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Xie Q, Kasahara K, Higo J, Takahashi T. Molecular Mechanisms of Functional Modulation of Transcriptional Coactivator PC4 via Phosphorylation on Its Intrinsically Disordered Region. ACS OMEGA 2023; 8:14572-14582. [PMID: 37125110 PMCID: PMC10134458 DOI: 10.1021/acsomega.3c00364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
To investigate the effects of phosphorylation on the function of the human positive cofactor 4 (PC4), an enhanced molecular dynamics (MD) simulation was performed. The simulation system consists of the N-terminal intrinsic disordered region (IDR) of PC4 and a complex that comprises the C-terminal acidic activation domain of a herpes simplex virion protein 16 (VP16ad) and a homodimer of the C-terminal structured core domain of PC4 (PC4ctd). An earlier report of an experimental study reported that the PC4-VP16ad interaction is modulated by incremental phosphorylation of the IDR. That report also proposed a dynamic model where phosphorylated serine residues of a segment (SEAC) in the IDR contact positively charged residues (lysin and arginine) of another segment (K-rich) in the IDR. This contact formation induced by the phosphorylation results in variation of PC4-VP16ad interaction. However, this contact formation has not yet been measured directly because it is transiently formed and because the SEAC and K-rich segments are unstructured with high flexibility. We performed two simulations to mimic the incremental phosphorylation: the IDR was not phosphorylated in one simulation and only partially phosphorylated in the other. Our simulation results indicate that the phosphorylation weakens the IDR-VP16ad contact considerably with the induction of a compact structure in the IDR. This structure was stabilized by electrostatic interactions between the phosphorylated serine residues of a segment and lysine or arginine residues of another segment in the IDR, but the conformational fluctuation of this compact structure was considerably large. Consequently, the present study supports the experimentally proposed dynamic model. Results of this study can be important for computational elucidation of the functional modulation of PC4.
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Affiliation(s)
- Qilin Xie
- Graduate
School of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Kota Kasahara
- College
of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Junichi Higo
- Graduate
School of Information Science, University
of Hyogo, 7-1-28 minatojima
Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Research
Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Takuya Takahashi
- College
of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
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2
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Collin A, González-Jiménez A, González-Jiménez MDC, Alfonso MJ, Calvo O. The Role of S. cerevisiae Sub1/PC4 in Transcription Elongation Depends on the C-Terminal Region and Is Independent of the ssDNA Binding Domain. Cells 2022; 11:cells11203320. [PMID: 36291192 PMCID: PMC9600219 DOI: 10.3390/cells11203320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
Saccharomyces cerevisiae Sub1 (ScSub1) has been defined as a transcriptional stimulatory protein due to its homology to the ssDNA binding domain (ssDBD) of human PC4 (hPC4). Recently, PC4/Sub1 orthologues have been elucidated in eukaryotes, prokaryotes, and bacteriophages with functions related to DNA metabolism. Additionally, ScSub1 contains a unique carboxyl–terminal region (CT) of unknown function up to date. Specifically, it has been shown that Sub1 is required for transcription activation, as well as other processes, throughout the transcription cycle. Despite the progress that has been made in understanding the mechanism underlying Sub1′s functions, some questions remain unanswered. As a case in point: whether Sub1’s roles in initiation and elongation are differentially predicated on distinct regions of the protein or how Sub1′s functions are regulated. Here, we uncover some residues that are key for DNA–ScSub1 interaction in vivo, localized in the ssDBD, and required for Sub1 recruitment to promoters. Furthermore, using an array of genetic and molecular techniques, we demonstrate that the CT region is required for transcription elongation by RNA polymerase II (RNAPII). Altogether, our data indicate that Sub1 plays a dual role during transcription—in initiation through the ssDBD and in elongation through the CT region.
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Affiliation(s)
- Alejandro Collin
- Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas-INICSA, CONICET-Universidad Nacional de Córdoba, Haya de la Torre s/n, Pabellón Argentina, 2º piso. Ciudad Universitaria, Cordoba CP5000, Argentina
| | - Araceli González-Jiménez
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
| | | | - Manuel J. Alfonso
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
- Correspondence:
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3
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Rojas DA, Urbina F, Solari A, Maldonado E. The Catalytic Subunit of Schizosaccharomyces pombe CK2 (Cka1) Negatively Regulates RNA Polymerase II Transcription through Phosphorylation of Positive Cofactor 4 (PC4). Int J Mol Sci 2022; 23:ijms23169499. [PMID: 36012759 PMCID: PMC9409219 DOI: 10.3390/ijms23169499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 01/04/2023] Open
Abstract
Positive cofactor 4 (PC4) is a transcriptional coactivator that plays important roles in transcription and DNA replication. In mammals, PC4 is phosphorylated by CK2, and this event downregulates its RNA polymerase II (RNAPII) coactivator function. This work describes the effect of fission yeast PC4 phosphorylation on RNAPII transcription in a cell extract, which closely resembles the cellular context. We found that fission yeast PC4 is strongly phosphorylated by the catalytic subunit of CK2 (Cka1), while the regulatory subunit (Ckb1) downregulates the PC4 phosphorylation. The addition of Cka1 to an in vitro transcription assay can diminish the basal transcription from the Ad-MLP promoter; however, the addition of recombinant fission yeast PC4 or Ckb1 can stimulate the basal transcription in a cell extract. Fission yeast PC4 is phosphorylated in a domain which has consensus phosphorylation sites for CK2, and two serine residues were identified as critical for CK2 phosphorylation. Mutation of one of the serine residues in PC4 does not completely abolish the phosphorylation; however, when the two serine residues are mutated, CK2 is no longer able to phosphorylate PC4. The mutant which is not phosphorylated is able to stimulate transcription even though it is previously phosphorylated by Cka1, while the wild type and the point mutant are inactivated by Cka1 phosphorylation, and they cannot stimulate transcription by RNAPII in cell extracts. Those results demonstrate that CK2 can regulate the coactivator function of fission yeast PC4 and suggests that this event could be important in vivo as well.
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Affiliation(s)
- Diego A. Rojas
- Instituto de Ciencias Biomédicas (ICB), Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8910132, Chile
- Correspondence: (D.A.R.); (E.M.)
| | - Fabiola Urbina
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Aldo Solari
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Edio Maldonado
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile
- Correspondence: (D.A.R.); (E.M.)
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4
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Mustafi P, Hu M, Kumari S, Das C, Li G, Kundu T. Phosphorylation-dependent association of human chromatin protein PC4 to linker histone H1 regulates genome organization and transcription. Nucleic Acids Res 2022; 50:6116-6136. [PMID: 35670677 PMCID: PMC9226532 DOI: 10.1093/nar/gkac450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 05/08/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Human Positive Coactivator 4 (PC4) is a multifaceted chromatin protein involved in diverse cellular processes including genome organization, transcription regulation, replication, DNA repair and autophagy. PC4 exists as a phospho-protein in cells which impinges on its acetylation by p300 and thereby affects its transcriptional co-activator functions via double-stranded DNA binding. Despite the inhibitory effects, the abundance of phosphorylated PC4 in cells intrigued us to investigate its role in chromatin functions in a basal state of the cell. We found that casein kinase-II (CKII)-mediated phosphorylation of PC4 is critical for its interaction with linker histone H1. By employing analytical ultracentrifugation and electron microscopy imaging of in vitro reconstituted nucleosomal array, we observed that phospho-mimic (PM) PC4 displays a superior chromatin condensation potential in conjunction with linker histone H1. ATAC-sequencing further unveiled the role of PC4 phosphorylation to be critical in inducing chromatin compaction of a wide array of coding and non-coding genes in vivo. Concordantly, phospho-PC4 mediated changes in chromatin accessibility led to gene repression and affected global histone modifications. We propose that the abundance of PC4 in its phosphorylated state contributes to genome compaction contrary to its co-activator function in driving several cellular processes like gene transcription and autophagy.
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Affiliation(s)
- Pallabi Mustafi
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Mingli Hu
- National laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Sujata Kumari
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Chandrima Das
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Guohong Li
- National laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Jankipuram Extension, Lucknow 226031, India
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5
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Zhang J, Liao H, Xun X, Hou X, Zhu X, Xing Q, Huang X, Hu J, Bao Z. Identification, characterization and expression analyses of PC4 genes in Yesso scallop (Patinopecten yessoensis) reveal functional differentiations in response to ocean acidification. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 244:106099. [PMID: 35114458 DOI: 10.1016/j.aquatox.2022.106099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/15/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Transcriptional coactivator p15 (PC4), considered a multifunctional chromosome associated protein, is actively involved in transcription regulation, DNA replication, damage repair and chromosome formation. Although studies have reported significant effects of PC4 in most vertebrates and some invertebrates, the complete PC4 gene members are less systematically identified and characterized in scallops. In this study, seven PC4 genes (PyPC4s) were identified in the Yesso scallop Patinopecten yessoensis using whole-genome scanning via bioinformatic analyses. Phylogenetic and protein structural analyses were performed to determine the identities and evolutionary relationships of the seven genes. Expression profiles of PyPC4s were further investigated in embryos/larvae at all developmental stages, healthy adult tissues, and mantles that were exposed to low pH stress (pH 6.5 and 7.5) with different time durations (3, 6, 12 and 24 h). Spatiotemporal expression patterns indicated the functional roles of PyPC4s at all development stages and in healthy adult tissues, with PY-3235.33 demonstrating remarkably high constitutive expressions. Expression regulations (up- and down-regulation) of PyPC4s under low pH stress levels demonstrated a time-dependent pattern with functional complementation and/or enhancement, revealing that PyPC4s exhibited differentiated functions in response to ocean acidification (OA). Collectively, our data offer a novel perspective stating that low pH is a potential inducer leading to functional differentiation of PyPC4s in scallops. The results provide preliminary information on the versatile roles of PC4(s) in bivalves in response to OA.
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Affiliation(s)
- Junhao Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaogang Xun
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Qilu University of Technology (Shandong Academy of Sciences), China
| | - Xiujiang Hou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xinghai Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution of the Ocean University of China (SOI-OUC), Sanya 572000, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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6
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Huang R, Hu Z, Chen X, Cao Y, Li H, Zhang H, Li Y, Liang L, Feng Y, Wang Y, Su W, Kong Z, Melgiri ND, Jiang L, Li X, Du J, Chen Y. The Transcription Factor SUB1 Is a Master Regulator of the Macrophage TLR Response in Atherosclerosis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004162. [PMID: 34378353 PMCID: PMC8498911 DOI: 10.1002/advs.202004162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/24/2021] [Indexed: 12/26/2022]
Abstract
Toll-like receptor 2 and 4 (TLR2, TLR4) signaling is implicated in atherosclerotic plaque formation. The two-stage master regulator Virtual Inference of Protein-activity by Enriched Regulon (VIPER) analysis of macrophage TLR2 and TLR4 signature genes integrated with coexpression network genes derived from 371 patient-derived carotid specimens identifies activated RNA polymerase II transcriptional coactivator p15 (SUB1/Sub1, PC4) as a master regulon in the atherogenic TLR response. It is found that TLR2 and TLR4 signaling is proinflammatory and proatherosclerotic in chow-fed apolipoprotein E-deficient (ApoE-/- ) mice. Through transgenic myeloid-specific Sub1 knockout in ApoE-/- mice, it is discovered that these proatherosclerotic effects of TLR2 and TLR4 signaling are mediated by Sub1. Sub1 knockout in macrophages enhances anti-inflammatory M2 macrophage polarization and cholesterol efflux. Irradiated low density lipoprotein receptor-deficient (Ldlr-/- ) mice transplanted with Sub1-/- murine bone marrow display reduced atherosclerosis. Promoter analysis reveals Sub1-dependent activation of interferon regulatory factor 1 (Irf1) transcription in a casein kinase 2 (Ck2)-dependent manner, and Sub1-knockout macrophages display decreased Irf1 expression. Artificial Irf1 overexpression in Sub1-knockout macrophages enhances proinflammatory M1 skewing and lowers cholesterol clearance. In conclusion, the TLR master regulon Sub1, and its downstream effect on the transcription factor Irf1, promotes a proinflammatory M1 macrophage phenotype and enhances atherosclerotic burden in vivo.
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Affiliation(s)
- Rongzhong Huang
- Department of Geriatric MedicineThe Second Affiliated Hospital of Chongqing Medical UniversityChongqing400010China
| | - Zicheng Hu
- Institute of Ultrasound ImagingThe Second Affiliated Hospital of Chongqing Medical UniversityChongqing400010China
| | - Xiaorui Chen
- Department of Pulmonary and Critical Care MedicineThe Second Affiliated Hospital of Chongqing Medical UniversityChongqing400010China
| | - Yu Cao
- Department of Cardiothoracic SurgeryThe First People's Hospital of Yunnan ProvinceKunming650032China
| | - Hongrong Li
- Department of Cardiothoracic SurgeryThe First People's Hospital of Yunnan ProvinceKunming650032China
| | - Hong Zhang
- Department of CardiologyThe First People's Hospital of Yunnan ProvinceKunming650032China
| | - Yongyong Li
- Department of Geriatric MedicineThe Second Affiliated Hospital of Chongqing Medical UniversityChongqing400010China
| | - Liwen Liang
- Department of CardiologyThe First People's Hospital of Yunnan ProvinceKunming650032China
| | - Yuxing Feng
- Department of Rehabilitation and Pain MedicineThe Ninth People's Hospital of ChongqingChongqing400700China
| | - Ying Wang
- Department of Rehabilitation MedicineThe Second Affiliated Hospital of Chongqing Medical UniversityChongqing400010China
| | - Wenhua Su
- Department of CardiologyThe First People's Hospital of Yunnan ProvinceKunming650032China
| | - Zerui Kong
- Department of Cardiothoracic SurgeryThe Affiliated Yan An Hospital of Kunming Medical UniversityKunming650000China
- Yunnan Key Laboratory of Primate Biomedical ResearchKunming650500China
| | - ND Melgiri
- Impactys Foundation for Biomedical ResearchSan DiegoCA92121USA
| | - Lihong Jiang
- Department of Cardiothoracic SurgeryThe First People's Hospital of Yunnan ProvinceKunming650032China
| | - Xingsheng Li
- Department of Geriatric MedicineThe Second Affiliated Hospital of Chongqing Medical UniversityChongqing400010China
| | - Jianlin Du
- Department of CardiologyThe Second Affiliated Hospital of Chongqing Medical UniversityChongqing400010China
| | - Yunqing Chen
- Department of CardiologyThe Second Affiliated Hospital of Chongqing Medical UniversityChongqing400010China
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7
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Chen L, Liao F, Wu J, Wang Z, Jiang Z, Zhang C, Luo P, Ma L, Gong Q, Wang Y, Wang Q, Luo M, Yang Z, Han S, Shi C. Acceleration of ageing via disturbing mTOR-regulated proteostasis by a new ageing-associated gene PC4. Aging Cell 2021; 20:e13370. [PMID: 33957702 PMCID: PMC8208792 DOI: 10.1111/acel.13370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/21/2021] [Accepted: 03/31/2021] [Indexed: 01/08/2023] Open
Abstract
Research on ageing‐associated genes is important for investigating ageing and anti‐ageing strategies. Here, we firstly reported that the human positive cofactor 4 (PC4), a multifunctional and highly conserved nucleoprotein, is accumulated and activated during ageing and causes global accelerated ageing process by disrupting proteostasis. Mechanistically, PC4 interacts with Sin3‐HDAC complex and inhibits its deacetylated activity, leads to hyper‐acetylation of the histones at the promoters of mTOR‐related genes and causes mTOR signalling activation. Accordingly, mTOR activation causes excessive protein synthesis, resulting in impaired proteostasis and accelerated senescence. These results reveal a new biological function of PC4 in vivo, recognizes PC4 as a new ageing‐associated gene and provides a genetically engineered mouse model to simulate natural ageing. More importantly, our findings also indicate that PC4 is involved in histone acetylation and serves as a potential target to improve proteostasis and delay ageing.
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Affiliation(s)
- Long Chen
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Fengying Liao
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Jie Wu
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Ziwen Wang
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
- Department of Cardiology Geriatric Cardiovascular Disease Research and Treatment Center 252 Hospital of PLA (82nd Group Army Hospital of PLA) Baoding China
| | - Zhongyong Jiang
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Chi Zhang
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Peng Luo
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Le Ma
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Qiang Gong
- Department of Hematology Southwest Hospital Third Military Medical University Chongqing China
| | - Yang Wang
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Qing Wang
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Min Luo
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Zeyu Yang
- Breast and Thyroid Surgical Department Chongqing General Hospital University of Chinese Academy of Sciences Chongqing China
| | - Shiqian Han
- Institute of Tropical Medicine Third Military Medical University Chongqing China
| | - Chunmeng Shi
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
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8
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Ochiai K, Yamaoka M, Swaminathan A, Shima H, Hiura H, Matsumoto M, Kurotaki D, Nakabayashi J, Funayama R, Nakayama K, Arima T, Ikawa T, Tamura T, Sciammas R, Bouvet P, Kundu TK, Igarashi K. Chromatin Protein PC4 Orchestrates B Cell Differentiation by Collaborating with IKAROS and IRF4. Cell Rep 2020; 33:108517. [PMID: 33357426 DOI: 10.1016/j.celrep.2020.108517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/10/2020] [Accepted: 11/22/2020] [Indexed: 12/24/2022] Open
Abstract
The chromatin protein positive coactivator 4 (PC4) has multiple functions, including chromatin compaction. However, its role in immune cells is largely unknown. We show that PC4 orchestrates chromatin structure and gene expression in mature B cells. B-cell-specific PC4-deficient mice show impaired production of antibody upon antigen stimulation. The PC4 complex purified from B cells contains the transcription factors (TFs) IKAROS and IRF4. IKAROS protein is reduced in PC4-deficient mature B cells, resulting in de-repression of their target genes in part by diminished interactions with gene-silencing components. Upon activation, the amount of IRF4 protein is not increased in PC4-deficient B cells, resulting in reduction of plasma cells. Importantly, IRF4 reciprocally induces PC4 expression via a super-enhancer. PC4 knockdown in human B cell lymphoma and myeloma cells reduces IKAROS protein as an anticancer drug, lenalidomide. Our findings establish PC4 as a chromatin regulator of B cells and a possible therapeutic target adjoining IKAROS in B cell malignancies.
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Affiliation(s)
- Kyoko Ochiai
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan.
| | - Mari Yamaoka
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Amrutha Swaminathan
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Hitoshi Hiura
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Mitsuyo Matsumoto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Daisuke Kurotaki
- Department of Immunology, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Yokohama 236-0004, Japan
| | - Jun Nakabayashi
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Yokohama 236-0004, Japan
| | - Ryo Funayama
- Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan; Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Keiko Nakayama
- Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan; Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Tomokatsu Ikawa
- Division of Immunobiology, Tokyo University of Science, Yamazaki 2669, Noda 278-0022, Japan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Yokohama 236-0004, Japan; Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Yokohama 236-0004, Japan
| | - Roger Sciammas
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA
| | - Philippe Bouvet
- Université de Lyon, Ecole Normale Supérieure de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India.
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan.
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9
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Efficacy of a small molecule inhibitor of the transcriptional cofactor PC4 in prevention and treatment of non-small cell lung cancer. PLoS One 2020; 15:e0230670. [PMID: 32231397 PMCID: PMC7108703 DOI: 10.1371/journal.pone.0230670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 03/05/2020] [Indexed: 12/19/2022] Open
Abstract
The human positive coactivator 4 (PC4) was originally identified as a multi-functional cofactor capable of mediating transcription activation by diverse gene- and tissue-specific activators. Recent studies suggest that PC4 might also function as a novel cancer biomarker and therapeutic target for different types of cancers. siRNA knockdown studies indicated that down-regulation of PC4 expression could inhibit tumorigeneicity of A549 non-small cell lung cancer tumor model in nude mice. Here we show that AG-1031, a small molecule identified by high throughput screening, can inhibit the double-stranded DNA binding activity of PC4, more effectively than its single-stranded DNA binding activity. AG-1031 also specifically inhibited PC4-dependent transcriptional activation in vitro using purified transcription factors. AG-1031 inhibited proliferation of several cultured cell lines derived from non-small cell lung cancers (NSCLC) and growth of tumors that formed from A549 cell xenografts in immuno-compromised mice. Moreover, pre-injection of AG-1031 in these mice not only reduced tumor size, but also prevented tumor formation in 20% of the animals. AG-1031 treated A549 cells and tumors from AG-1031 treated animals showed a significant decrease in the levels of both PC4 and VEGFC, a key mediator of angiogenesis in cancer. On the other hand, all tested mice remained constant weight during animal trials. These results demonstrated that AG-1031 could be a potential therapy for PC4-positive NSCLC.
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10
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Zhao Y, Zhang Y, Huang J, Wang S, Yi L, Zhang X, Xu M, Fang X, Liu J. The effect of phosphate ion on the ssDNA binding mode of MoSub1, a Sub1/PC4 homolog from rice blast fungus. Proteins 2018; 87:257-264. [PMID: 30561148 DOI: 10.1002/prot.25647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/21/2018] [Accepted: 12/12/2018] [Indexed: 11/09/2022]
Abstract
MoSub1 is an ortholog of yeast single stranded DNA binding protein Sub1 or human PC4 from rice blast fungus. All of them share a similar DNA binding region and may have similar biological roles. The well-studied Sub1/PC4 has been reported to play multiple roles in DNA metabolic processes, such as transcription and DNA repair and their DNA binding capacity is significantly affected by phosphorylation. Here, we determined the crystal structure of MoSub1 complexed with ssDNA in a phosphate solution. The crystal structure of the MoSub1-ssDNA complex was solved to a resolution of 2.04 Å. A phosphate ion at the interface of the protein-DNA interaction of the complex bridged the lys84 of the protein and two nucleotides. The DNA was bound in novel mode (L mode) in the MoSub1 complex in the presence of phosphate ions, while DNA bound in the straight mode in the absence of the phosphate ion and in U mode in the same binding motif of the PC4-ssDNA complex. The crystal structure of the complex and a small-angle X-ray scattering analysis revealed that the phosphate ion at the protein-DNA interface affected the DNA binding mode of MoSub1 to oligo-DNA and provided a new structural clue for studying its functions.
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Affiliation(s)
- Yanxiang Zhao
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China.,College of Plant Health and Medicine, and Key Lab of Integrated Crop Disease and Pest Management of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yikan Zhang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinguang Huang
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China.,College of Plant Health and Medicine, and Key Lab of Integrated Crop Disease and Pest Management of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Shanshan Wang
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China
| | - Long Yi
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China.,Nanxiong Tobacco Research Institute of Guangdong, Nanxiong, Guangdong, China
| | - Xin Zhang
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China
| | - Min Xu
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Junfeng Liu
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China
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11
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Abstract
Sub1 was initially identified as a coactivator factor with a role during transcription initiation. However, over the last years, many evidences showed that it influences processes downstream during mRNA biogenesis, such as elongation, termination, and RNAPII phosphorylation. The recent discover that Sub1 directly interacts with the RNAPII stalk adds new insights into how it achieves all these tasks.
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Affiliation(s)
- Olga Calvo
- a Instituto de Biología Funcional y Genómica (CSIC) , Salamanca , Spain
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12
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Sub1/PC4, a multifaceted factor: from transcription to genome stability. Curr Genet 2017; 63:1023-1035. [DOI: 10.1007/s00294-017-0715-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 10/19/2022]
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13
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Shammas SL. Mechanistic roles of protein disorder within transcription. Curr Opin Struct Biol 2017; 42:155-161. [PMID: 28262589 DOI: 10.1016/j.sbi.2017.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/26/2017] [Accepted: 02/13/2017] [Indexed: 12/28/2022]
Abstract
Understanding the interactions of proteins involved in transcriptional regulation is critical to describing biological systems because they control the expression profile of the cell. Yet sadly they belong to a less well biophysically characterized subset of proteins; they frequently contain long disordered regions that are highly dynamic. A key question therefore is, why? What functional roles does protein disorder play in transcriptional regulation? Experimental data exemplifying these roles are starting to emerge, with common themes being enabling complexity within networks and quick responses. Most recently a role for disorder in mediating phase transitions of membrane-less organelles has been proposed.
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Affiliation(s)
- Sarah L Shammas
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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14
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Akimoto Y, Yamamoto S, Iida S, Hirose Y, Tanaka A, Hanaoka F, Ohkuma Y. Transcription cofactor PC4 plays essential roles in collaboration with the small subunit of general transcription factor TFIIE. Genes Cells 2014; 19:879-90. [PMID: 25308091 DOI: 10.1111/gtc.12187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 09/01/2014] [Indexed: 11/27/2022]
Abstract
In eukaryotes, positive cofactor 4 (PC4) stimulates activator-dependent transcription by facilitating transcription initiation and the transition from initiation to elongation. It also forms homodimers and binds to single-stranded DNA and various transcriptional activators, including the general transcription factor TFIIH. In this study, we further investigated PC4 from Homo sapiens and the nematode Caenorhabditis elegans (hPC4 and cePC4, respectively). hPC4 strongly stimulated transcription on a linearized template, whereas it alleviated transcription on a supercoiled template. Transcriptional stimulation by PC4 was also alleviated by increasing the amount of TFIID. GST pull-down studies with general transcription factors indicated that both hPC4 and cePC4 bind strongly to TFIIB, TFIIEβ, TFIIFα, TFIIFβ and TFIIH XPB subunits and weakly to TBP and TFIIH p62. However, only hPC4 bound to CDK7. The effect of each PC4 on transcription was studied in combination with TFIIEβ. hPC4 stimulated both basal and activated transcription, whereas cePC4 primarily stimulated activated transcription, especially in the presence of TFIIEβ from C. elegans. Finally, hPC4 bound to the C-terminal region of hTFIIEβ adjacent to the basic region. These results indicate that PC4 plays essential roles in the transition step from transcription initiation to elongation by binding to melted DNA in collaboration with TFIIEβ.
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Affiliation(s)
- Yusuke Akimoto
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
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15
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Steigemann B, Schulz A, Werten S. Bacteriophage T5 Encodes a Homolog of the Eukaryotic Transcription Coactivator PC4 Implicated in Recombination-Dependent DNA Replication. J Mol Biol 2013; 425:4125-33. [DOI: 10.1016/j.jmb.2013.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 08/24/2013] [Accepted: 09/02/2013] [Indexed: 11/30/2022]
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16
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García A, Collin A, Calvo O. Sub1 associates with Spt5 and influences RNA polymerase II transcription elongation rate. Mol Biol Cell 2012; 23:4297-312. [PMID: 22973055 PMCID: PMC3484106 DOI: 10.1091/mbc.e12-04-0331] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The transcriptional coactivator Sub1 has been implicated in several steps of mRNA metabolism in yeast, such as the activation of transcription, termination, and 3'-end formation. In addition, Sub1 globally regulates RNA polymerase II phosphorylation, and most recently it has been shown that it is a functional component of the preinitiation complex. Here we present evidence that Sub1 plays a significant role in transcription elongation by RNA polymerase II (RNAPII). We show that SUB1 genetically interacts with the gene encoding the elongation factor Spt5, that Sub1 influences Spt5 phosphorylation of the carboxy-terminal domain of RNAPII largest subunit by the kinase Bur1, and that both Sub1 and Spt5 copurify in the same complex, likely during early transcription elongation. Indeed, our data indicate that Sub1 influences Spt5-Rpb1 interaction. In addition, biochemical and molecular data show that Sub1 influences transcription elongation of constitutive and inducible genes and associates with coding regions in a transcription-dependent manner. Taken together, our results indicate that Sub1 associates with Spt5 and influences Spt5-Rpb1 complex levels and consequently transcription elongation rate.
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Affiliation(s)
- Alicia García
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, 37007 Salamanca, Spain
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17
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Rajagopal C, Mains RE, Eipper BA. Signaling from the secretory granule to the nucleus. Crit Rev Biochem Mol Biol 2012; 47:391-406. [PMID: 22681236 DOI: 10.3109/10409238.2012.694845] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Neurons and endocrine cells use a complex array of signaling molecules to communicate with each other and with various targets. The majority of these signaling molecules are stored in specialized organelles awaiting release on demand: 40-60 nm vesicles carry conventional or small molecule neurotransmitters, and 200-400 nm granules contain bioactive peptides. The supply of small molecule neurotransmitters is tightly regulated by local feedback of synthetic rates and transport processes at sites of release. The larger granules that contain bioactive peptides present the secretory cell with special challenges, as the peptide precursors are inserted into the lumen of the secretory pathway in the cell soma and undergo biosynthetic processing while being transported to distant sites for eventual secretion. One solution to this dilemma in information handling has been to employ proteolytic cleavage of secretory granule membrane proteins to produce cytosolic fragments that can signal to the nucleus, affecting gene expression. The use of regulated intramembrane proteolysis to signal from secretory granules to the nucleus is compared to its much better understood role in relaying information from the endoplasmic reticulum by SREBP and ATF6 and from the plasma membrane by cadherins, Notch and ErbB4.
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Affiliation(s)
- Chitra Rajagopal
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT, USA
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18
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Affiliation(s)
- Monika Fuxreiter
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary.
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19
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Vuzman D, Levy Y. Intrinsically disordered regions as affinity tuners in protein–DNA interactions. ACTA ACUST UNITED AC 2012; 8:47-57. [DOI: 10.1039/c1mb05273j] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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20
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Sub1 and RPA associate with RNA polymerase II at different stages of transcription. Mol Cell 2011; 44:397-409. [PMID: 22055186 DOI: 10.1016/j.molcel.2011.09.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 06/06/2011] [Accepted: 09/30/2011] [Indexed: 01/24/2023]
Abstract
Single-stranded DNA-binding proteins play many roles in nucleic acid metabolism, but their importance during transcription remains unclear. Quantitative proteomic analysis of RNA polymerase II (RNApII) preinitiation complexes (PICs) identified Sub1 and the replication protein A complex (RPA), both of which bind single-stranded DNA (ssDNA). Sub1, homolog of mammalian coactivator PC4, exhibits strong genetic interactions with factors necessary for promoter melting. Sub1 localizes near the transcription bubble in vitro and binds to promoters in vivo dependent upon PIC assembly. In contrast, RPA localizes to transcribed regions of active genes, strongly correlated with transcribing RNApII but independently of replication. RFA1 interacts genetically with transcription elongation factor genes. Interestingly, RPA levels increase at active promoters in cells carrying a Sub1 deletion or ssDNA-binding mutant, suggesting competition for a common binding site. We propose that Sub1 and RPA interact with the nontemplate strand of RNApII complexes during initiation and elongation, respectively.
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21
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Fuxreiter M, Simon I, Bondos S. Dynamic protein-DNA recognition: beyond what can be seen. Trends Biochem Sci 2011; 36:415-23. [PMID: 21620710 DOI: 10.1016/j.tibs.2011.04.006] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Revised: 04/15/2011] [Accepted: 04/15/2011] [Indexed: 12/28/2022]
Abstract
Traditionally, specific DNA recognition is thought to rely on static contacts with the bases or phosphates. Recent results, however, indicate that residues far outside the binding context can crucially influence selectivity or binding affinity via transient, dynamic interactions with the DNA binding interface. These regions usually do not adopt a well-defined structure, even when bound to DNA, and thus form a fuzzy complex. Here, we propose the existence of a dynamic DNA readout mechanism, wherein distant segments modulate conformational preferences, flexibility or spacing of the DNA binding motifs or serve as competitive partners. Despite their low sequence similarity, these intrinsically disordered regions are often conserved at the structural level, and exploited for regulation of the transcription machinery via protein-protein interactions, post-translational modifications or alternative splicing.
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Affiliation(s)
- Monika Fuxreiter
- Department of Biological Chemistry, Weizmann Institute of Science, 7600 Rehovot, Israel.
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22
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Debnath S, Chatterjee S, Arif M, Kundu TK, Roy S. Peptide-protein interactions suggest that acetylation of lysines 381 and 382 of p53 is important for positive coactivator 4-p53 interaction. J Biol Chem 2011; 286:25076-87. [PMID: 21586571 DOI: 10.1074/jbc.m110.205328] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human transcriptional positive coactivator 4 (PC4) activates several p53-dependent genes. It has been demonstrated that this is a consequence of direct interaction with p53. Previously, we have concluded that PC4 interacts mainly with the C-terminal negative regulatory domain of p53 through its DNA binding C-terminal half. NMR chemical shift perturbation studies with peptide fragments indicated that amino acids 380-386 of p53 are crucial for interaction with PC4. This was verified by fluorescence anisotropy and sedimentation velocity studies. A peptide consisting of p53-(380-386) sequence, when attached to a cell penetration tag and nuclear localization signal, localizes to the nucleus and inhibits luciferase gene expression from a transfected plasmid carrying a Luc gene under a p53-dependent promoter. Acetylation of lysine 382/381 enhanced the binding of this peptide to PC4 by about an order of magnitude. NMR and mutagenesis studies indicated that serine 73 of PC4 is an important residue for recognition of p53. Intermolecular nuclear Overhauser effect placed aspartate 76 in the vicinity of lysine 381, indicating that the region around residues 73-76 of PC4 is important for p53 recognition. We conclude that the 380-386 region of p53 interacts with the region around residues 73-76 of PC4, and acetylation of lysine 382/381 of p53 may play an important role in modulating p53-PC4 interaction and as a consequence PC4 mediated activation of p53 target genes.
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Affiliation(s)
- Subrata Debnath
- Division of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research (India), 4, Raja S. C. Mullick Road, Kolkata 700032, India
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23
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Rajagopal C, Stone KL, Francone VP, Mains RE, Eipper BA. Secretory granule to the nucleus: role of a multiply phosphorylated intrinsically unstructured domain. J Biol Chem 2009; 284:25723-34. [PMID: 19635792 DOI: 10.1074/jbc.m109.035782] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Intrinsically unstructured domains occur in one-third of all proteins and are characterized by conformational flexibility, protease sensitivity, and the occurrence of multiple phosphorylation. They provide large interfaces for diverse protein-protein interactions. Peptidylglycine alpha-amidating monooxygenase (PAM), an enzyme essential for neuropeptide biosynthesis, is a secretory granule membrane protein. As one of the few proteins spanning the granule membrane, PAM is a candidate to relay information about the status of the granule pool and conditions in the granule lumen. Here, we show that the PAM cytosolic domain is unstructured. Mass spectroscopy and two-dimensional gel electrophoresis demonstrated phosphorylation at 10-12 sites in the cytosolic domain. Stimulation of exocytosis resulted in coupled phosphorylation and dephosphorylation of specific sites and in the endoproteolytic release of a soluble, proteasome-sensitive cytosolic domain fragment. Analysis of granule-rich tissues, such as pituitary and heart, showed that a similar fragment was generated endogenously and translocated to the nucleus. This multiply phosphorylated unstructured domain may act as a signaling molecule that relays information from secretory granules to both cytosol and nucleus.
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Affiliation(s)
- Chitra Rajagopal
- Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
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24
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Abstract
Multisite phosphorylation is an important mechanism for fine-tuned regulation of protein function. Mathematical models developed over recent years have contributed to elucidation of the functional consequences of a variety of molecular mechanisms involved in processing of the phosphorylation sites. Here we review the results of such models, together with salient experimental findings on multisite protein phosphorylation. We discuss how molecular mechanisms that can be distinguished with respect to the order and processivity of phosphorylation, as well as other factors, regulate changes in the sensitivity and kinetics of the response, the synchronization of molecular events, signalling specificity, and other functional implications.
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Affiliation(s)
- Carlos Salazar
- Research Group Modeling of Biological Systems (B086), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany.
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25
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Batta K, Kundu TK. Activation of p53 function by human transcriptional coactivator PC4: role of protein-protein interaction, DNA bending, and posttranslational modifications. Mol Cell Biol 2007; 27:7603-14. [PMID: 17785449 PMCID: PMC2169069 DOI: 10.1128/mcb.01064-07] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tumor suppressor p53 controls cell cycle checkpoints and apoptosis via the transactivation of several genes that are involved in these processes. The functions of p53 are regulated by a wide variety of proteins, which interact with it either directly or indirectly. The multifunctional human transcriptional coactivator PC4 interacts with p53 in vivo and in vitro and regulates its function. Here we report the molecular mechanisms of the PC4-mediated activation of p53 function. PC4 interacts with the DNA binding and C-terminal domains of p53 through its DNA binding domain, which is essential for the stimulation of p53 DNA binding. Remarkably, ligation-mediated circularization assays reveal that PC4 induces significant bending in the DNA double helix. Deletion mutants defective in DNA bending are found to be impaired in activating p53-mediated DNA binding and apoptosis. Furthermore, acetylation of PC4 enhances, while phosphorylation abolishes, its ability to bend DNA, activate p53 DNA binding, and, thereby, regulate p53 functions. In conclusion, PC4 activates p53 recruitment to p53-responsive promoters (Bax and p21) in vivo through its interaction with p53 and by providing bent substrate for p53 recruitment. These results elucidate the general molecular mechanisms of activation of p53 function, mediated by its coactivators.
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Affiliation(s)
- Kiran Batta
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, P.O. Bangalore-560064, India
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26
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Salazar C, Höfer T. Versatile regulation of multisite protein phosphorylation by the order of phosphate processing and protein-protein interactions. FEBS J 2007; 274:1046-61. [PMID: 17257173 DOI: 10.1111/j.1742-4658.2007.05653.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multisite protein phosphorylation is a common regulatory mechanism in cell signaling, and dramatically increases the possibilities for protein-protein interactions, conformational regulation, and phosphorylation pathways. However, there is at present no comprehensive picture of how these factors shape the response of a protein's phosphorylation state to changes in kinase and phosphatase activities. Here we provide a mathematical theory for the regulation of multisite protein phosphorylation based on the mechanistic description of elementary binding and catalytic steps. Explicit solutions for the steady-state response curves and characteristic (de)phosphorylation times have been obtained in special cases. The order of phosphate processing and the characteristics of protein-protein interactions turn out to be of overriding importance for both sensitivity and speed of response. Random phosphate processing gives rise to shallow response curves, favoring intermediate phosphorylation states of the target, and rapid kinetics. Sequential processing is characterized by steeper response curves and slower kinetics. We show systematically how qualitative differences in target phosphorylation--including graded, switch-like and bistable responses--are determined by the relative concentrations of enzyme and target as well as the enzyme-target affinities. In addition to collective effects of several phosphorylation sites, our analysis predicts that distinct phosphorylation patterns can be finely tuned by a single kinase. Taken together, this study suggests a versatile regulation of protein activation by the combined effect of structural, kinetic and thermodynamic aspects of multisite phosphorylation.
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Affiliation(s)
- Carlos Salazar
- Theoretical Biophysics, Institute for Biology, Humboldt University Berlin, Germany
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