancient role for SURF in regulating UPF1, and the intriguing possibility of undiscovered NMD regulatory pathways.
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Affiliation(s)
- Barry Causier
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Gent, Belgium
| | - Riet De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Gent, Belgium
| | - James P B Lloyd
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Gent, Belgium.,Department of Genetics, Genomics Research Institute, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Brendan Davies
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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Quek H, Lim YC, Lavin MF, Roberts TL. PIKKing a way to regulate inflammation. Immunol Cell Biol 2017; 96:8-20. [DOI: 10.1111/imcb.1001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/31/2017] [Accepted: 09/02/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Hazel Quek
- The University of Queensland Centre for Clinical Research; Herston Qld Australia
- QIMR Berghofer Medical Research Institute; Herston Qld Australia
| | - Yi Chieh Lim
- QIMR Berghofer Medical Research Institute; Herston Qld Australia
| | - Martin F Lavin
- The University of Queensland Centre for Clinical Research; Herston Qld Australia
| | - Tara L Roberts
- The University of Queensland Centre for Clinical Research; Herston Qld Australia
- The Ingham Institute for Applied Medical Research and School of Medicine; Western Sydney University; Liverpool New South Wales Australia
- South West Sydney Clinical School; Sydney UNSW Australia
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48
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Li Y, Zhao L, Yuan S, Zhang J, Sun Z. Axonemal dynein assembly requires the R2TP complex component Pontin. Development 2017; 144:4684-4693. [PMID: 29113992 DOI: 10.1242/dev.152314] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 10/30/2017] [Indexed: 01/03/2023]
Abstract
Pontin (Ruvbl1) and Reptin (Ruvbl2) are closely related AAA ATPases. They are components of the Ruvbl1-Ruvbl2-Tah1-Pih1 (R2TP) complexes that function as co-chaperones for the assembly of multiple macromolecular protein complexes. Here, we show that Pontin is essential for cilia motility in both zebrafish and mouse and that Pontin and Reptin function cooperatively in this process. Zebrafish pontin mutants display phenotypes tightly associated with cilia defects, and cilia motility is lost in a number of ciliated tissues along with a reduction in the number of outer and inner dynein arms. Pontin protein is enriched in cytosolic puncta in ciliated cells in zebrafish embryos. In mouse testis, Pontin is essential for the stabilization of axonemal dynein intermediate chain 1 (DNAI1) and DNAI2, the first appreciated step in axonemal dynein arm assembly. Strikingly, multiple dynein arm assembly factors show structural similarities to either Tah1 or Pih1, the other two components of the R2TP complex. Based on these results, we propose that Pontin and Reptin function to facilitate dynein arm assembly in cytosolic foci enriched with R2TP-like complexes.
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Affiliation(s)
- Yuanyuan Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shiaulou Yuan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jiefang Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University of Medicine, Hangzhou 310016, Zhejiang, PR China
| | - Zhaoxia Sun
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
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Baron BW, Baron RM, Baron JM. Reticulocytes Are an Enriched Source of the RUVBL1 Protein. Acta Haematol 2017; 138:162-165. [PMID: 28982102 DOI: 10.1159/000480449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 08/19/2017] [Indexed: 11/19/2022]
Affiliation(s)
- Beverly W Baron
- Department of Pathology, The University of Chicago, Chicago, IL, USA
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Tian S, Yu G, He H, Zhao Y, Liu P, Marshall AG, Demeler B, Stagg SM, Li H. Pih1p-Tah1p Puts a Lid on Hexameric AAA+ ATPases Rvb1/2p. Structure 2017; 25:1519-1529.e4. [PMID: 28919439 PMCID: PMC6625358 DOI: 10.1016/j.str.2017.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/11/2017] [Accepted: 08/07/2017] [Indexed: 11/21/2022]
Abstract
The Saccharomyces cerevisiae (Sc) R2TP complex affords an Hsp90-mediated and nucleotide-driven chaperone activity to proteins of small ribonucleoprotein particles (snoRNPs). The current lack of structural information on the ScR2TP complex, however, prevents a mechanistic understanding of this biological process. We characterized the structure of the ScR2TP complex made up of two AAA+ ATPases, Rvb1/2p, and two Hsp90 binding proteins, Tah1p and Pih1p, and its interaction with the snoRNP protein Nop58p by a combination of analytical ultracentrifugation, isothermal titration calorimetry, chemical crosslinking, hydrogen-deuterium exchange, and cryoelectron microscopy methods. We find that Pih1p-Tah1p interacts with Rvb1/2p cooperatively through the nucleotide-sensitive domain of Rvb1/2p. Nop58p further binds Pih1p-Tahp1 on top of the dome-shaped R2TP. Consequently, nucleotide binding releases Pih1p-Tah1p from Rvb1/2p, which offers a mechanism for nucleotide-driven binding and release of snoRNP intermediates.
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Affiliation(s)
- Shaoxiong Tian
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Ge Yu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Huan He
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Peilu Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Ion Cyclotron Resonance Program, The National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Scott M Stagg
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hong Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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