1
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Chen W, Chu J, Miao Y, Jiang W, Wang F, Zhang N, Jin J, Cai Y. MOF-mediated acetylation of CDK9 promotes global transcription by modulating P-TEFb complex formation. FEBS J 2024. [PMID: 39250546 DOI: 10.1111/febs.17264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/25/2024] [Accepted: 08/22/2024] [Indexed: 09/11/2024]
Abstract
Cyclin-dependent kinase 9 (CDK9), a catalytic subunit of the positive transcription elongation factor b (P-TEFb) complex, is a global transcriptional elongation factor associated with cell proliferation. CDK9 activity is regulated by certain histone acetyltransferases, such as p300, GCN5 and P/CAF. However, the impact of males absent on the first (MOF) (also known as KAT8 or MYST1) on CDK9 activity has not been reported. Therefore, the present study aimed to elucidate the regulatory role of MOF on CDK9. We present evidence from systematic biochemical assays and molecular biology approaches arguing that MOF interacts with and acetylates CDK9 at the lysine 35 (i.e. K35) site, and that this acetyl-group can be removed by histone deacetylase HDAC1. Notably, MOF-mediated acetylation of CDK9 at K35 promotes the formation of the P-TEFb complex through stabilizing CDK9 protein and enhancing its association with cyclin T1, which further increases RNA polymerase II serine 2 residues levels and global transcription. Our study reveals for the first time that MOF promotes global transcription by acetylating CDK9, providing a new strategy for exploring the comprehensive mechanism of the MOF-CDK9 axis in cellular processes.
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Affiliation(s)
- Wenqi Chen
- School of Life Sciences, Jilin University, Changchun, China
| | - Jinmeng Chu
- School of Life Sciences, Jilin University, Changchun, China
| | - Yujuan Miao
- School of Life Sciences, Jilin University, Changchun, China
| | - Wenwen Jiang
- School of Life Sciences, Jilin University, Changchun, China
| | - Fei Wang
- School of Life Sciences, Jilin University, Changchun, China
| | - Na Zhang
- School of Life Sciences, Jilin University, Changchun, China
| | - Jingji Jin
- School of Life Sciences, Jilin University, Changchun, China
| | - Yong Cai
- School of Life Sciences, Jilin University, Changchun, China
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2
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Vishwakarma KK, Kolthur US, Venkatramani R. Multiple Functional Protein-Protein Interaction Interfaces Allosterically Regulate ATP-Binding in Cyclin-Dependent Kinase-1. Proteins 2024. [PMID: 39012208 DOI: 10.1002/prot.26729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/30/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024]
Abstract
The ATP-dependent phosphorylation activity of cyclin-dependent kinase 1 (CDK1), an essential enzyme for cell cycle progression, is regulated by interactions with Cyclin-B, substrate, and Cks proteins. We have recently shown that active site acetylation in CDK1 abrogated binding to Cyclin-B which posits an intriguing long-range communication between the catalytic site and the protein-protein interaction (PPI) interface. Now, we demonstrate a general allosteric link between the CDK1 active site and all three of its PPI interfaces through atomistic molecular dynamics (MD) simulations. Specifically, we examined ATP binding free energies to CDK1 in native nonacetylated (K33wt) and acetylated (K33Ac) forms as well as the acetyl-mimic K33Q and the acetyl-null K33R mutant forms, which are accessible in vitro. In agreement with experiments, ATP binding is stronger in K33wt relative to the other three perturbed states. Free energy decomposition reveals, in addition to expected local changes, significant and selective nonlocal entropic responses to ATP binding/perturbation of K33 from theαC $$ \alpha C $$ -helix, activation loop (A-loop), andαG $$ \alpha G $$ -α $$ \alpha $$ H segments in CDK1 which interface with Cyclin-B, substrate, and Cks proteins, respectively. Statistical analysis reveals that while entropic responses of protein segments to active site perturbations are on average correlated with their dynamical changes, such correlations are lost in about 9%-48% of the dataset depending on the segment. Besides proving the bi-directional communication between the active site and the CDK1:Cyclin-B interface, our study uncovers a hitherto unknown mode of ATP binding regulation by multiple PPI interfaces in CDK1.
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Affiliation(s)
| | - Ullas Seetharam Kolthur
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- Tata Institute of Fundamental Research, Hyderabad, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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3
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Betsinger CN, Justice JL, Tyl MD, Edgar JE, Budayeva HG, Abu YF, Cristea IM. Sirtuin 2 promotes human cytomegalovirus replication by regulating cell cycle progression. mSystems 2023; 8:e0051023. [PMID: 37916830 PMCID: PMC10734535 DOI: 10.1128/msystems.00510-23] [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: 05/19/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE This study expands the growing understanding that protein acetylation is a highly regulated molecular toggle of protein function in both host anti-viral defense and viral replication. We describe a pro-viral role for the human enzyme SIRT2, showing that its deacetylase activity supports HCMV replication. By integrating quantitative proteomics, flow cytometry cell cycle assays, microscopy, and functional virology assays, we investigate the temporality of SIRT2 functions and substrates. We identify a pro-viral role for the SIRT2 deacetylase activity via regulation of CDK2 K6 acetylation and the G1-S cell cycle transition. These findings highlight a link between viral infection, protein acetylation, and cell cycle progression.
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Affiliation(s)
- Cora N. Betsinger
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey, USA
| | - Joshua L. Justice
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey, USA
| | - Matthew D. Tyl
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey, USA
| | - Julia E. Edgar
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey, USA
| | - Hanna G. Budayeva
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey, USA
| | - Yaa F. Abu
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey, USA
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey, USA
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4
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Silonov SA, Mokin YI, Nedelyaev EM, Smirnov EY, Kuznetsova IM, Turoverov KK, Uversky VN, Fonin AV. On the Prevalence and Roles of Proteins Undergoing Liquid-Liquid Phase Separation in the Biogenesis of PML-Bodies. Biomolecules 2023; 13:1805. [PMID: 38136675 PMCID: PMC10741438 DOI: 10.3390/biom13121805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
The formation and function of membrane-less organelles (MLOs) is one of the main driving forces in the molecular life of the cell. These processes are based on the separation of biopolymers into phases regulated by multiple specific and nonspecific inter- and intramolecular interactions. Among the realm of MLOs, a special place is taken by the promyelocytic leukemia nuclear bodies (PML-NBs or PML bodies), which are the intranuclear compartments involved in the regulation of cellular metabolism, transcription, the maintenance of genome stability, responses to viral infection, apoptosis, and tumor suppression. According to the accepted models, specific interactions, such as SUMO/SIM, the formation of disulfide bonds, etc., play a decisive role in the biogenesis of PML bodies. In this work, a number of bioinformatics approaches were used to study proteins found in the proteome of PML bodies for their tendency for spontaneous liquid-liquid phase separation (LLPS), which is usually caused by weak nonspecific interactions. A total of 205 proteins found in PML bodies have been identified. It has been suggested that UBC9, P53, HIPK2, and SUMO1 can be considered as the scaffold proteins of PML bodies. It was shown that more than half of the proteins in the analyzed proteome are capable of spontaneous LLPS, with 85% of the analyzed proteins being intrinsically disordered proteins (IDPs) and the remaining 15% being proteins with intrinsically disordered protein regions (IDPRs). About 44% of all proteins analyzed in this study contain SUMO binding sites and can potentially be SUMOylated. These data suggest that weak nonspecific interactions play a significantly larger role in the formation and biogenesis of PML bodies than previously expected.
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Affiliation(s)
- Sergey A. Silonov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| | - Yakov I. Mokin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| | - Eugene M. Nedelyaev
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| | - Eugene Y. Smirnov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Alexander V. Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
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5
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Xu X, Ding Y, Jin J, Xu C, Hu W, Wu S, Ding G, Cheng R, Cao L, Jia S. Post-translational modification of CDK1-STAT3 signaling by fisetin suppresses pancreatic cancer stem cell properties. Cell Biosci 2023; 13:176. [PMID: 37743465 PMCID: PMC10518106 DOI: 10.1186/s13578-023-01118-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND Pancreatic cancer stem cells (CSCs) promote pancreatic ductal adenocarcinoma (PDAC) tumorigenesis and chemoresistance. Cyclin-dependent kinase 1 (CDK1) plays an important role in tumor initiation in other tumors, but the function of CDK1 in PDAC remains unclear. Fisetin is a bioactive flavonoid with anti-tumor properties in multiple tumors, while its function in CSCs remains elusive. RESULTS In this study, we demonstrated that CDK1 was correlated with prognosis and was highly expressed in pancreatic cancer tissue and gemcitabine-resistant cells. Silencing CDK1 impaired tumor stemness and reduced a subset of CSCs. We found that fisetin blocked the kinase pocket domain of CDK1 and inhibited pancreatic CSC characteristics. Using acetylation proteomics analysis and phosphorylation array assay, we confirmed that fisetin reduced CDK1 expression and increased CDK1 acetylation at lysine 33 (K33), which resulted in the suppression of CDK1 phosphorylation. Silencing CDK1 or STAT3 suppressed tumor stemness properties, while overexpressing CDK1 or STAT3 showed the opposite effect. Mutation or acetylation of CDK1 at K33 weakened STAT3 phosphorylation at Y705, impairing the expression of stem-related genes and pancreatic cancer stemness. In addition, lack of histone deacetylase 3 (HDAC3), which deacetylates CDK1, contributed to weakening STAT3 phosphorylation by regulating the post-translational modification of CDK1, thereby decreasing the stemness of PDAC. Moreover, our results revealed that fisetin enhanced the effect of gemcitabine through eliminating a subpopulation of pancreatic CSCs by inhibiting the CDK1-STAT3 axis in vitro and in vivo. CONCLUSION Our findings highlight the role of post-translational modifications of CDK1-STAT3 signaling in maintaining cancer stemness of PDAC, and indicated that targeting the CDK1-STAT3 axis with inhibitors such as fisetin is a potential therapeutic strategy to diminish drug resistance and eliminate PDAC.
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Affiliation(s)
- Xiaodong Xu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, 310014, Zhejiang, China
| | - Yimin Ding
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Junbin Jin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Chengjie Xu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Wenyi Hu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Songtao Wu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Guoping Ding
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Rui Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Liping Cao
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.
- Innovation Center for Minimally Invasive Technique and Device, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
| | - Shengnan Jia
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.
- Innovation Center for Minimally Invasive Technique and Device, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
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6
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Liu R. Brd4-dependent CDK9 expression induction upon sustained pharmacological inhibition of P-TEFb kinase activity. Biochem Biophys Res Commun 2023; 671:75-79. [PMID: 37295357 DOI: 10.1016/j.bbrc.2023.05.114] [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: 05/18/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
CDK9 is the kinase subunit of P-TEFb (positive transcription elongation factor b), which is crucial for effective transcriptional elongation. The activity of P-TEFb is well maintained, mainly through dynamic association with several larger protein complexes. Here, we show that CDK9 expression is induced upon inhibition of P-TEFb activity, a process dependent on Brd4 as later revealed. Brd4 inhibition synergizes with CDK9 inhibitor to suppress P-TEFb activity and tumor cell growth. Our study suggests that combined inhibition of Brd4 and CDK9 can be evaluated as a potential therapeutic strategy.
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Affiliation(s)
- Rongdiao Liu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
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7
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Tabassum Z, Tseng JH, Isemann C, Tian X, Chen Y, Herring LE, Cohen TJ. Identification of a reciprocal negative feedback loop between tau-modifying proteins MARK2 kinase and CBP acetyltransferase. J Biol Chem 2022; 298:101977. [PMID: 35469920 PMCID: PMC9136110 DOI: 10.1016/j.jbc.2022.101977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 11/30/2022] Open
Abstract
The posttranslational regulation of the neuronal proteome is critical for brain homeostasis but becomes dysregulated in the aged or diseased brain, in which abnormal posttranslational modifications (PTMs) are frequently observed. While the full extent of modified substrates that comprise the "PTM-ome" are slowly emerging, how the upstream enzymes catalyzing these processes are regulated themselves is not well understood, particularly in the context of neurodegeneration. Here, we describe the reciprocal regulation of a kinase, the microtubule affinity-regulating kinase 2 (MARK2), and an acetyltransferase, CREB-binding protein (CBP), two enzymes known to extensively modify tau proteins in the progression of Alzheimer's disease. We found that MARK2 negatively regulates CBP and, conversely, CBP directly acetylates and inhibits MARK2 kinase activity. These findings highlight a reciprocal negative feedback loop between a kinase and an acetyltransferase, which has implications for how PTM interplay is coordinated on substrates including tau. Our study suggests that PTM profiles occur through the posttranslational control of the master PTM remodeling enzymes themselves.
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Affiliation(s)
- Zarin Tabassum
- Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jui-Heng Tseng
- Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Camryn Isemann
- Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Xu Tian
- Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Youjun Chen
- Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Laura E Herring
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Todd J Cohen
- Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA.
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8
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Heterogeneity of Latency Establishment in the Different Human CD4
+
T Cell Subsets Stimulated with IL-15. J Virol 2022; 96:e0037922. [PMID: 35499323 PMCID: PMC9131862 DOI: 10.1128/jvi.00379-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
HIV integrates into the host genome, creating a viral reservoir of latently infected cells that persists despite effective antiretroviral treatment. CD4-positive (CD4+) T cells are the main contributors to the HIV reservoir. CD4+ T cells are a heterogeneous population, and the mechanisms of latency establishment in the different subsets, as well as their contribution to the reservoir, are still unclear. In this study, we analyzed HIV latency establishment in different CD4+ T cell subsets stimulated with interleukin 15 (IL-15), a cytokine that increases both susceptibility to infection and reactivation from latency. Using a dual-reporter virus that allows discrimination between latent and productive infection at the single-cell level, we found that IL-15-treated primary human CD4+ T naive and CD4+ T stem cell memory (TSCM) cells are less susceptible to HIV infection than CD4+ central memory (TCM), effector memory (TEM), and transitional memory (TTM) cells but are also more likely to harbor transcriptionally silent provirus. The propensity of these subsets to harbor latent provirus compared to the more differentiated memory subsets was independent of differential expression of pTEFb components. Microscopy analysis of NF-κB suggested that CD4+ T naive cells express smaller amounts of nuclear NF-κB than the other subsets, partially explaining the inefficient long terminal repeat (LTR)-driven transcription. On the other hand, CD4+ TSCM cells display similar levels of nuclear NF-κB to CD4+ TCM, CD4+ TEM, and CD4+ TTM cells, indicating the availability of transcription initiation and elongation factors is not solely responsible for the inefficient HIV gene expression in the CD4+ TSCM subset. IMPORTANCE The formation of a latent reservoir is the main barrier to HIV cure. Here, we investigated how HIV latency is established in different CD4+ T cell subsets in the presence of IL-15, a cytokine that has been shown to efficiently induce latency reversal. We observed that, even in the presence of IL-15, the less differentiated subsets display lower levels of productive HIV infection than the more differentiated subsets. These differences were not related to different expression of pTEFb, and modest differences in NF-κB were observed for CD4+ T naive cells only, implying the involvement of other mechanisms. Understanding the molecular basis of latency establishment in different CD4+ T cell subsets might be important for tailoring specific strategies to reactivate HIV transcription in all the CD4+ T subsets that compose the latent reservoir.
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9
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Fournier JCL, Evans JP, Zappacosta F, Thomas DA, Patel VK, White GV, Campos S, Tomkinson NCO. Acetylation of the Catalytic Lysine Inhibits Kinase Activity in PI3Kδ. ACS Chem Biol 2021; 16:1644-1653. [PMID: 34397208 DOI: 10.1021/acschembio.1c00225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covalent inhibition is a powerful strategy to develop potent and selective small molecule kinase inhibitors. Targeting the conserved catalytic lysine is an attractive method for selective kinase inactivation. We have developed novel, selective inhibitors of phosphoinositide 3-kinase δ (PI3Kδ) which acylate the catalytic lysine, Lys779, using activated esters as the reactive electrophiles. The acylating agents were prepared by adding the activated ester motif to a known selective dihydroisobenzofuran PI3Kδ inhibitor. Three esters were designed, including an acetate ester which was the smallest lysine modification evaluated in this work. Covalent binding to the enzyme was characterized by intact protein mass spectrometry of the PI3Kδ-ester adducts. An enzymatic digest coupled with tandem mass spectrometry identified Lys779 as the covalent binding site, and a biochemical activity assay confirmed that PI3Kδ inhibition was a direct result of covalent lysine acylation. These results indicate that a simple chemical modification such as lysine acetylation is sufficient to inhibit kinase activity. The selectivity of the compounds was evaluated against lipid kinases in cell lysates using a chemoproteomic binding assay. Due to the conserved nature of the catalytic lysine across the kinome, we believe the covalent inhibition strategy presented here could be applicable to a broad range of clinically relevant targets.
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Affiliation(s)
- Julie C. L. Fournier
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - John P. Evans
- Arctoris, 120E Olympic Avenue, Milton Park, Oxford, OX14 4SA, United Kingdom
| | | | - Daniel A. Thomas
- Arctoris, 120E Olympic Avenue, Milton Park, Oxford, OX14 4SA, United Kingdom
| | - Vipulkumar K. Patel
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Gemma V. White
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Sebastien Campos
- Pharmaron, West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire EN11 9FH, United Kingdom
| | - Nicholas C. O. Tomkinson
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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10
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The GCN5: its biological functions and therapeutic potentials. Clin Sci (Lond) 2021; 135:231-257. [PMID: 33443284 DOI: 10.1042/cs20200986] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022]
Abstract
General control non-depressible 5 (GCN5) or lysine acetyltransferase 2A (KAT2A) is one of the most highly studied histone acetyltransferases. It acts as both histone acetyltransferase (HAT) and lysine acetyltransferase (KAT). As an HAT it plays a pivotal role in the epigenetic landscape and chromatin modification. Besides, GCN5 regulates a wide range of biological events such as gene regulation, cellular proliferation, metabolism and inflammation. Imbalance in the GCN5 activity has been reported in many disorders such as cancer, metabolic disorders, autoimmune disorders and neurological disorders. Therefore, unravelling the role of GCN5 in different diseases progression is a prerequisite for both understanding and developing novel therapeutic agents of these diseases. In this review, we have discussed the structural features, the biological function of GCN5 and the mechanical link with the diseases associated with its imbalance. Moreover, the present GCN5 modulators and their limitations will be presented in a medicinal chemistry perspective.
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11
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De A, Maity A, Mazumder M, Mondal B, Mukherjee A, Ghosh S, Ray P, Polley S, Dastidar SG, Basu D. Overexpression of LYK4, a lysin motif receptor with non-functional kinase domain, enhances tolerance to Alternaria brassicicola and increases trichome density in Brassica juncea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 309:110953. [PMID: 34134846 DOI: 10.1016/j.plantsci.2021.110953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
Lysin motif receptor-like kinases (LYKs) are involved in the recognition of chitin and activation of plant immune response. In this study, we found LYK4 to be strongly induced in resistant Sinapis alba compared with susceptible Brassica juncea on challenge with Alternaria brassicicola. In silico analysis and in vitro kinase assay revealed that despite the presence of canonical protein kinase fold, B.juncea LYK4 (BjLYK4) lacks several key residues of a prototype protein kinase which renders it catalytically inactive. Transient expression analysis confirmed that fluorescently tagged BjLYK4 localizes specifically to the plasma membrane. Overexpression (OE) of BjLYK4 in B. juncea enhanced tolerance against A. brassicicola. Interestingly, the OE lines also exhibited a novel trichome dense phenotype and increased jasmonic acid (JA) responsiveness. We further showed that many chitin responsive WRKY transcription factors and JA biosynthetic genes were strongly induced in the OE lines on challenge with the pathogen. Moreover, several JA inducible trichome developmental genes constituting the WD-repeat/bHLH/MYB activator complex were also upregulated in the OE lines compared with vector control and RNA interference line. These results suggest that BjLYK4 plays an essential role in chitin-dependent activation of defense response and chitin independent trichome development likely by influencing the JA signaling pathway.
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Affiliation(s)
- Aishee De
- Division of Plant Biology, Bose Institute, P1/12 C.I.T. Scheme-VIIM, Kankurgachi, Kolkata, 700054, India.
| | - Atanu Maity
- Division of Bioinformatics, Bose Institute, P1/12 C.I.T. Scheme-VIIM, Kankurgachi, Kolkata, 700054, India.
| | - Mrinmoy Mazumder
- Department of Biological Sciences, National University of Singapore (NUS), Singapore, 119077.
| | - Banani Mondal
- Division of Plant Biology, Bose Institute, P1/12 C.I.T. Scheme-VIIM, Kankurgachi, Kolkata, 700054, India.
| | - Amrita Mukherjee
- Division of Plant Biology, Bose Institute, P1/12 C.I.T. Scheme-VIIM, Kankurgachi, Kolkata, 700054, India.
| | - Swagata Ghosh
- Division of Plant Biology, Bose Institute, P1/12 C.I.T. Scheme-VIIM, Kankurgachi, Kolkata, 700054, India.
| | - Pranita Ray
- Department of Biophysics, Bose Institute, P1/12 C.I.T. Scheme-VIIM, Kankurgachi, Kolkata, 700054, India.
| | - Smarajit Polley
- Department of Biophysics, Bose Institute, P1/12 C.I.T. Scheme-VIIM, Kankurgachi, Kolkata, 700054, India.
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, P1/12 C.I.T. Scheme-VIIM, Kankurgachi, Kolkata, 700054, India.
| | - Debabrata Basu
- Division of Plant Biology, Bose Institute, P1/12 C.I.T. Scheme-VIIM, Kankurgachi, Kolkata, 700054, India.
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12
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Anshabo AT, Milne R, Wang S, Albrecht H. CDK9: A Comprehensive Review of Its Biology, and Its Role as a Potential Target for Anti-Cancer Agents. Front Oncol 2021; 11:678559. [PMID: 34041038 PMCID: PMC8143439 DOI: 10.3389/fonc.2021.678559] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/16/2021] [Indexed: 12/25/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are proteins pivotal to a wide range of cellular functions, most importantly cell division and transcription, and their dysregulations have been implicated as prominent drivers of tumorigenesis. Besides the well-established role of cell cycle CDKs in cancer, the involvement of transcriptional CDKs has been confirmed more recently. Most cancers overtly employ CDKs that serve as key regulators of transcription (e.g., CDK9) for a continuous production of short-lived gene products that maintain their survival. As such, dysregulation of the CDK9 pathway has been observed in various hematological and solid malignancies, making it a valuable anticancer target. This therapeutic potential has been utilized for the discovery of CDK9 inhibitors, some of which have entered human clinical trials. This review provides a comprehensive discussion on the structure and biology of CDK9, its role in solid and hematological cancers, and an updated review of the available inhibitors currently being investigated in preclinical and clinical settings.
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Affiliation(s)
- Abel Tesfaye Anshabo
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Robert Milne
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Shudong Wang
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Hugo Albrecht
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
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13
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Basu S, Nandy A, Biswas D. Keeping RNA polymerase II on the run: Functions of MLL fusion partners in transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194563. [PMID: 32348849 DOI: 10.1016/j.bbagrm.2020.194563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/13/2020] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Since the identification of key MLL fusion partners as transcription elongation factors regulating expression of HOX cluster genes during hematopoiesis, extensive work from the last decade has resulted in significant progress in our overall mechanistic understanding of role of MLL fusion partner proteins in transcriptional regulation of diverse set of genes beyond just the HOX cluster. In this review, we are going to detail overall understanding of role of MLL fusion partner proteins in transcriptional regulation and thus provide mechanistic insights into possible MLL fusion protein-mediated transcriptional misregulation leading to aberrant hematopoiesis and leukemogenesis.
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Affiliation(s)
- Subham Basu
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India
| | - Arijit Nandy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India.
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14
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AFF1 acetylation by p300 temporally inhibits transcription during genotoxic stress response. Proc Natl Acad Sci U S A 2019; 116:22140-22151. [PMID: 31611376 PMCID: PMC6823056 DOI: 10.1073/pnas.1907097116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mammalian cells are constantly exposed to genotoxic agents that can lead to DNA damage, genomic instability, and diseases, including cancers. Maintenance of genomic stability, a prerequisite for survival and proper functions of cells, is facilitated by the cellular DNA repair machinery. One of the earliest responses to DNA damage is a transient inhibition of transcription to avoid fatal collisions between the DNA repair and transcriptional machineries. However, the mechanisms underlying this early transcriptional inhibition are poorly understood. Our study establishes a critical role for AFF1, a key component of super elongation complex, in early transcription inhibition and cell survival upon DNA damage, as well as a mechanism involving p300-mediated acetylation of AFF1 and consequent inactivation of the super elongation complex. Soon after exposure to genotoxic reagents, mammalian cells inhibit transcription to prevent collisions with repair machinery and to mount a proper DNA damage response. However, mechanisms underlying early transcriptional inhibition are poorly understood. In this report, we show that site-specific acetylation of super elongation complex (SEC) subunit AFF1 by p300 reduces its interaction with other SEC components and impairs P-TEFb−mediated C-terminal domain phosphorylation of RNA polymerase II both in vitro and in vivo. Reexpression of wild-type AFF1, but not an acetylation mimic mutant, restores SEC component recruitment and target gene expression in AFF1 knockdown cells. Physiologically, we show that, upon genotoxic exposure, p300-mediated AFF1 acetylation is dynamic and strongly correlated with concomitant global down-regulation of transcription—and that this can be reversed by overexpression of an acetylation-defective AFF1 mutant. Therefore, we describe a mechanism of dynamic transcriptional regulation involving p300-mediated acetylation of a key elongation factor during genotoxic stress.
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15
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Collesi C, Felician G, Secco I, Gutierrez MI, Martelletti E, Ali H, Zentilin L, Myers MP, Giacca M. Reversible Notch1 acetylation tunes proliferative signalling in cardiomyocytes. Cardiovasc Res 2019; 114:103-122. [PMID: 29186476 DOI: 10.1093/cvr/cvx228] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 11/23/2017] [Indexed: 01/07/2023] Open
Abstract
Aims The Notch signalling pathway regulates the balance between proliferation and differentiation in several tissues, including the heart. Our previous work has demonstrated that the proliferative potential of neonatal cardiomyocytes relies on Notch1 activity. A deep investigation on the biochemical regulation of the Notch signalling in cardiomyocytes is the focus of the current research. Methods and results We show that the Notch1 intracellular domain is acetylated in proliferating neonatal rat cardiomyocytes and that acetylation tightly controls the amplitude and duration of Notch signalling. We found that acetylation extends the half-life of the protein, and enhanced its transcriptional activity, therefore counteracting apoptosis and sustaining cardiomyocyte proliferation. Sirt1 acted as a negative modulator of Notch1 signalling; its overexpression in cardiomyocytes reverted Notch acetylation and dampened its stability. A constitutively acetylated fusion protein between Notch1 and the acetyltransferase domain of p300 promoted cardiomyocyte proliferation, which was remarkably sustained over time. Viral vector-mediated expression of this protein enhanced heart regeneration after apical resection in neonatal mice. Conclusion These results identify the reversible acetylation of Notch1 as a novel mechanism to modulate its signalling in the heart and tune the proliferative potential of cardiomyocytes.
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Affiliation(s)
- Chiara Collesi
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy.,Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume 447, 34100 Trieste, Italy.,Center for Translational Cardiology, Azienda Sanitaria Universitaria Integrata, Via Valdoni 7, 34100 Trieste, Italy; and
| | - Giulia Felician
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Ilaria Secco
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Maria Ines Gutierrez
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Elisa Martelletti
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Hashim Ali
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Lorena Zentilin
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Michael P Myers
- Protein Networks Laboratories, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy.,Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume 447, 34100 Trieste, Italy.,Center for Translational Cardiology, Azienda Sanitaria Universitaria Integrata, Via Valdoni 7, 34100 Trieste, Italy; and
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16
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Deota S, Rathnachalam S, Namrata K, Boob M, Fulzele A, Radhika S, Ganguli S, Balaji C, Kaypee S, Vishwakarma KK, Kundu TK, Bhandari R, Gonzalez de Peredo A, Mishra M, Venkatramani R, Kolthur-Seetharam U. Allosteric Regulation of Cyclin-B Binding by the Charge State of Catalytic Lysine in CDK1 Is Essential for Cell-Cycle Progression. J Mol Biol 2019; 431:2127-2142. [PMID: 30974121 DOI: 10.1016/j.jmb.2019.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 01/19/2023]
Abstract
Cyclin-dependent kinase 1 (CDK1) is essential for cell-cycle progression. While dependence of CDK activity on cyclin levels is well established, molecular mechanisms that regulate their binding are less understood. Here, we report for the first time that CDK1:cyclin-B binding is not default but rather determined by the evolutionarily conserved catalytic residue, lysine-33 in CDK1. We demonstrate that the charge state of this lysine allosterically remodels the CDK1:cyclin-B interface. Cell cycle-dependent acetylation of lysine-33 or its mutation to glutamine, which mimics acetylation, abrogates cyclin-B binding. Using biochemical approaches and atomistic molecular dynamics simulations, we have uncovered both short-range and long-range effects of perturbing the charged state of the catalytic lysine, which lead to inhibition of kinase activity. Specifically, although loss of the charge state of catalytic lysine did not impact ATP binding significantly, it altered its orientation in the active site. In addition, the catalytic lysine also acts as an intra-molecular electrostatic tether at the active site to orient structural elements interfacing with cyclin-B. Physiologically, opposing activities of SIRT1 and P300 regulate acetylation and thus control the charge state of lysine-33. Importantly, cells expressing acetylation mimic mutant of Cdc2/CDK1 in yeast are arrested in G2 and fail to divide, indicating the requirement of the deacetylated state of the catalytic lysine for cell division. Thus, by illustrating the molecular role of the catalytic lysine and cell cycle-dependent deacetylation as a determinant of CDK1:cyclin-B interaction, our results redefine the current model of CDK1 activation and cell-cycle progression.
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Affiliation(s)
- Shaunak Deota
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Sivasudhan Rathnachalam
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Kanojia Namrata
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Mayank Boob
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Amit Fulzele
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Toulouse 31400, France
| | - S Radhika
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Shubhra Ganguli
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad 500039, India; Graduate Studies, Manipal Academy of Higher Education, Manipal 576104, India
| | - Chinthapalli Balaji
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Stephanie Kaypee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Krishna Kant Vishwakarma
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Tapas Kumar Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad 500039, India
| | | | - Mithilesh Mishra
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India.
| | - Ullas Kolthur-Seetharam
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India.
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17
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Ma X, Yang T, Luo Y, Wu L, Jiang Y, Song Z, Pan T, Liu B, Liu G, Liu J, Yu F, He Z, Zhang W, Yang J, Liang L, Guan Y, Zhang X, Li L, Cai W, Tang X, Gao S, Deng K, Zhang H. TRIM28 promotes HIV-1 latency by SUMOylating CDK9 and inhibiting P-TEFb. eLife 2019; 8:42426. [PMID: 30652970 PMCID: PMC6361614 DOI: 10.7554/elife.42426] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/16/2019] [Indexed: 12/19/2022] Open
Abstract
Comprehensively elucidating the molecular mechanisms of human immunodeficiency virus type 1 (HIV-1) latency is a priority to achieve a functional cure. As current 'shock' agents failed to efficiently reactivate the latent reservoir, it is important to discover new targets for developing more efficient latency-reversing agents (LRAs). Here, we found that TRIM28 potently suppresses HIV-1 expression by utilizing both SUMO E3 ligase activity and epigenetic adaptor function. Through global site-specific SUMO-MS study and serial SUMOylation assays, we identified that P-TEFb catalytic subunit CDK9 is significantly SUMOylated by TRIM28 with SUMO4. The Lys44, Lys56 and Lys68 residues on CDK9 are SUMOylated by TRIM28, which inhibits CDK9 kinase activity or prevents P-TEFb assembly by directly blocking the interaction between CDK9 and Cyclin T1, subsequently inhibits viral transcription and contributes to HIV-1 latency. The manipulation of TRIM28 and its consequent SUMOylation pathway could be the target for developing LRAs. The human immunodeficiency virus-1, or HIV-1, infects certain human cells, including white blood cells. One reason the infection is incurable is because the virus can integrate its genetic information into its host, and essentially ‘sleep’ within the host cell, a process called latency. This helps to hide HIV-1 from the immune system and stops it getting destroyed. Latency represents a critical challenge in treating and curing HIV-1. One proposed cure for HIV-1 involves ‘shocking’ the viruses out of latency so that they can be eliminated. Applying this so-called shock and kill approach means scientists need to understand more about how latency is maintained. Previous evidence shows that latency requires proteins known as histone deacetylases and histone methyltransferases. Certain gene-silencing proteins called transcription suppressors are also involved. Ma et al. have now examined latent HIV-1 in several kinds of human cells grown in the laboratory. The cells were modified to make certain proteins at much lower levels than normal. The experiments showed that the loss of a protein called TRIM28 ‘wakes up’ latent HIV-1. TRIM28 attaches chemical marks called SUMOylations to gene regulators in the cell. These SUMOylations restrict the activity of HIV-1’s genes, which is important to maintain latency. Specifically, TRIM28 adds SUMOylations to a protein named CDK9 at three key positions. Reducing the levels of TRIM28 made it easier to shock many HIV-1 in infected cells out of latency. With further investigation, targeting TRIM28 may one day be used to treat HIV-1 infection through a shock and kill method.
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Affiliation(s)
- Xiancai Ma
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Tao Yang
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuewen Luo
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Liyang Wu
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yawen Jiang
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zheng Song
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ting Pan
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Bingfeng Liu
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Guangyan Liu
- College of Basic Medical Sciences, Shenyang Medical College, Shenyang, China
| | - Jun Liu
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Fei Yu
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhangping He
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wanying Zhang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jinyu Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Liting Liang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuanjun Guan
- Core Laboratory Platform for Medical Science, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xu Zhang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Linghua Li
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou, China
| | - Weiping Cai
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou, China
| | - Xiaoping Tang
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kai Deng
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hui Zhang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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18
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Habibian J, Ferguson BS. The Crosstalk between Acetylation and Phosphorylation: Emerging New Roles for HDAC Inhibitors in the Heart. Int J Mol Sci 2018; 20:E102. [PMID: 30597863 PMCID: PMC6337125 DOI: 10.3390/ijms20010102] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/20/2018] [Accepted: 12/22/2018] [Indexed: 12/22/2022] Open
Abstract
Approximately five million United States (U.S.) adults are diagnosed with heart failure (HF), with eight million U.S. adults projected to suffer from HF by 2030. With five-year mortality rates following HF diagnosis approximating 50%, novel therapeutic treatments are needed for HF patients. Pre-clinical animal models of HF have highlighted histone deacetylase (HDAC) inhibitors as efficacious therapeutics that can stop and potentially reverse cardiac remodeling and dysfunction linked with HF development. HDACs remove acetyl groups from nucleosomal histones, altering DNA-histone protein electrostatic interactions in the regulation of gene expression. However, HDACs also remove acetyl groups from non-histone proteins in various tissues. Changes in histone and non-histone protein acetylation plays a key role in protein structure and function that can alter other post translational modifications (PTMs), including protein phosphorylation. Protein phosphorylation is a well described PTM that is important for cardiac signal transduction, protein activity and gene expression, yet the functional role for acetylation-phosphorylation cross-talk in the myocardium remains less clear. This review will focus on the regulation and function for acetylation-phosphorylation cross-talk in the heart, with a focus on the role for HDACs and HDAC inhibitors as regulators of acetyl-phosphorylation cross-talk in the control of cardiac function.
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Affiliation(s)
- Justine Habibian
- Cellular and Molecular Biology, University of Nevada, Reno, NV 89557, USA.
- Department of Nutrition, University of Nevada, Reno, NV 89557, USA.
- Center for Cardiovascular Research, University of Nevada, Reno, NV 89557, USA.
| | - Bradley S Ferguson
- Department of Nutrition, University of Nevada, Reno, NV 89557, USA.
- Center for Cardiovascular Research, University of Nevada, Reno, NV 89557, USA.
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19
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Identification and targeting of novel CDK9 complexes in acute myeloid leukemia. Blood 2018; 133:1171-1185. [PMID: 30587525 DOI: 10.1182/blood-2018-08-870089] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/07/2018] [Indexed: 01/09/2023] Open
Abstract
Aberrant activation of mTOR signaling in acute myeloid leukemia (AML) results in a survival advantage that promotes the malignant phenotype. To improve our understanding of factors that contribute to mammalian target of rapamycin (mTOR) signaling activation and identify novel therapeutic targets, we searched for unique interactors of mTOR complexes through proteomics analyses. We identify cyclin dependent kinase 9 (CDK9) as a novel binding partner of the mTOR complex scaffold protein, mLST8. Our studies demonstrate that CDK9 is present in distinct mTOR-like (CTOR) complexes in the cytoplasm and nucleus. In the nucleus, CDK9 binds to RAPTOR and mLST8, forming CTORC1, to promote transcription of genes important for leukemogenesis. In the cytoplasm, CDK9 binds to RICTOR, SIN1, and mLST8, forming CTORC2, and controls messenger RNA (mRNA) translation through phosphorylation of LARP1 and rpS6. Pharmacological targeting of CTORC complexes results in suppression of growth of primitive human AML progenitors in vitro and elicits strong antileukemic responses in AML xenografts in vivo.
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20
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The acetylation of cyclin-dependent kinase 5 at lysine 33 regulates kinase activity and neurite length in hippocampal neurons. Sci Rep 2018; 8:13676. [PMID: 30209341 PMCID: PMC6135752 DOI: 10.1038/s41598-018-31785-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/19/2018] [Indexed: 01/06/2023] Open
Abstract
Cyclin-dependent kinase 5 (CDK5) plays a pivotal role in neural development and neurodegeneration. CDK5 activity can be regulated by posttranslational modifications, including phosphorylation and S-nitrosylation. In this study, we demonstrate a novel mechanism by which the acetylation of CDK5 at K33 (Ac-CDK5) results in the loss of ATP binding and impaired kinase activity. We identify GCN5 and SIRT1 as critical factor controlling Ac-CDK5 levels. Ac-CDK5 achieved its lowest levels in rat fetal brains but was dramatically increased during postnatal periods. Intriguingly, nuclear Ac-CDK5 levels negatively correlated with neurite length in embryonic hippocampal neurons. Either treatment with the SIRT1 activator SRT1720 or overexpression of SIRT1 leads to increases in neurite length, whereas SIRT1 inhibitor EX527 or ectopic expression of acetyl-mimetic (K33Q) CDK5 induced the opposite effect. Furthermore, the expression of nuclear-targeted CDK5 K33Q abolished the SRT1720-induced neurite outgrowth, showing that SIRT1 positively regulates neurite outgrowth via deacetylation of nuclear CDK5. The CDK5 activity-dependent increase of neurite length was mediated by enhanced transcriptional regulation of BDNF via unknown mechanism(s). Our findings identify a novel mechanism by which acetylation-mediated regulation of nuclear CDK5 activity plays a critical role in determining neurite length in embryonic neurons.
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21
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Chen L, Keppler OT, Schölz C. Post-translational Modification-Based Regulation of HIV Replication. Front Microbiol 2018; 9:2131. [PMID: 30254620 PMCID: PMC6141784 DOI: 10.3389/fmicb.2018.02131] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Human immunodeficiency virus (HIV) relies heavily on the host cellular machinery for production of viral progeny. To exploit cellular proteins for replication and to overcome host factors with antiviral activity, HIV has evolved a set of regulatory and accessory proteins to shape an optimized environment for its replication and to facilitate evasion from the immune system. Several cellular pathways are hijacked by the virus to modulate critical steps during the viral life cycle. Thereby, post-translational modifications (PTMs) of viral and cellular proteins gain increasingly attention as modifying enzymes regulate virtually every step of the viral replication cycle. This review summarizes the current knowledge of HIV-host interactions influenced by PTMs with a special focus on acetylation, ubiquitination, and phosphorylation of proteins linked to cellular signaling and viral replication. Insights into these interactions are surmised to aid development of new intervention strategies.
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Affiliation(s)
- Lin Chen
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Christian Schölz
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
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22
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Bachs O, Gallastegui E, Orlando S, Bigas A, Morante-Redolat JM, Serratosa J, Fariñas I, Aligué R, Pujol MJ. Role of p27 Kip1 as a transcriptional regulator. Oncotarget 2018; 9:26259-26278. [PMID: 29899857 PMCID: PMC5995243 DOI: 10.18632/oncotarget.25447] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 05/01/2018] [Indexed: 12/16/2022] Open
Abstract
The protein p27Kip1 is a member of the Cip/Kip family of cyclin-dependent kinase (Cdk) inhibitors. It interacts with both the catalytic and the regulatory subunit (cyclin) and introduces a region into the catalytic cleave of the Cdk inducing its inactivation. Its inhibitory capacity can be modulated by specific tyrosine phosphorylations. p27Kip1 also behaves as a transcriptional regulator. It associates with specific chromatin domains through different transcription factors. ChIP on chip, ChIP-seq and expression microarray analysis allowed the identification of the transcriptional programs regulated by p27Kip1. Thus, important cellular functions as cell division cycle, respiration, RNA processing, translation and cell adhesion, are under p27Kip1 regulation. Moreover, genes involved in pathologies as cancer and neurodegeneration are also regulated by p27Kip1, suggesting its implication in these pathologies. The carboxyl moiety of p27Kip1 can associate with different proteins, including transcriptional regulators. In contrast, its NH2-terminal region specifically interacts with cyclin-Cdk complexes. The general mechanistic model of how p27Kip1 regulates transcription is that it associates by its COOH region to the transcriptional regulators on the chromatin and by the NH2-domain to cyclin-Cdk complexes. After Cdk activation it would phosphorylate the specific targets on the chromatin leading to gene expression. This model has been demonstrated to apply in the transcriptional regulation of p130/E2F4 repressed genes involved in cell cycle progression. We summarize in this review our current knowledge on the role of p27Kip1 in the regulation of transcription, on the transcriptional programs under its regulation and on its relevance in pathologies as cancer and neurodegeneration.
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Affiliation(s)
- Oriol Bachs
- Department of Biomedical Sciences, Faculty of Medicine, University of Barcelona, IDIBAPS, CIBERONC, Barcelona, Spain
| | - Edurne Gallastegui
- Department of Biomedical Sciences, Faculty of Medicine, University of Barcelona, IDIBAPS, CIBERONC, Barcelona, Spain
| | - Serena Orlando
- Department of Biomedical Sciences, Faculty of Medicine, University of Barcelona, IDIBAPS, CIBERONC, Barcelona, Spain
| | - Anna Bigas
- Program in Cancer Research, Institut Hospital Del Mar d'Investigacions Mèdiques (IMIM), CIBERONC, Barcelona, Spain
| | - José Manuel Morante-Redolat
- Departamento de Biología Celular, Biología Funcional y Antropología Física and ERI de Biotecnología y Biomedicina, CIBERNED, Universidad de Valencia, Valencia, Spain
| | - Joan Serratosa
- Department of Cerebral Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), IDIBAPS, Barcelona, Spain
| | - Isabel Fariñas
- Departamento de Biología Celular, Biología Funcional y Antropología Física and ERI de Biotecnología y Biomedicina, CIBERNED, Universidad de Valencia, Valencia, Spain
| | - Rosa Aligué
- Department of Biomedical Sciences, Faculty of Medicine, University of Barcelona, IDIBAPS, CIBERONC, Barcelona, Spain
| | - Maria Jesús Pujol
- Department of Biomedical Sciences, Faculty of Medicine, University of Barcelona, IDIBAPS, CIBERONC, Barcelona, Spain
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23
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
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24
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Di Martile M, Del Bufalo D, Trisciuoglio D. The multifaceted role of lysine acetylation in cancer: prognostic biomarker and therapeutic target. Oncotarget 2018; 7:55789-55810. [PMID: 27322556 PMCID: PMC5342454 DOI: 10.18632/oncotarget.10048] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/01/2016] [Indexed: 12/28/2022] Open
Abstract
Lysine acetylation is a post-translational modification that regulates gene transcription by targeting histones as well as a variety of transcription factors in the nucleus. Recently, several reports have demonstrated that numerous cytosolic proteins are also acetylated and that this modification, affecting protein activity, localization and stability has profound consequences on their cellular functions. Interestingly, most non-histone proteins targeted by acetylation are relevant for tumorigenesis. In this review, we will analyze the functional implications of lysine acetylation in different cellular compartments, and will examine our current understanding of lysine acetyltransferases family, highlighting the biological role and prognostic value of these enzymes and their substrates in cancer. The latter part of the article will address challenges and current status of molecules targeting lysine acetyltransferase enzymes in cancer therapy.
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Affiliation(s)
- Marta Di Martile
- Preclinical Models and New Therapeutic Agents Unit, Research, Advanced Diagnostics and Technological Innovation Department, Regina Elena National Cancer Institute, Rome, Italy
| | - Donatella Del Bufalo
- Preclinical Models and New Therapeutic Agents Unit, Research, Advanced Diagnostics and Technological Innovation Department, Regina Elena National Cancer Institute, Rome, Italy
| | - Daniela Trisciuoglio
- Preclinical Models and New Therapeutic Agents Unit, Research, Advanced Diagnostics and Technological Innovation Department, Regina Elena National Cancer Institute, Rome, Italy
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25
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Perearnau A, Orlando S, Islam ABMMK, Gallastegui E, Martínez J, Jordan A, Bigas A, Aligué R, Pujol MJ, Bachs O. p27Kip1, PCAF and PAX5 cooperate in the transcriptional regulation of specific target genes. Nucleic Acids Res 2017; 45:5086-5099. [PMID: 28158851 PMCID: PMC5435914 DOI: 10.1093/nar/gkx075] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 01/26/2017] [Indexed: 12/13/2022] Open
Abstract
The cyclin-dependent kinase inhibitor p27Kip1 (p27) also behaves as a transcriptional repressor. Data showing that the p300/CBP-associated factor (PCAF) acetylates p27 inducing its degradation suggested that PCAF and p27 could collaborate in the regulation of transcription. However, this possibility remained to be explored. We analyzed here the transcriptional programs regulated by PCAF and p27 in the colon cancer cell line HCT116 by chromatin immunoprecipitation sequencing (ChIP-seq). We identified 269 protein-encoding genes that contain both p27 and PCAF binding sites being the majority of these sites different for PCAF and p27. PCAF or p27 knock down revealed that both regulate the expression of these genes, PCAF as an activator and p27 as a repressor. The double knock down of PCAF and p27 strongly reduced their expression indicating that the activating role of PCAF overrides the repressive effect of p27. We also observed that the transcription factor Pax5 interacts with both p27 and PCAF and that the knock down of Pax5 induces the expression of p27/PCAF target genes indicating that it also participates in the transcriptional regulation mediated by p27/PCAF. In summary, we report here a previously unknown mechanism of transcriptional regulation mediated by p27, Pax5 and PCAF.
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Affiliation(s)
- Anna Perearnau
- Department of Biomedical Sciences, University of Barcelona-IDIBAPS, CIBERONC, 08036 Barcelona, Spain
| | - Serena Orlando
- Department of Biomedical Sciences, University of Barcelona-IDIBAPS, CIBERONC, 08036 Barcelona, Spain
| | - Abul B M M K Islam
- Department of Genetic Engineering and Biotechnology University of Dhaka, Dhaka 1000, Bangladesh
| | - Edurne Gallastegui
- Department of Biomedical Sciences, University of Barcelona-IDIBAPS, CIBERONC, 08036 Barcelona, Spain
| | - Jonatan Martínez
- Department of Biomedical Sciences, University of Barcelona-IDIBAPS, CIBERONC, 08036 Barcelona, Spain
| | - Albert Jordan
- Department of Molecular Genomics, Molecular Biology Institute of Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), 08029 Barcelona, Spain
| | - Anna Bigas
- Program in Cancer Research, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), CIBERONC, 08003 Barcelona, Spain
| | - Rosa Aligué
- Department of Biomedical Sciences, University of Barcelona-IDIBAPS, CIBERONC, 08036 Barcelona, Spain
| | - Maria Jesús Pujol
- Department of Biomedical Sciences, University of Barcelona-IDIBAPS, CIBERONC, 08036 Barcelona, Spain
| | - Oriol Bachs
- Department of Biomedical Sciences, University of Barcelona-IDIBAPS, CIBERONC, 08036 Barcelona, Spain
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26
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Blank MF, Chen S, Poetz F, Schnölzer M, Voit R, Grummt I. SIRT7-dependent deacetylation of CDK9 activates RNA polymerase II transcription. Nucleic Acids Res 2017; 45:2675-2686. [PMID: 28426094 PMCID: PMC5389538 DOI: 10.1093/nar/gkx053] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/20/2017] [Indexed: 01/08/2023] Open
Abstract
SIRT7 is an NAD+-dependent protein deacetylase that regulates cell growth and proliferation. Previous studies have shown that SIRT7 is required for RNA polymerase I (Pol I) transcription and pre-rRNA processing. Here, we took a proteomic approach to identify novel molecular targets and characterize the role of SIRT7 in non-nucleolar processes. We show that SIRT7 interacts with numerous proteins involved in transcriptional regulation and RNA metabolism, the majority of interactions requiring ongoing transcription. In addition to its role in Pol I transcription, we found that SIRT7 also regulates transcription of snoRNAs and mRNAs. Mechanistically, SIRT7 promotes the release of P-TEFb from the inactive 7SK snRNP complex and deacetylates CDK9, a subunit of the elongation factor P-TEFb, which activates transcription by phosphorylating serine 2 within the C-terminal domain (CTD) of Pol II. SIRT7 counteracts GCN5-directed acetylation of lysine 48 within the catalytic domain of CDK9, deacetylation promoting CTD phosphorylation and transcription elongation.
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Affiliation(s)
- Maximilian F Blank
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Sifan Chen
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Fabian Poetz
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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27
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Paparidis NFDS, Durvale MC, Canduri F. The emerging picture of CDK9/P-TEFb: more than 20 years of advances since PITALRE. MOLECULAR BIOSYSTEMS 2017; 13:246-276. [PMID: 27833949 DOI: 10.1039/c6mb00387g] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CDK9 is a prominent member of the transcriptional CDKs subfamily, a group of kinases whose function is to control the primary steps of mRNA synthesis and processing by eukaryotic RNA polymerase II. As a cyclin-dependent kinase, CDK9 activation in vivo depends upon its association with T-type cyclins to assemble the positive transcription elongation factor (P-TEFb). Although CDK9/P-TEFb phosphorylates the C-terminal domain of RNAP II in the same positions targeted by CDK7 (TFIIH) and CDK8 (Mediator), the former does not participate in the transcription initiation, but rather plays a unique role by driving the polymerase to productive elongation. In addition to RNAP II CTD, the negative transcription elongation factors DSIF and NELF also represent major CDK9 substrates, whose phosphorylation is required to overcome the proximal pause of the polymerase. CDK9 is recruited to specific genes through proteins that interact with both P-TEFb and distinct elements in DNA, RNA or chromatin, where it modulates the activity of individual RNAP II transcription complexes. The regulation of CDK9 function is an intricate network that includes post-translational modifications (phosphorylation/dephosphorylation and acetylation/deacetylation of key residues) as well as the association of P-TEFb with various proteins that can stimulate or inhibit its kinase activity. Several cases of CDK9 deregulation have been linked to important human diseases, including various types of cancer and also AIDS (due to its essential role in HIV replication). Not only HIV, but also many other human viruses have been shown to depend strongly on CDK9 activity to be transcribed within host cells. This review summarizes the main advances made on CDK9/P-TEFb field in more than 20 years, introducing the structural, functional and genetic aspects that have been elucidated ever since.
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Affiliation(s)
- Nikolas Ferreira Dos Santos Paparidis
- Department of Chemistry and Molecular Physics, Institute of Chemistry of Sao Carlos, Sao Paulo University, Av. Trabalhador Sãocarlense, 400, Zip Code 780, 13560-970, São Carlos-SP, Brazil.
| | - Maxwell Castro Durvale
- Department of Biochemistry, Institute of Chemistry, Sao Paulo University, Av. Prof. Lineu Prestes, 748, 05508-000, Butantã - São Paulo - SP, Brazil
| | - Fernanda Canduri
- Department of Chemistry and Molecular Physics, Institute of Chemistry of Sao Carlos, Sao Paulo University, Av. Trabalhador Sãocarlense, 400, Zip Code 780, 13560-970, São Carlos-SP, Brazil.
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28
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Caron D, Byrne DP, Thebault P, Soulet D, Landry CR, Eyers PA, Elowe S. Mitotic phosphotyrosine network analysis reveals that tyrosine phosphorylation regulates Polo-like kinase 1 (PLK1). Sci Signal 2016; 9:rs14. [PMID: 27965426 DOI: 10.1126/scisignal.aah3525] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tyrosine phosphorylation is closely associated with cell proliferation. During the cell cycle, serine and threonine phosphorylation plays the leading role, and such phosphorylation events are most dynamic during the mitotic phase of the cell cycle. However, mitotic phosphotyrosine is not well characterized. Although a few functionally-relevant mitotic phosphotyrosine sites have been characterized, evidence suggests that this modification may be more prevalent than previously appreciated. Here, we examined tyrosine phosphorylation in mitotic human cells including those on spindle-associated proteins.? Database mining confirmed ~2000 mitotic phosphotyrosine sites, and network analysis revealed a number of subnetworks that were enriched in tyrosine-phosphorylated proteins, including components of the kinetochore or spindle and SRC family kinases. We identified Polo-like kinase 1 (PLK1), a major signaling hub in the spindle subnetwork, as phosphorylated at the conserved Tyr217 in the kinase domain. Substitution of Tyr217 with a phosphomimetic residue eliminated PLK1 activity in vitro and in cells. Further analysis showed that Tyr217 phosphorylation reduced the phosphorylation of Thr210 in the activation loop, a phosphorylation event necessary for PLK1 activity. Our data indicate that mitotic tyrosine phosphorylation regulated a key serine/threonine kinase hub in mitotic cells and suggested that spatially separating tyrosine phosphorylation events can reveal previously unrecognized regulatory events and complexes associated with specific structures of the cell cycle.
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Affiliation(s)
- Danielle Caron
- Department of Pediatrics, Faculty of Medicine, Université Laval, Centre Hospitalier Universitaire de Québec Research Center, Quebec City, Quebec G1V 4G2, Canada
| | - Dominic P Byrne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Philippe Thebault
- Department of Pediatrics, Faculty of Medicine, Université Laval, Centre Hospitalier Universitaire de Québec Research Center, Quebec City, Quebec G1V 4G2, Canada
| | - Denis Soulet
- Department of Psychiatry et Neurosciences, Faculty of Medicine, Université Laval, Centre Hospitalier Universitaire de Québec Research Center, Quebec City, Quebec G1V 4G2, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, Department of Biology, PROTEO, Université Laval, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine, Quebec City, Quebec G1V 0A6, Canada
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Sabine Elowe
- Department of Pediatrics, Faculty of Medicine, Université Laval, Centre Hospitalier Universitaire de Québec Research Center, Quebec City, Quebec G1V 4G2, Canada.
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29
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Abstract
To complete its life cycle, HIV-1 enters the nucleus of the host cell as reverse-transcribed viral DNA. The nucleus is a complex environment, in which chromatin is organized to support different structural and functional aspects of cell physiology. As such, it represents a challenge for an incoming viral genome, which needs to be integrated into cellular DNA to ensure productive infection. Integration of the viral genome into host DNA depends on the enzymatic activity of HIV-1 integrase and involves different cellular factors that influence the selection of integration sites. The selection of integration site has functional consequences for viral transcription, which usually follows the integration event. However, in resting CD4+ T cells, the viral genome can be silenced for long periods of time, which leads to the generation of a latent reservoir of quiescent integrated HIV-1 DNA. Integration represents the only nuclear event in the viral life cycle that can be pharmacologically targeted with current therapies, and the aspects that connect HIV-1 nuclear entry to HIV-1 integration and viral transcription are only beginning to be elucidated.
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30
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Fournier M, Orpinell M, Grauffel C, Scheer E, Garnier JM, Ye T, Chavant V, Joint M, Esashi F, Dejaegere A, Gönczy P, Tora L. KAT2A/KAT2B-targeted acetylome reveals a role for PLK4 acetylation in preventing centrosome amplification. Nat Commun 2016; 7:13227. [PMID: 27796307 PMCID: PMC5095585 DOI: 10.1038/ncomms13227] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/14/2016] [Indexed: 12/12/2022] Open
Abstract
Lysine acetylation is a widespread post-translational modification regulating various biological processes. To characterize cellular functions of the human lysine acetyltransferases KAT2A (GCN5) and KAT2B (PCAF), we determined their acetylome by shotgun proteomics. One of the newly identified KAT2A/2B substrate is polo-like kinase 4 (PLK4), a key regulator of centrosome duplication. We demonstrate that KAT2A/2B acetylate the PLK4 kinase domain on residues K45 and K46. Molecular dynamics modelling suggests that K45/K46 acetylation impairs kinase activity by shifting the kinase to an inactive conformation. Accordingly, PLK4 activity is reduced upon in vitro acetylation of its kinase domain. Moreover, the overexpression of the PLK4 K45R/K46R mutant in cells does not lead to centrosome overamplification, as observed with wild-type PLK4. We also find that impairing KAT2A/2B-acetyltransferase activity results in diminished phosphorylation of PLK4 and in excess centrosome numbers in cells. Overall, our study identifies the global human KAT2A/2B acetylome and uncovers that KAT2A/2B acetylation of PLK4 prevents centrosome amplification. The acetyltransferases KAT2A and KAT2B are essential regulators of transcription, cell cycle progression and DNA repair. Here the authors describe a KAT2A/2B-dependent acetylome, and show that acetylation of the protein kinase PLK4 contributes to the regulation of centrosome number.
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Affiliation(s)
- Marjorie Fournier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Meritxell Orpinell
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Cédric Grauffel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Jean-Marie Garnier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Virginie Chavant
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Mathilde Joint
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Annick Dejaegere
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
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31
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Ahmad K, Scholz B, Capelo R, Schweighöfer I, Kahnt AS, Marschalek R, Steinhilber D. AF4 and AF4-MLL mediate transcriptional elongation of 5-lipoxygenase mRNA by 1, 25-dihydroxyvitamin D3. Oncotarget 2016; 6:25784-800. [PMID: 26329759 PMCID: PMC4694866 DOI: 10.18632/oncotarget.4703] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/10/2015] [Indexed: 12/22/2022] Open
Abstract
The human 5-lipoxygenase (5-LO), encoded by the ALOX5 gene, is the key enzyme in the formation of pro-inflammatory leukotrienes. ALOX5 gene transcription is strongly stimulated by calcitriol (1α, 25-dihydroxyvitamin D3) and TGFβ (transforming growth factor-β). Here, we investigated the influence of MLL (activator of transcript initiation), AF4 (activator of transcriptional elongation) as well as of the leukemogenic fusion proteins MLL-AF4 (ectopic activator of transcript initiation) and AF4-MLL (ectopic activator of transcriptional elongation) on calcitriol/TGFβ-dependent 5-LO transcript elongation. We present evidence that the AF4 complex directly interacts with the vitamin D receptor (VDR) and promotes calcitriol-dependent ALOX5 transcript elongation. Activation of transcript elongation was strongly enhanced by the AF4-MLL fusion protein but was sensitive to Flavopiridol. By contrast, MLL-AF4 displayed no effect on transcriptional elongation. Furthermore, HDAC class I inhibitors inhibited the ectopic effects caused by AF4-MLL on transcriptional elongation, suggesting that HDAC class I inhibitors are potential therapeutics for the treatment of t(4;11)(q21;q23) leukemia.
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Affiliation(s)
- Khalil Ahmad
- Institute of Pharmaceutical Chemistry / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
| | - Bastian Scholz
- Institute of Pharmaceutical Biology / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
| | - Ricardo Capelo
- Institute of Pharmaceutical Chemistry / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
| | - Ilona Schweighöfer
- Institute of Pharmaceutical Chemistry / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
| | - Astrid Stefanie Kahnt
- Institute of Pharmaceutical Chemistry / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
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32
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Lucic B, Lusic M. Connecting HIV-1 integration and transcription: a step toward new treatments. FEBS Lett 2016; 590:1927-39. [PMID: 27224516 DOI: 10.1002/1873-3468.12226] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/17/2016] [Accepted: 05/24/2016] [Indexed: 12/12/2022]
Abstract
Thanks to the current combined antiretroviral therapy (cART), HIV-1 infection has become a manageable although chronic disease. The reason for this lies in the fact that long-lived cellular reservoirs persist in patients on cART. Despite numerous efforts to understand molecular mechanisms that contribute to viral latency, the important question of how and when latency is established remains unanswered. Related to this is the connection between HIV-1 integration and the capacity of the provirus to enter the latent state. In this review, we will give an overview of these nuclear events in the viral life cycle in the light of current therapeutic approaches, which aim to either reactivate the provirus or even excise the proviral DNA from the cellular genome.
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Affiliation(s)
- Bojana Lucic
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg and German Center for Infection Research (DZIF), Germany
| | - Marina Lusic
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg and German Center for Infection Research (DZIF), Germany
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33
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Persistent human Borna disease virus infection modifies the acetylome of human oligodendroglia cells towards higher energy and transporter levels. Virology 2015. [DOI: 10.1016/j.virol.2015.06.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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34
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Bose D, Gagnon J, Chebloune Y. Comparative Analysis of Tat-Dependent and Tat-Deficient Natural Lentiviruses. Vet Sci 2015; 2:293-348. [PMID: 29061947 PMCID: PMC5644649 DOI: 10.3390/vetsci2040293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 01/10/2023] Open
Abstract
The emergence of human immunodeficiency virus (HIV) causing acquired immunodeficiency syndrome (AIDS) in infected humans has resulted in a global pandemic that has killed millions. HIV-1 and HIV-2 belong to the lentivirus genus of the Retroviridae family. This genus also includes viruses that infect other vertebrate animals, among them caprine arthritis-encephalitis virus (CAEV) and Maedi-Visna virus (MVV), the prototypes of a heterogeneous group of viruses known as small ruminant lentiviruses (SRLVs), affecting both goat and sheep worldwide. Despite their long host-SRLV natural history, SRLVs were never found to be responsible for immunodeficiency in contrast to primate lentiviruses. SRLVs only replicate productively in monocytes/macrophages in infected animals but not in CD4+ T cells. The focus of this review is to examine and compare the biological and pathological properties of SRLVs as prototypic Tat-independent lentiviruses with HIV-1 as prototypic Tat-dependent lentiviruses. Results from this analysis will help to improve the understanding of why and how these two prototypic lentiviruses evolved in opposite directions in term of virulence and pathogenicity. Results may also help develop new strategies based on the attenuation of SRLVs to control the highly pathogenic HIV-1 in humans.
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Affiliation(s)
- Deepanwita Bose
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
| | - Jean Gagnon
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
| | - Yahia Chebloune
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
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35
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Jeng MY, Ali I, Ott M. Manipulation of the host protein acetylation network by human immunodeficiency virus type 1. Crit Rev Biochem Mol Biol 2015; 50:314-25. [PMID: 26329395 PMCID: PMC4816045 DOI: 10.3109/10409238.2015.1061973] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Over the past 15 years, protein acetylation has emerged as a globally important post-translational modification that fine-tunes major cellular processes in many life forms. This dynamic regulatory system is critical both for complex eukaryotic cells and for the viruses that infect them. HIV-1 accesses the host acetylation network by interacting with several key enzymes, thereby promoting infection at multiple steps during the viral life cycle. Inhibitors of host histone deacetylases and bromodomain-containing proteins are now being pursued as therapeutic strategies to enhance current antiretroviral treatment. As more acetylation-targeting compounds are reaching clinical trials, it is time to review the role of reversible protein acetylation in HIV-infected CD4(+) T cells.
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Affiliation(s)
- Mark Y. Jeng
- Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94158, USA
| | - Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94158, USA
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94158, USA
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36
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Proietto M, Bianchi MM, Ballario P, Brenna A. Epigenetic and Posttranslational Modifications in Light Signal Transduction and the Circadian Clock in Neurospora crassa. Int J Mol Sci 2015; 16:15347-83. [PMID: 26198228 PMCID: PMC4519903 DOI: 10.3390/ijms160715347] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/24/2015] [Accepted: 06/30/2015] [Indexed: 12/15/2022] Open
Abstract
Blue light, a key abiotic signal, regulates a wide variety of physiological processes in many organisms. One of these phenomena is the circadian rhythm presents in organisms sensitive to the phase-setting effects of blue light and under control of the daily alternation of light and dark. Circadian clocks consist of autoregulatory alternating negative and positive feedback loops intimately connected with the cellular metabolism and biochemical processes. Neurospora crassa provides an excellent model for studying the molecular mechanisms involved in these phenomena. The White Collar Complex (WCC), a blue-light receptor and transcription factor of the circadian oscillator, and Frequency (FRQ), the circadian clock pacemaker, are at the core of the Neurospora circadian system. The eukaryotic circadian clock relies on transcriptional/translational feedback loops: some proteins rhythmically repress their own synthesis by inhibiting the activity of their transcriptional factors, generating self-sustained oscillations over a period of about 24 h. One of the basic mechanisms that perpetuate self-sustained oscillations is post translation modification (PTM). The acronym PTM generically indicates the addition of acetyl, methyl, sumoyl, or phosphoric groups to various types of proteins. The protein can be regulatory or enzymatic or a component of the chromatin. PTMs influence protein stability, interaction, localization, activity, and chromatin packaging. Chromatin modification and PTMs have been implicated in regulating circadian clock function in Neurospora. Research into the epigenetic control of transcription factors such as WCC has yielded new insights into the temporal modulation of light-dependent gene transcription. Here we report on epigenetic and protein PTMs in the regulation of the Neurospora crassa circadian clock. We also present a model that illustrates the molecular mechanisms at the basis of the blue light control of the circadian clock.
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Affiliation(s)
- Marco Proietto
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
| | - Michele Maria Bianchi
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
| | - Paola Ballario
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
- Pasteur Institute, Cenci Bolognetti Foundation and Department of Biology and Biotechnology "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
| | - Andrea Brenna
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
- Pasteur Institute, Cenci Bolognetti Foundation and Department of Biology and Biotechnology "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
- Department of Biology, Division of Biochemistry, University of Fribourg, Chemin du Musée 5, Fribourg 1700, Switzerland.
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Melo-Braga MN, Meyer M, Zeng X, Larsen MR. Characterization of human neural differentiation from pluripotent stem cells using proteomics/PTMomics-Current state-of-the-art and challenges. Proteomics 2015; 15:656-74. [DOI: 10.1002/pmic.201400388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/11/2014] [Accepted: 11/19/2014] [Indexed: 01/18/2023]
Affiliation(s)
- Marcella Nunes Melo-Braga
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
- Center for Clinical Proteomics; University of Southern Denmark; Odense Denmark
| | - Morten Meyer
- Department of Neurobiology Research; Institute of Molecular Medicine; University of Southern Denmark; Odense Denmark
| | | | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
- Center for Clinical Proteomics; University of Southern Denmark; Odense Denmark
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38
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Rahimi N, Costello CE. Emerging roles of post-translational modifications in signal transduction and angiogenesis. Proteomics 2014; 15:300-9. [PMID: 25161153 DOI: 10.1002/pmic.201400183] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/14/2014] [Accepted: 08/20/2014] [Indexed: 01/02/2023]
Abstract
The vascular endothelial growth factor receptor-2 (VEGFR-2) belongs to the family of receptor tyrosine kinases and is a key player in vasculogenesis and pathological angiogenesis. An emerging picture of PTMs of VEGFR-2 suggests that they play central roles in generating a highly dynamic and complex signaling system that regulates key angiogenic responses ranging from endothelial cell differentiation, proliferation, migration to permeability. Recent MS analysis of VEGFR-2 uncovered previously unrecognized PTMs on VEGFR-2 with a distinct function. The ligand binding extracellular domain of VEGFR-2 is composed of seven immunoglobulin-like domains highly decorated with N-glycosylation, while its cytoplasmic domain is subject to multiple PTMs including Tyr, Ser/Thr phosphorylation, Arg and Lys methylation, acetylation and ubiquitination. Here we review the PTMs on VEGFR-2, their importance in angiogenic signaling relays and possible novel therapeutic potentials.
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Affiliation(s)
- Nader Rahimi
- Department of Pathology, Boston University School of Medicine, Boston, MA, USA
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39
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Gcn5 and PCAF regulate PPARγ and Prdm16 expression to facilitate brown adipogenesis. Mol Cell Biol 2014; 34:3746-53. [PMID: 25071153 DOI: 10.1128/mcb.00622-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The acetyltransferase Gcn5 is critical for embryogenesis and shows partial functional redundancy with its homolog PCAF. However, the tissue- and cell lineage-specific functions of Gcn5 and PCAF are still not well defined. Here we probe the functions of Gcn5 and PCAF in adipogenesis. We found that the double knockout (DKO) of Gcn5/PCAF inhibits expression of the master adipogenic transcription factor gene PPARγ, thereby preventing adipocyte differentiation. The adipogenesis defects in Gcn5/PCAF DKO cells are rescued by ectopic expression of peroxisome proliferator-activated receptor γ (PPARγ), suggesting Gcn5/PCAF act upstream of PPARγ to facilitate adipogenesis. The requirement of Gcn5/PCAF for PPARγ expression was unexpectedly bypassed by prolonged treatment with an adipogenic inducer, 3-isobutyl-1-methylxanthine (IBMX). However, neither PPARγ ectopic expression nor prolonged IBMX treatment rescued defects in Prdm16 expression in DKO cells, indicating that Gcn5/PCAF are essential for normal Prdm16 expression. Gcn5/PCAF regulate PPARγ and Prdm16 expression at different steps in the transcription process, facilitating RNA polymerase II recruitment to Prdm16 and elongation of PPARγ transcripts. Overall, our study reveals that Gcn5/PCAF facilitate adipogenesis through regulation of PPARγ expression and regulate brown adipogenesis by influencing Prdm16 expression.
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40
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Lusic M, Giacca M. Regulation of HIV-1 latency by chromatin structure and nuclear architecture. J Mol Biol 2014; 427:688-94. [PMID: 25073101 DOI: 10.1016/j.jmb.2014.07.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/25/2014] [Accepted: 07/16/2014] [Indexed: 11/16/2022]
Abstract
Current antiretroviral therapies fail to cure HIV-1 (human immunodeficiency virus type 1) infection because HIV-1 persists as a transcriptionally inactive provirus in resting memory CD4(+) T cells. Multiple molecular events are known to regulate HIV-1 gene expression, yet the mechanisms governing the establishment and maintenance of latency remain incompletely understood. Here we summarize different molecular aspects of viral latency, from its establishment in resting CD4(+) T cells to the mechanisms involved in the reactivation of latent viral reservoirs. We focus on the relevance of chromatin structure and nuclear architecture in determining the transcriptional fate of integrated HIV-1 genomes, in light of recent findings indicating that proximity to specific subnuclear neighborhoods regulates HIV-1 gene expression.
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Affiliation(s)
- Marina Lusic
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy.
| | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy.
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41
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Safronova OS, Nakahama KI, Morita I. Acute hypoxia affects P-TEFb through HDAC3 and HEXIM1-dependent mechanism to promote gene-specific transcriptional repression. Nucleic Acids Res 2014; 42:8954-69. [PMID: 25056306 PMCID: PMC4132729 DOI: 10.1093/nar/gku611] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Hypoxia is associated with a variety of physiological and pathological conditions and elicits specific transcriptional responses. The elongation competence of RNA Polymerase II is regulated by the positive transcription elongation factor b (P-TEFb)-dependent phosphorylation of Ser2 residues on its C-terminal domain. Here, we report that hypoxia inhibits transcription at the level of elongation. The mechanism involves enhanced formation of inactive complex of P-TEFb with its inhibitor HEXIM1 in an HDAC3-dependent manner. Microarray transcriptome profiling of hypoxia primary response genes identified ∼79% of these genes being HEXIM1-dependent. Hypoxic repression of P-TEFb was associated with reduced acetylation of its Cdk9 and Cyclin T1 subunits. Hypoxia caused nuclear translocation and co-localization of the Cdk9 and HDAC3/N-CoR repressor complex. We demonstrated that the described mechanism is involved in hypoxic repression of the monocyte chemoattractant protein-1 (MCP-1) gene. Thus, HEXIM1 and HDAC-dependent deacetylation of Cdk9 and Cyclin T1 in response to hypoxia signalling alters the P-TEFb functional equilibrium, resulting in repression of transcription.
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Affiliation(s)
- Olga S Safronova
- Department of Cellular Physiological Chemistry, Graduate School, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan Global Center of Excellence Program, International Research Center for Molecular Science in Tooth and Bone Diseases, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Ken-Ichi Nakahama
- Department of Cellular Physiological Chemistry, Graduate School, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Ikuo Morita
- Department of Cellular Physiological Chemistry, Graduate School, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan Global Center of Excellence Program, International Research Center for Molecular Science in Tooth and Bone Diseases, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
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42
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Parker BL, Shepherd NE, Trefely S, Hoffman NJ, White MY, Engholm-Keller K, Hambly BD, Larsen MR, James DE, Cordwell SJ. Structural basis for phosphorylation and lysine acetylation cross-talk in a kinase motif associated with myocardial ischemia and cardioprotection. J Biol Chem 2014; 289:25890-906. [PMID: 25008320 DOI: 10.1074/jbc.m114.556035] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Myocardial ischemia and cardioprotection by ischemic pre-conditioning induce signal networks aimed at survival or cell death if the ischemic period is prolonged. These pathways are mediated by protein post-translational modifications that are hypothesized to cross-talk with and regulate each other. Phosphopeptides and lysine-acetylated peptides were quantified in isolated rat hearts subjected to ischemia or ischemic pre-conditioning, with and without splitomicin inhibition of lysine deacetylation. We show lysine acetylation (acetyl-Lys)-dependent activation of AMP-activated protein kinase, AKT, and PKA kinases during ischemia. Phosphorylation and acetyl-Lys sites mapped onto tertiary structures were proximal in >50% of proteins investigated, yet they were mutually exclusive in 50 ischemic pre-conditioning- and/or ischemia-associated peptides containing the KXXS basophilic protein kinase consensus motif. Modifications in this motif were modeled in the C terminus of muscle-type creatine kinase. Acetyl-Lys increased proximal dephosphorylation by 10-fold. Structural analysis of modified muscle-type creatine kinase peptide variants by two-dimensional NMR revealed stabilization via a lysine-phosphate salt bridge, which was disrupted by acetyl-Lys resulting in backbone flexibility and increased phosphatase accessibility.
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Affiliation(s)
- Benjamin L Parker
- From the Discipline of Pathology, School of Medical Sciences, University of Sydney, Sydney 2006, Australia, the Diabetes and Obesity Program, Biological Mass Spectrometry Unit, Garvan Institute of Medical Research, 2010 Australia
| | | | | | - Nolan J Hoffman
- the Diabetes and Obesity Program, Biological Mass Spectrometry Unit, Garvan Institute of Medical Research, 2010 Australia
| | - Melanie Y White
- the School of Molecular Bioscience and the Charles Perkins Centre, University of Sydney, Sydney 2006, Australia, and
| | | | - Brett D Hambly
- From the Discipline of Pathology, School of Medical Sciences, University of Sydney, Sydney 2006, Australia, the Charles Perkins Centre, University of Sydney, Sydney 2006, Australia, and
| | - Martin R Larsen
- the Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - David E James
- the Diabetes and Obesity Program, Biological Mass Spectrometry Unit, Garvan Institute of Medical Research, 2010 Australia, the Charles Perkins Centre, University of Sydney, Sydney 2006, Australia, and
| | - Stuart J Cordwell
- From the Discipline of Pathology, School of Medical Sciences, University of Sydney, Sydney 2006, Australia, the School of Molecular Bioscience and the Charles Perkins Centre, University of Sydney, Sydney 2006, Australia, and
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43
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Dikfidan A, Loll B, Zeymer C, Magler I, Clausen T, Meinhart A. RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase Clp1. Mol Cell 2014; 54:975-986. [PMID: 24813946 DOI: 10.1016/j.molcel.2014.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/27/2014] [Accepted: 04/03/2014] [Indexed: 12/19/2022]
Abstract
RNA-specific polynucleotide kinases of the Clp1 subfamily are key components of various RNA maturation pathways. However, the structural basis explaining their substrate specificity and the enzymatic mechanism is elusive. Here, we report crystal structures of Clp1 from Caenorhabditis elegans (ceClp1) in a number of nucleotide- and RNA-bound states along the reaction pathway. The combined structural and biochemical analysis of ceClp1 elucidates the RNA specificity and lets us derive a general model for enzyme catalysis of RNA-specific polynucleotide kinases. We identified an RNA binding motif referred to as "clasp" as well as a conformational switch that involves the essential Walker A lysine (Lys127) and regulates the enzymatic activity of ceClp1. Structural comparison with other P loop proteins, such as kinases, adenosine triphosphatases (ATPases), and guanosine triphosphatases (GTPases), suggests that the observed conformational switch of the Walker A lysine is a broadly relevant mechanistic feature.
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Affiliation(s)
- Aytac Dikfidan
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Bernhard Loll
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg 69120, Germany; Institute for Chemistry and Biochemistry/Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Cathleen Zeymer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Iris Magler
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Tim Clausen
- Research Institute of Molecular Pathology, Vienna 1030, Austria
| | - Anton Meinhart
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg 69120, Germany.
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44
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Lee J, Yun N, Kim C, Song MY, Park KS, Oh YJ. Acetylation of cyclin-dependent kinase 5 is mediated by GCN5. Biochem Biophys Res Commun 2014; 447:121-7. [PMID: 24704205 DOI: 10.1016/j.bbrc.2014.03.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 11/19/2022]
Abstract
Cyclin-dependent kinase 5 (CDK5), a member of atypical serine/threonine cyclin-dependent kinase family, plays a crucial role in pathophysiology of neurodegenerative disorders. Its kinase activity and substrate specificity are regulated by several independent pathways including binding with its activator, phosphorylation and S-nitrosylation. In the present study, we report that acetylation of CDK5 comprises an additional posttranslational modification within the cells. Among many candidates, we confirmed that its acetylation is enhanced by GCN5, a member of the GCN5-related N-acetyl-transferase family of histone acetyltransferase. Co-immunoprecipitation assay and fluorescent localization study indicated that GCN5 physically interacts with CDK5 and they are co-localized at the specific nuclear foci. Furthermore, liquid chromatography in conjunction with a mass spectrometry indicated that CDK5 is acetylated at Lys33 residue of ATP binding domain. Considering this lysine site is conserved among a wide range of species and other related cyclin-dependent kinases, therefore, we speculate that acetylation may alter the kinase activity of CDK5 via affecting efficacy of ATP coordination.
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Affiliation(s)
- Juhyung Lee
- Department of Systems Biology, Yonsei University College of Life Science and Biotechnology, Seoul 120-749, Republic of Korea
| | - Nuri Yun
- Department of Systems Biology, Yonsei University College of Life Science and Biotechnology, Seoul 120-749, Republic of Korea
| | - Chiho Kim
- Department of Systems Biology, Yonsei University College of Life Science and Biotechnology, Seoul 120-749, Republic of Korea
| | - Min-Young Song
- Department of Physiology and Biomedical Science Institute, Kyung Hee University School of Medicine, Seoul 130-701, Republic of Korea
| | - Kang-Sik Park
- Department of Physiology and Biomedical Science Institute, Kyung Hee University School of Medicine, Seoul 130-701, Republic of Korea
| | - Young J Oh
- Department of Systems Biology, Yonsei University College of Life Science and Biotechnology, Seoul 120-749, Republic of Korea.
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45
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Zhu R, Lu X, Pradhan M, Armstrong S, Storchan GB, Chow C, Simons SS. A kinase-independent activity of Cdk9 modulates glucocorticoid receptor-mediated gene induction. Biochemistry 2014; 53:1753-67. [PMID: 24559102 PMCID: PMC3985961 DOI: 10.1021/bi5000178] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/20/2014] [Indexed: 12/18/2022]
Abstract
A gene induction competition assay has recently uncovered new inhibitory activities of two transcriptional cofactors, NELF-A and NELF-B, in glucocorticoid-regulated transactivation. NELF-A and -B are also components of the NELF complex, which participates in RNA polymerase II pausing shortly after the initiation of gene transcription. We therefore asked if cofactors (Cdk9 and ELL) best known to affect paused polymerase could reverse the effects of NELF-A and -B. Unexpectedly, Cdk9 and ELL augmented, rather than prevented, the effects of NELF-A and -B. Furthermore, Cdk9 actions are not blocked either by Ckd9 inhibitors (DRB or flavopiridol) or by two Cdk9 mutants defective in kinase activity. The mode and site of action of NELF-A and -B mutants with an altered NELF domain are similarly affected by wild-type and kinase-dead Cdk9. We conclude that Cdk9 is a new modulator of GR action, that Ckd9 and ELL have novel activities in GR-regulated gene expression, that NELF-A and -B can act separately from the NELF complex, and that Cdk9 possesses activities that are independent of Cdk9 kinase activity. Finally, the competition assay has succeeded in ordering the site of action of several cofactors of GR transactivation. Extension of this methodology should be helpful in determining the site and mode of action of numerous additional cofactors and in reducing unwanted side effects.
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Affiliation(s)
- Rong Zhu
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Xinping Lu
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Madhumita Pradhan
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Stephen
P. Armstrong
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Geoffrey B. Storchan
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Carson
C. Chow
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - S. Stoney Simons
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
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Zecchin A, Pattarini L, Gutierrez MI, Mano M, Mai A, Valente S, Myers MP, Pantano S, Giacca M. Reversible acetylation regulates vascular endothelial growth factor receptor-2 activity. J Mol Cell Biol 2014; 6:116-27. [PMID: 24620033 DOI: 10.1093/jmcb/mju010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The tyrosine kinase receptor vascular endothelial growth factor receptor 2 (VEGFR2) is a key regulator of angiogenesis. Here we show that VEGFR2 is acetylated in endothelial cells both at four lysine residues forming a dense cluster in the kinase insert domain and at a single lysine located in the receptor activation loop. These modifications are under dynamic control of the acetyltransferase p300 and two deacetylases HDAC5 and HDAC6. We demonstrate that VEGFR2 acetylation essentially regulates receptor phosphorylation. In particular, VEGFR2 acetylation significantly alters the kinetics of receptor phosphorylation after ligand binding, allowing receptor phosphorylation and intracellular signaling upon prolonged stimulation with VEGF. Molecular dynamics simulations indicate that acetylation of the lysine in the activation loop contributes to the transition to an open active state, in which tyrosine phosphorylation is favored by better exposure of the kinase target residues. These findings indicate that post-translational modification by acetylation is a critical mechanism that directly affects VEGFR2 function.
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Affiliation(s)
- Annalisa Zecchin
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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Lusic M, Marini B, Ali H, Lucic B, Luzzati R, Giacca M. Proximity to PML nuclear bodies regulates HIV-1 latency in CD4+ T cells. Cell Host Microbe 2013; 13:665-77. [PMID: 23768491 DOI: 10.1016/j.chom.2013.05.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 03/05/2013] [Accepted: 04/26/2013] [Indexed: 12/21/2022]
Abstract
Nuclear bodies (NBs), characterized by the presence of the promyelocytic leukemia (PML) protein, are important components of the nuclear architecture, contributing to genetic and epigenetic control of gene expression. In investigating the mechanisms mediating HIV-1 latency, we determined that silenced but transcriptionally competent HIV-1 proviruses reside in close proximity to PML NBs and that this association inhibits HIV-1 gene expression. PML binds to the latent HIV-1 promoter, which coincides with transcriptionally inactive facultative heterochromatic marks, notably H3K9me2, at the viral genome. PML degradation and NB disruption result in strong activation of viral transcription as well as release of G9a, the major methyltransferase responsible for H3K9me2, and loss of facultative heterochromatin marks from the proviral DNA. Additionally, HIV-1 transcriptional activation requires proviral displacement from PML NBs by active nuclear actin polymerization. Thus, nuclear topology and active gene movement mediate HIV-1 transcriptional regulation and have implications for controlling HIV-1 latency and eradication.
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Affiliation(s)
- Marina Lusic
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology ICGEB, 34149 Trieste, Italy.
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Beltrao P, Bork P, Krogan NJ, van Noort V. Evolution and functional cross-talk of protein post-translational modifications. Mol Syst Biol 2013; 9:714. [PMID: 24366814 PMCID: PMC4019982 DOI: 10.1002/msb.201304521] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 11/18/2013] [Accepted: 11/22/2013] [Indexed: 12/19/2022] Open
Abstract
Protein post-translational modifications (PTMs) allow the cell to regulate protein activity and play a crucial role in the response to changes in external conditions or internal states. Advances in mass spectrometry now enable proteome wide characterization of PTMs and have revealed a broad functional role for a range of different types of modifications. Here we review advances in the study of the evolution and function of PTMs that were spurred by these technological improvements. We provide an overview of studies focusing on the origin and evolution of regulatory enzymes as well as the evolutionary dynamics of modification sites. Finally, we discuss different mechanisms of altering protein activity via post-translational regulation and progress made in the large-scale functional characterization of PTM function.
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Affiliation(s)
- Pedro Beltrao
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Peer Bork
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Max‐Delbruck‐Centre for Molecular MedicineBerlin‐BuchGermany
| | - Nevan J. Krogan
- Department of Cellular and Molecular PharmacologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- California Institute for Quantitative BiosciencesSan FranciscoCaliforniaUSA
- J. David Gladstone InstitutesSan FranciscoCaliforniaUSA
| | - Vera van Noort
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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Sancineto L, Iraci N, Massari S, Attanasio V, Corazza G, Barreca ML, Sabatini S, Manfroni G, Avanzi NR, Cecchetti V, Pannecouque C, Marcello A, Tabarrini O. Computer-Aided Design, Synthesis and Validation of 2-Phenylquinazolinone Fragments as CDK9 Inhibitors with Anti-HIV-1 Tat-Mediated Transcription Activity. ChemMedChem 2013; 8:1941-53. [DOI: 10.1002/cmdc.201300287] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Indexed: 12/20/2022]
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SIRT2 directs the replication stress response through CDK9 deacetylation. Proc Natl Acad Sci U S A 2013; 110:13546-51. [PMID: 23898190 DOI: 10.1073/pnas.1301463110] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Sirtuin 2 (SIRT2) is a sirtuin family deacetylase that directs acetylome signaling, protects genome integrity, and is a murine tumor suppressor. We show that SIRT2 directs replication stress responses by regulating the activity of cyclin-dependent kinase 9 (CDK9), a protein required for recovery from replication arrest. SIRT2 deficiency results in replication stress sensitivity, impairment in recovery from replication arrest, spontaneous accumulation of replication protein A to foci and chromatin, and a G2/M checkpoint deficit. SIRT2 interacts with and deacetylates CDK9 at lysine 48 in response to replication stress in a manner that is partially dependent on ataxia telangiectasia and Rad3 related (ATR) but not cyclin T or K, thereby stimulating CDK9 kinase activity and promoting recovery from replication arrest. Moreover, wild-type, but not acetylated CDK9, alleviates the replication stress response impairment of SIRT2 deficiency. Collectively, our results define a function for SIRT2 in regulating checkpoint pathways that respond to replication stress through deacetylation of CDK9, providing insight into how SIRT2 maintains genome integrity and a unique mechanism by which SIRT2 may function, at least in part, as a tumor suppressor protein.
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