1
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Gutiérrez-Santiago F, Martínez-Fernández V, Garrido-Godino AI, Colino-Palomino C, Clemente-Blanco A, Conesa C, Acker J, Navarro F. Maf1 phosphorylation is regulated through the action of prefoldin-like Bud27 on PP4 phosphatase in Saccharomyces cerevisiae. Nucleic Acids Res 2024:gkae414. [PMID: 38864693 DOI: 10.1093/nar/gkae414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/12/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024] Open
Abstract
Bud27 is a prefoldin-like protein that participates in transcriptional regulation mediated by the three RNA polymerases in Saccharomyces cerevisiae. Lack of Bud27 significantly affects RNA pol III transcription, although the involved mechanisms have not been characterized. Here, we show that Bud27 regulates the phosphorylation state of the RNA pol III transcriptional repressor, Maf1, influences its nuclear localization, and likely its activity. We demonstrate that Bud27 is associated with the Maf1 main phosphatase PP4 in vivo, and that this interaction is required for proper Maf1 dephosphorylation. Lack of Bud27 decreases the interaction among PP4 and Maf1, Maf1 dephosphorylation, and its nuclear entry. Our data uncover a new nuclear function of Bud27, identify PP4 as a novel Bud27 interactor and demonstrate the effect of this prefoldin-like protein on the posttranslational regulation of Maf1. Finally, our data reveal a broader effect of Bud27 on PP4 activity by influencing, at least, the phosphorylation of Rad53.
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Affiliation(s)
- Francisco Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética; Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071. Jaén, Spain
| | - Verónica Martínez-Fernández
- Departamento de Biología Experimental-Genética; Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071. Jaén, Spain
| | - Ana Isabel Garrido-Godino
- Departamento de Biología Experimental-Genética; Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071. Jaén, Spain
| | - Cristina Colino-Palomino
- Departamento de Biología Experimental-Genética; Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071. Jaén, Spain
| | | | - Christine Conesa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Joël Acker
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética; Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071. Jaén, Spain
- Instituto Universitario de Investigación en Olivar y Aceites de Oliva (INUO). Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071. Jaén, Spain
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2
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Sarkar GC, Rautela U, Goyala A, Datta S, Anand N, Singh A, Singh P, Chamoli M, Mukhopadhyay A. DNA damage signals from somatic uterine tissue arrest oogenesis through activated DAF-16. Development 2023; 150:dev201472. [PMID: 37577954 DOI: 10.1242/dev.201472] [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: 11/24/2022] [Accepted: 07/21/2023] [Indexed: 08/15/2023]
Abstract
Germ line integrity is crucial for progeny fitness. Organisms deploy the DNA damage response (DDR) signaling to protect the germ line from genotoxic stress, facilitating the cell-cycle arrest of germ cells and DNA repair or their apoptosis. Cell-autonomous regulation of germ line quality in response to DNA damage is well studied; however, how quality is enforced cell non-autonomously on sensing somatic DNA damage is less known. Using Caenorhabditis elegans, we show that DDR disruption, only in the uterus, when insulin/IGF-1 signaling (IIS) is low, arrests oogenesis in the pachytene stage of meiosis I, in a FOXO/DAF-16 transcription factor-dependent manner. Without FOXO/DAF-16, germ cells of the IIS mutant escape the arrest to produce poor-quality oocytes, showing that the transcription factor imposes strict quality control during low IIS. Activated FOXO/DAF-16 senses DDR perturbations during low IIS to lower ERK/MPK-1 signaling below a threshold to promote germ line arrest. Altogether, we elucidate a new surveillance role for activated FOXO/DAF-16 that ensures optimal germ cell quality and progeny fitness in response to somatic DNA damage.
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Affiliation(s)
- Gautam Chandra Sarkar
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Umanshi Rautela
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anita Goyala
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sudeshna Datta
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nikhita Anand
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anupama Singh
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Prachi Singh
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manish Chamoli
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Arnab Mukhopadhyay
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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3
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Hua X, Feng X, Liang G, Chao J, Wang D. Long-term exposure to 6-PPD quinone reduces reproductive capacity by enhancing germline apoptosis associated with activation of both DNA damage and cell corpse engulfment in Caenorhabditis elegans. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131495. [PMID: 37119572 DOI: 10.1016/j.jhazmat.2023.131495] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/13/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023]
Abstract
Recently, 6-PPD quinone (6-PPDQ), a derivative of tire antioxidant 6-PPD, was reported to have acute toxicity for organisms. However, the possible reproductive toxicity of 6-PPDQ is still largely unclear. In this study, the reproductive toxicity of 6-PPDQ after long-term exposure was further investigated in Caenorhabditis elegans. Exposure to 1 and 10 μg/L 6-PPDQ reduced the reproductive capacity. Meanwhile, exposure to 1 and 10 μg/L 6-PPDQ enhanced the germline apoptosis, which was accompanied by upregulation of ced-3, ced-4, and egl-1 expressions and downregulation of ced-9 expression. The observed increase in germline apoptosis in 1 and 10 μg/L 6-PPDQ exposed nematodes was associated with the enhancement in DNA damage and increase in expressions of related genes of cep-1, clk-2, hus-1, and mrt-2. The detected enhancement in germline apoptosis in 1 and 10 μg/L 6-PPDQ exposed nematodes was further associated with the increase in expressions of ced-1 and ced-6 governing the cell corpse engulfment process. Molecular docking analysis indicated the binding potentials of 6-PPDQ with three DNA damage checkpoints (CLK-2, HUS-1, and MRT-2) and corpse-recognizing phagocytic receptor CED-1. Therefore, our data suggested the toxicity on reproductive capacity by 6-PPDQ at environmentally relevant concentrations by enhancing DNA damage- and cell corpse engulfment-induced germline apoptosis in organisms.
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Affiliation(s)
- Xin Hua
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
| | - Xiao Feng
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
| | - Geyu Liang
- School of Public Health, Southeast University, Nanjing 210009, China
| | - Jie Chao
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
| | - Dayong Wang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Medical School, Southeast University, Nanjing 210009, China.
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4
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Hanna R, Rozenberg A, Saied L, Ben-Yosef D, Lavy T, Kleifeld O. In-Depth Characterization of Apoptosis N-terminome Reveals a Link Between Caspase-3 Cleavage and Post-Translational N-terminal Acetylation. Mol Cell Proteomics 2023:100584. [PMID: 37236440 PMCID: PMC10362333 DOI: 10.1016/j.mcpro.2023.100584] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 05/28/2023] Open
Abstract
The N-termini of proteins contain information about their biochemical properties and functions. These N-termini can be processed by proteases, and can undergo other co- or post-translational modifications. We have developed LATE (LysN Amino Terminal Enrichment), a method that uses selective chemical derivatization of α-amines to isolate the N-terminal peptides, in order to improve N-terminome identification in conjunction with other enrichment strategies. We applied LATE alongside another N-terminomic method to study caspase-3 mediated proteolysis both in vitro and during apoptosis in cells. This has enabled us to identify many unreported caspase-3 cleavages, some of which cannot be identified by other methods. Moreover, we have found direct evidence that neo-N-termini generated by caspase-3 cleavage can be further modified by Nt-acetylation. Some of these neo-Nt-acetylation events occur in the early phase of the apoptotic process and may have a role in translation inhibition. This has provided a comprehensive overview of the caspase-3 degradome and has uncovered previously unrecognized crosstalk between post-translational Nt-acetylation and caspase proteolytic pathways.
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Affiliation(s)
- Rawad Hanna
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Layla Saied
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Daniel Ben-Yosef
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Tali Lavy
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Oded Kleifeld
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel.
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5
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Yang Y, Liu F, Liu L, Zhu M, Yuan J, Mai YX, Zou JJ, Le J, Wang Y, Palme K, Li X, Wang Y, Wang L. The unconventional prefoldin RPB5 interactor mediates the gravitropic response by modulating cytoskeleton organization and auxin transport in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1916-1934. [PMID: 35943836 DOI: 10.1111/jipb.13341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Gravity-induced root curvature involves the asymmetric distribution of the phytohormone auxin. This response depends on the concerted activities of the auxin transporters such as PIN-FORMED (PIN) proteins for auxin efflux and AUXIN RESISTANT 1 (AUX1) for auxin influx. However, how the auxin gradient is established remains elusive. Here we identified a new mutant with a short root, strong auxin distribution in the lateral root cap and an impaired gravitropic response. The causal gene encoded an Arabidopsis homolog of the human unconventional prefoldin RPB5 interactor (URI). AtURI interacted with prefoldin 2 (PFD2) and PFD6, two β-type PFD members that modulate actin and tubulin patterning in roots. The auxin reporter DR5rev :GFP showed that asymmetric auxin redistribution after gravistimulation is disordered in aturi-1 root tips. Treatment with the endomembrane protein trafficking inhibitor brefeldin A indicated that recycling of the auxin transporter PIN2 is disrupted in aturi-1 roots as well as in pfd mutants. We propose that AtURI cooperates with PFDs to recycle PIN2 and modulate auxin distribution.
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Affiliation(s)
- Yi Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, China
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Fang Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Faculty of Biology, Institute of Biology II/Molecular Plant Physiology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, Freiburg, D-79104, Germany
| | - Le Liu
- Faculty of Biology, Institute of Biology II/Molecular Plant Physiology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, Freiburg, D-79104, Germany
| | - Mingyue Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Jinfeng Yuan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Yan-Xia Mai
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China
| | - Jun-Jie Zou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Le
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yonghong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Klaus Palme
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Faculty of Biology, Institute of Biology II/Molecular Plant Physiology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, Freiburg, D-79104, Germany
| | - Xugang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Long Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China
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6
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Kropp P, Rhodehouse K, Golden A. TUNEL Labeling to Detect Double-stranded DNA Breaks in Caenorhabditis elegans Gonads. Bio Protoc 2022; 12:e4351. [DOI: 10.21769/bioprotoc.4351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 11/15/2021] [Accepted: 01/20/2022] [Indexed: 11/02/2022] Open
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7
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Herranz-Montoya I, Park S, Djouder N. A comprehensive analysis of prefoldins and their implication in cancer. iScience 2021; 24:103273. [PMID: 34761191 PMCID: PMC8567396 DOI: 10.1016/j.isci.2021.103273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Prefoldins (PFDNs) are evolutionary conserved co-chaperones, initially discovered in archaea but universally present in eukaryotes. PFDNs are prevalently organized into hetero-hexameric complexes. Although they have been overlooked since their discovery and their functions remain elusive, several reports indicate they act as co-chaperones escorting misfolded or non-native proteins to group II chaperonins. Unlike the eukaryotic PFDNs which interact with cytoskeletal components, the archaeal PFDNs can bind and stabilize a wide range of substrates, possibly due to their great structural diversity. The discovery of the unconventional RPB5 interactor (URI) PFDN-like complex (UPC) suggests that PFDNs have versatile functions and are required for different cellular processes, including an important role in cancer. Here, we summarize their functions across different species. Moreover, a comprehensive analysis of PFDNs genomic alterations across cancer types by using large-scale cancer genomic data indicates that PFDNs are a new class of non-mutated proteins significantly overexpressed in some cancer types.
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Affiliation(s)
- Irene Herranz-Montoya
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Solip Park
- Computational Cancer Genomics Group, Structural Biology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Nabil Djouder
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
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8
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Allele-specific mitochondrial stress induced by Multiple Mitochondrial Dysfunctions Syndrome 1 pathogenic mutations modeled in Caenorhabditis elegans. PLoS Genet 2021; 17:e1009771. [PMID: 34449775 PMCID: PMC8428684 DOI: 10.1371/journal.pgen.1009771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 09/09/2021] [Accepted: 08/10/2021] [Indexed: 01/18/2023] Open
Abstract
Multiple Mitochondrial Dysfunctions Syndrome 1 (MMDS1) is a rare, autosomal recessive disorder caused by mutations in the NFU1 gene. NFU1 is responsible for delivery of iron-sulfur clusters (ISCs) to recipient proteins which require these metallic cofactors for their function. Pathogenic variants of NFU1 lead to dysfunction of its target proteins within mitochondria. To date, 20 NFU1 variants have been reported and the unique contributions of each variant to MMDS1 pathogenesis is unknown. Given that over half of MMDS1 individuals are compound heterozygous for different NFU1 variants, it is valuable to investigate individual variants in an isogenic background. In order to understand the shared and unique phenotypes of NFU1 variants, we used CRISPR/Cas9 gene editing to recreate exact patient variants of NFU1 in the orthologous gene, nfu-1 (formerly lpd-8), in C. elegans. Five mutant C. elegans alleles focused on the presumptive iron-sulfur cluster interaction domain were generated and analyzed for mitochondrial phenotypes including respiratory dysfunction and oxidative stress. Phenotypes were variable between the mutant nfu-1 alleles and generally presented as an allelic series indicating that not all variants have lost complete function. Furthermore, reactive iron within mitochondria was evident in some, but not all, nfu-1 mutants indicating that iron dyshomeostasis may contribute to disease pathogenesis in some MMDS1 individuals. Functional mitochondria are essential to life in eukaryotes, but they can be perterbured by inherent dysfunction of important proteins or stressors. Mitochondrial dysfunction is the root cause of dozens of diseases many of which involve complex phenotypes. One such disease is Multiple Mitochondrial Dysfunctions Syndrome 1, a pediatric-fatal disease that is poorly understood in part due to the lack of clarity about how mutations in the causative gene, NFU1, affect protein function and phenotype development and severity. Here we employ the power of CRISPR/Cas9 gene editing in the small nematode Caenorhabditis elegans to recreate five patient-specific mutations known to cause Multiple Mitochondrial Dysfunctions Syndrome 1. We are able to analyze each of these mutations individually, evaluate how mitochondrial dysfunction differs between them, and whether or not the phenotypes can be improved. We find that there are meaningful differences between each mutation which not only effects the types of stress that develop, but also the ability to rescue deleterious phenotypes. This work thus provides insight into disease pathogenesis and establishes a foundation for potential future therapeutic intervention.
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9
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Martónez-Ferníndez V, Navarro F. Rpb5, a subunit shared by eukaryotic RNA polymerases, cooperates with prefoldin-like Bud27/URI. AIMS GENETICS 2021. [DOI: 10.3934/genet.2018.1.63] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AbstractRpb5 is one of the five common subunits to all eukaryotic RNA polymerases, which is conserved in archaea, but not in bacteria. Among these common subunits, it is the only one that is not interchangeable between yeasts and humans, and accounts for the functional incompatibility of yeast and human subunits. Rpb5 has been proposed to contribute to the gene-specific activation of RNA pol II, notably during the infectious cycle of the hepatitis B virus, and also to participate in general transcription mediated by all eukaryotic RNA pol. The structural analysis of Rpb5 and its interaction with different transcription factors, regulators and DNA, accounts for Rpb5 being necessary to maintain the correct conformation of the shelf module of RNA pol II, which favors the proper organization of the transcription bubble and the clamp closure of the enzyme.In this work we provide details about subunit Rpb5's structure, conservation and the role it plays in transcription regulation by analyzing the different interactions with several factors, as well as its participation in the assembly of the three RNA pols, in cooperation with prefoldin-like Bud27/URI.
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Affiliation(s)
- Veránica Martónez-Ferníndez
- Department of Experimental Biology, Faculty of Experimental Sciences, University of JaÉn, Paraje de las Lagunillas, s/n, 23071, JaÉn, Spain
| | - Francisco Navarro
- Department of Experimental Biology, Faculty of Experimental Sciences, University of JaÉn, Paraje de las Lagunillas, s/n, 23071, JaÉn, Spain
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10
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Garcia-Muse T, Galindo-Diaz U, Garcia-Rubio M, Martin JS, Polanowska J, O'Reilly N, Aguilera A, Boulton SJ. A Meiotic Checkpoint Alters Repair Partner Bias to Permit Inter-sister Repair of Persistent DSBs. Cell Rep 2020; 26:775-787.e5. [PMID: 30650366 PMCID: PMC6334227 DOI: 10.1016/j.celrep.2018.12.074] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/28/2018] [Accepted: 12/17/2018] [Indexed: 11/30/2022] Open
Abstract
Accurate meiotic chromosome segregation critically depends on the formation of inter-homolog crossovers initiated by double-strand breaks (DSBs). Inaccuracies in this process can drive aneuploidy and developmental defects, but how meiotic cells are protected from unscheduled DNA breaks remains unexplored. Here we define a checkpoint response to persistent meiotic DSBs in C. elegans that phosphorylates the synaptonemal complex (SC) to switch repair partner from the homolog to the sister chromatid. A key target of this response is the core SC component SYP-1, which is phosphorylated in response to ionizing radiation (IR) or unrepaired meiotic DSBs. Failure to phosphorylate (syp-16A) or dephosphorylate (syp-16D) SYP-1 in response to DNA damage results in chromosome non-dysjunction, hyper-sensitivity to IR-induced DSBs, and synthetic lethality with loss of brc-1BRCA1. Since BRC-1 is required for inter-sister repair, these observations reveal that checkpoint-dependent SYP-1 phosphorylation safeguards the germline against persistent meiotic DSBs by channelling repair to the sister chromatid. Meiotic DNA damage triggers phosphorylation of the synaptonemal complex (SC) ATM-ATR kinases phosphorylate the SC in response to excessive meiotic DSBs SC phosphorylation channels DNA repair to the sister chromatid
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Affiliation(s)
- Tatiana Garcia-Muse
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain; Clare Hall Laboratories, Blanche Lane, South Mimms EN6 3LD, UK.
| | - U Galindo-Diaz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain
| | - M Garcia-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain
| | - J S Martin
- Clare Hall Laboratories, Blanche Lane, South Mimms EN6 3LD, UK
| | - J Polanowska
- Clare Hall Laboratories, Blanche Lane, South Mimms EN6 3LD, UK
| | - N O'Reilly
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - A Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain.
| | - Simon J Boulton
- Clare Hall Laboratories, Blanche Lane, South Mimms EN6 3LD, UK; DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK.
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11
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Chaves-Pérez A, Yilmaz M, Perna C, de la Rosa S, Djouder N. URI is required to maintain intestinal architecture during ionizing radiation. Science 2019; 364:364/6443/eaaq1165. [PMID: 31147493 DOI: 10.1126/science.aaq1165] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 08/13/2018] [Accepted: 04/10/2019] [Indexed: 12/16/2022]
Abstract
Ionizing radiation (IR) can cause gastrointestinal syndrome (GIS), a lethal disorder, by means of unknown mechanisms. We show that high-dose irradiation increases unconventional prefoldin RPB5 interactor (URI) levels in mouse intestinal crypt, but organ regeneration correlates with URI reductions. URI overexpression in intestine protects mice from radiation-induced GIS, whereas halving URI expression sensitizes mice to IR. URI specifically inhibits β-catenin in stem cell-like label-retaining (LR) cells, which are essential for organ regeneration after IR. URI reduction activates β-catenin-induced c-MYC expression, causing proliferation of and DNA damage to LR cells, rendering them radiosensitive. Therefore, URI labels LR cells which promote tissue regeneration in response to high-dose irradiation, and c-MYC inhibitors could be countermeasures for humans at risk of developing GIS.
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Affiliation(s)
- Almudena Chaves-Pérez
- Cancer Cell Biology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Mahmut Yilmaz
- Cancer Cell Biology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Cristian Perna
- Department of Pathology, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid 28034, Spain
| | - Sergio de la Rosa
- Cancer Cell Biology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Nabil Djouder
- Cancer Cell Biology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas, CNIO, Madrid 28029, Spain.
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12
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Lee BR, Rengaraj D, Choi HJ, Han JY. A novel F-box domain containing cyclin F like gene is required for maintaining the genome stability and survival of chicken primordial germ cells. FASEB J 2019; 34:1001-1017. [PMID: 31914591 DOI: 10.1096/fj.201901294r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/25/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022]
Abstract
The stability and survival of germ cells are controlled by the germline-specific genes, however, such genes are less known in the avian species. Using a microarray-based the National Center for Biotechnology Information Gene Expression Omnibus dataset, we found an unigene (Gga.9721) that upregulated in the chicken primordial germ cells (PGCs). The unigene showed 97% identities with an uncharacterized chicken cyclin F like gene. The predicted chicken cyclin F like gene was further characterized through expression and regulation in the chicken PGCs. The sequence analysis revealed that the gene shows identities with cyclin F gene and contains an F-box domain. The expression of chicken cyclin F like was detected specifically in the gonads, PGCs, and germline cells. The knockdown of cyclin F like gene resulted in DNA damage and apoptosis in the PGCs. The genes related to stemness and germness were downregulated, whereas, genes related to apoptosis and DNA damage response were increased in the PGCs after the knockdown of chicken cyclin F like. We further observed that the Nanog homeobox controlled the transcriptional activity of chicken cyclin F like gene in PGCs. Collectively, the chicken cyclin F like gene, which is not reported in any other species, is required for maintaining the genome stability of germ cells.
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Affiliation(s)
- Bo Ram Lee
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.,Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Korea
| | - Deivendran Rengaraj
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Hee Jung Choi
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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13
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Chen S, Feng Y, Zhang B, Chen X, Wei W, Ma H. RMP promotes the proliferation and radioresistance of esophageal carcinoma. J Cancer 2019; 10:3698-3705. [PMID: 31333787 PMCID: PMC6636304 DOI: 10.7150/jca.32680] [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: 12/30/2018] [Accepted: 05/16/2019] [Indexed: 11/11/2022] Open
Abstract
RMP is a RNA polymerase II Subunit RPB-5 associated protein shown to act as an oncogene in several cancer. However, the mechanism of the involvement of RMP in esophageal cancer (EC) remains unclear. We analyzed RMP expression in EC cell lines and EC tissues. The connection between RMP and clinical pathological features of EC was also elucidated. To investigate the role of RMP in EC, We performed CCK-8 assay to evaluate cell proliferation, and Annexin V/PI double-staining to evaluate cell apoptosis. Effect of RMP on tumor progression in nude mouse models was assessed by measurement of volume and weight of tumors. Expression of RMP, CEA and CA199 in vivo were measured by Inmunohistochemical staining. First of all, our study showed that RMP was highly expressed in EC cell lines (compared with normal cells) and tumor tissues (compare with corresponding normal tissues). Then, we found that RMP was bound up with the status of nodal and T stage which indicating that RMP may be related to the growth and malignant degree of EC. Moreover upregulation of RMP could contribute to tumor growth in vitro and vivo. In addition, the results also showed that overexpression of RMP could significantly reduce the susceptibility to radiotherapy. Taken together, all these further suggested that RMP would play a chance-promoting in EC which may provide us a powerful goal for gene targeting treatment of esophageal cancer.
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Affiliation(s)
- Shaomu Chen
- Department of Cell Biology, School of Medicine, Soochow University, Suzhou, Jiangsu, China.,Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yu Feng
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Biao Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiaochun Chen
- Department of Cardiothoracic surgery, Suzhou Science & Technology Town Hospital, Suzhou, Jiangsu, China
| | - Wenxiang Wei
- Department of Cell Biology, School of Medicine, Soochow University, Suzhou, Jiangsu, China
| | - Haitao Ma
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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14
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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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15
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Son HG, Seo K, Seo M, Park S, Ham S, An SWA, Choi ES, Lee Y, Baek H, Kim E, Ryu Y, Ha CM, Hsu AL, Roh TY, Jang SK, Lee SJV. Prefoldin 6 mediates longevity response from heat shock factor 1 to FOXO in C. elegans. Genes Dev 2018; 32:1562-1575. [PMID: 30478249 PMCID: PMC6295163 DOI: 10.1101/gad.317362.118] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/02/2018] [Indexed: 12/31/2022]
Abstract
Heat shock factor 1 (HSF-1) and forkhead box O (FOXO) are key transcription factors that protect cells from various stresses. In Caenorhabditis elegans, HSF-1 and FOXO together promote a long life span when insulin/IGF-1 signaling (IIS) is reduced. However, it remains poorly understood how HSF-1 and FOXO cooperate to confer IIS-mediated longevity. Here, we show that prefoldin 6 (PFD-6), a component of the molecular chaperone prefoldin-like complex, relays longevity response from HSF-1 to FOXO under reduced IIS. We found that PFD-6 was specifically required for reduced IIS-mediated longevity by acting in the intestine and hypodermis. We showed that HSF-1 increased the levels of PFD-6 proteins, which in turn directly bound FOXO and enhanced its transcriptional activity. Our work suggests that the prefoldin-like chaperone complex mediates longevity response from HSF-1 to FOXO to increase the life span in animals with reduced IIS.
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Affiliation(s)
- Heehwa G Son
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Keunhee Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Mihwa Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea.,Center for plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, South Korea.,Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, South Korea
| | - Sangsoon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Seokjin Ham
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Seon Woo A An
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Eun-Seok Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Yujin Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Haeshim Baek
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Eunju Kim
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Youngjae Ryu
- Research Division, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Chang Man Ha
- Research Division, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Ao-Lin Hsu
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA.,Research Center for Healthy Aging, China Medical University, Taichung 404, Taiwan.,Institute of New Drug Development, China Medical University, Taichung 404, Taiwan
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Sung Key Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Seung-Jae V Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
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16
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Schafler ED, Thomas PA, Ha S, Wang Y, Bermudez-Hernandez K, Tang Z, Fenyö D, Vigodner M, Logan SK. UXT is required for spermatogenesis in mice. PLoS One 2018; 13:e0195747. [PMID: 29649254 PMCID: PMC5896988 DOI: 10.1371/journal.pone.0195747] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 03/28/2018] [Indexed: 12/25/2022] Open
Abstract
Male mammals must simultaneously produce prodigious numbers of sperm and maintain an adequate reserve of stem cells to ensure continuous production of gametes throughout life. Failures in the mechanisms responsible for balancing germ cell differentiation and spermatogonial stem cell (SSC) self-renewal can result in infertility. We discovered a novel requirement for Ubiquitous Expressed Transcript (UXT) in spermatogenesis by developing the first knockout mouse model for this gene. Constitutive deletion of Uxt is embryonic lethal, while conditional knockout in the male germline results in a Sertoli cell-only phenotype during the first wave of spermatogenesis that does not recover in the adult. This phenotype begins to manifest between 6 and 7 days post-partum, just before meiotic entry. Gene expression analysis revealed that Uxt deletion downregulates the transcription of genes governing SSC self-renewal, differentiation, and meiosis, consistent with its previously defined role as a transcriptional co-factor. Our study has revealed the first in vivo function for UXT in the mammalian germline as a regulator of distinct transcriptional programs in SSCs and differentiating spermatogonia.
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Affiliation(s)
- Eric D. Schafler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States of America
- Pathobiology and Translational Medicine Training Program, New York University School of Medicine, New York, NY, United States of America
| | - Phillip A. Thomas
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States of America
| | - Susan Ha
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States of America
- Department of Urology, New York University School of Medicine, New York, NY, United States of America
| | - Yu Wang
- Department of Urology, New York University School of Medicine, New York, NY, United States of America
- Department of Microbiology, New York University School of Medicine, New York, NY, United States of America
| | - Keria Bermudez-Hernandez
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States of America
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, United States of America
| | - Zuojian Tang
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States of America
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, United States of America
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States of America
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States of America
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, United States of America
| | - Margarita Vigodner
- Department of Biology, Stern College, Yeshiva University, New York, NY, United States of America
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Susan K. Logan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States of America
- Department of Urology, New York University School of Medicine, New York, NY, United States of America
- * E-mail:
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17
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Martínez-Fernández V, Navarro F. Rpb5, a subunit shared by eukaryotic RNA polymerases, cooperates with prefoldin-like Bud27/URI. AIMS GENETICS 2018; 5:63-74. [PMID: 31435513 PMCID: PMC6690254 DOI: 10.3934/genet.2018.1.74] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/05/2018] [Indexed: 12/28/2022]
Abstract
Rpb5 is one of the five common subunits to all eukaryotic RNA polymerases, which is conserved in archaea, but not in bacteria. Among these common subunits, it is the only one that is not interchangeable between yeasts and humans, and accounts for the functional incompatibility of yeast and human subunits. Rpb5 has been proposed to contribute to the gene-specific activation of RNA pol II, notably during the infectious cycle of the hepatitis B virus, and also to participate in general transcription mediated by all eukaryotic RNA pol. The structural analysis of Rpb5 and its interaction with different transcription factors, regulators and DNA, accounts for Rpb5 being necessary to maintain the correct conformation of the shelf module of RNA pol II, which favors the proper organization of the transcription bubble and the clamp closure of the enzyme. In this work we provide details about subunit Rpb5's structure, conservation and the role it plays in transcription regulation by analyzing the different interactions with several factors, as well as its participation in the assembly of the three RNA pols, in cooperation with prefoldin-like Bud27/URI.
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Affiliation(s)
- Verónica Martínez-Fernández
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Paraje de las Lagunillas, s/n, 23071, Jaén, Spain
| | - Francisco Navarro
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Paraje de las Lagunillas, s/n, 23071, Jaén, Spain
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18
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Thomas PA, Mita P, Ha S, Logan SK. Role of the Unconventional Prefoldin Proteins URI and UXT in Transcription Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1106:85-94. [PMID: 30484154 DOI: 10.1007/978-3-030-00737-9_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Unconventional prefoldin RPB5 interacting protein (URI), also known as RPB5-Mediating Protein (RMP) has been shown to play several regulatory roles in different cellular compartments including the mitochondria, as a phosphatase binding protein; in the cytoplasm, as a chaperone-like protein; and in the nucleus, as a transcriptional regulator through binding to RPB5 and RNA polymerase II (polII). This chapter focuses on the role URI plays in transcriptional regulation in the prostate cell. In prostate cells, URI is tightly bound to another prefoldin-like protein called UXT, a known androgen receptor (AR) cofactor. Part of a multiprotein complex, URI and UXT act as transcriptional repressors, and URI regulates KAP1 through PP2A phosphatase activity. The discovery of the interaction of URI and UXT with KAP1, AR, and PP2A, as well as the numerous interactions between URI and components of the R2TP/prefoldin-like complex, RPB5, and nuclear proteins involved in DNA damage response, chromatin remodeling and gene transcription, reveal a pleiotropic effect of the URI/UXT complex on nuclear processes. The mechanisms by which URI/UXT affect transcription, chromatin structure and regulation, and genome stability, remain to be elucidated but will be of fundamental importance considering the many processes affected by alterations of URI/UXT and other prefoldins and prefoldin-like proteins.
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Affiliation(s)
- Phillip A Thomas
- Departments of Urology, and Biochemistry and Molecular Biology, New York University School of Medicine, New York, NY, USA
| | - Paolo Mita
- Institute for Systems Genetics, New York University School of Medicine, New York, NY, USA
| | - Susan Ha
- Departments of Urology, and Biochemistry and Molecular Biology, New York University School of Medicine, New York, NY, USA
| | - Susan K Logan
- Departments of Urology, and Biochemistry and Molecular Biology, New York University School of Medicine, New York, NY, USA.
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19
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Roles and Functions of the Unconventional Prefoldin URI. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1106:95-108. [PMID: 30484155 DOI: 10.1007/978-3-030-00737-9_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Almost 15 years ago, the URI prefoldin-like complex was discovered by Krek and colleagues in immunoprecipitation experiments conducted in mammalian cells with the aim of identifying new binding partners of the E3 ubiquitin-protein ligase S-phase kinase-associated protein 2 (SKP2) (Gstaiger et al. Science 302(5648):1208-1212, 2003). The URI prefoldin-like complex is a heterohexameric chaperone complex comprising two α and four β subunits (α2β4). The α subunits are URI and STAP1, while the β subunits are PFDN2, PFDN6, and PFDN4r, one of which is probably present in duplicate. Elucidating the roles and functions of these components in vitro and in vivo will help to clarify the mechanistic behavior of what appears to be a remarkably important cellular machine.
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20
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Zhang H, Ye J, Shi Z, Bu C, Bao F. Quantitative analyses of the global proteome and phosphoproteome reveal the different impacts of propofol and dexmedetomidine on HT22 cells. Sci Rep 2017; 7:46455. [PMID: 28418008 PMCID: PMC5394455 DOI: 10.1038/srep46455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 03/17/2017] [Indexed: 02/07/2023] Open
Abstract
Propofol and dexmedetomidine are both commonly used anaesthetics. Although they employ two different mechanisms to induce anaesthesia, both compounds influence the hippocampus and the HT22 cell line. HT22 cells are broadly used in neurobiological research. In this study, we assessed the effects of propofol and dexmedetomidine on signalling in HT22 cells. Using the SILAC (stable isotope labelling with amino acids in cell culture) labelling technique, IMAC (immobilized metal affinity chromatography) enrichment and high-resolution LC-MS/MS (liquid chromatography tandem mass spectrometry) analysis, we investigated the quantitative proteome and phosphoproteome in HT22 cells treated with propofol or dexmedetomidine. In total, 4,527 proteins and 6,824 phosphosites were quantified in cells treated with these two anaesthetics. With the assistance of intensive bioinformatics, the propofol and dexmedetomidine treatments were shown to induce distinct proteome and phosphoproteome profiles in HT22 cells. Consistent with our bioinformatics analysis, dexmedetomidine had a smaller effect than propofol on cell survival. These findings deepen our understanding of drug-induced anaesthesia.
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Affiliation(s)
- Honggang Zhang
- Department of Anesthesiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Juan Ye
- Department of Pediatrics, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Zhaomei Shi
- Jingjie PTM Biolab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Chen Bu
- Jingjie PTM Biolab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Fangping Bao
- Department of Anesthesiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
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21
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Mita P, Savas JN, Briggs EM, Ha S, Gnanakkan V, Yates JR, Robins DM, David G, Boeke JD, Garabedian MJ, Logan SK. URI Regulates KAP1 Phosphorylation and Transcriptional Repression via PP2A Phosphatase in Prostate Cancer Cells. J Biol Chem 2016; 291:25516-25528. [PMID: 27780869 PMCID: PMC5207251 DOI: 10.1074/jbc.m116.741660] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/21/2016] [Indexed: 11/06/2022] Open
Abstract
URI (unconventional prefoldin RPB5 interactor protein) is an unconventional prefoldin, RNA polymerase II interactor that functions as a transcriptional repressor and is part of a larger nuclear protein complex. The components of this complex and the mechanism of transcriptional repression have not been characterized. Here we show that KAP1 (KRAB-associated protein 1) and the protein phosphatase PP2A interact with URI. Mechanistically, we show that KAP1 phosphorylation is decreased following recruitment of PP2A by URI. We functionally characterize the novel URI-KAP1-PP2A complex, demonstrating a role of URI in retrotransposon repression, a key function previously demonstrated for the KAP1-SETDB1 complex. Microarray analysis of annotated transposons revealed a selective increase in the transcription of LINE-1 and L1PA2 retroelements upon knockdown of URI. These data unveil a new nuclear function of URI and identify a novel post-transcriptional regulation of KAP1 protein that may have important implications in reactivation of transposable elements in prostate cancer cells.
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Affiliation(s)
- Paolo Mita
- From the Institute of Systems Genetics and
- the Departments of Biochemistry and Molecular Pharmacology
| | - Jeffrey N Savas
- the Department of Chemical Physiology, Scripps Research Institute, La Jolla, California 92037
| | - Erica M Briggs
- the Departments of Biochemistry and Molecular Pharmacology
| | - Susan Ha
- Urology, and
- the Departments of Biochemistry and Molecular Pharmacology
| | - Veena Gnanakkan
- the Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and
| | - John R Yates
- the Department of Chemical Physiology, Scripps Research Institute, La Jolla, California 92037
| | - Diane M Robins
- the Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Gregory David
- the Departments of Biochemistry and Molecular Pharmacology
| | - Jef D Boeke
- From the Institute of Systems Genetics and
- the Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and
- the Departments of Biochemistry and Molecular Pharmacology
| | - Michael J Garabedian
- Urology, and
- Microbiology at New York University School of Medicine, New York, New York 10016
| | - Susan K Logan
- Urology, and
- the Departments of Biochemistry and Molecular Pharmacology
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22
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Wang Y, Xu MY, Liu JP, Wang MG, Yin HQ, Tu JM. Molecular identification and interaction assay of the gene (OsUbc13) encoding a ubiquitin-conjugating enzyme in rice. J Zhejiang Univ Sci B 2015; 15:624-37. [PMID: 25001222 DOI: 10.1631/jzus.b1300273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The ubiquitin (Ub)-conjugating enzyme, Ubc13, has been known to be involved in error-free DNA damage tolerance (or post-replication repair) via catalyzing Lys63-linked polyubiquitin chains formation together with a Ubc variant. However, its functions remain largely unknown in plant species, especially in monocotyledons. In this study, we cloned a Ub-conjugating enzyme, OsUbc13, that shares the conserved domain of Ubc with AtUBC13B in Oryza sativa L., which encodes a protein of 153 amino acids; the deduced sequence shares high similarities with other homologs. Real-time quantitative polymerase chain reaction (PCR) indicated that OsUbc13 transcripts could be detected in all tissues examined, and the expression level was higher in palea, pistil, stamen, and leaf, and lower in root, stem, and lemma; the expression of OsUbc13 was induced by low temperature, methylmethane sulfate (MMS), and H(2)O(2), but repressed by mannitol, abscisic acid (ABA), and NaCl. OsUbc13 was probably localized in the plasma and nuclear membranes. About 20 proteins, which are responsible for the positive yeast two-hybrid interaction of OsUbc13, were identified. These include the confirmed OsVDAC (correlated with apoptosis), OsMADS1 (important for development of floral organs), OsB22EL8 (related to reactive oxygen species (ROS) scavenging and DNA protection), and OsCROC-1 (required for formation of Lys63 polyubiquitylation and error-free DNA damage tolerance). The molecular characterization provides a foundation for the functional study of OsUbc13.
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Affiliation(s)
- Ya Wang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
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23
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Abstract
Prefoldin is a cochaperone, present in all eukaryotes, that cooperates with the chaperonin CCT. It is known mainly for its functional relevance in the cytoplasmic folding of actin and tubulin monomers during cytoskeleton assembly. However, both canonical and prefoldin-like subunits of this heterohexameric complex have also been found in the nucleus, and are functionally connected with nuclear processes in yeast and metazoa. Plant prefoldin has also been detected in the nucleus and physically associated with a gene regulator. In this review, we summarize the information available on the involvement of prefoldin in nuclear phenomena, place special emphasis on gene transcription, and discuss the possibility of a global coordination between gene regulation and cytoplasmic dynamics mediated by prefoldin.
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Affiliation(s)
- Gonzalo Millán-Zambrano
- Instituto de Biomedicina de Sevilla, Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
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24
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Wang Q, Xu Y, Zhou W, Zhong L, Wen Z, Yu H, Chen S, Shen J, Chen H, She Q, Jiang J, Miao J, Wei W. The viral oncoprotein HBx of Hepatitis B virus promotes the growth of hepatocellular carcinoma through cooperating with the cellular oncoprotein RMP. Int J Biol Sci 2014; 10:1181-92. [PMID: 25516716 PMCID: PMC4261202 DOI: 10.7150/ijbs.10275] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 10/14/2014] [Indexed: 01/28/2023] Open
Abstract
The smallest gene HBx of Hepatitis B virus (HBV) is recognized as an important viral oncogene (V-oncogene) in the hepatocarcinogenesis. Our previous work demonstrated that RMP is a cellular oncogene (C-oncogene) required for the proliferation of hepatocellular carcinoma (HCC) cells. Here we presented the collaboration between V-oncogene HBx and C-oncogene RMP in the development of HCC. The coexpression of HBx and RMP resulted in the cooperative effect of antiapoptosis and proliferation of HCC cells. In vivo, overexpression of RMP accelerated the growth of HBx-induced xenograft tumors in nude mice and vice versa HBx promoted the growth of RMP-driven xenograft tumors. Although HBx didn't regulate the expression of RMP, HBx and RMP interact with each other and collocalized in the cytoplasm of HCC cells. HBx and RMP collaboratively inhibited the expression of apoptotic factors and promoted the expression of antiapoptotic factors. This finding suggests that HBV may induce, or at least partially contributes to the carcinogenesis of HCC, through its V-oncoprotein HBx interacting with the C-oncoprotein RMP.
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Affiliation(s)
- Qi Wang
- 1. Department of Cell Biology, School of Medicine, Soochow University, Suzhou, 215123 China ; 2. Department of Tumor Biotherapy, Third Affiliated Hospital of Soochow University, Changzhou, 213003 China
| | - Yi Xu
- 1. Department of Cell Biology, School of Medicine, Soochow University, Suzhou, 215123 China
| | - Wei Zhou
- 1. Department of Cell Biology, School of Medicine, Soochow University, Suzhou, 215123 China
| | - Lei Zhong
- 1. Department of Cell Biology, School of Medicine, Soochow University, Suzhou, 215123 China
| | - Zengqing Wen
- 3. Eastern Hepatobiliary Surgery Hospital, Shanghai, 200433, China
| | - Huijun Yu
- 1. Department of Cell Biology, School of Medicine, Soochow University, Suzhou, 215123 China
| | - Shaomu Chen
- 1. Department of Cell Biology, School of Medicine, Soochow University, Suzhou, 215123 China
| | - Jian Shen
- 1. Department of Cell Biology, School of Medicine, Soochow University, Suzhou, 215123 China
| | - Han Chen
- 1. Department of Cell Biology, School of Medicine, Soochow University, Suzhou, 215123 China
| | - Qinying She
- 1. Department of Cell Biology, School of Medicine, Soochow University, Suzhou, 215123 China
| | - Jingting Jiang
- 2. Department of Tumor Biotherapy, Third Affiliated Hospital of Soochow University, Changzhou, 213003 China
| | - Jingcheng Miao
- 1. Department of Cell Biology, School of Medicine, Soochow University, Suzhou, 215123 China
| | - Wenxiang Wei
- 1. Department of Cell Biology, School of Medicine, Soochow University, Suzhou, 215123 China
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Mirón-García MC, Garrido-Godino AI, Martínez-Fernández V, Fernández-Pevida A, Cuevas-Bermúdez A, Martín-Expósito M, Chávez S, de la Cruz J, Navarro F. The yeast prefoldin-like URI-orthologue Bud27 associates with the RSC nucleosome remodeler and modulates transcription. Nucleic Acids Res 2014; 42:9666-76. [PMID: 25081216 PMCID: PMC4150788 DOI: 10.1093/nar/gku685] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Bud27, the yeast orthologue of human URI/RMP, is a member of the prefoldin-like family of ATP-independent molecular chaperones. It has recently been shown to mediate the assembly of the three RNA polymerases in an Rpb5-dependent manner. In this work, we present evidence of Bud27 modulating RNA pol II transcription elongation. We show that Bud27 associates with RNA pol II phosphorylated forms (CTD-Ser5P and CTD-Ser2P), and that its absence affects RNA pol II occupancy of transcribed genes. We also reveal that Bud27 associates in vivo with the Sth1 component of the chromatin remodeling complex RSC and mediates its association with RNA pol II. Our data suggest that Bud27, in addition of contributing to Rpb5 folding within the RNA polymerases, also participates in the correct assembly of other chromatin-associated protein complexes, such as RSC, thereby modulating their activity.
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Affiliation(s)
- María Carmen Mirón-García
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Paraje de las Lagunillas, s/n, 23071, Jaén, Spain
| | - Ana Isabel Garrido-Godino
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Paraje de las Lagunillas, s/n, 23071, Jaén, Spain
| | - Verónica Martínez-Fernández
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Paraje de las Lagunillas, s/n, 23071, Jaén, Spain
| | - Antonio Fernández-Pevida
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Sevilla, Spain Departamento de Genética, Universidad de Sevilla, E41012 Sevilla, Spain
| | - Abel Cuevas-Bermúdez
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Paraje de las Lagunillas, s/n, 23071, Jaén, Spain
| | - Manuel Martín-Expósito
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Paraje de las Lagunillas, s/n, 23071, Jaén, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Sevilla, Spain Departamento de Genética, Universidad de Sevilla, E41012 Sevilla, Spain
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Sevilla, Spain Departamento de Genética, Universidad de Sevilla, E41012 Sevilla, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Paraje de las Lagunillas, s/n, 23071, Jaén, Spain
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Zhang J, Pan YF, Ding ZW, Yang GZ, Tan YX, Yang C, Jiang TY, Liu LJ, Zhang B, Han T, Cao D, Yang T, Yang N, Wu MC, Dong LW, Wang HY. RMP promotes venous metastases of hepatocellular carcinoma through promoting IL-6 transcription. Oncogene 2014; 34:1575-83. [DOI: 10.1038/onc.2014.84] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 01/31/2014] [Accepted: 02/25/2014] [Indexed: 02/07/2023]
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27
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URI regulates tumorigenicity and chemotherapeutic resistance of multiple myeloma by modulating IL-6 transcription. Cell Death Dis 2014; 5:e1126. [PMID: 24625985 PMCID: PMC3973192 DOI: 10.1038/cddis.2014.93] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/27/2014] [Accepted: 01/28/2014] [Indexed: 01/26/2023]
Abstract
Unconventional prefoldin RPB5 interactor (URI), which acts as an oncoprotein in solid tumors, is associated with RNA polymerase II subunit 5. However, its impact on multiple myeloma (MM) has not been determined. We demonstrate here that URI is overexpressed in MM compared with plasma cells derived from healthy volunteers. Side population (SP) cells sorted from MM cells showed a much higher level of URI than non-SP cells. Using lentivirus-delivered shRNA, we established stable URI knockdown MM cell lines. URI inhibition significantly attenuated the proliferation of MM cells and decreased colony formation compared with the control cells. Tumor growth assays in NOD/SCID mice further confirmed the promotion role of URI during MM development in vivo. Furthermore, URI knockdown markedly reduced the abundance of SP in MM cell lines and enhanced the chemotherapeutic sensitivity of MM towards bortezomib. Mechanically, URI appears to be critically involved in modulating STAT3 activity through regulating interleukin (IL)-6 transcription via interaction with NFκBp65. In conclusion, URI may have an important role in the development of MM and chemotherapeutic resistance through activating the IL-6/STAT3 pathway.
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28
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Afanasyeva A, Hirtreiter A, Schreiber A, Grohmann D, Pobegalov G, McKay AR, Tsaneva I, Petukhov M, Käs E, Grigoriev M, Werner F. Lytic water dynamics reveal evolutionarily conserved mechanisms of ATP hydrolysis by TIP49 AAA+ ATPases. Structure 2014; 22:549-59. [PMID: 24613487 PMCID: PMC3991330 DOI: 10.1016/j.str.2014.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/29/2014] [Accepted: 02/01/2014] [Indexed: 11/24/2022]
Abstract
Eukaryotic TIP49a (Pontin) and TIP49b (Reptin) AAA+ ATPases play essential roles in key cellular processes. How their weak ATPase activity contributes to their important functions remains largely unknown and difficult to analyze because of the divergent properties of TIP49a and TIP49b proteins and of their homo- and hetero-oligomeric assemblies. To circumvent these complexities, we have analyzed the single ancient TIP49 ortholog found in the archaeon Methanopyrus kandleri (mkTIP49). All-atom homology modeling and molecular dynamics simulations validated by biochemical assays reveal highly conserved organizational principles and identify key residues for ATP hydrolysis. An unanticipated crosstalk between Walker B and Sensor I motifs impacts the dynamics of water molecules and highlights a critical role of trans-acting aspartates in the lytic water activation step that is essential for the associative mechanism of ATP hydrolysis. We have studied the single TIP49 ortholog (mkTIP49) from the archaeon M. kandleri We propose a model for assembly of the pre-transition state for ATP hydrolysis Trans-aspartates downregulate ATP hydrolysis by mkTIP49 hexamers Mutational analysis confirms a highly conserved mechanism for lytic water activation
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Affiliation(s)
- Arina Afanasyeva
- Department of Biophysics, Saint Petersburg State Polytechnical University, Saint Petersburg 195251, Russia; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina 188300, Russia
| | - Angela Hirtreiter
- Division of Biosciences, Institute for Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Anne Schreiber
- Division of Biosciences, Institute for Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Dina Grohmann
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Georgii Pobegalov
- Department of Biophysics, Saint Petersburg State Polytechnical University, Saint Petersburg 195251, Russia
| | - Adam R McKay
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Irina Tsaneva
- Division of Biosciences, Institute for Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Michael Petukhov
- Department of Biophysics, Saint Petersburg State Polytechnical University, Saint Petersburg 195251, Russia; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina 188300, Russia
| | - Emmanuel Käs
- UMR 5099, CNRS, Toulouse F-31000, France; Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, Toulouse F-31000, France.
| | - Mikhail Grigoriev
- UMR 5099, CNRS, Toulouse F-31000, France; Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, Toulouse F-31000, France.
| | - Finn Werner
- Division of Biosciences, Institute for Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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29
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Yang S, Wang H, Guo Y, Chen S, Zhang MY, Shen J, Yu H, Miao J, Wang HY, Wei W. RMP plays distinct roles in the proliferation of hepatocellular carcinoma cells and normal hepatic cells. Int J Biol Sci 2013; 9:637-48. [PMID: 23847445 PMCID: PMC3708043 DOI: 10.7150/ijbs.6439] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 06/17/2013] [Indexed: 12/25/2022] Open
Abstract
RMP has been shown to function in the transcription regulation through association with RNA polymerase (RNAP) II subunit RPB5. It also has been shown to be required for the proliferation of hepatocellular carcinoma (HCC) cells with an antiapoptotic property. In this article, we further demonstrate that RMP displays distinct features in HCC cells compared with normal hepatic cells. RMP expression is remarkably increased in various cancer cell lines including HCC cells when compared with normal cells. Depletion of RMP could inhibit the proliferation of HCC cells, but not the normal hepatic cells. RMP significantly prevented apoptosis of HCC cells in SMMC-7721 and HepG2, but had little effect on apoptosis in the normal hepatic cells. The mechanisms of RMP's distinct features rely on different responsive expressions of apoptosis factors induced by RMP in HCC and hepatic cells. Either overexpression or depletion of RMP significantly affected the expression of apoptosis factors in HCC cells. However, normal hepatic cells showed a tendency to resist RMP for the regulation of apoptosis. In the clinical samples, the increased expression of RMP in HCCs was also observed when compared with the matched non-tumor tissues from 30 HCC patients. The different expression levels of and distinct responses to RMP between HCC and hepatic cells suggest that RMP might serve as not only a biomarker for the diagnosis of HCC, but also a potential target for the HCC therapy.
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Affiliation(s)
- Sijun Yang
- Department of Cell Biology, School of Medicine, Soochow University, Suzhou, 215123 China
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30
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Izumi N, Yamashita A, Ohno S. Integrated regulation of PIKK-mediated stress responses by AAA+ proteins RUVBL1 and RUVBL2. Nucleus 2012; 3:29-43. [PMID: 22540023 PMCID: PMC3337166 DOI: 10.4161/nucl.18926] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Proteins of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family are activated by various cellular stresses, including DNA damage, premature termination codon and nutritional status, and induce appropriate cellular responses. The importance of PIKK functions in the maintenance of genome integrity, accurate gene expression and the proper control of cell growth/proliferation is established. Recently, ATPase associated diverse cellular activities (AAA+) proteins RUVBL1 and RUVBL2 (RUVBL1/2) have been shown to be common regulators of PIKKs. The RUVBL1/2 complex regulates PIKK-mediated stress responses through physical interactions with PIKKs and by controlling PIKK mRNA levels. In this review, the functions of PIKKs in stress responses are outlined and the physiological significance of the integrated regulation of PIKKs by the RUVBL1/2 complex is presented. We also discuss a putative "PIKK regulatory chaperone complex" including other PIKK regulators, Hsp90 and the Tel2 complex.
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Affiliation(s)
- Natsuko Izumi
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama, Japan
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31
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Wang Y, Jian F, Wu J, Wang S. Stress-response protein expression and DAF-16 translocation were induced in tributyltin-exposed Caenorhabditis elegans. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2012; 89:704-11. [PMID: 22875284 DOI: 10.1007/s00128-012-0760-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 07/20/2012] [Indexed: 05/05/2023]
Abstract
Exposure to tributyltin (TBT) with graded sublethal doses (0, 1, 10, 50 and 200 nM) resulted in the release of reactive oxygen species (ROS) and DNA damage in the nematode Caenorhabditis elegans. After the worms carrying transgenic reporters were exposed to TBT, the expressions of superoxide dismutase (SOD-3), glutathione S-transferase (GST-4) and heat shock proteins (HSP-4, HSP-16.2 and HSP-70) were semi-quantified after exposure. The results indicated that TBT caused dose-dependent induction of SOD-3, GST-4, HSP-4 and HSP-70. Furthermore, TBT exposure also induced DAF-16 translocation from cytoplasm to nucleus. The results implicated that C. elegans might be a potential animal model for TBT level monitoring and toxicity assessment.
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Affiliation(s)
- Yun Wang
- Department of Life Sciences, Huainan Normal University, Huainan 232001, Anhui, China.
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32
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Ueno S, Yasutake K, Tohyama D, Fujimori T, Ayusawa D, Fujii M. Systematic screen for genes involved in the regulation of oxidative stress in the nematode Caenorhabditis elegans. Biochem Biophys Res Commun 2012; 420:552-7. [DOI: 10.1016/j.bbrc.2012.03.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 03/07/2012] [Indexed: 01/29/2023]
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33
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Schøler LV, Møller TH, Nørgaard S, Vestergaard L, Olsen A. Isolating genes involved with genotoxic drug response in the nematode Caenorhabditis elegans using genome-wide RNAi screening. Methods Mol Biol 2012; 920:27-38. [PMID: 22941594 DOI: 10.1007/978-1-61779-998-3_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The soil nematode Caenorhabditis elegans has become a popular genetic model organism used to study a broad range of complex biological processes, including development, aging, apoptosis, and DNA damage responses. Many genetic tools and tricks have been developed in C. elegans including knock down of gene expression via RNA interference (RNAi). In C. elegans RNAi can effectively be administrated via feeding the nematodes bacteria expressing double-stranded RNA targeting the gene of interest. Several commercial C. elegans RNAi libraries are available and hence gene inactivation using RNAi can relatively easily be performed in a genome-wide fashion. In this chapter we give a protocol for using genome-wide RNAi screening to identify genes involved with the response to genotoxic stress.
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Affiliation(s)
- Lone Vedel Schøler
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus, Denmark
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34
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Regulation of androgen receptor-mediated transcription by RPB5 binding protein URI/RMP. Mol Cell Biol 2011; 31:3639-52. [PMID: 21730289 DOI: 10.1128/mcb.05429-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Androgen receptor (AR)-mediated transcription is modulated by interaction with coregulatory proteins. We demonstrate that the unconventional prefoldin RPB5 interactor (URI) is a new regulator of AR transcription and is critical for antagonist (bicalutamide) action. URI is phosphorylated upon androgen treatment, suggesting communication between the URI and AR signaling pathways. Whereas depletion of URI enhances AR-mediated gene transcription, overexpression of URI suppresses AR transcriptional activation and anchorage-independent prostate cancer cell growth. Repression of AR-mediated transcription is achieved, in part, by URI binding and regulation of androgen receptor trapped clone 27 (Art-27), a previously characterized AR corepressor. Consistent with this idea, genome-wide expression profiling in prostate cancer cells upon depletion of URI or Art-27 reveals substantially overlapping patterns of gene expression. Further, depletion of URI increases the expression of the AR target gene NKX-3.1, decreases the recruitment of Art-27, and increases AR occupancy at the NKX-3.1 promoter. While Art-27 can bind AR directly, URI is bound to chromatin prior to hormone-dependent recruitment of AR, suggesting a role for URI in modulating AR recruitment to target genes.
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35
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Grigoletto A, Lestienne P, Rosenbaum J. The multifaceted proteins Reptin and Pontin as major players in cancer. Biochim Biophys Acta Rev Cancer 2011; 1815:147-57. [DOI: 10.1016/j.bbcan.2010.11.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 11/17/2010] [Accepted: 11/17/2010] [Indexed: 01/29/2023]
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36
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Yang H, Gu J, Zheng Q, Li M, Lian X, Miao J, Jiang J, Wei W. RPB5-mediating protein is required for the proliferation of hepatocellular carcinoma cells. J Biol Chem 2011; 286:11865-74. [PMID: 21310960 DOI: 10.1074/jbc.m110.136929] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RPB5-mediating protein (RMP) is associated with the RNA polymerase II subunit RPB5. RMP functionally counteracts the transcriptional activation of hepatitis B virus X protein that has been shown to play a role in the development of hepatocellular carcinoma (HCC). However, the effect of RMP on the growth of HCC remains unclear. In this study, we characterized the potential role of RMP in the proliferation of human HCC cells using two cell lines, SMMC-7721 and HepG2. We found that RMP expression increased when HCC cells were treated with (60)Co γ-irradiation. Cell growth and colony formation assays suggest that RMP plays an antiapoptotic role in the proliferation and growth of HCC cells. We also show that RMP depletion induced the G(2) arrest of HCC cells characterized by the decreased expression of Cdk1 and Cyclin B. Tumor formation assays further confirmed the in vivo requirement of RMP during HCC growth. In conclusion, our results demonstrate that RMP is a radiation-sensitive factor, and it may play essential roles in HCC growth by affecting the proliferation and apoptosis of HCC cells.
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Affiliation(s)
- Huicui Yang
- Department of Cell Biology, School of Medicine, Soochow University, Suzhou, China
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37
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Horejsí Z, Takai H, Adelman CA, Collis SJ, Flynn H, Maslen S, Skehel JM, de Lange T, Boulton SJ. CK2 phospho-dependent binding of R2TP complex to TEL2 is essential for mTOR and SMG1 stability. Mol Cell 2010; 39:839-50. [PMID: 20864032 DOI: 10.1016/j.molcel.2010.08.037] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 08/25/2010] [Accepted: 08/26/2010] [Indexed: 11/30/2022]
Abstract
TEL2 interacts with and is essential for the stability of all phosphatidylinositol 3-kinase-related kinases (PIKKs), but its mechanism of action remains unclear. Here, we show that TEL2 is constitutively phosphorylated on conserved serines 487 and 491 by casein kinase 2 (CK2). Proteomic analyses establish that the CK2 phosphosite of TEL2 confers binding to the R2TP/prefoldin-like complex, which possesses chaperon/prefoldin activities required during protein complex assembly. The PIH1D1 subunit of the R2TP complex binds directly to the CK2 phosphosite of TEL2 in vitro and is required for the TEL2-R2TP/prefoldin-like complex interaction in vivo. Although the CK2 phosphosite mutant of TEL2 retains association with the PIKKs and HSP90 in cells, failure to interact with the R2TP/prefoldin-like complex results in instability of the PIKKs, principally mTOR and SMG1. We propose that TEL2 acts as a scaffold to coordinate the activities of R2TP/prefoldin-like and HSP90 chaperone complexes during the assembly of the PIKKs.
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Affiliation(s)
- Zuzana Horejsí
- DNA Damage Response Laboratory, London Research Institute, Clare Hall, South Mimms, UK
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38
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Etemadmoghadam D, George J, Cowin PA, Cullinane C, Kansara M, Gorringe KL, Smyth GK, Bowtell DDL. Amplicon-dependent CCNE1 expression is critical for clonogenic survival after cisplatin treatment and is correlated with 20q11 gain in ovarian cancer. PLoS One 2010; 5:e15498. [PMID: 21103391 PMCID: PMC2980490 DOI: 10.1371/journal.pone.0015498] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 10/17/2010] [Indexed: 01/02/2023] Open
Abstract
Genomic amplification of 19q12 occurs in several cancer types including ovarian cancer where it is associated with primary treatment failure. We systematically attenuated expression of genes within the minimally defined 19q12 region in ovarian cell lines using short-interfering RNAs (siRNA) to identify driver oncogene(s) within the amplicon. Knockdown of CCNE1 resulted in G1/S phase arrest, reduced cell viability and apoptosis only in amplification-carrying cells. Although CCNE1 knockdown increased cisplatin resistance in short-term assays, clonogenic survival was inhibited after treatment. Gain of 20q11 was highly correlated with 19q12 amplification and spanned a 2.5 Mb region including TPX2, a centromeric protein required for mitotic spindle function. Expression of TPX2 was highly correlated with gene amplification and with CCNE1 expression in primary tumors. siRNA inhibition of TPX2 reduced cell viability but this effect was not amplicon-dependent. These findings demonstrate that CCNE1 is a key driver in the 19q12 amplicon required for survival and clonogenicity in cells with locus amplification. Co-amplification at 19q12 and 20q11 implies the presence of a cooperative mutational network. These observations have implications for the application of targeted therapies in CCNE1 dependent ovarian cancers.
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Affiliation(s)
| | - Joshy George
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
- Department of Biochemistry, University of Melbourne, Parkville, Australia
| | - Prue A. Cowin
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | - Carleen Cullinane
- Translational Research Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | - Maya Kansara
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | | | - Kylie L. Gorringe
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
- Department of Pathology, University of Melbourne, Parkville, Australia
| | - Gordon K. Smyth
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - David D. L. Bowtell
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
- Department of Biochemistry, University of Melbourne, Parkville, Australia
- * E-mail:
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39
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Cloutier P, Coulombe B. New insights into the biogenesis of nuclear RNA polymerases? Biochem Cell Biol 2010; 88:211-21. [PMID: 20453924 DOI: 10.1139/o09-173] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
More than 30 years of research on nuclear RNA polymerases (RNAP I, II, and III) has uncovered numerous factors that regulate the activity of these enzymes during the transcription reaction. However, very little is known about the machinery that regulates the fate of RNAPs before or after transcription. In particular, the mechanisms of biogenesis of the 3 nuclear RNAPs, which comprise both common and specific subunits, remains mostly uncharacterized and the proteins involved are yet to be discovered. Using protein affinity purification coupled to mass spectrometry (AP-MS), we recently unraveled a high-density interaction network formed by nuclear RNAP subunits from the soluble fraction of human cell extracts. Validation of the dataset using a machine learning approach trained to minimize the rate of false positives and false negatives yielded a high-confidence dataset and uncovered novel interactors that regulate the RNAP II transcription machinery, including a set of proteins we named the RNAP II-associated proteins (RPAPs). One of the RPAPs, RPAP3, is part of an 11-subunit complex we termed the RPAP3/R2TP/prefoldin-like complex. Here, we review the literature on the subunits of this complex, which points to a role in nuclear RNAP biogenesis.
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Affiliation(s)
- Philippe Cloutier
- Laboratory of Gene Transcription and Proteomics, Institut de recherches cliniques de Montreal, 110 avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada
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40
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Huen J, Kakihara Y, Ugwu F, Cheung KLY, Ortega J, Houry WA. Rvb1–Rvb2: essential ATP-dependent helicases for critical complexesThis paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process. Biochem Cell Biol 2010; 88:29-40. [DOI: 10.1139/o09-122] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Rvb1 and Rvb2 are highly conserved, essential AAA+ helicases found in a wide range of eukaryotes. The versatility of these helicases and their central role in the biology of the cell is evident from their involvement in a wide array of critical cellular complexes. Rvb1 and Rvb2 are components of the chromatin-remodeling complexes INO80, Swr-C, and BAF. They are also members of the histone acetyltransferase Tip60 complex, and the recently identified R2TP complex present in Saccharomyces cerevisiae and Homo sapiens; a complex that is involved in small nucleolar ribonucleoprotein (snoRNP) assembly. Furthermore, in humans, Rvb1 and Rvb2 have been identified in the URI prefoldin-like complex. In Drosophila, the Polycomb Repressive complex 1 contains Rvb2, but not Rvb1, and the Brahma complex contains Rvb1 and not Rvb2. Both of these complexes are involved in the regulation of growth and development genes in Drosophila. Rvbs are therefore crucial factors in various cellular processes. Their importance in chromatin remodeling, transcription regulation, DNA damage repair, telomerase assembly, mitotic spindle formation, and snoRNP biogenesis is discussed in this review.
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Affiliation(s)
- Jennifer Huen
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Yoshito Kakihara
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Francisca Ugwu
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Kevin L. Y. Cheung
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Joaquin Ortega
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
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Moniaux N, Nemos C, Deb S, Zhu B, Dornreiter I, Hollingsworth MA, Batra SK. The human RNA polymerase II-associated factor 1 (hPaf1): a new regulator of cell-cycle progression. PLoS One 2009; 4:e7077. [PMID: 19771162 PMCID: PMC2740866 DOI: 10.1371/journal.pone.0007077] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 08/19/2009] [Indexed: 11/18/2022] Open
Abstract
Background The human PAF (hPAF) complex is part of the RNA polymerase II transcription apparatus and regulates multiple steps in gene expression. Further, the yeast homolog of hPaf1 has a role in regulating the expression of a subset of genes involved in the cell-cycle. We therefore investigated the role of hPaf1 during progression of the cell-cycle. Methodology/Findings Herein, we report that the expression of hPaf1, a subunit of the hPAF complex, increases with cell-cycle progression and is regulated in a cell-cycle dependant manner. hPaf1 specifically regulates a subclass of genes directly implicated in cell-cycle progression during G1/S, S/G2, and G2/M. In prophase, hPaf1 aligns in filament-like structures, whereas in metaphase it is present within the pole forming a crown-like structure, surrounding the centrosomes. Moreover, hPaf1 is degraded during the metaphase to anaphase transition. In the nucleus, hPaf1 regulates the expression of cyclins A1, A2, D1, E1, B1, and Cdk1. In addition, expression of hPaf1 delays DNA replication but favors the G2/M transition, in part through microtubule assembly and mitotic spindle formation. Conclusion/Significance Our results identify hPaf1 and the hPAF complex as key regulators of cell-cycle progression. Mutation or loss of stoichiometry of at least one of the members may potentially lead to cancer development.
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Affiliation(s)
- Nicolas Moniaux
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Christophe Nemos
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Shonali Deb
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Bing Zhu
- Howard Hughes Medical Institute, Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey, United States of America
| | | | - Michael A. Hollingsworth
- Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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Ni L, Saeki M, Xu L, Nakahara H, Saijo M, Tanaka K, Kamisaki Y. RPAP3 interacts with Reptin to regulate UV-induced phosphorylation of H2AX and DNA damage. J Cell Biochem 2009; 106:920-8. [PMID: 19180575 DOI: 10.1002/jcb.22073] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have previously reported that Monad, a novel WD40 repeat protein, potentiates apoptosis induced by tumor necrosis factor-alpha and cycloheximide. By affinity purification and mass spectrometry, RNA polymerase II-associated protein 3 (RPAP3) was identified as a Monad binding protein and may function with Monad as a novel modulator of apoptosis pathways. Here we report that Reptin, a highly conserved AAA + ATPase that is part of various chromatin-remodeling complexes, is also involved in the association of RPAP3 by immunoprecipitation and confocal microscopic analysis. Overexpression of RPAP3 induced HEK293 cells to death after UV-irradiation. Loss of RPAP3 by RNAi improved HeLa cell survival after UV-induced DNA damage and attenuated the phosphorylation of H2AX. Depletion of Reptin reduced cell survival and facilitated the phosphorylation on H2AX. These results suggest that RPAP3 modulates UV-induced DNA damage by regulating H2AX phosphorylation.
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Affiliation(s)
- Lin Ni
- Department of Pharmacology, Graduate School of Dentistry, Osaka University, Suita, Osaka, Japan
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43
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Moser SC, von Elsner S, Büssing I, Alpi A, Schnabel R, Gartner A. Functional dissection of Caenorhabditis elegans CLK-2/TEL2 cell cycle defects during embryogenesis and germline development. PLoS Genet 2009; 5:e1000451. [PMID: 19360121 PMCID: PMC2660272 DOI: 10.1371/journal.pgen.1000451] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Accepted: 03/11/2009] [Indexed: 12/31/2022] Open
Abstract
CLK-2/TEL2 is essential for viability from yeasts to vertebrates, but its essential functions remain ill defined. CLK-2/TEL2 was initially implicated in telomere length regulation in budding yeast, but work in Caenorhabditis elegans has uncovered a function in DNA damage response signalling. Subsequently, DNA damage signalling defects associated with CLK-2/TEL2 have been confirmed in yeast and human cells. The CLK-2/TEL2 interaction with the ATM and ATR DNA damage sensor kinases and its requirement for their stability led to the proposal that CLK-2/TEL2 mutants might phenocopy ATM and/or ATR depletion. We use C. elegans to dissect developmental and cell cycle related roles of CLK-2. Temperature sensitive (ts) clk-2 mutants accumulate genomic instability and show a delay of embryonic cell cycle timing. This delay partially depends on the worm p53 homolog CEP-1 and is rescued by co-depletion of the DNA replication checkpoint proteins ATL-1 (C. elegans ATR) and CHK-1. In addition, clk-2 ts mutants show a spindle orientation defect in the eight cell stages that lead to major cell fate transitions. clk-2 deletion worms progress through embryogenesis and larval development by maternal rescue but become sterile and halt germ cell cycle progression. Unlike ATL-1 depleted germ cells, clk-2–null germ cells do not accumulate DNA double-strand breaks. Rather, clk-2 mutant germ cells arrest with duplicated centrosomes but without mitotic spindles in an early prophase like stage. This germ cell cycle arrest does not depend on cep-1, the DNA replication, or the spindle checkpoint. Our analysis shows that CLK-2 depletion does not phenocopy PIKK kinase depletion. Rather, we implicate CLK-2 in multiple developmental and cell cycle related processes and show that CLK-2 and ATR have antagonising functions during early C. elegans embryonic development. PI3K-related protein kinases (PIKKs) ATM and ATR are essential upstream components of DNA damage signalling pathways, while TOR-1 acts as a nutrient sensor. CLK-2/TEL2 is a conserved gene initially implicated in budding yeast telomere length regulation and uncovered in the same genetic screen as the yeast TEL1 ATM like kinase. CLK-2/TEL2 was first implicated in DNA damage response signalling by C. elegans genetics, a function confirmed in yeast and human cells. In addition, CLK-2/TEL2 is essential for cellular and organismal survival from yeasts to vertebrates, but the essential phenotypes were not defined. A direct interaction between CLK-2/TEL2 and all PI3K-related protein kinases and the reduction of PIKK protein levels upon CLK-2/TEL2 depletion lead to the widely discussed notion that CLK-2/TEL2 mutants might phenocopy PIKK depletion phenotypes. We take advantage of embryonic lineage analysis and germline cytology to dissect developmental and cell cycle related functions of CLK-2. CLK-2 depletion does not phenocopy PIKK kinase depletion. We rather link CLK-2 to multiple developmental and cell cycle related processes and show that CLK-2 and ATR have antagonising functions during early C. elegans embryonic development. Furthermore, we implicate CLK-2 in a distinct cell lineage decision and show that its depletion leads to a novel germline cell cycle arrest phenotype.
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Affiliation(s)
- Sandra C. Moser
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Sophie von Elsner
- Developmental Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ingo Büssing
- Developmental Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Arno Alpi
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Ralf Schnabel
- Developmental Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Anton Gartner
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
- * E-mail:
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Nwachukwu JC, Mita P, Ruoff R, Ha S, Wang Q, Huang SJ, Taneja SS, Brown M, Gerald WL, Garabedian MJ, Logan SK. Genome-wide impact of androgen receptor trapped clone-27 loss on androgen-regulated transcription in prostate cancer cells. Cancer Res 2009; 69:3140-7. [PMID: 19318562 DOI: 10.1158/0008-5472.can-08-3738] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The androgen receptor (AR) directs diverse biological processes through interaction with coregulators such as AR trapped clone-27 (ART-27). Our results show that ART-27 is recruited to AR-binding sites by chromatin immunoprecipitation analysis. In addition, the effect of ART-27 on genome-wide transcription was examined. The studies indicate that loss of ART-27 enhances expression of many androgen-regulated genes, suggesting that ART-27 inhibits gene expression. Surprisingly, classes of genes that are up-regulated upon ART-27 depletion include regulators of DNA damage checkpoint and cell cycle progression, suggesting that ART-27 functions to keep expression levels of these genes low. Consistent with this idea, stable reduction of ART-27 by short-hairpin RNA enhances LNCaP cell proliferation compared with control cells. The effect of ART-27 loss was also examined in response to the antiandrogen bicalutamide. Unexpectedly, cells treated with ART-27 siRNA no longer exhibited gene repression in response to bicalutamide. To examine ART-27 loss in prostate cancer progression, immunohistochemistry was conducted on a tissue array containing samples from primary tumors of individuals who were clinically followed and later shown to have either recurrent or nonrecurrent disease. Comparison of ART-27 and AR staining indicated that nuclear ART-27 expression was lost in the majority of AR-positive recurrent prostate cancers. Our studies show that reduction of ART-27 protein levels in prostate cancer may facilitate antiandrogen-resistant disease.
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Affiliation(s)
- Jerome C Nwachukwu
- Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
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Alternative induction of meiotic recombination from single-base lesions of DNA deaminases. Genetics 2009; 182:41-54. [PMID: 19237686 DOI: 10.1534/genetics.109.101683] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination enhances genetic diversity as well as ensures proper segregation of homologous chromosomes, requiring Spo11-initiated double-strand breaks (DSBs). DNA deaminases act on regions of single-stranded DNA and deaminate cytosine to uracil (dU). In the immunoglobulin locus, this lesion will initiate point mutations, gene conversion, and DNA recombination. To begin to delineate the effect of induced base lesions on meiosis, we analyzed the effect of expressing DNA deaminases (activation-induced deaminase, AID, and APOBEC3C) in germ cells. We show that meiotic dU:dG lesions can partially rescue a spo11Delta phenotype in yeast and worm. In rec12 Schizosaccharomyces pombe, AID expression increased proper chromosome segregation, thereby enhancing spore viability, and induced low-frequency meiotic crossovers. Expression of AID in the germ cells of Caenorhabditis elegans spo-11 induced meiotic RAD-51 foci formation and chromosomal bivalency and segregation, as well as an increase in viability. RNAi experiments showed that this rescue was dependent on uracil DNA-glycosylase (Ung). Furthermore, unlike ionizing radiation-induced spo-11 rescue, AID expression did not induce large numbers of DSBs during the rescue. This suggests that the products of DNA deamination and base excision repair, such as uracil, an abasic site, or a single-stranded nick, are sufficient to initiate and alter meiotic recombination in uni- and multicellular organisms.
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Grigsby IF, Rutledge EM, Morton CA, Finger FP. Functional redundancy of two C. elegans homologs of the histone chaperone Asf1 in germline DNA replication. Dev Biol 2009; 329:64-79. [PMID: 19233156 DOI: 10.1016/j.ydbio.2009.02.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 01/30/2009] [Accepted: 02/11/2009] [Indexed: 11/20/2022]
Abstract
Eukaryotic genomes contain either one or two genes encoding homologs of the highly conserved histone chaperone Asf1, however, little is known of their in vivo roles in animal development. UNC-85 is one of the two Caenorhabditis elegans Asf1 homologs and functions in post-embryonic replication in neuroblasts. Although UNC-85 is broadly expressed in replicating cells, the specificity of the mutant phenotype suggested possible redundancy with the second C. elegans Asf1 homolog, ASFL-1. The asfl-1 mRNA is expressed in the meiotic region of the germline, and mutants in either Asf1 genes have reduced brood sizes and low penetrance defects in gametogenesis. The asfl-1, unc-85 double mutants are sterile, displaying defects in oogenesis and spermatogenesis, and analysis of DNA synthesis revealed that DNA replication in the germline is blocked. Analysis of somatic phenotypes previously observed in unc-85 mutants revealed that they are neither observed in asfl-1 mutants, nor enhanced in the double mutants, with the exception of enhanced male tail abnormalities in the double mutants. These results suggest that the two Asf1 homologs have partially overlapping functions in the germline, while UNC-85 is primarily responsible for several Asf1 functions in somatic cells, and is more generally involved in replication throughout development.
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Affiliation(s)
- Iwen F Grigsby
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Biotech-BCHM-2, Troy, NY 12180, USA
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Balaji S, Iyer LM, Aravind L. HPC2 and ubinuclein define a novel family of histone chaperones conserved throughout eukaryotes. MOLECULAR BIOSYSTEMS 2009; 5:269-75. [PMID: 19225618 PMCID: PMC2898643 DOI: 10.1039/b816424j] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Using sensitive protein sequence profile analyses we investigated the evolution of some histone chaperones and showed that Hir3p and Hpc2p have a much wider phyletic pattern than was previously known.
While histone chaperones have been intensely studied, the roles of components of the Hir–Asf1 histone chaperone complex such as Hir3p and Hpc2p are poorly understood. Using sensitive protein sequence profile analyses we investigated the evolution of these proteins and showed that Hir3p and Hpc2p have a much wider phyletic pattern than was previously known. We established the animal histone-deacetylase-complex-interacting proteins, CAIN/CABIN, to be orthologs of Hir3p. They contain a conserved core of around 30 TPR-like bi-helical repeats that are likely to form a super-helical scaffold. We identified a conserved domain, the HUN domain, in all Hpc2p homologs, including animal ubinuclein/yemanuclein and the recently discovered vertebrate cell-cycle regulator FLJ25778. The HUN domain has a characteristic pattern of conserved acidic residues based on which we predict that it is a previously unrecognized histone-tail-binding chaperone. By analyzing various high-throughput data sets, such as RNAi knock-downs, genetic and protein interaction maps and cell-cycle-specific gene expression data, we present evidence that Hpc2p homologs might be deployed in specific processes of chromatin dynamics relating to cell-cycle progression in vertebrates and schizogony in Plasmodium. Beyond the conserved HUN domain these proteins show extensive divergence patterns in different eukaryotic lineages. Hence, we propose that Hpc2p homologs are probably involved in recruitment of the ancient conserved histone-loading Hir–Asf1 complex to different lineage-specific chromatin reorganization processes.
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Affiliation(s)
- S Balaji
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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Kirchner J, Vissi E, Gross S, Szoor B, Rudenko A, Alphey L, White-Cooper H. Drosophila Uri, a PP1alpha binding protein, is essential for viability, maintenance of DNA integrity and normal transcriptional activity. BMC Mol Biol 2008; 9:36. [PMID: 18412953 PMCID: PMC2346476 DOI: 10.1186/1471-2199-9-36] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Accepted: 04/15/2008] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Protein phosphatase 1 (PP1) is involved in diverse cellular processes, and is targeted to substrates via interaction with many different protein binding partners. PP1 catalytic subunits (PP1c) fall into PP1alpha and PP1beta subfamilies based on sequence analysis, however very few PP1c binding proteins have been demonstrated to discriminate between PP1alpha and PP1beta. RESULTS URI (unconventional prefoldin RPB5 interactor) is a conserved molecular chaperone implicated in a variety of cellular processes, including the transcriptional response to nutrient signalling and maintenance of DNA integrity. We show that Drosophila Uri binds PP1alpha with much higher affinity than PP1beta, and that this ability to discriminate between PP1c forms is conserved to humans. Most Uri is cytoplasmic, however we found some protein associated with active RNAPII on chromatin. We generated a uri loss of function allele, and show that uri is essential for viability in Drosophila. uri mutants have transcriptional defects, reduced cell viability and differentiation in the germline, and accumulate DNA damage in their nuclei. CONCLUSION Uri is the first PP1alpha specific binding protein to be described in Drosophila. Uri protein plays a role in transcriptional regulation. Activity of uri is required to maintain DNA integrity and cell survival in normal development.
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Affiliation(s)
- Jasmin Kirchner
- Department of Zoology, University of Oxford, South Parks Rd, Oxford, OX1 3PS. UK
| | - Emese Vissi
- Department of Zoology, University of Oxford, South Parks Rd, Oxford, OX1 3PS. UK
| | - Sascha Gross
- Abbott Laboratories, Global Pharmaceutical Regulatory Affairs, Abbott Park, IL 60064-6157, USA
- Department of Zoology, University of Oxford, South Parks Rd, Oxford, OX1 3PS. UK
| | - Balazs Szoor
- Institute of Immunology and Infection Research, University of Edinburgh, EH9 3JT, UK
- Department of Zoology, University of Oxford, South Parks Rd, Oxford, OX1 3PS. UK
| | - Andrey Rudenko
- Harvard University, FAS Molecular & Cell Biology, Sherman Fairchild Biochemistry Bldg, 7 Divinity Ave, Cambridge MA, 02138, USA
- Department of Zoology, University of Oxford, South Parks Rd, Oxford, OX1 3PS. UK
| | - Luke Alphey
- Department of Zoology, University of Oxford, South Parks Rd, Oxford, OX1 3PS. UK
| | - Helen White-Cooper
- Department of Zoology, University of Oxford, South Parks Rd, Oxford, OX1 3PS. UK
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Lin L, Czapiga M, Nini L, Zhang JH, Simonds WF. Nuclear localization of the parafibromin tumor suppressor protein implicated in the hyperparathyroidism-jaw tumor syndrome enhances its proapoptotic function. Mol Cancer Res 2007; 5:183-93. [PMID: 17314275 DOI: 10.1158/1541-7786.mcr-06-0129] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Parafibromin is a tumor suppressor protein encoded by HRPT2, a gene recently implicated in the hereditary hyperparathyroidism-jaw tumor syndrome, parathyroid cancer, and a subset of kindreds with familial isolated hyperparathyroidism. Human parafibromin binds to RNA polymerase II as part of a PAF1 transcriptional regulatory complex. The mechanism by which loss of parafibromin function can lead to neoplastic transformation is poorly understood. Because the subcellular localization of parafibromin is likely to be critical for its function with the nuclear PAF1 complex, we sought to experimentally define the nuclear localization signal (NLS) of parafibromin and examine its potential role in parafibromin function. Using site-directed mutagenesis, we define a dominant bipartite NLS and a secondary NLS, both in the NH(2)-terminal region of parafibromin whose combined mutation nearly abolishes nuclear targeting. The NLS-mutant parafibromin is significantly impaired in its association with endogenous Paf1 and Leo1. We further report that overexpression of wild-type but not NLS-mutant parafibromin induces apoptosis in transfected cells. Inhibition of endogenous parafibromin expression by RNA interference inhibits the basal rate of apoptosis and apoptosis resulting from DNA damage induced by camptothecin, a topoisomerase I inhibitor. These experiments identify for the first time a proapoptotic activity of endogenous parafibromin likely to be important in its role as a tumor suppressor and show a functional role for the NLS of parafibromin in this activity.
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Affiliation(s)
- Ling Lin
- Metabolic Diseases Branch/National Institutes of Diabetes, Digestive and Kidney Diseases, NIH, Room 8C-101, Building 10, 10 Center Drive, MSC 1752, Bethesda, MD 20892-1752, USA
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50
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Gallant P. Control of transcription by Pontin and Reptin. Trends Cell Biol 2007; 17:187-92. [PMID: 17320397 DOI: 10.1016/j.tcb.2007.02.005] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 01/24/2007] [Accepted: 02/09/2007] [Indexed: 11/26/2022]
Abstract
Pontin and Reptin are two closely related members of the AAA+ family of DNA helicases. They have roles in diverse cellular processes, including the response to DNA double-strand breaks and the control of gene expression. The two proteins share residence in different multiprotein complexes, such as the Tip60, Ino80, SRCAP and Uri1 complexes in animals, which are involved (directly or indirectly) in transcriptional regulation, but they also function independently from each other. Both Reptin and Pontin repress certain transcriptional targets of Myc, but only Reptin is required for the repression of specific beta-catenin and nuclear factor-kappaB targets. Here, I review recent studies that have addressed the mechanisms of transcriptional control by Pontin and Reptin.
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Affiliation(s)
- Peter Gallant
- Zoologisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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