1
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Bortoletto S, Nunes-Souza E, Marchi R, Ruthes MO, Okano LM, Tofolo MV, Centa A, Fonseca AS, Rosolen D, Cavalli LR. MicroRNAs role in telomere length maintenance and telomerase activity in tumor cells. J Mol Med (Berl) 2024:10.1007/s00109-024-02467-z. [PMID: 39042290 DOI: 10.1007/s00109-024-02467-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/24/2024]
Abstract
MiRNAs, a class of non-coding RNA molecules, have emerged as critical modulators of telomere length and telomerase activity by finely tuning the expression of target genes (and not gene targets) within signaling pathways involved in telomere homeostasis. The primary objective of this systematic review was to compile and synthesize the existing body of knowledge on the role, association, and involvement of miRNAs in telomere length. Additionally, the review explored the regulation, function, and activation mechanism of the human telomerase reverse transcriptase (hTERT) gene and telomerase activity in tumor cells. A comprehensive analysis of 47 selected articles revealed 40 distinct miRNAs involved in these processes. These miRNAs were shown to exert their function, in both clinical cases and cell line models, either directly or indirectly, regulating hTERT and telomerase activity through distinct molecular mechanisms. The regulatory roles of these miRNAs significantly affected major cancer phenotypes, with outcomes largely dependent on the tissue type and the cellular actions within the tumor cells, whereby they functioned as oncogenes or tumor suppressors. These findings strongly support the pivotal role of miRNAs in modulating telomere length and telomerase activity, thereby contributing to the intricate and complex regulation of telomere homeostasis in tumor cells. Moreover, they emphasize the potential of targeting miRNAs and key regulatory genes as therapeutic strategies to disrupt cancer cell growth and promote senescence, offering promising avenues for novel cancer treatments.
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Affiliation(s)
- Stéfanne Bortoletto
- Faculdades Pequeno Príncipe, Research Institute Pelé Pequeno Príncipe, Curitiba, PR, Brazil
| | - Emanuelle Nunes-Souza
- Faculdades Pequeno Príncipe, Research Institute Pelé Pequeno Príncipe, Curitiba, PR, Brazil
| | - Rafael Marchi
- Faculdades Pequeno Príncipe, Research Institute Pelé Pequeno Príncipe, Curitiba, PR, Brazil
| | - Mayara Oliveira Ruthes
- Faculdades Pequeno Príncipe, Research Institute Pelé Pequeno Príncipe, Curitiba, PR, Brazil
| | - Larissa M Okano
- Faculdades Pequeno Príncipe, Research Institute Pelé Pequeno Príncipe, Curitiba, PR, Brazil
| | - Maria Vitoria Tofolo
- Faculdades Pequeno Príncipe, Research Institute Pelé Pequeno Príncipe, Curitiba, PR, Brazil
| | - Ariana Centa
- Universidade Alto Vale do Rio do Peixe (UNIARP), Caçador, SC, Brazil
| | - Aline S Fonseca
- Faculdades Pequeno Príncipe, Research Institute Pelé Pequeno Príncipe, Curitiba, PR, Brazil
| | - Daiane Rosolen
- Faculdades Pequeno Príncipe, Research Institute Pelé Pequeno Príncipe, Curitiba, PR, Brazil
| | - Luciane R Cavalli
- Faculdades Pequeno Príncipe, Research Institute Pelé Pequeno Príncipe, Curitiba, PR, Brazil.
- Oncology Department, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
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2
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Lozano-Vidal N, Stanicek L, Bink DI, Juni RP, Hooglugt A, Kremer V, Phelp P, van Bergen A, MacInnes AW, Dimmeler S, Boon RA. Aging-regulated PNUTS maintains endothelial barrier function via SEMA3B suppression. Commun Biol 2024; 7:541. [PMID: 38714838 PMCID: PMC11076560 DOI: 10.1038/s42003-024-06230-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Age-related diseases pose great challenges to health care systems worldwide. During aging, endothelial senescence increases the risk for cardiovascular disease. Recently, it was described that Phosphatase 1 Nuclear Targeting Subunit (PNUTS) has a central role in cardiomyocyte aging and homeostasis. Here, we determine the role of PNUTS in endothelial cell aging. We confirm that PNUTS is repressed in senescent endothelial cells (ECs). Moreover, PNUTS silencing elicits several of the hallmarks of endothelial aging: senescence, reduced angiogenesis and loss of barrier function. Findings are validate in vivo using endothelial-specific inducible PNUTS-deficient mice (Cdh5-CreERT2;PNUTSfl/fl), termed PNUTSEC-KO. Two weeks after PNUTS deletion, PNUTSEC-KO mice present severe multiorgan failure and vascular leakage. Transcriptomic analysis of PNUTS-silenced HUVECs and lungs of PNUTSEC-KO mice reveal that the PNUTS-PP1 axis tightly regulates the expression of semaphorin 3B (SEMA3B). Indeed, silencing of SEMA3B completely restores barrier function after PNUTS loss-of-function. These results reveal a pivotal role for PNUTS in endothelial homeostasis through a SEMA3B downstream pathway that provides a potential target against the effects of aging in ECs.
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Affiliation(s)
- Noelia Lozano-Vidal
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Laura Stanicek
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
- Institute of Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Diewertje I Bink
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Rio P Juni
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Aukie Hooglugt
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands
| | - Veerle Kremer
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Philippa Phelp
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Anke van Bergen
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Alyson W MacInnes
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Potsdamer Strasse 58, 10785, Berlin, Germany
| | - Reinier A Boon
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
- Institute of Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Potsdamer Strasse 58, 10785, Berlin, Germany.
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3
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Hein JB, Nguyen HT, Garvanska DH, Nasa I, Kruse T, Feng Y, Lopez Mendez B, Davey N, Kettenbach AN, Fordyce PM, Nilsson J. Phosphatase specificity principles uncovered by MRBLE:Dephos and global substrate identification. Mol Syst Biol 2023; 19:e11782. [PMID: 37916966 PMCID: PMC10698503 DOI: 10.15252/msb.202311782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
Phosphoprotein phosphatases (PPPs) regulate major signaling pathways, but the determinants of phosphatase specificity are poorly understood. This is because methods to investigate this at scale are lacking. Here, we develop a novel in vitro assay, MRBLE:Dephos, that allows multiplexing of dephosphorylation reactions to determine phosphatase preferences. Using MRBLE:Dephos, we establish amino acid preferences of the residues surrounding the dephosphorylation site for PP1 and PP2A-B55, which reveals common and unique preferences. To compare the MRBLE:Dephos results to cellular substrates, we focused on mitotic exit that requires extensive dephosphorylation by PP1 and PP2A-B55. We use specific inhibition of PP1 and PP2A-B55 in mitotic exit lysates coupled with phosphoproteomics to identify more than 2,000 regulated sites. Importantly, the sites dephosphorylated during mitotic exit reveal key signatures that are consistent with MRBLE:Dephos. Furthermore, integration of our phosphoproteomic data with mitotic interactomes of PP1 and PP2A-B55 provides insight into how binding of phosphatases to substrates shapes dephosphorylation. Collectively, we develop novel approaches to investigate protein phosphatases that provide insight into mitotic exit regulation.
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Affiliation(s)
- Jamin B Hein
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Hieu T Nguyen
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Dimitriya H Garvanska
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Isha Nasa
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Thomas Kruse
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Yinnian Feng
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Blanca Lopez Mendez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Norman Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Arminja N Kettenbach
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Polly M Fordyce
- Department of BioengineeringStanford UniversityStanfordCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
- Sarafan ChEM‐HStanford UniversityStanfordCAUSA
- Chan Zuckerberg BiohubSan FranciscoCAUSA
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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4
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Zhang Y, Sabatini R. Leishmania PNUTS discriminates between PP1 catalytic subunits through an RVxF-ΦΦ-F motif and polymorphisms in the PP1 C-tail and catalytic domain. J Biol Chem 2023; 299:105432. [PMID: 37926279 PMCID: PMC10731240 DOI: 10.1016/j.jbc.2023.105432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/10/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023] Open
Abstract
Phosphoprotein phosphatase 1 (PP1) associates with specific regulatory subunits to achieve, among other functions, substrate selectivity. Among the eight PP1 isotypes in Leishmania, PP1-8e associates with the regulatory protein PNUTS along with the structural factors JBP3 and Wdr82 in the PJW/PP1 complex that modulates RNA polymerase II (pol II) phosphorylation and transcription termination. Little is known regarding interactions involved in PJW/PP1 complex formation, including how PP1-8e is the selective isotype associated with PNUTS. Here, we show that PNUTS uses an established RVxF-ΦΦ-F motif to bind the PP1 catalytic domain with similar interfacial interactions as mammalian PP1-PNUTS and noncanonical motifs. These atypical interactions involve residues within the PP1-8e catalytic domain and N and C terminus for isoform-specific regulator binding. This work advances our understanding of PP1 isoform selectivity and reveals key roles of PP1 residues in regulator binding. We also explore the role of PNUTS as a scaffold protein for the complex by identifying the C-terminal region involved in binding JBP3 and Wdr82 and impact of PNUTS on the stability of complex components and function in pol II transcription in vivo. Taken together, these studies provide a potential mechanism where multiple motifs within PNUTS are used combinatorially to tune binding affinity to PP1, and the C terminus for JBP3 and Wdr82 association, in the Leishmania PJW/PP1 complex. Overall, our data provide insights in the formation of the PJW/PP1 complex involved in regulating pol II transcription in divergent protozoans where little is understood.
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Affiliation(s)
- Yang Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
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5
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The PNUTS-PP1 complex acts as an intrinsic barrier to herpesvirus KSHV gene expression and replication. Nat Commun 2022; 13:7447. [PMID: 36460671 PMCID: PMC9718767 DOI: 10.1038/s41467-022-35268-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Control of RNA Polymerase II (pol II) elongation is a critical component of gene expression in mammalian cells. The PNUTS-PP1 complex controls elongation rates, slowing pol II after polyadenylation sites to promote termination. The Kaposi's sarcoma-associated herpesvirus (KSHV) co-opts pol II to express its genes, but little is known about its regulation of pol II elongation. We identified PNUTS as a suppressor of a KSHV reporter gene in a genome-wide CRISPR screen. PNUTS depletion enhances global KSHV gene expression and overall viral replication. Mechanistically, PNUTS requires PP1 interaction, binds viral RNAs downstream of polyadenylation sites, and restricts transcription readthrough of viral genes. Surprisingly, PNUTS also represses productive elongation at the 5´ ends of the KSHV reporter and the KSHV T1.4 RNA. From these data, we conclude that PNUTS' activity constitutes an intrinsic barrier to KSHV replication likely by suppressing pol II elongation at promoter-proximal regions.
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6
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Structure and function of cancer-related developmentally regulated GTP-binding protein 1 (DRG1) is conserved between sponges and humans. Sci Rep 2022; 12:11379. [PMID: 35790840 PMCID: PMC9256742 DOI: 10.1038/s41598-022-15242-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/21/2022] [Indexed: 11/08/2022] Open
Abstract
Cancer is a disease caused by errors within the multicellular system and it represents a major health issue in multicellular organisms. Although cancer research has advanced substantially, new approaches focusing on fundamental aspects of cancer origin and mechanisms of spreading are necessary. Comparative genomic studies have shown that most genes linked to human cancer emerged during the early evolution of Metazoa. Thus, basal animals without true tissues and organs, such as sponges (Porifera), might be an innovative model system for understanding the molecular mechanisms of proteins involved in cancer biology. One of these proteins is developmentally regulated GTP-binding protein 1 (DRG1), a GTPase stabilized by interaction with DRG family regulatory protein 1 (DFRP1). This study reveals a high evolutionary conservation of DRG1 gene/protein in metazoans. Our biochemical analysis and structural predictions show that both recombinant sponge and human DRG1 are predominantly monomers that form complexes with DFRP1 and bind non-specifically to RNA and DNA. We demonstrate the conservation of sponge and human DRG1 biological features, including intracellular localization and DRG1:DFRP1 binding, function of DRG1 in α-tubulin dynamics, and its role in cancer biology demonstrated by increased proliferation, migration and colonization in human cancer cells. These results suggest that the ancestor of all Metazoa already possessed DRG1 that is structurally and functionally similar to the human DRG1, even before the development of real tissues or tumors, indicating an important function of DRG1 in fundamental cellular pathways.
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7
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Wei Y, Redel C, Ahlner A, Lemak A, Johansson-Åkhe I, Houliston S, Kenney TMG, Tamachi A, Morad V, Duan S, Andrews DW, Wallner B, Sunnerhagen M, Arrowsmith CH, Penn LZ. The MYC oncoprotein directly interacts with its chromatin cofactor PNUTS to recruit PP1 phosphatase. Nucleic Acids Res 2022; 50:3505-3522. [PMID: 35244724 PMCID: PMC8989513 DOI: 10.1093/nar/gkac138] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 01/11/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023] Open
Abstract
Despite MYC dysregulation in most human cancers, strategies to target this potent oncogenic driver remain an urgent unmet need. Recent evidence shows the PP1 phosphatase and its regulatory subunit PNUTS control MYC phosphorylation, chromatin occupancy, and stability, however the molecular basis remains unclear. Here we demonstrate that MYC interacts directly with PNUTS through the MYC homology Box 0 (MB0), a highly conserved region recently shown to be important for MYC oncogenic activity. By NMR we identified a distinct peptide motif within MB0 that interacts with PNUTS residues 1–148, a functional unit, here termed PNUTS amino-terminal domain (PAD). Using NMR spectroscopy we determined the solution structure of PAD, and characterised its MYC-binding patch. Point mutations of residues at the MYC-PNUTS interface significantly weaken their interaction both in vitro and in vivo, leading to elevated MYC phosphorylation. These data demonstrate that the MB0 region of MYC directly interacts with the PAD of PNUTS, which provides new insight into the control mechanisms of MYC as a regulator of gene transcription and a pervasive cancer driver.
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Affiliation(s)
- Yong Wei
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Structural Genomics Consortium (SGC), University of Toronto, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada.,Sunnybrook Research Institute, 2075 Bayview Ave. Toronto, ON, M4N 3M5, Canada
| | - Cornelia Redel
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Alexandra Ahlner
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Alexander Lemak
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Structural Genomics Consortium (SGC), University of Toronto, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada
| | - Isak Johansson-Åkhe
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Scott Houliston
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Structural Genomics Consortium (SGC), University of Toronto, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada
| | - Tristan M G Kenney
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Aaliya Tamachi
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada
| | - Vivian Morad
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | | | - David W Andrews
- Sunnybrook Research Institute, 2075 Bayview Ave. Toronto, ON, M4N 3M5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Björn Wallner
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Maria Sunnerhagen
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Structural Genomics Consortium (SGC), University of Toronto, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
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8
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Schreiter T, Gieseler RK, Vílchez-Vargas R, Jauregui R, Sowa JP, Klein-Scory S, Broering R, Croner RS, Treckmann JW, Link A, Canbay A. Transcriptome-Wide Analysis of Human Liver Reveals Age-Related Differences in the Expression of Select Functional Gene Clusters and Evidence for a PPP1R10-Governed 'Aging Cascade'. Pharmaceutics 2021; 13:pharmaceutics13122009. [PMID: 34959291 PMCID: PMC8709089 DOI: 10.3390/pharmaceutics13122009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/17/2021] [Accepted: 11/21/2021] [Indexed: 12/27/2022] Open
Abstract
A transcriptome-wide analysis of human liver for demonstrating differences between young and old humans has not yet been performed. However, identifying major age-related alterations in hepatic gene expression may pinpoint ontogenetic shifts with important hepatic and systemic consequences, provide novel pharmacogenetic information, offer clues to efficiently counteract symptoms of old age, and improve the overarching understanding of individual decline. Next-generation sequencing (NGS) data analyzed by the Mann-Whitney nonparametric test and Ensemble Feature Selection (EFS) bioinformatics identified 44 transcripts among 60,617 total and 19,986 protein-encoding transcripts that significantly (p = 0.0003 to 0.0464) and strikingly (EFS score > 0.3:16 transcripts; EFS score > 0.2:28 transcripts) differ between young and old livers. Most of these age-related transcripts were assigned to the categories 'regulome', 'inflammaging', 'regeneration', and 'pharmacogenes'. NGS results were confirmed by quantitative real-time polymerase chain reaction. Our results have important implications for the areas of ontogeny/aging and the age-dependent increase in major liver diseases. Finally, we present a broadly substantiated and testable hypothesis on a genetically governed 'aging cascade', wherein PPP1R10 acts as a putative ontogenetic master regulator, prominently flanked by IGFALS and DUSP1. This transcriptome-wide analysis of human liver offers potential clues towards developing safer and improved therapeutic interventions against major liver diseases and increased insights into key mechanisms underlying aging.
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Affiliation(s)
- Thomas Schreiter
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Laboratory of Immunology & Molecular Biology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
| | - Robert K. Gieseler
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Laboratory of Immunology & Molecular Biology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
| | - Ramiro Vílchez-Vargas
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (R.V.-V.); (A.L.)
| | - Ruy Jauregui
- Data Science Grasslands, Grasslands Research Centre, AgResearch, Palmerston North 4410, New Zealand;
| | - Jan-Peter Sowa
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Laboratory of Immunology & Molecular Biology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
| | - Susanne Klein-Scory
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Laboratory of Immunology & Molecular Biology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
| | - Ruth Broering
- Department of Gastroenterology and Hepatology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Roland S. Croner
- Department of General, Visceral, Vascular and Transplantation Surgery, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany;
| | - Jürgen W. Treckmann
- Department of General, Visceral and Transplantation Surgery, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Alexander Link
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (R.V.-V.); (A.L.)
| | - Ali Canbay
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Section of Hepatology and Gastroenterology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
- Correspondence: ; Tel.: +49-234-299-3401
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9
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Benjamin B, Sanchez AM, Garg A, Schwer B, Shuman S. Structure-function analysis of fission yeast cleavage and polyadenylation factor (CPF) subunit Ppn1 and its interactions with Dis2 and Swd22. PLoS Genet 2021; 17:e1009452. [PMID: 33711009 PMCID: PMC7990198 DOI: 10.1371/journal.pgen.1009452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/24/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022] Open
Abstract
Fission yeast Cleavage and Polyadenylation Factor (CPF), a 13-subunit complex, executes the cotranscriptional 3' processing of RNA polymerase II (Pol2) transcripts that precedes transcription termination. The three-subunit DPS sub-complex of CPF, consisting of a PP1-type phosphoprotein phosphatase Dis2, a WD-repeat protein Swd22, and a putative phosphatase regulatory factor Ppn1, associates with the CPF core to form the holo-CPF assembly. Here we probed the functional, physical, and genetic interactions of DPS by focusing on the Ppn1 subunit, which mediates association of DPS with the core. Transcriptional profiling by RNA-seq defined limited but highly concordant sets of protein-coding genes that were dysregulated in ppn1Δ, swd22Δ and dis2Δ cells, which included the DPSΔ down-regulated phosphate homeostasis genes pho1 and pho84 that are controlled by lncRNA-mediated transcriptional interference. Essential and inessential modules of the 710-aa Ppn1 protein were defined by testing the effects of Ppn1 truncations in multiple genetic backgrounds in which Ppn1 is required for growth. An N-terminal 172-aa disordered region was dispensable and its deletion alleviated hypomorphic phenotypes caused by deleting C-terminal aa 640-710. A TFIIS-like domain (aa 173-330) was not required for viability but was important for Ppn1 activity in phosphate homeostasis. Distinct sites within Ppn1 for binding to Dis2 (spanning Ppn1 aa 506 to 532) and Swd22 (from Ppn1 aa 533 to 578) were demarcated by yeast two-hybrid assays. Dis2 interaction-defective missense mutants of full-length Ppn1 (that retained Swd22 interaction) were employed to show that binding to Dis2 (or its paralog Sds21) was necessary for Ppn1 biological activity. Ppn1 function was severely compromised by missense mutations that selectively affected its binding to Swd22.
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Affiliation(s)
- Bradley Benjamin
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, United States of America
| | - Ana M. Sanchez
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, United States of America
| | - Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
| | - Beate Schwer
- Dept. of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail: (BS); (SS)
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
- * E-mail: (BS); (SS)
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10
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Abstract
Unlike most other eukaryotes, Leishmania and other trypanosomatid protozoa have largely eschewed transcriptional control of gene expression, relying instead on posttranscriptional regulation of mRNAs derived from polycistronic transcription units (PTUs). In these parasites, a novel modified nucleotide base (β-d-glucopyranosyloxymethyluracil) known as J plays a critical role in ensuring that transcription termination occurs only at the end of each PTU, rather than at the polyadenylation sites of individual genes. To further understand the biology of J-associated processes, we used tandem affinity purification (TAP) tagging and mass spectrometry to reveal proteins that interact with the glucosyltransferase performing the final step in J synthesis. These studies identified four proteins reminiscent of subunits in the PTW/PP1 complex that controls transcription termination in higher eukaryotes. Moreover, bioinformatic analyses identified the DNA-binding subunit of Leishmania PTW/PP1 as a novel J-binding protein (JBP3), which is also part of another complex containing proteins with domains suggestive of a role in chromatin modification/remodeling. Additionally, JBP3 associates (albeit transiently and/or indirectly) with the trypanosomatid equivalent of the PAF1 complex involved in the regulation of transcription in other eukaryotes. The downregulation of JBP3 expression levels in Leishmania resulted in a substantial increase in transcriptional readthrough at the 3′ end of most PTUs. We propose that JBP3 recruits one or more of these complexes to the J-containing regions at the end of PTUs, where they halt the progression of the RNA polymerase. This decoupling of transcription termination from the splicing of individual genes enables the parasites’ unique reliance on polycistronic transcription and posttranscriptional regulation of gene expression. IMPORTANCELeishmania parasites cause a variety of serious human diseases, with no effective vaccine and emerging resistance to current drug therapy. We have previously shown that a novel DNA base called J is critical for transcription termination at the ends of the polycistronic gene clusters that are a hallmark of Leishmania and related trypanosomatids. Here, we describe a new J-binding protein (JBP3) associated with three different protein complexes that are reminiscent of those involved in the control of transcription in other eukaryotes. However, the parasite complexes have been reprogrammed to regulate transcription and gene expression in trypanosomatids differently than in the mammalian hosts, providing new opportunities to develop novel chemotherapeutic treatments against these important pathogens.
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11
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Platholi J, Hemmings HC. Modulation of dendritic spines by protein phosphatase-1. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2020; 90:117-144. [PMID: 33706930 DOI: 10.1016/bs.apha.2020.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Protein phosphatase-1 (PP-1), a highly conserved multifunctional serine/threonine phosphatase, is enriched in dendritic spines where it plays a major role in modulating excitatory synaptic activity. In addition to established functions in spine maturation and development, multi-subunit holoenzyme forms of PP-1 modulate higher-order cognitive functions such learning and memory. Mechanisms involved in regulating PP-1 activity and localization in spines include interactions with neurabin and spinophilin, structurally related synaptic scaffolding proteins associated with the actin cytoskeleton. Since PP-1 is a critical element in synaptic development, signaling, and plasticity, alterations in PP-1 signaling in dendritic spines are implicated in various neurological and psychiatric disorders. The effects of PP-1 depend on its isoform-specific association with regulatory proteins and activation of downstream signaling pathways. Here we review the role of PP-1 and its binding proteins neurabin and spinophilin in both developing and established dendritic spines, as well as some of the disorders that result from its dysregulation.
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Affiliation(s)
- Jimcy Platholi
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, United States
| | - Hugh C Hemmings
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States; Department of Pharmacology, Weill Cornell Medicine, New York, NY, United States.
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12
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Schieweck R, Ninkovic J, Kiebler MA. RNA-binding proteins balance brain function in health and disease. Physiol Rev 2020; 101:1309-1370. [PMID: 33000986 DOI: 10.1152/physrev.00047.2019] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Posttranscriptional gene expression including splicing, RNA transport, translation, and RNA decay provides an important regulatory layer in many if not all molecular pathways. Research in the last decades has positioned RNA-binding proteins (RBPs) right in the center of posttranscriptional gene regulation. Here, we propose interdependent networks of RBPs to regulate complex pathways within the central nervous system (CNS). These are involved in multiple aspects of neuronal development and functioning, including higher cognition. Therefore, it is not sufficient to unravel the individual contribution of a single RBP and its consequences but rather to study and understand the tight interplay between different RBPs. In this review, we summarize recent findings in the field of RBP biology and discuss the complex interplay between different RBPs. Second, we emphasize the underlying dynamics within an RBP network and how this might regulate key processes such as neurogenesis, synaptic transmission, and synaptic plasticity. Importantly, we envision that dysfunction of specific RBPs could lead to perturbation within the RBP network. This would have direct and indirect (compensatory) effects in mRNA binding and translational control leading to global changes in cellular expression programs in general and in synaptic plasticity in particular. Therefore, we focus on RBP dysfunction and how this might cause neuropsychiatric and neurodegenerative disorders. Based on recent findings, we propose that alterations in the entire regulatory RBP network might account for phenotypic dysfunctions observed in complex diseases including neurodegeneration, epilepsy, and autism spectrum disorders.
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Affiliation(s)
- Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Jovica Ninkovic
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Michael A Kiebler
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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13
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Casamayor A, Ariño J. Controlling Ser/Thr protein phosphatase PP1 activity and function through interaction with regulatory subunits. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:231-288. [PMID: 32951813 DOI: 10.1016/bs.apcsb.2020.06.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein phosphatase 1 is a major Ser/Thr protein phosphatase activity in eukaryotic cells. It is composed of a catalytic polypeptide (PP1C), with little substrate specificity, that interacts with a large variety of proteins of diverse structure (regulatory subunits). The diversity of holoenzymes that can be formed explain the multiplicity of cellular functions under the control of this phosphatase. In quite a few cases, regulatory subunits have an inhibitory role, downregulating the activity of the phosphatase. In this chapter we shall introduce PP1C and review the most relevant families of PP1C regulatory subunits, with particular emphasis in describing the structural basis for their interaction.
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Affiliation(s)
- Antonio Casamayor
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola, del Vallès, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola, del Vallès, Spain
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Upregulation of Phosphatase 1 Nuclear-Targeting Subunit (PNUTS) Is an Independent Predictor of Poor Prognosis in Prostate Cancer. DISEASE MARKERS 2020; 2020:7050146. [PMID: 32377272 PMCID: PMC7196962 DOI: 10.1155/2020/7050146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 01/17/2020] [Indexed: 01/07/2023]
Abstract
Protein phosphatase 1 nuclear-targeting subunit (PNUTS) is ubiquitously expressed and associates with PTEN and protein phosphatase 1 (PP1) to control its activity. The role of PNUTS overexpression has hardly been studied in cancer. In this study, we used immunohistochemistry to quantitate PNUTS expression on a tissue microarray containing 17,747 clinical prostate cancer specimens. As compared to normal prostate epithelium, PNUTS expression was often higher in cancer. Among 12,235 interpretable tumors, PNUTS staining was negative in 21%, weak in 34%, moderate in 35%, and strong in 10% of cases. High PNUTS expression was associated with higher tumor stage, classical and quantitative Gleason grade, nodal stage, surgical margin, Ki67 labeling index, and early biochemical recurrence (p < 0.0001 each). PNUTS expression proved to be a moderate prognostic parameter with a maximal univariable Cox proportional hazard for PSA recurrence-free survival of 2.21 compared with 5.91 for Gleason grading. It was independent from established prognostic parameters in multivariable analysis. Comparison with molecular data available from earlier studies using the same TMA identified associations between high PNUTS expression and elevated androgen receptor expression (p < 0.0001), presence of TMPRSS2:ERG fusion (p < 0.0001), and 8 of 11 chromosomal deletions (3p13, 5q21, 8p21, 10q23, 12p13, 13q14, 16q24, and 17p13; p < 0.05 each). Particularly strong associations with PTEN and 12p13 deletions (p < 0.0001 each) may indicate a functional relationship, which has already been established for PNUTS and PTEN. PNUTS had no additional role on outcome in PTEN-deleted cancers. In conclusion, the results of our study identify high PNUTS protein levels as a predictor of poor prognosis possibly linked to increased levels of genomic instability. PNUTS measurement, either alone or in combination, might be of clinical utility in prostate cancers.
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Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription. Mol Cell 2020; 77:1322-1339.e11. [PMID: 32006464 PMCID: PMC7086158 DOI: 10.1016/j.molcel.2020.01.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 12/09/2019] [Accepted: 01/07/2020] [Indexed: 01/19/2023]
Abstract
Deregulated expression of MYC induces a dependence on the NUAK1 kinase, but the molecular mechanisms underlying this dependence have not been fully clarified. Here, we show that NUAK1 is a predominantly nuclear protein that associates with a network of nuclear protein phosphatase 1 (PP1) interactors and that PNUTS, a nuclear regulatory subunit of PP1, is phosphorylated by NUAK1. Both NUAK1 and PNUTS associate with the splicing machinery. Inhibition of NUAK1 abolishes chromatin association of PNUTS, reduces spliceosome activity, and suppresses nascent RNA synthesis. Activation of MYC does not bypass the requirement for NUAK1 for spliceosome activity but significantly attenuates transcription inhibition. Consequently, NUAK1 inhibition in MYC-transformed cells induces global accumulation of RNAPII both at the pause site and at the first exon-intron boundary but does not increase mRNA synthesis. We suggest that NUAK1 inhibition in the presence of deregulated MYC traps non-productive RNAPII because of the absence of correctly assembled spliceosomes. Nuclear NUAK1 associates with PP1 and phosphorylates its targeting subunit PNUTS NUAK1, PP1, and PNUTS form a trimer that associates with the splicing machinery Inhibition of NUAK1 reduces spliceosome activity and nascent RNA synthesis When MYC is deregulated, NUAK1 inhibition traps RNAPII at the intron-exon boundary
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16
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Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a "Sitting Duck Torpedo" Mechanism. Mol Cell 2019; 76:896-908.e4. [PMID: 31677974 DOI: 10.1016/j.molcel.2019.09.031] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/14/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022]
Abstract
Control of transcription speed, which influences many co-transcriptional processes, is poorly understood. We report that PNUTS-PP1 phosphatase is a negative regulator of RNA polymerase II (Pol II) elongation rate. The PNUTS W401A mutation, which disrupts PP1 binding, causes genome-wide acceleration of transcription associated with hyper-phosphorylation of the Spt5 elongation factor. Immediately downstream of poly(A) sites, Pol II decelerates from >2 kb/min to <1 kb/min, which correlates with Spt5 dephosphorylation. Pol II deceleration and Spt5 dephosphorylation require poly(A) site recognition and the PNUTS-PP1 complex, which is in turn necessary for transcription termination. These results lead to a model for termination, the "sitting duck torpedo" mechanism, where poly(A) site-dependent deceleration caused by PNUTS-PP1 and Spt5 dephosphorylation is required to convert Pol II into a viable target for the Xrn2 terminator exonuclease. Spt5 and its bacterial homolog NusG therefore have related functions controlling kinetic competition between RNA polymerases and the termination factors that pursue them.
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17
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Smith RJ, Cordeiro MH, Davey NE, Vallardi G, Ciliberto A, Gross F, Saurin AT. PP1 and PP2A Use Opposite Phospho-dependencies to Control Distinct Processes at the Kinetochore. Cell Rep 2019; 28:2206-2219.e8. [PMID: 31433993 PMCID: PMC6715587 DOI: 10.1016/j.celrep.2019.07.067] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/18/2019] [Accepted: 07/18/2019] [Indexed: 12/12/2022] Open
Abstract
PP1 and PP2A-B56 are major serine/threonine phosphatase families that achieve specificity by colocalizing with substrates. At the kinetochore, however, both phosphatases localize to an almost identical molecular space and yet they still manage to regulate unique pathways and processes. By switching or modulating the positions of PP1/PP2A-B56 at kinetochores, we show that their unique downstream effects are not due to either the identity of the phosphatase or its precise location. Instead, these phosphatases signal differently because their kinetochore recruitment can be either inhibited (PP1) or enhanced (PP2A) by phosphorylation inputs. Mathematical modeling explains how these inverse phospho-dependencies elicit unique forms of cross-regulation and feedback, which allows otherwise indistinguishable phosphatases to produce distinct network behaviors and control different mitotic processes. Furthermore, our genome-wide analysis suggests that these major phosphatase families may have evolved to respond to phosphorylation inputs in opposite ways because many other PP1 and PP2A-B56-binding motifs are also phospho-regulated.
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Affiliation(s)
- Richard J Smith
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Marilia H Cordeiro
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Giulia Vallardi
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | | | - Fridolin Gross
- Istituto Firc di Oncologia Molecolare, IFOM, Milano, Italy
| | - Adrian T Saurin
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK.
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18
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Nahalka J. The role of the protein-RNA recognition code in neurodegeneration. Cell Mol Life Sci 2019; 76:2043-2058. [PMID: 30980111 PMCID: PMC11105320 DOI: 10.1007/s00018-019-03096-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/14/2019] [Accepted: 04/08/2019] [Indexed: 12/14/2022]
Abstract
MicroRNAs are small endogenous RNAs that pair and bind to sites on mRNAs to direct post-transcriptional repression. However, there is a possibility that microRNAs directly influence protein structure and activity, and this influence can be termed post-translational riboregulation. This conceptual review explores the literature on neurodegenerative disorders. Research on the association between neurodegeneration and RNA-repeat toxicity provides data that support a protein-RNA recognition code. For example, this code explains why hnRNP H and SFPQ proteins, which are involved in amyotrophic lateral sclerosis, are sequestered by the (GGGGCC)n repeat sequence. Similarly, it explains why MNBL proteins and (CTG)n repeats in RNA, which are involved in myotonic dystrophy, are sequestered into RNA foci. Using this code, proteins involved in diseases can be identified. A simple protein BLAST search of the human genome for amino acid repeats that correspond to the nucleotide repeats reveals new proteins among already known proteins that are involved in diseases. For example, the (CAG)n repeat sequence, when transcribed into possible peptide sequences, leads to the identification of PTCD3, Rem2, MESP2, SYPL2, WDR33, COL23A1, and others. After confirming this approach on RNA repeats, in the next step, the code was used in the opposite manner. Proteins that are involved in diseases were compared with microRNAs involved in those diseases. For example, a reasonable correspondence of microRNA 9 and 107 with amyloid-β-peptide (Aβ42) was identified. In the last step, a miRBase search for micro-nucleotides, obtained by transcription of a prion amino acid sequence, revealed new microRNAs and microRNAs that have previously been identified as involved in prion diseases. This concept provides a useful key for designing RNA or peptide probes.
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Affiliation(s)
- Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, 84538, Bratislava, Slovak Republic.
- Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, 94976, Nitra, Slovak Republic.
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19
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Brautigan DL, Shenolikar S. Protein Serine/Threonine Phosphatases: Keys to Unlocking Regulators and Substrates. Annu Rev Biochem 2019; 87:921-964. [PMID: 29925267 DOI: 10.1146/annurev-biochem-062917-012332] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein serine/threonine phosphatases (PPPs) are ancient enzymes, with distinct types conserved across eukaryotic evolution. PPPs are segregated into types primarily on the basis of the unique interactions of PPP catalytic subunits with regulatory proteins. The resulting holoenzymes dock substrates distal to the active site to enhance specificity. This review focuses on the subunit and substrate interactions for PPP that depend on short linear motifs. Insights about these motifs from structures of holoenzymes open new opportunities for computational biology approaches to elucidate PPP networks. There is an expanding knowledge base of posttranslational modifications of PPP catalytic and regulatory subunits, as well as of their substrates, including phosphorylation, acetylation, and ubiquitination. Cross talk between these posttranslational modifications creates PPP-based signaling. Knowledge of PPP complexes, signaling clusters, as well as how PPPs communicate with each other in response to cellular signals should unlock the doors to PPP networks and signaling "clouds" that orchestrate and coordinate different aspects of cell physiology.
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Affiliation(s)
- David L Brautigan
- Center for Cell Signaling and Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA;
| | - Shirish Shenolikar
- Signature Research Programs in Cardiovascular and Metabolic Disorders and Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore 169857
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20
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Yu D, An X, Fan W, Wang X, He Y, Li B. PNUTS mediates ionizing radiation-induced CNE-2 nasopharyngeal carcinoma cell migration, invasion, and epithelial-mesenchymal transition via the PI3K/AKT signaling pathway. Onco Targets Ther 2019; 12:1205-1214. [PMID: 30863088 PMCID: PMC6388972 DOI: 10.2147/ott.s188571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Purpose Ionizing radiation (IR) is widely used for treating nasopharyngeal carcinoma (NPC). However, recent studies indicate that IR can also promote the migration and invasion of malignant tumors. Phosphatase 1 nuclear-targeting subunit (PNUTS), a novel interacting protein, was recently demonstrated to be involved in tumorigenesis and metastasis formation. This protein was hypothesized to take part in IR-induced migration and invasion in NPC cells in this study. Materials and methods Western blotting was used to detect how PNUTS was expressed in NPC cells with or without IR treatment. Wound-healing and Transwell assays were used to measure cell migration and invasion. Quantitative real-time PCR and Western blotting were used to determine the expression levels of PNUTS and epithelial–mesenchymal transition (EMT) proteins, respectively, after CNE-2 cells were infected with an adenovirus vector, ad-PNUTS, or transfected with PNUTS-specific siRNA. Finally, the expression levels of PI3K/AKT signaling-related proteins were detected by Western blotting. Results IR significantly promoted PNUTS expression and the migration and invasion in CNE-2 cells. Moreover, after exposure to IR, expression of the mesenchymal markers N-cadherin and vimentin increased, while that of the epithelial marker E-cadherin decreased. Silencing PNUTS remarkably attenuated IR-induced increases in cell migration and invasion and reversed the EMT process. Additionally, the overexpression of PNUTS restored the mobility and invasiveness of CNE-2 cells, which regained EMT characteristics. Furthermore, we found that PNUTS regulated IR-induced EMT via the PI3K/AKT signaling pathway. Conclusion Our research illustrates a relationship between PNUTS and IR-induced cell migration and invasion and provides a novel therapeutic target for preventing radiotherapy-induced metastasis in NPC patients.
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Affiliation(s)
- Dan Yu
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China,
| | - Xiang An
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China,
| | - Wanlin Fan
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China,
| | - Xin Wang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China,
| | - Yuxing He
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China,
| | - Bing Li
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China,
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21
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Wang F, Zhu S, Fisher LA, Wang L, Eurek NJ, Wahl JK, Lan L, Peng A. Phosphatase 1 Nuclear Targeting Subunit Mediates Recruitment and Function of Poly (ADP-Ribose) Polymerase 1 in DNA Repair. Cancer Res 2019; 79:2526-2535. [PMID: 30733193 DOI: 10.1158/0008-5472.can-18-1673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/26/2018] [Accepted: 01/31/2019] [Indexed: 12/17/2022]
Abstract
PARP, particularly PARP1, plays an essential role in the detection and repair of DNA single-strand breaks and double-strand breaks. PARP1 accumulates at DNA damage sites within seconds after DNA damage to catalyze the massive induction of substrate protein poly ADP-ribosylation (PARylation). However, the molecular mechanisms underlying the recruitment and activation of PARP1 in DNA repair are not fully understood. Here we show that phosphatase 1 nuclear targeting subunit 1 (PNUTS) is a robust binding partner of PARP1. Inhibition of PNUTS led to strong accumulation of endogenous DNA damage and sensitized the cellular response to a wide range of DNA-damaging agents, implicating PNUTS as an essential and multifaceted regulator of DNA repair. Recruitment of PNUTS to laser-induced DNA damage was similar to that of PARP1, and depletion or inhibition of PARP1 abrogated recruitment of PNUTS to sites of DNA damage. Conversely, PNUTS was required for efficient induction of substrate PARylation after DNA damage. PNUTS bound the BRCA1 C-terminal (BRCT) domain of PARP1 and was required for the recruitment of PARP1 to sites of DNA damage. Finally, depletion of PNUTS rendered cancer cells hypersensitive to PARP inhibition. Taken together, our study characterizes PNUTS as an essential partner of PARP1 in DNA repair and a potential drug target in cancer therapy. SIGNIFICANCE: These findings reveal PNUTS as an essential functional partner of PARP1 in DNA repair and suggest its inhibition as a potential therapeutic strategy in conjunction with DNA-damaging agents or PARP inhibitors.See related commentary by Murai and Pommier, p. 2460.
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Affiliation(s)
- Feifei Wang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, P.R. China.,Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Songli Zhu
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Laura A Fisher
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Ling Wang
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Nicholas J Eurek
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - James K Wahl
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Li Lan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Aimin Peng
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska.
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White CR, Dungan M, Carrithers MD. Activation of human macrophage sodium channels regulates RNA processing to increase expression of the DNA repair protein PPP1R10. Immunobiology 2019; 224:80-93. [DOI: 10.1016/j.imbio.2018.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/12/2018] [Accepted: 10/16/2018] [Indexed: 11/26/2022]
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Thomas NA, Abraham RG, Dedi B, Krucher NA. Targeting retinoblastoma protein phosphorylation in combination with EGFR inhibition in pancreatic cancer cells. Int J Oncol 2018; 54:527-536. [PMID: 30535494 PMCID: PMC6317693 DOI: 10.3892/ijo.2018.4658] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/16/2018] [Indexed: 12/24/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains a particularly lethal disease that is resistant to targeted therapies. Tyrosine kinase inhibitors (TKIs), including erlotinib and gefitinib, which block the action of the human epidermal growth factor receptor type 1 receptor, provide small increases in patient survival when administered with gemcitabine. The retinoblastoma (Rb) tumor suppressor protein is an additional target in pancreatic cancer, due to its documented inactivation in PDAC. The present study, using cell number, apoptosis and immunoblotting assays, aimed to evaluate the effects of activation of the Rb tumor suppressor via dephosphorylation by small interfering RNA-mediated phosphatase activation. In the Panc1, MIAPaCa-2 and Capan-2 pancreatic cancer cell lines, and in normal H6c7 cells, the effects of phosphatase activation on Rb were revealed to be dependent on expression of the p16 tumor suppressor, which regulates Rb phosphorylation. Phosphatase activation had no effect on non-transformed pancreatic epithelial cells. When comparing kinase inhibition with phosphatase activation, it was demonstrated that kinase inhibition reduced proliferation, whereas phosphatase activation induced apoptosis. Both treatments together resulted in a greater reduction of pancreatic cancer cells than either treatment alone. In addition, the effects of combination treatment of phosphatase activation with TKIs on cell number and activation of the signal transducer and activator of transcription 3 (STAT3) resistance pathway were determined. The combination of Rb phosphatase activation with TKIs resulted in a greater reduction in cell number compared with either treatment alone, without STAT3 pathway activation. These data suggested that targeting Rb phosphorylation by activating phosphatase may be a rational strategy to inhibit pancreatic tumor cell growth, without activation of acquired resistance.
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Affiliation(s)
- Nimmi A Thomas
- Department of Biology, Pace University, Pleasantville, NY 10570, USA
| | - Rita G Abraham
- Department of Biology, Pace University, Pleasantville, NY 10570, USA
| | - Brixhilda Dedi
- Department of Biology, Pace University, Pleasantville, NY 10570, USA
| | - Nancy A Krucher
- Department of Biology, Pace University, Pleasantville, NY 10570, USA
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24
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Wang F, Wang L, Fisher LA, Li C, Wang W, Peng A. Phosphatase 1 Nuclear Targeting Subunit (PNUTS) Regulates Aurora Kinases and Mitotic Progression. Mol Cancer Res 2018; 17:10-19. [PMID: 30190438 DOI: 10.1158/1541-7786.mcr-17-0670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 05/31/2018] [Accepted: 08/27/2018] [Indexed: 11/16/2022]
Abstract
Mitotic progression is regulated largely by reversible phosphorylation events that are mediated by mitotic kinases and phosphatases. Protein phosphatase 1 (PP1) has been shown to play a crucial role in regulation of mitotic entry, progression, and exit. We previously observed, in Xenopus egg extracts, that phosphatase 1 nuclear targeting subunit (PPP1R10/PNUTS) acts as a mitotic regulator by negatively modulating PP1. This study investigates the role of PNUTS in mitotic progression in mammalian cells, and demonstrates that PNUTS expression is elevated in mitosis and depletion partially blocks mitotic entry. Cells that enter mitosis after PNUTS knockdown exhibit frequent chromosome mis-segregation. Aurora A/B kinase complexes and several kinetochore components are identified as PNUTS-associated proteins. PNUTS depletion suppresses the activation of Aurora A/B kinases, and disrupts the spatiotemporal regulation of the chromosomal passenger complex (CPC). PNUTS dynamically localizes to kinetochores, and is required for the activation of the spindle assembly checkpoint. Finally, PNUTS depletion sensitizes the tumor cell response to Aurora inhibition, suggesting that PNUTS is a potential drug target in combination anticancer therapy. IMPLICATIONS: Delineation of how PNUTS governs the mitotic activation and function of Aurora kinases will improve the understanding of the complex phospho-regulation in mitotic progression, and suggest new options to enhance the therapeutic efficacy of Aurora inhibitors.
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Affiliation(s)
- Feifei Wang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China.,Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska.,Institute of Hypertension, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ling Wang
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Laura A Fisher
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Chunling Li
- Institute of Hypertension, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Weidong Wang
- Institute of Hypertension, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Aimin Peng
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska.
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25
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Zhu S, Fisher LA, Bessho T, Peng A. Protein phosphatase 1 and phosphatase 1 nuclear targeting subunit-dependent regulation of DNA-dependent protein kinase and non-homologous end joining. Nucleic Acids Res 2017; 45:10583-10594. [PMID: 28985363 PMCID: PMC5737533 DOI: 10.1093/nar/gkx686] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 07/28/2017] [Indexed: 12/29/2022] Open
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) plays a key role in mediating non-homologous end joining (NHEJ), a major repair pathway for DNA double-strand breaks (DSBs). The activation, function and dynamics of DNA-PKcs is regulated largely by its reversible phosphorylation at numerous residues, many of which are targeted by DNA-PKcs itself. Interestingly, these DNA-PKcs phosphorylation sites function in a distinct, and sometimes opposing manner, suggesting that they are differentially regulated via complex actions of both kinases and phosphatases. In this study we identified several phosphatase subunits as potential DSB-associated proteins. In particular, protein phosphatase 1 (PP1) is recruited to a DSB-mimicking substrate in Xenopus egg extracts and sites of laser microirradiation in human cells. Depletion of PP1 impairs NHEJ in both Xenopus egg extracts and human cells. PP1 binds multiple motifs of DNA-PKcs, regulates DNA-PKcs phosphorylation, and is required for DNA-PKcs activation after DNA damage. Interestingly, phosphatase 1 nuclear targeting subunit (PNUTS), an inhibitory regulator of PP1, is also recruited to DNA damage sites to promote NHEJ. PNUTS associates with the DNA-PK complex and is required for DNA-PKcs phosphorylation at Ser-2056 and Thr-2609. Thus, PNUTS and PP1 together fine-tune the dynamic phosphorylation of DNA-PKcs after DNA damage to mediate NHEJ.
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Affiliation(s)
- Songli Zhu
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, USA
| | - Laura A Fisher
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, USA
| | - Tadayoshi Bessho
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Aimin Peng
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, USA
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26
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Liu S, Xu T, Wu X, Lin Y, Bao D, Di Y, Ma T, Dang Y, Jia P, Xian J, Wang A, Liu Y. Pomegranate peel extract attenuates D-galactose-induced oxidative stress and hearing loss by regulating PNUTS/PP1 activity in the mouse cochlea. Neurobiol Aging 2017; 59:30-40. [PMID: 28837860 DOI: 10.1016/j.neurobiolaging.2017.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 07/11/2017] [Accepted: 07/15/2017] [Indexed: 01/20/2023]
Abstract
Oxidative stress is considered to be a major contributor to age-related hearing loss (ARHL). Here, we investigated whether pomegranate peel extract (PPE) protected against hearing loss by decreased oxidative stress in the cochlea of D-galactose-induced accelerated aging mice. The aging mice exhibited an increase in hearing threshold shifts and hair cells loss, which were improved in the PPE-treated aging mice. The aging mice also exhibited an increase in 4-hydroxynonenal, the expression of protein phosphatase 1 nuclear targeting subunit (PNUTS), p53 and caspase-3, and a decrease in protein phosphatase 1 (PP1) and MDM2 in the cochlea. PPE treatment reversed the changes in aforementioned molecules. Our results suggested that PPE can protect against ARHL, the underlying mechanisms may involve in the inhibition of oxidative damage of cochlea, possibly by regulating PNUTS/PP1 pathway. The results from the present study provide a new therapeutic strategy to use PPE for prevention of ARHL.
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Affiliation(s)
- Shuangyue Liu
- Department of Physiology, Jinzhou Medical University, Jinzhou, P.R. China
| | - Tao Xu
- Life Science Institute, Jinzhou Medical University, Jinzhou, P.R. China
| | - Xidi Wu
- Department of Physiology, Jinzhou Medical University, Jinzhou, P.R. China
| | - Yuhan Lin
- Department of Physiology, Jinzhou Medical University, Jinzhou, P.R. China
| | - Dongyan Bao
- Department of Physiology, Jinzhou Medical University, Jinzhou, P.R. China
| | - Yang Di
- Department of Physiology, Jinzhou Medical University, Jinzhou, P.R. China
| | - Tingting Ma
- Department of Physiology, Jinzhou Medical University, Jinzhou, P.R. China
| | - Yan Dang
- Department of Physiology, Jinzhou Medical University, Jinzhou, P.R. China
| | - Peili Jia
- Department of Physiology, Jinzhou Medical University, Jinzhou, P.R. China
| | - Jianqiao Xian
- Department of Physiology, Jinzhou Medical University, Jinzhou, P.R. China
| | - Aimei Wang
- Department of Physiology, Jinzhou Medical University, Jinzhou, P.R. China.
| | - Yongxin Liu
- Department of Otorhinolaryngology-Head and Neck Surgery, the First Hospital of Jinzhou Medical University, Jinzhou, P.R. China.
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27
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NBS1 Phosphorylation Status Dictates Repair Choice of Dysfunctional Telomeres. Mol Cell 2017; 65:801-817.e4. [PMID: 28216226 PMCID: PMC5639704 DOI: 10.1016/j.molcel.2017.01.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 11/22/2016] [Accepted: 01/05/2017] [Indexed: 01/07/2023]
Abstract
Telomeres employ TRF2 to protect chromosome ends from activating the DNA damage sensor MRE11-RAD50-NBS1 (MRN), thereby repressing ATM-dependent DNA damage checkpoint responses. How TRF2 prevents MRN activation at dysfunctional telomeres is unclear. Here, we show that the phosphorylation status of NBS1 determines the repair pathway choice of dysfunctional telomeres. The crystal structure of the TRF2-NBS1 complex at 3.0 Å resolution shows that the NBS1 429YQLSP433 motif interacts specifically with the TRF2TRFH domain. Phosphorylation of NBS1 serine 432 by CDK2 in S/G2 dissociates NBS1 from TRF2, promoting TRF2-Apollo/SNM1B complex formation and the protection of leading-strand telomeres. Classical-NHEJ-mediated repair of telomeres lacking TRF2 requires phosphorylated NBS1S432 to activate ATM, while interaction of de-phosphorylated NBS1S432 with TRF2 promotes alternative-NHEJ repair of telomeres lacking POT1-TPP1. Our work advances understanding of how the TRF2TRFH domain orchestrates telomere end protection and reveals how the phosphorylation status of the NBS1S432 dictates repair pathway choice of dysfunctional telomeres.
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28
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Wang X, Bajaj R, Bollen M, Peti W, Page R. Expanding the PP2A Interactome by Defining a B56-Specific SLiM. Structure 2016; 24:2174-2181. [PMID: 27998540 DOI: 10.1016/j.str.2016.09.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/11/2016] [Accepted: 10/03/2016] [Indexed: 11/18/2022]
Abstract
Specific interactions between proteins govern essential physiological processes including signaling. Many enzymes, especially the family of serine/threonine phosphatases (PSPs: PP1, PP2A, and PP2B/calcineurin/CN), recruit substrates and regulatory proteins by binding short linear motifs (SLiMs), short sequences found within intrinsically disordered regions that mediate specific protein-protein interactions. While tremendous progress had been made in identifying where and how SLiMs bind PSPs, especially PP1 and CN, essentially nothing is known about how SLiMs bind PP2A, a validated cancer drug target. Here we describe three structures of a PP2A-SLiM interaction (B56:pS-RepoMan, B56:pS-BubR1, and B56:pSpS-BubR1), show that this PP2A-specific SLiM is defined as LSPIxE, and then use these data to discover scores of likely PP2A regulators and substrates. Together, these data provide a powerful approach not only for dissecting PP2A interaction networks in cells but also for targeting PP2A diseases, such as cancer.
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Affiliation(s)
- Xinru Wang
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Rakhi Bajaj
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA; Department Chemistry, Brown University, Providence, RI 02912, USA
| | - Rebecca Page
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.
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29
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Brieño-Enríquez MA, Moak SL, Toledo M, Filter JJ, Gray S, Barbero JL, Cohen PE, Holloway JK. Cohesin Removal along the Chromosome Arms during the First Meiotic Division Depends on a NEK1-PP1γ-WAPL Axis in the Mouse. Cell Rep 2016; 17:977-986. [PMID: 27760328 PMCID: PMC5123770 DOI: 10.1016/j.celrep.2016.09.059] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/25/2016] [Accepted: 09/16/2016] [Indexed: 12/25/2022] Open
Abstract
Mammalian NIMA-like kinase-1 (NEK1) is a dual-specificity kinase highly expressed in mouse germ cells during prophase I of meiosis. Loss of NEK1 induces retention of cohesin on chromosomes at meiotic prophase I. Timely deposition and removal of cohesin is essential for accurate chromosome segregation. Two processes regulate cohesin removal: a non-proteolytic mechanism involving WAPL, sororin, and PDS5B and direct cleavage by separase. Here, we demonstrate a role for NEK1 in the regulation of WAPL loading during meiotic prophase I, via an interaction between NEK1 and PDS5B. This regulation of WAPL by NEK1-PDS5B is mediated by protein phosphatase 1 gamma (PP1γ), which both interacts with and is a phosphotarget of NEK1. Taken together, our results reveal that NEK1 phosphorylates PP1γ, leading to the dephosphorylation of WAPL, which, in turn, results in its retention on chromosome cores to promote loss of cohesion at the end of prophase I in mammals.
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Affiliation(s)
- Miguel A Brieño-Enríquez
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, NY 14853, USA
| | - Stefannie L Moak
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, NY 14853, USA
| | - Melissa Toledo
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, NY 14853, USA
| | - Joshua J Filter
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Stephen Gray
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, NY 14853, USA
| | - José L Barbero
- Department of Cellular and Molecular Biology, Laboratory of Chromosomal Dynamics in Meiosis, Centro de Investigaciones Biológicas (CSIC), Madrid 28040, Spain
| | - Paula E Cohen
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, NY 14853, USA.
| | - J Kim Holloway
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, NY 14853, USA.
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30
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Egger JV, Lane MV, Antonucci LA, Dedi B, Krucher NA. Dephosphorylation of the Retinoblastoma protein (Rb) inhibits cancer cell EMT via Zeb. Cancer Biol Ther 2016; 17:1197-1205. [PMID: 27645778 PMCID: PMC5137485 DOI: 10.1080/15384047.2016.1235668] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The tumor suppressor Retinoblastoma (Rb) protein is highly phosphorylated in cancer cells largely due to the overexpression of cyclins or the loss of expression of cyclin dependent kinase inhibitors (cdki). Hyperphosphorylation of Rb promotes proliferation, and plays a role in the regulation of apoptosis. Recently, inhibition of cyclin dependent activity toward Rb has been identified as a strategy that has shown clinical efficacy. We utilized a method to induce phosphatase activity toward Rb in cells by shRNA silencing of PNUTS (Phosphatase Nuclear Targeting Subunit) that regulates PP1-mediated dephosphorylation of Rb. In this study, the effect of Rb dephosphorylation on the epithelial to mesenchymal transition (EMT) was determined. The EMT transition is observed in cancer cells that have acquired invasive characteristics. In breast cancer cells grown in 3D Matrigel cultures, MCF7 cells undergo apoptosis in response to Rb dephosphorylation, whereas MDA-MB-231 and Hs578T cells exhibit a reduction in the EMT. Cells devoid of phosphorylated Rb (nontransformed MCF10A and Rb-null MDA-MB-468) lacked any response to PNUTS depletion, showing the effect is Rb-dependent. In addition, these studies showed that Rb dephosphorylation in 3D Matrigel cultures of highly invasive HT1080 cells led to the inhibition of the EMT. Furthermore we observed association between dephosphorylated Rb with ZEB1, a zinc-finger E-box-binding transcription factor that regulates expression of E- and N-cadherins. Finally Rb dephosphorylation led to inhibition of ZEB1 transcriptional activity, this data supports the notion that Rb dephosphorylation modulates the EMT. These studies suggest targeting Rb phosphorylation in mesenchymal cancer cells may decrease invasiveness.
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Affiliation(s)
- Jacklynn V Egger
- a Department of Biology , Dyson Hall, Pace University , Pleasantville , NY , USA
| | - Maria V Lane
- a Department of Biology , Dyson Hall, Pace University , Pleasantville , NY , USA
| | - Lisa A Antonucci
- a Department of Biology , Dyson Hall, Pace University , Pleasantville , NY , USA
| | - Brixhilda Dedi
- a Department of Biology , Dyson Hall, Pace University , Pleasantville , NY , USA
| | - Nancy A Krucher
- a Department of Biology , Dyson Hall, Pace University , Pleasantville , NY , USA
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31
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Biophysical Analysis of the N-Terminal Domain from the Human Protein Phosphatase 1 Nuclear Targeting Subunit PNUTS Suggests an Extended Transcription Factor TFIIS-Like Fold. Protein J 2016; 35:340-345. [DOI: 10.1007/s10930-016-9677-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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32
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Rebelo S, Santos M, Martins F, da Cruz e Silva EF, da Cruz e Silva OA. Protein phosphatase 1 is a key player in nuclear events. Cell Signal 2015; 27:2589-98. [DOI: 10.1016/j.cellsig.2015.08.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/31/2015] [Accepted: 08/10/2015] [Indexed: 12/17/2022]
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33
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The miRNA miR-34a enhances HIV-1 replication by targeting PNUTS/PPP1R10, which negatively regulates HIV-1 transcriptional complex formation. Biochem J 2015; 470:293-302. [PMID: 26188041 DOI: 10.1042/bj20150700] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/16/2015] [Indexed: 12/20/2022]
Abstract
HIV-1 relies heavily on the host cellular machinery for its replication. During infection, HIV-1 is known to modulate the host-cell miRNA profile. One of the miRNAs, miR-34a, is up-regulated by HIV-1 in T-cells as suggested by miRNA microarray studies. However, the functional consequences and the mechanism behind this phenomenon were not explored. The present study shows that HIV-1 enhances miR-34a in a time-dependent manner in T-cells. Our overexpression and knockdown-based experimental results suggest that miR-34a promotes HIV-1 replication in T-cells. Hence, there is a positive feedback loop between miR-34a and HIV-1 replication. We show that the mechanism of action of miR-34a in HIV-1 replication involves a cellular protein, the phosphatase 1 nuclear-targeting subunit (PNUTS). PNUTS expression levels decrease with the progression of HIV-1 infection in T-cells. Also, the overexpression of PNUTS potently inhibits HIV-1 replication in a dose-dependent manner. We report for the first time that PNUTS negatively regulates HIV-1 transcription by inhibiting the assembly of core components of the transcription elongation factor P-TEFb, i.e. cyclin T1 and CDK9. Thus, HIV-1 increases miR-34a expression in cells to overcome the inhibitory effect of PNUTS on HIV-1 transcription. So, the present study provides new mechanistic details with regard to our understanding of a complex interplay between miR-34a and the HIV-1 transcription machinery involving PNUTS.
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Felgueiras J, Fardilha M. Phosphoprotein phosphatase 1-interacting proteins as therapeutic targets in prostate cancer. World J Pharmacol 2014; 3:120-139. [DOI: 10.5497/wjp.v3.i4.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 09/01/2014] [Accepted: 09/24/2014] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer is a major public health concern worldwide, being one of the most prevalent cancers in men. Great improvements have been made both in terms of early diagnosis and therapeutics. However, there is still an urgent need for reliable biomarkers that could overcome the lack of cancer-specificity of prostate-specific antigen, as well as alternative therapeutic targets for advanced metastatic cases. Reversible phosphorylation of proteins is a post-translational modification critical to the regulation of numerous cellular processes. Phosphoprotein phosphatase 1 (PPP1) is a major serine/threonine phosphatase, whose specificity is determined by its interacting proteins. These interactors can be PPP1 substrates, regulators, or even both. Deregulation of this protein-protein interaction network alters cell dynamics and underlies the development of several cancer hallmarks. Therefore, the identification of PPP1 interactome in specific cellular context is of crucial importance. The knowledge on PPP1 complexes in prostate cancer remains scarce, with only 4 holoenzymes characterized in human prostate cancer models. However, an increasing number of PPP1 interactors have been identified as expressed in human prostate tissue, including the tumor suppressors TP53 and RB1. Efforts should be made in order to identify the role of such proteins in prostate carcinogenesis, since only 26 have yet well-recognized roles. Here, we revise literature and human protein databases to provide an in-depth knowledge on the biological significance of PPP1 complexes in human prostate carcinogenesis and their potential use as therapeutic targets for the development of new therapies for prostate cancer.
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35
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Xing Z, Lin A, Li C, Liang K, Wang S, Liu Y, Park PK, Qin L, Wei Y, Hawke DH, Hung MC, Lin C, Yang L. lncRNA directs cooperative epigenetic regulation downstream of chemokine signals. Cell 2014; 159:1110-1125. [PMID: 25416949 DOI: 10.1016/j.cell.2014.10.013] [Citation(s) in RCA: 336] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 07/07/2014] [Accepted: 09/24/2014] [Indexed: 11/17/2022]
Abstract
lncRNAs are known to regulate a number of different developmental and tumorigenic processes. Here, we report a role for lncRNA BCAR4 in breast cancer metastasis that is mediated by chemokine-induced binding of BCAR4 to two transcription factors with extended regulatory consequences. BCAR4 binding of SNIP1 and PNUTS in response to CCL21 releases the SNIP1's inhibition of p300-dependent histone acetylation, which in turn enables the BCAR4-recruited PNUTS to bind H3K18ac and relieve inhibition of RNA Pol II via activation of the PP1 phosphatase. This mechanism activates a noncanonical Hedgehog/GLI2 transcriptional program that promotes cell migration. BCAR4 expression correlates with advanced breast cancers, and therapeutic delivery of locked nucleic acids (LNAs) targeting BCAR4 strongly suppresses breast cancer metastasis in mouse models. The findings reveal a disease-relevant lncRNA mechanism consisting of both direct coordinated protein recruitment and indirect regulation of transcription factors.
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Affiliation(s)
- Zhen Xing
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aifu Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunlai Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ke Liang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shouyu Wang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yang Liu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter K Park
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Li Qin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yongkun Wei
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David H Hawke
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Cancer Biology Program, The University of Texas Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Cancer Biology Program, The University of Texas Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Cancer Biology Program, The University of Texas Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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36
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Jérôme M, Paudel HK. 14-3-3ζ regulates nuclear trafficking of protein phosphatase 1α (PP1α) in HEK-293 cells. Arch Biochem Biophys 2014; 558:28-35. [DOI: 10.1016/j.abb.2014.06.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/09/2014] [Accepted: 06/11/2014] [Indexed: 12/24/2022]
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37
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Di Giammartino DC, Manley JL. New links between mRNA polyadenylation and diverse nuclear pathways. Mol Cells 2014; 37:644-9. [PMID: 25081038 PMCID: PMC4179132 DOI: 10.14348/molcells.2014.0177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 06/28/2014] [Indexed: 11/27/2022] Open
Abstract
The 3' ends of most eukaryotic messenger RNAs must undergo a maturation step that includes an endonuc-leolytic cleavage followed by addition of a polyadenylate tail. While this reaction is catalyzed by the action of only two enzymes it is supported by an unexpectedly large number of proteins. This complexity reflects the necessity of coordinating this process with other nuclear events, and growing evidence indicates that even more factors than previously thought are necessary to connect 3' processing to additional cellular pathways. In this review we summarize the current understanding of the molecular machinery involved in this step of mRNA maturation, focusing on new core and auxiliary proteins that connect polyadenylation to splicing, DNA damage, transcription and cancer.
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Affiliation(s)
| | - James L Manley
- Columbia University, Department of Biological Sciences, New York NY, 10027, USA
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Fisher LA, Wang L, Wu L, Peng A. Phosphatase 1 nuclear targeting subunit is an essential regulator of M-phase entry, maintenance, and exit. J Biol Chem 2014; 289:23745-52. [PMID: 25002584 DOI: 10.1074/jbc.m114.572149] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitotic progression is regulated largely through dynamic and reversible protein phosphorylation that is modulated by opposing actions of protein kinases and phosphatases. In this study, we show that phosphatase 1 nuclear targeting subunit (Pnuts) functions as a master regulator of mitosis by modulating protein phosphatase 1 (PP1). Overexpression of Pnuts in Xenopus egg extracts inhibited both mitotic and meiotic exit. Immunodepletion of Pnuts from egg extracts revealed its essential functions in mitotic entry and maintenance. The level of Pnuts oscillates during the cell cycle and peaks in mitosis. Pnuts destruction during M-phase exit is mediated by the anaphase-promoting complex/cyclosome (APC/C)-targeted ubiquitination and proteolysis, and conserved destruction motifs of Pnuts. Disruption of Pnuts degradation delayed M-phase exit, suggesting it as an important mechanism to permit M-phase exit.
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Affiliation(s)
- Laura A Fisher
- From the Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska 68583
| | - Ling Wang
- From the Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska 68583
| | - Lan Wu
- From the Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska 68583
| | - Aimin Peng
- From the Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska 68583
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Understanding the antagonism of retinoblastoma protein dephosphorylation by PNUTS provides insights into the PP1 regulatory code. Proc Natl Acad Sci U S A 2014; 111:4097-102. [PMID: 24591642 DOI: 10.1073/pnas.1317395111] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The serine/threonine protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets by associating with nearly 200 regulatory proteins to form highly specific holoenzymes. However, how these proteins direct PP1 specificity and the ability to predict how these PP1 interacting proteins bind PP1 from sequence alone is still missing. PP1 nuclear targeting subunit (PNUTS) is a PP1 targeting protein that, with PP1, plays a central role in the nucleus, where it regulates chromatin decondensation, RNA processing, and the phosphorylation state of fundamental cell cycle proteins, including the retinoblastoma protein (Rb), p53, and MDM2. The molecular function of PNUTS in these processes is completely unknown. Here, we show that PNUTS, which is intrinsically disordered in its free form, interacts strongly with PP1 in a highly extended manner. Unexpectedly, PNUTS blocks one of PP1's substrate binding grooves while leaving the active site accessible. This interaction site, which we have named the arginine site, allowed us to define unique PP1 binding motifs, which advances our ability to predict how more than a quarter of the known PP1 regulators bind PP1. Additionally, the structure shows how PNUTS inhibits the PP1-mediated dephosphorylation of critical substrates, especially Rb, by blocking their binding sites on PP1, insights that are providing strategies for selectively enhancing Rb activity.
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Ciurciu A, Duncalf L, Jonchere V, Lansdale N, Vasieva O, Glenday P, Rudenko A, Vissi E, Cobbe N, Alphey L, Bennett D. PNUTS/PP1 regulates RNAPII-mediated gene expression and is necessary for developmental growth. PLoS Genet 2013; 9:e1003885. [PMID: 24204300 PMCID: PMC3814315 DOI: 10.1371/journal.pgen.1003885] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 09/03/2013] [Indexed: 12/25/2022] Open
Abstract
In multicellular organisms, tight regulation of gene expression ensures appropriate tissue and organismal growth throughout development. Reversible phosphorylation of the RNA Polymerase II (RNAPII) C-terminal domain (CTD) is critical for the regulation of gene expression states, but how phosphorylation is actively modified in a developmental context remains poorly understood. Protein phosphatase 1 (PP1) is one of several enzymes that has been reported to dephosphorylate the RNAPII CTD. However, PP1's contribution to transcriptional regulation during animal development and the mechanisms by which its activity is targeted to RNAPII have not been fully elucidated. Here we show that the Drosophila orthologue of the PP1 Nuclear Targeting Subunit (dPNUTS) is essential for organismal development and is cell autonomously required for growth of developing tissues. The function of dPNUTS in tissue development depends on its binding to PP1, which we show is targeted by dPNUTS to RNAPII at many active sites of transcription on chromosomes. Loss of dPNUTS function or specific disruption of its ability to bind PP1 results in hyperphosphorylation of the RNAPII CTD in whole animal extracts and on chromosomes. Consistent with dPNUTS being a global transcriptional regulator, we find that loss of dPNUTS function affects the expression of the majority of genes in developing 1st instar larvae, including those that promote proliferative growth. Together, these findings shed light on the in vivo role of the PNUTS-PP1 holoenzyme and its contribution to the control of gene expression during early Drosophila development. During development, cells rely on appropriate patterns of gene expression to regulate metabolism in order to meet cellular demands and maintain rapid tissue growth. Conversely, dysregulation of gene expression is critical in various disease states, such as cancer, and during ageing. A key mechanism that is ubiquitously employed to control gene expression is reversible phosphorylation, a molecular switch that is used to regulate the activity of the transcriptional machinery. Here we identify an enzyme that binds to and regulates the phosphorylation state of RNA Polymerase II, a central component of the general transcription machinery. We also show that an essential role of this enzyme is to support normal patterns of gene expression that facilitate organismal growth. These findings are not only of relevance to the understanding of normal enzyme function but may also assist in the development of therapeutic strategies for the treatment of aberrant patterns of gene expression that occur during ageing and disease progression.
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Affiliation(s)
- Anita Ciurciu
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Louise Duncalf
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Vincent Jonchere
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Nick Lansdale
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Olga Vasieva
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Peter Glenday
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Department of Zoology, Oxford University, Oxford, United Kingdom
| | - Andreii Rudenko
- Department of Zoology, Oxford University, Oxford, United Kingdom
| | - Emese Vissi
- Department of Zoology, Oxford University, Oxford, United Kingdom
| | - Neville Cobbe
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Luke Alphey
- Department of Zoology, Oxford University, Oxford, United Kingdom
| | - Daimark Bennett
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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41
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Korrodi-Gregório L, Ferreira M, Vintém AP, Wu W, Muller T, Marcus K, Vijayaraghavan S, Brautigan DL, da Cruz E Silva OAB, Fardilha M, da Cruz E Silva EF. Identification and characterization of two distinct PPP1R2 isoforms in human spermatozoa. BMC Cell Biol 2013; 14:15. [PMID: 23506001 PMCID: PMC3606321 DOI: 10.1186/1471-2121-14-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 03/11/2013] [Indexed: 11/29/2022] Open
Abstract
Background Protein Ser/Thr Phosphatase PPP1CC2 is an alternatively spliced isoform of PPP1C that is highly enriched in testis and selectively expressed in sperm. Addition of the phosphatase inhibitor toxins okadaic acid or calyculin A to caput and caudal sperm triggers and stimulates motility, respectively. Thus, the endogenous mechanisms of phosphatase inhibition are fundamental for controlling sperm function and should be characterized. Preliminary results have shown a protein phosphatase inhibitor activity resembling PPP1R2 in bovine and primate spermatozoa. Results Here we show conclusively, for the first time, that PPP1R2 is present in sperm. In addition, we have also identified a novel protein, PPP1R2P3. The latter was previously thought to be an intron-less pseudogene. We show that the protein corresponding to the pseudogene is expressed. It has PPP1 inhibitory potency similar to PPP1R2. The potential phosphosites in PPP1R2 are substituted by non-phosphorylable residues, T73P and S87R, in PPP1R2P3. We also confirm that PPP1R2/PPP1R2P3 are phosphorylated at Ser121 and Ser122, and report a novel phosphorylation site, Ser127. Subfractionation of sperm structures show that PPP1CC2, PPP1R2/PPP1R2P3 are located in the head and tail structures. Conclusions The conclusive identification and localization of sperm PPP1R2 and PPP1R2P3 lays the basis for future studies on their roles in acrosome reaction, sperm motility and hyperactivation. An intriguing possibility is that a switch in PPP1CC2 inhibitory subunits could be the trigger for sperm motility in the epididymis and/or sperm hyperactivation in the female reproductive tract.
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Affiliation(s)
- Luis Korrodi-Gregório
- Laboratory of Signal Transduction, Centre for Cell Biology, Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal
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Kavela S, Shinde SR, Ratheesh R, Viswakalyan K, Bashyam MD, Gowrishankar S, Vamsy M, Pattnaik S, Rao S, Sastry RA, Srinivasulu M, Chen J, Maddika S. PNUTS functions as a proto-oncogene by sequestering PTEN. Cancer Res 2013; 73:205-14. [PMID: 23117887 PMCID: PMC3538077 DOI: 10.1158/0008-5472.can-12-1394] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PTEN is a well-defined tumor suppressor gene that antagonizes the PI3K/Akt pathway to regulate a multitude of cellular processes, such as survival, growth, motility, invasiveness, and angiogenesis. While the functions of PTEN have been studied extensively, the regulation of its activity during normal and disease conditions still remains incompletely understood. In this study, we identified the protein phosphatase-1 nuclear targeting subunit PNUTS (PPP1R10) as a PTEN-associated protein. PNUTS directly interacted with the lipid-binding domain (C2 domain) of PTEN and sequestered it in the nucleus. Depletion of PNUTS leads to increased apoptosis and reduced cellular proliferation in a PTEN-dependent manner. PNUTS expression was elevated in certain cancers compared with matched normal tissues. Collectively, our studies reveal PNUTS as a novel PTEN regulator and a likely oncogene.
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Affiliation(s)
- Sridhar Kavela
- Laboratory of Cell Death & Cell Survival, Nampally, Hyderabad 500001, INDIA
| | - Swapnil R Shinde
- Laboratory of Cell Death & Cell Survival, Nampally, Hyderabad 500001, INDIA
| | - Raman Ratheesh
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, INDIA
| | - Kotapalli Viswakalyan
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, INDIA
| | - Murali D Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, INDIA
| | | | - Mohana Vamsy
- Indo-American Cancer Institute and Research centre, Hyderabad 500034, INDIA
| | - Sujit Pattnaik
- Indo-American Cancer Institute and Research centre, Hyderabad 500034, INDIA
| | | | | | - Mukta Srinivasulu
- MNJ Institute of Oncology and regional cancer centre, Hyderabad 500004, INDIA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Subbareddy Maddika
- Laboratory of Cell Death & Cell Survival, Nampally, Hyderabad 500001, INDIA
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Pinheiro AS, Marsh JA, Forman-Kay JD, Peti W. Structural signature of the MYPT1-PP1 interaction. J Am Chem Soc 2010; 133:73-80. [PMID: 21142030 DOI: 10.1021/ja107810r] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Muscle relaxation is triggered by the dephosphorylation of Ser19 in the myosin regulatory light chain. This reaction is catalyzed by the holoenzyme myosin phosphatase (MP), which includes the catalytic subunit protein phosphatase 1 (PP1) and the regulatory targeting subunit (MYPT). MYPT1 (myosin phosphatase targeting subunit 1) is responsible for both targeting the holoenzyme to subcellular compartments in the muscle and directing PP1 specificity toward myosin. To understand the molecular events leading to the MYPT1-PP1 holoenzyme formation, we used NMR spectroscopy to determine the structural and dynamic characteristics of unbound MYPT1. This allowed the conformations of MYPT1 in the free, unbound state to be directly compared to the PP1-bound state. Our results show that MYPT1(1-98) behaves like a two-domain protein in solution. The first 40 residues of MYPT1(1-98), the disordered region, are intrinsically disordered and highly dynamic, whereas residues 41-98, the folded ankyrin-repeat region, are well-structured and rigid. Furthermore, the integrated use of NMR and biophysical data enabled us to calculate an ensemble model for MYPT1(1-98). The most prominent structural feature of the MYPT1(1-98) ensemble is a 25% populated transient α-helix in the disordered region of MYPT1(1-98). This α-helix becomes fully populated when bound to PP1 and, as we show, likely plays a central role in the formation of the MYPT1-PP1 holoenzyme complex. Finally, this combined analysis shows that the structural and dynamic behaviors exhibited by MYPT1 for PP1 are distinct from those of any other previously analyzed PP1 regulatory protein. Collectively, these data enable us to present a new model of the molecular events that drive MYPT1-PP1 holoenzyme formation and demonstrate that there are structural differences in unbound PP1 regulators that have not been previously observed. Thus, this work adds significant insights to the currently limited data for molecular structures and dynamics of PP1 regulators.
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Affiliation(s)
- Anderson S Pinheiro
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island 02903, USA
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44
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De Leon G, Cavino M, D'Angelo M, Krucher NA. PNUTS knockdown potentiates the apoptotic effect of Roscovitine in breast and colon cancer cells. Int J Oncol 2010; 36:1269-75. [PMID: 20372802 DOI: 10.3892/ijo_00000611] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The phosphorylation state of Retinoblastoma protein (Rb) plays a role in cell proliferation and apoptosis. Within cells, cyclin dependent kinases (cdks) phosphorylate Rb in response to growth stimulatory signals, whereas protein phosphatase 1 (PP1) dephosphorylates Rb when cells stop proliferating or undergo apoptosis in response to anti-proliferative or stress signals. Stimulation of PP1 activity via siRNA mediated knockdown of its interacting protein PNUTS (Phosphatase Nuclear Targeting Subunit) leads to Rb dephosphorylation and apoptosis in cancer cells. We utilized two separate methods to modulate the phosphorylation state of Rb in cancer cells. Kinase activity toward Rb is inhibited by the clinically relevant cdk inhibitor, Roscovitine. In addition, siRNA mediated PNUTS knockdown stimulates phosphatase activity toward Rb. Either of these treatments in cancer cells causes a 2-fold stimulation of apoptosis. When activation of phosphatase activity is combined with inhibition of cdk activity toward Rb, however, cells exhibit a 4-fold increase in apoptosis. The mechanism by which PNUTS knockdown mediated PP1 activation leads to apoptosis was determined to be dependent on the activity of the transcription factor E2F1. The Rb phosphorylation profiles resulting from each treatment were analyzed and found to be similar but not identical. In addition, the two treatments differentially effect the expression of bcl-2 family proteins. Thus inhibition of cdk activity and activation of PP1 activity toward pRb are functionally distinct processes that together increase the apoptotic effect in cells.
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Affiliation(s)
- Gabriel De Leon
- Department of Biology and Health Science, Pace University, Pleasantville, NY 10570, USA
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45
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The protein phosphatase 1 regulator PNUTS is a new component of the DNA damage response. EMBO Rep 2010; 11:868-75. [PMID: 20890310 DOI: 10.1038/embor.2010.134] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 08/09/2010] [Accepted: 08/11/2010] [Indexed: 12/17/2022] Open
Abstract
The function of protein phosphatase 1 nuclear-targeting subunit (PNUTS)--one of the most abundant nuclear-targeting subunits of protein phosphatase 1 (PP1c)--remains largely uncharacterized. We show that PNUTS depletion by small interfering RNA activates a G2 checkpoint in unperturbed cells and prolongs G2 checkpoint and Chk1 activation after ionizing-radiation-induced DNA damage. Overexpression of PNUTS-enhanced green fluorescent protein (EGFP)--which is rapidly and transiently recruited at DNA damage sites--inhibits G2 arrest. Finally, γH2AX, p53-binding protein 1, replication protein A and Rad51 foci are present for a prolonged period and clonogenic survival is decreased in PNUTS-depleted cells after ionizing radiation treatment. We identify the PP1c regulatory subunit PNUTS as a new and integral component of the DNA damage response involved in DNA repair.
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46
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Lee JH, You J, Dobrota E, Skalnik DG. Identification and characterization of a novel human PP1 phosphatase complex. J Biol Chem 2010; 285:24466-76. [PMID: 20516061 DOI: 10.1074/jbc.m110.109801] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mammalian Wdr82 is a regulatory component of the Setd1a and Setd1b histone H3-lysine 4 methyltransferase complexes and is implicated in the tethering of Setd1 complexes to transcriptional start sites of active genes. In the studies reported here, immunoprecipitation and mass spectrometry analyses reveal that Wdr82 additionally associates with multiple protein complexes, including an RNA polymerase II complex, four distinct histone H3-Lys(4) methyltransferase complexes, protein phosphatase 1 (PP1)-associated proteins, a chaperonin-containing Tcp1 complex, and other uncharacterized proteins. Further characterization of the PP1-associated proteins identified a stable multimeric complex composed of regulatory subunits PNUTS, Tox4, and Wdr82 and a PP1 catalytic subunit (denoted as the PTW/PP1 phosphatase complex). The PTW/PP1 complex exhibits in vitro phosphatase activity in a PP1-dependent manner. Analysis of protein-protein interactions reveals that PNUTS mediates phosphatase complex formation by providing a binding platform to each component. The PNUTS and Tox4 subunits are predominantly associated with the PTW/PP1 phosphatase complex in HEK293 cells, and the integrity of this complex remains intact throughout cell cycle progression. Inducible expression of a PP1 interaction-defective form of PNUTS (W401A) or small interfering RNA-mediated depletion of PNUTS in HEK293 cells causes cell cycle arrest at mitotic exit and apoptotic cell death. PNUTS (W401A) shows normal association with chromosomes but causes defects in the process of chromosome decondensation at late telophase. These data reveal that mammalian Wdr82 functions in a variety of cellular processes and reveal a potential role of the PTW/PP1 phosphatase complex in the regulation of chromatin structure during the transition from mitosis into interphase.
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Affiliation(s)
- Jeong-Heon Lee
- Wells Center for Pediatric Research, Section of Pediatric Hematology/Oncology, Department of Pediatrics and Biochemistry, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.
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Bollen M, Peti W, Ragusa MJ, Beullens M. The extended PP1 toolkit: designed to create specificity. Trends Biochem Sci 2010; 35:450-8. [PMID: 20399103 DOI: 10.1016/j.tibs.2010.03.002] [Citation(s) in RCA: 381] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 03/03/2010] [Accepted: 03/04/2010] [Indexed: 01/03/2023]
Abstract
Protein Ser/Thr phosphatase-1 (PP1) catalyzes the majority of eukaryotic protein dephosphorylation reactions in a highly regulated and selective manner. Recent studies have identified an unusually diversified PP1 interactome with the properties of a regulatory toolkit. PP1-interacting proteins (PIPs) function as targeting subunits, substrates and/or inhibitors. As targeting subunits, PIPs contribute to substrate selection by bringing PP1 into the vicinity of specific substrates and by modulating substrate specificity via additional substrate docking sites or blocking substrate-binding channels. Many of the nearly 200 established mammalian PIPs are predicted to be intrinsically disordered, a property that facilitates their binding to a large surface area of PP1 via multiple docking motifs. These novel insights offer perspectives for the therapeutic targeting of PP1 by interfering with the binding of PIPs or substrates.
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Affiliation(s)
- Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, Department of Molecular Cell Biology, University of Leuven, B-3000 Leuven, Belgium.
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48
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Lee SJ, Lee JK, Maeng YS, Kim YM, Kwon YG. Langerhans cell protein 1 (LCP1) binds to PNUTS in the nucleus: implications for this complex in transcriptional regulation. Exp Mol Med 2009; 41:189-200. [PMID: 19293638 DOI: 10.3858/emm.2009.41.3.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Protein phosphatase-1 (PP1) nuclear targeting subunit (PNUTS), also called PP1R10, p99, or CAT 53 was originally isolated as a mammalian nuclear PP1-binding protein. In this study, we performed yeast two-hybrid screens to identify PNUTS-interacting proteins. Here, we report that LCP1 (epidermal Langerhans cell protein 1), a novel member of the HMG-box protein family, binds tightly to PNUTS. Co-immunoprecipitation of deletion constructs revealed that the C-terminus of LCP1 is sufficient for the interaction with an N-terminal region of PNUTS that is distinct from its PP1-binding domain. Furthermore, immunofluorescence studies showed that a subpopulation of LCP1 co-localizes with PNUTS in nuclear speckles. Importantly, we found that the N-terminus of LCP1 has a strong trans-activation activity in a GAL4-based heterologous transcription assay. The transcriptional activity of LCP1 is markedly suppressed by its interaction with PNUTS, in a PP1-independent manner. These findings suggest that the coordinated spatial and temporal regulation of LCP1 and PNUTS may be a novel mechanism to control the expression of genes that are critical for certain physiological and pathological processes.
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Affiliation(s)
- Shin Jeong Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-752, Korea
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Liersch T, Grade M, Gaedcke J, Varma S, Difilippantonio MJ, Langer C, Hess CF, Becker H, Ried T, Ghadimi BM. Preoperative chemoradiotherapy in locally advanced rectal cancer: correlation of a gene expression-based response signature with recurrence. ACTA ACUST UNITED AC 2009; 190:57-65. [PMID: 19380020 DOI: 10.1016/j.cancergencyto.2008.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Revised: 11/10/2008] [Accepted: 11/10/2008] [Indexed: 10/20/2022]
Abstract
Preoperative chemoradiotherapy is recommended for locally advanced rectal cancer (UICC stage II/III). We recently demonstrated that responsive and nonresponsive tumors showed differential expression levels of 54 genes. In this follow-up study, we investigated the relationship between this gene set and disease-free (DFS) and overall survival (OS). Pretherapeutic biopsies from 30 participants in the CAO/ARO/AIO-94 trial of the German Rectal Cancer Study Group were analyzed using gene expression microarrays. Statistical analysis was performed to identify differentially expressed genes between recurrent and nonrecurrent tumors and to correlate these changes with disease recurrence and outcome. After a median follow-up of 59 months, seven of eight patients with recurrent disease was a nonresponder, and one responsive tumor recurred. Response to chemoradiotherapy was significantly correlated with an improved DFS (log rank P=0.028), whereas OS did not differ significantly (P=0.11). Applying a class comparison analysis, we identified 20 genes that were differentially expressed between recurrent and nonrecurrent tumors (P<0.001). Analyzing the first two principal components of the 54 genes previously identified to predict response, we observed that this response signature correlated with an increased risk of cancer recurrence. These data suggest that the genetic basis of local response also affects the genetic basis of tumor recurrence. Genes that are indicative of nonresponse to preoperative chemoradiotherapy might also be linked to an increased risk of tumor recurrence.
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Affiliation(s)
- Torsten Liersch
- Department of General and Visceral Surgery, University Medical Center, Georg-August-University, Robert Koch Str. 40, 37075 Göttingen, Germany
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50
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Mellström B, Savignac M, Gomez-Villafuertes R, Naranjo JR. Ca2+-Operated Transcriptional Networks: Molecular Mechanisms and In Vivo Models. Physiol Rev 2008; 88:421-49. [DOI: 10.1152/physrev.00041.2005] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Calcium is the most universal signal used by living organisms to convey information to many different cellular processes. In this review we present well-known and recently identified proteins that sense and decode the calcium signal and are key elements in the nucleus to regulate the activity of various transcriptional networks. When possible, the review also presents in vivo models in which the genes encoding these calcium sensors-transducers have been modified, to emphasize the critical role of these Ca2+-operated mechanisms in many physiological functions.
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