101
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Sloutsky R, Naegle KM. Proteome-Level Analysis Indicates Global Mechanisms for Post-Translational Regulation of RRM Domains. J Mol Biol 2017; 430:41-44. [PMID: 29146174 DOI: 10.1016/j.jmb.2017.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/19/2017] [Accepted: 11/06/2017] [Indexed: 12/22/2022]
Abstract
RRM, or RNA-recognition motif, domains are the largest class of single-stranded RNA binding domains in the human proteome and play important roles in RNA processing, splicing, export, stability, packaging, and degradation. Using a current database of post-translational modifications (PTMs), ProteomeScout, we found that RRM domains are also one of the most heavily modified domains in the human proteome. Here, we present two interesting findings about RRM domain modifications, found by mapping known PTMs onto RRM domain alignments and structures. First, we find significant overlap of ubiquitination and acetylation within RRM domains, suggesting the possibility for ubiquitination-acetylation crosstalk. Additionally, an analysis of quantitative study of ubiquitination changes in response to proteasome inhibition highlights the uniqueness of RRM domain ubiquitination - RRM domain ubiquitination decreases in response to proteasome inhibition, whereas the majority of sites increase. Second, we found conservation of tyrosine phosphorylation within the RNP1 and RNP2 consensus sequences, which coordinate RNA binding - suggesting a possible role for regulation of RNA binding by tyrosine kinase signaling. These observations suggest there are unique regulatory mechanisms of RRM function that have yet to be uncovered and that the RRM domain represents a model system for further studies on understanding PTM crosstalk.
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Affiliation(s)
- Roman Sloutsky
- Biomedical Engineering and the Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kristen M Naegle
- Biomedical Engineering and the Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
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102
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Oxidative stress promotes SIRT1 recruitment to the GADD34/PP1α complex to activate its deacetylase function. Cell Death Differ 2017; 25:255-267. [PMID: 28984870 DOI: 10.1038/cdd.2017.152] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/01/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022] Open
Abstract
Phosphorylation of the eukaryotic translation initiation factor, eIF2α, by stress-activated protein kinases and dephosphorylation by the growth arrest and DNA damage-inducible protein (GADD34)-containing phosphatase is a central node in the integrated stress response. Mass spectrometry demonstrated GADD34 acetylation at multiple lysines. Substituting K315 and K322 with alanines or glutamines did not impair GADD34's ability to recruit protein phosphatase 1α (PP1α) or eIF2α, suggesting that GADD34 acetylation did not modulate eIF2α phosphatase activity. Arsenite (Ars)-induced oxidative stress increased cellular GADD34 levels and enhanced Sirtuin 1 (SIRT1) recruitment to assemble a cytoplasmic complex containing GADD34, PP1α, eIF2α and SIRT1. Induction of GADD34 in WT MEFs paralleled the dephosphorylation of eIF2α (phosphoserine-51) and SIRT1 (phosphoserine-47). By comparison, eIF2α and SIRT1 were persistently phosphorylated in Ars-treated GADD34-/- MEFs. Expressing WT GADD34, but not a mutant unable to bind PP1α in GADD34-/- MEFs restored both eIF2α and SIRT1 dephosphorylation. SIRT1 dephosphorylation increased its deacetylase activity, measured in vitro and in cells. Loss of function of GADD34 or SIRT1 enhanced cellular p-eIF2α levels and attenuated cell death following Ars exposure. These results highlighted a novel role for the GADD34/PP1α complex in coordinating the dephosphorylation and reactivation of eIF2α and SIRT1 to determine cell fate following oxidative stress.
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103
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Xie S, Yang Y, Lin X, Zhou J, Li D, Liu M. Characterization of a novel EB1 acetylation site important for the regulation of microtubule dynamics and cargo recruitment. J Cell Physiol 2017; 233:2581-2589. [DOI: 10.1002/jcp.26133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/03/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Songbo Xie
- Shandong Provincial Key Laboratory of Animal Resistance Biology; Institute of Biomedical Sciences; College of Life Sciences; Shandong Normal University; Jinan Shandong China
| | - Yang Yang
- State Key Laboratory of Medicinal Chemical Biology; College of Life Sciences; Nankai University; Tianjin China
| | - Xiaochen Lin
- State Key Laboratory of Medicinal Chemical Biology; College of Life Sciences; Nankai University; Tianjin China
| | - Jun Zhou
- Shandong Provincial Key Laboratory of Animal Resistance Biology; Institute of Biomedical Sciences; College of Life Sciences; Shandong Normal University; Jinan Shandong China
- State Key Laboratory of Medicinal Chemical Biology; College of Life Sciences; Nankai University; Tianjin China
| | - Dengwen Li
- State Key Laboratory of Medicinal Chemical Biology; College of Life Sciences; Nankai University; Tianjin China
| | - Min Liu
- Shandong Provincial Key Laboratory of Animal Resistance Biology; Institute of Biomedical Sciences; College of Life Sciences; Shandong Normal University; Jinan Shandong China
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104
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Bell RAV, Storey KB. Purification and characterization of skeletal muscle pyruvate kinase from the hibernating ground squirrel, Urocitellus richardsonii: potential regulation by posttranslational modification during torpor. Mol Cell Biochem 2017; 442:47-58. [DOI: 10.1007/s11010-017-3192-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 09/09/2017] [Indexed: 10/18/2022]
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105
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Lai Y, Li J, Li X, Zou C. Lipopolysaccharide modulates p300 and Sirt1 to promote PRMT1 stability via an SCF Fbxl17-recognized acetyldegron. J Cell Sci 2017; 130:3578-3587. [PMID: 28883095 DOI: 10.1242/jcs.206904] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/25/2017] [Indexed: 12/19/2022] Open
Abstract
E3 ubiquitin ligase recognizes its protein substrates via specific molecular signatures for ubiquitin proteasomal degradation. However, the role of acetylation/deacetylation in the process of E3 ubiquitin ligase recognizing its protein substrates is not fully studied. Here, we report that a tandem IK motif in protein arginine methyltransferase 1 (PRMT1) forms an acetyldegron to recruit the F-box/LRR-repeat protein 17 (FBXL17), a component of the SKP1-CUL1-F-box protein (SCF)-type E3 ubiquitin ligase complex. PRMT1 is polyubiquitylated for proteasome degradation with a half-life of approximately 4 h in lung epithelial cells. SCFFbxl17 mediates PRMT1 polyubiquitylation at K117. SCFFbxl17 specifically binds PRMT1 via a unique motif IKxxxIK. Strikingly, the acetylation/deacetylation status of the lysine residues within the motif determines Fbxl17 binding. Deacetylation on both K200 and K205 by Sirtuin 1 (Sirt1) and acetylation of p300 (EP300) on K205 collaboratively prepare the motif for SCFFbxl17 binding thereby triggering PRMT1 protein degradation. Pathogen-derived lipopolysaccharide (LPS) downregulates Sirt1 and p300 to protect PRMT1 from degradation. This study demonstrates that LPS promotes PRMT1 stability by blockade of PRMT1 and SCFFbxl17 binding via an acetylation/deacetylation-modified acetyldegron; and LPS-elevated levels of PRMT1 lead to bronchial epithelial cell overgrowth in pulmonary inflammatory diseases.
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Affiliation(s)
- Yandong Lai
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jin Li
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Xiuying Li
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Chunbin Zou
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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106
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Engle SM, Crowder JJ, Watts SG, Indovina CJ, Coffey SZ, Rubenstein EM. Acetylation of N-terminus and two internal amino acids is dispensable for degradation of a protein that aberrantly engages the endoplasmic reticulum translocon. PeerJ 2017; 5:e3728. [PMID: 28848693 PMCID: PMC5571791 DOI: 10.7717/peerj.3728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/02/2017] [Indexed: 12/26/2022] Open
Abstract
Conserved homologues of the Hrd1 ubiquitin ligase target for degradation proteins that persistently or aberrantly engage the endoplasmic reticulum translocon, including mammalian apolipoprotein B (apoB; the major protein component of low-density lipoproteins) and the artificial yeast protein Deg1-Sec62. A complete understanding of the molecular mechanism by which translocon-associated proteins are recognized and degraded may inform the development of therapeutic strategies for cholesterol-related pathologies. Both apoB and Deg1-Sec62 are extensively post-translationally modified. Mass spectrometry of a variant of Deg1-Sec62 revealed that the protein is acetylated at the N-terminal methionine and two internal lysine residues. N-terminal and internal acetylation regulates the degradation of a variety of unstable proteins. However, preventing N-terminal and internal acetylation had no detectable consequence for Hrd1-mediated proteolysis of Deg1-Sec62. Our data highlight the importance of empirically validating the role of post-translational modifications and sequence motifs on protein degradation, even when such elements have previously been demonstrated sufficient to destine other proteins for destruction.
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Affiliation(s)
- Sarah M Engle
- Department of Biology, Ball State University, Muncie, IN, United States of America.,Immunology-Translational Science, Eli Lilly and Company, Indianapolis, IN, United States of America
| | - Justin J Crowder
- Department of Biology, Ball State University, Muncie, IN, United States of America.,Center for Medical Education, Indiana University School of Medicine, Muncie, IN, United States of America
| | - Sheldon G Watts
- Department of Biology, Ball State University, Muncie, IN, United States of America.,Marian University College of Osteopathic Medicine, Indianapolis, IN, United States of America
| | | | - Samuel Z Coffey
- Department of Biology, Ball State University, Muncie, IN, United States of America.,Medpace Reference Laboratories, Cincinnati, OH, United States of America
| | - Eric M Rubenstein
- Department of Biology, Ball State University, Muncie, IN, United States of America
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107
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Srivastava S, Mohibi S, Mirza S, Band H, Band V. Epidermal Growth Factor Receptor activation promotes ADA3 acetylation through the AKT-p300 pathway. Cell Cycle 2017; 16:1515-1525. [PMID: 28759294 PMCID: PMC5584872 DOI: 10.1080/15384101.2017.1339846] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The ADA3 (Alteration/Deficiency in Activation 3) protein is an essential adaptor component of several Lysine Acetyltransferase (KAT) complexes involved in chromatin modifications. Previously, we and others have demonstrated a crucial role of ADA3 in cell cycle progression and in maintenance of genomic stability. Recently, we have shown that acetylation of ADA3 is key to its role in cell cycle progression. Here, we demonstrate that AKT activation downstream of Epidermal Growth Factor Receptor (EGFR) family proteins stimulation leads to phosphorylation of p300, which in turn promotes the acetylation of ADA3. Inhibition of upstream receptor tyrosine kinases (RTKs), HER1 (EGFR)/HER2 by lapatinib and the accompanying reduction of phospho-AKT levels led to a decrease in p300 phosphorylation and ADA3 protein levels. The p300/PCAF inhibitor garcinol also destabilized the ADA3 protein in a proteasome-dependent manner and an ADA3 mutant with K→R mutations exhibited a marked increase in half-life, consistent with opposite role of acetylation and ubiquitination of ADA3 on shared lysine residues. ADA3 knockdown led to cell cycle inhibitory effects, as well as apoptosis similar to those induced by lapatinib treatment of HER2+ breast cancer cells, as seen by accumulation of CDK inhibitor p27, reduction in mitotic marker pH3(S10), and a decrease in the S-phase marker PCNA, as well as the appearance of cleaved PARP. Taken together our results reveal a novel RTK-AKT-p300-ADA3 signaling pathway involved in growth factor-induced cell cycle progression.
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Affiliation(s)
- Shashank Srivastava
- a Genetics, Cell Biology and Anatomy , University of Nebraska Medical Center , Omaha , NE , USA
| | - Shakur Mohibi
- a Genetics, Cell Biology and Anatomy , University of Nebraska Medical Center , Omaha , NE , USA
| | - Sameer Mirza
- a Genetics, Cell Biology and Anatomy , University of Nebraska Medical Center , Omaha , NE , USA
| | - Hamid Band
- a Genetics, Cell Biology and Anatomy , University of Nebraska Medical Center , Omaha , NE , USA.,b Pathology & Microbiology , University of Nebraska Medical Center , Omaha , NE , USA.,c Biochemistry & Molecular Biology , College of Medicine, University of Nebraska Medical Center , Omaha , NE , USA.,d Eppley Institute for Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha , NE , USA.,e Fred & Pamela Buffett Cancer Center; University of Nebraska Medical Center , Omaha , NE , USA
| | - Vimla Band
- a Genetics, Cell Biology and Anatomy , University of Nebraska Medical Center , Omaha , NE , USA.,d Eppley Institute for Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha , NE , USA.,e Fred & Pamela Buffett Cancer Center; University of Nebraska Medical Center , Omaha , NE , USA
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108
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Peroxisomes protect lymphoma cells from HDAC inhibitor-mediated apoptosis. Cell Death Differ 2017; 24:1912-1924. [PMID: 28731463 PMCID: PMC5635217 DOI: 10.1038/cdd.2017.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/23/2017] [Accepted: 06/07/2017] [Indexed: 01/12/2023] Open
Abstract
Peroxisomes are a critical rheostat of reactive oxygen species (ROS), yet their role in drug sensitivity and resistance remains unexplored. Gene expression analysis of clinical lymphoma samples suggests that peroxisomes are involved in mediating drug resistance to the histone deacetylase inhibitor (HDACi) Vorinostat (Vor), which promotes ROS-mediated apoptosis. Vor augments peroxisome numbers in cultured lymphoma cells, concomitant with increased levels of peroxisomal proteins PEX3, PEX11B, and PMP70. Genetic inhibition of peroxisomes, using PEX3 knockdown, reveals that peroxisomes protect lymphoma cells against Vor-mediated cell death. Conversely, Vor-resistant cells were tolerant to elevated ROS levels and possess upregulated levels of (1) catalase, a peroxisomal antioxidant, and (2) plasmalogens, ether glycerophospholipids that represent peroxisome function and serve as antioxidants. Catalase knockdown induces apoptosis in Vor-resistant cells and potentiates ROS-mediated apoptosis in Vor-sensitive cells. These findings highlight the role of peroxisomes in resistance to therapeutic intervention in cancer, and provide a novel modality to circumvent drug resistance.
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109
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Han Z, Chou CW, Yang X, Bartlett MG, Zheng YG. Profiling Cellular Substrates of Lysine Acetyltransferases GCN5 and p300 with Orthogonal Labeling and Click Chemistry. ACS Chem Biol 2017; 12:1547-1555. [PMID: 28426192 DOI: 10.1021/acschembio.7b00114] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
p300 and GCN5 are two representative lysine acetyltransferases (KATs) in mammalian cells. It was recently reported that they possess multiple acyltransferase activities including acetylation, propionylation, and butyrylation of the ε-amino group of lysine residues of histones and non-histone protein substrates. Although thousands of acetylated substrates and acetylation sites have been identified by mass spectrometry-based proteomic screening, our knowledge about the causative connections between individual KAT members and their corresponding sub-acylomes remain very limited. Herein, we applied 3-azidopropionyl CoA (3AZ-CoA) as a bioorthogonal surrogate of acetyl-, propionyl- and butyryl-CoA for KAT substrate identification. We successfully attached the azide as a chemical warhead to cellular substrates of wild-type p300 and engineered GCN5. The substrates were subsequently labeled with biotin tag through the copper-catalyzed azide-alkyne cycloaddition (CuAAC). Following protein enrichment on streptavidin-coated resin, we conducted LC-MS/MS studies from which more than four hundred proteins were identified as GCN5 or p300 substrate candidates. These proteins are either p300- or GCN5-unique or shared by the two KATs and are extensively involved in various biological events including gene expression, cell cycle, and cellular metabolism. We also experimentally validated two novel substrates of GCN5, that is, IQGAP1 and SMC1. These results demonstrate extensive engagement of GCN5 and p300 in cellular pathways and provide new insights into understanding their functions in specific biological processes.
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Affiliation(s)
- Zhen Han
- Department of Pharmaceutical
and Biomedical Sciences and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Chau-wen Chou
- Department of Pharmaceutical
and Biomedical Sciences and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Xiangkun Yang
- Department of Pharmaceutical
and Biomedical Sciences and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Michael G. Bartlett
- Department of Pharmaceutical
and Biomedical Sciences and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Y. George Zheng
- Department of Pharmaceutical
and Biomedical Sciences and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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110
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Binding and inhibition of the ternary complex factor Elk-4/Sap1 by the adapter protein Dok-4. Biochem J 2017; 474:1509-1528. [PMID: 28275114 DOI: 10.1042/bcj20160832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 02/17/2017] [Accepted: 03/08/2017] [Indexed: 01/25/2023]
Abstract
The adapter protein Dok-4 (downstream of kinase-4) has been reported as both an activator and inhibitor of Erk and Elk-1, but lack of knowledge about the identity of its partner molecules has precluded any mechanistic insight into these seemingly conflicting properties. We report that Dok-4 interacts with the transactivation domain of Elk-4 through an atypical phosphotyrosine-binding domain-mediated interaction. Dok-4 possesses a nuclear export signal and can relocalize Elk-4 from nucleus to cytosol, whereas Elk-4 possesses two nuclear localization signals that restrict interaction with Dok-4. The Elk-4 protein, unlike Elk-1, is highly unstable in the presence of Dok-4, through both an interaction-dependent mechanism and a pleckstrin homology domain-dependent but interaction-independent mechanism. This is reversed by proteasome inhibition, depletion of endogenous Dok-4 or lysine-to-arginine mutation of putative Elk-4 ubiquitination sites. Finally, Elk-4 transactivation is potently inhibited by Dok-4 overexpression but enhanced by Dok-4 knockdown in MDCK renal tubular cells, which correlates with increased basal and EGF-induced expression of Egr-1, Fos and cylcinD1 mRNA, and cell proliferation despite reduced Erk activation. Thus, Dok-4 can target Elk-4 activity through multiple mechanisms, including binding of the transactivation domain, nuclear exclusion and protein destabilization, without a requirement for inhibition of Erk.
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111
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Ryan B, Logan BJ, Abraham WC, Williams JM. MicroRNAs, miR-23a-3p and miR-151-3p, Are Regulated in Dentate Gyrus Neuropil following Induction of Long-Term Potentiation In Vivo. PLoS One 2017; 12:e0170407. [PMID: 28125614 PMCID: PMC5268419 DOI: 10.1371/journal.pone.0170407] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/04/2017] [Indexed: 01/04/2023] Open
Abstract
Translation of synaptic mRNA contributes to alterations in the proteome necessary to consolidate long-term potentiation (LTP), a model of memory processes. Yet, how this process is controlled is not fully resolved. MicroRNAs are non-coding RNAs that negatively regulate gene expression by suppressing translation or promoting mRNA degradation. As specific microRNAs are synaptically located, we hypothesized that they are ideally suited to couple synaptic activation, translational regulation, and LTP persistence. The aim of this study was to identify LTP-regulated microRNAs at or near synapses. Accordingly, LTP was induced unilaterally at perforant path-dentate gyrus synapses in awake adult Sprague-Dawley rats. Five hours later, dentate gyrus middle molecular layer neuropil, containing potentiated synapses, was laser-microdissected. MicroRNA expression profiling, using TaqMan Low Density MicroRNA Microarrays (n = 4), identified eight regulated microRNAs. Subsequent individual TaqMan assays confirmed upregulation of miR-23a-3p (1.30 ± 0.10; p = 0.015) and miR-151-3p (1.17 ± 0.19; p = 0.045) in a second cohort (n = 7). Interestingly, bioinformatic analysis indicated that miR-151-3p and miR-23a-3p regulate synaptic reorganisation and transcription, respectively. In summary, we have demonstrated for the first time that microRNAs are regulated in isolated neuropil following LTP induction in vivo, supporting the hypothesis that synaptic, LTP-responsive microRNAs contribute to LTP persistence via regulation of the synaptic proteome.
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Affiliation(s)
- Brigid Ryan
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- The Brain Health Research Centre, University of Otago, Dunedin, New Zealand
- Brain Research New Zealand, Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Barbara J. Logan
- The Brain Health Research Centre, University of Otago, Dunedin, New Zealand
- Brain Research New Zealand, Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
- Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Wickliffe C. Abraham
- The Brain Health Research Centre, University of Otago, Dunedin, New Zealand
- Brain Research New Zealand, Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
- Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Joanna M. Williams
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- The Brain Health Research Centre, University of Otago, Dunedin, New Zealand
- Brain Research New Zealand, Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
- * E-mail:
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112
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Silmon de Monerri NC, Yakubu RR, Chen AL, Bradley PJ, Nieves E, Weiss LM, Kim K. The Ubiquitin Proteome of Toxoplasma gondii Reveals Roles for Protein Ubiquitination in Cell-Cycle Transitions. Cell Host Microbe 2016; 18:621-33. [PMID: 26567513 DOI: 10.1016/j.chom.2015.10.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/15/2015] [Accepted: 10/22/2015] [Indexed: 12/28/2022]
Abstract
Protein ubiquitination plays key roles in protein turnover, cellular signaling, and intracellular transport. The genome of Toxoplasma gondii encodes ubiquitination machinery, but the roles of this posttranslational modification (PTM) are unknown. To examine the prevalence and function of ubiquitination in T. gondii, we mapped the ubiquitin proteome of tachyzoites. Over 500 ubiquitin-modified proteins, with almost 1,000 sites, were identified on proteins with diverse localizations and functions. Enrichment analysis demonstrated that 35% of ubiquitinated proteins are cell-cycle regulated. Unexpectedly, most classic cell-cycle regulators conserved in T. gondii were not detected in the ubiquitinome. Furthermore, many ubiquitinated proteins localize to the cytoskeleton and inner membrane complex, a structure beneath the plasma membrane facilitating division and host invasion. Comparing the ubiquitinome with other PTM proteomes reveals waves of PTM enrichment during the cell cycle. Thus, T. gondii PTMs are implicated as critical regulators of cell division and cell-cycle transitions.
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Affiliation(s)
| | - Rama R Yakubu
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Allan L Chen
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095-1489, USA
| | - Peter J Bradley
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095-1489, USA
| | - Edward Nieves
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Louis M Weiss
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kami Kim
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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113
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Hong Y, Cao X, Han Q, Yuan C, Zhang M, Han Y, Zhu C, Lin T, Lu K, Li H, Fu Z, Lin J. Proteome-wide analysis of lysine acetylation in adult Schistosoma japonicum worm. J Proteomics 2016; 148:202-12. [PMID: 27535354 DOI: 10.1016/j.jprot.2016.08.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/30/2016] [Accepted: 08/09/2016] [Indexed: 12/14/2022]
Abstract
UNLABELLED Lysine acetylation, a ubiquitous and conserved posttranslational modification, has recently been shown to participate in many diverse non-chromatin-associated biological processes in prokaryotes and eukaryotes. However, the full extent and functional significance of acetylation in Schistosoma japonicum is still unknown. To investigate the nature, extent, and biological functions of lysine acetylation in schistosomes, immunoaffinity-based acetyl-lysine peptide enrichment, integrated with mass spectrometry, was used to comprehensively characterize the lysine-acetylated proteins in this parasite. In total, 1109 acetylated proteins and 2393 acetylation sites in S. japonicum were identified, representing the largest acetylome yet reported in a parasite. In a bioinformatic analysis showed that these acetylated proteins were mainly enriched in the biological process categories of metabolism, gene expression, translation, and transport. The classification according to molecular function revealed that the largest class involved the catalytic activity of different enzymes, including oxidoreductase, transferase, and pyrophosphatase activities. Most of the acetylated proteins in the cellular component category occurred in the cytoplasm, membrane, cytoskeleton, and nucleus. These data demonstrate the generality of lysine acetylation and provide the first global survey of acetylation in schistosomes. Our findings are an exciting starting point for the further exploration of the functions of acetylation in the biology of this parasite. SIGNIFICANCE Schistosomiasis is one of the world's most prevalent and neglected tropical parasitic zoonotic diseases, and it causes almost 200,000 deaths annually. To control and eradicate schistosomiasis, effective vaccines are urgently required, and drug targets that are essential for schistosome survival must be identified in fundamental studies of schistosome biology. Posttranslational modifications are complex, fundamental, and important mechanisms that regulate the physiological functions of organisms. Lysine acetylation, a ubiquitous and conserved posttranslational modification, has recently been shown to participate in many diverse non-chromatin-associated biological processes in prokaryotes and eukaryotes. However, the full extent and functional significance of acetylation in Schistosoma japonicum is still unknown. To investigate the nature, extent, and biological functions of lysine acetylation in S. japonicum, we employ immunoaffinity-based acetyl-lysine peptide enrichment, integrated with mass spectrometry to comprehensively characterize the lysine-acetylated proteins in this parasite. The results of our data demonstrate the generality of lysine acetylation and provide the first global survey of acetylation in schistosomes. Our findings are an exciting starting point for the further exploration of the functions of acetylation in the biology of this parasite. Meanwhile, identifying the mechanisms and proteins targeted by acetylation may also provide a promising avenue for specific drug design and the development of sophisticated therapeutic strategies.
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Affiliation(s)
- Yang Hong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Xiaodan Cao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Qian Han
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Chunxiu Yuan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Min Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan Province 471023, PR China
| | - Yanhui Han
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan Province 453003, PR China
| | - Chuangang Zhu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Tao Lin
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, United States
| | - Ke Lu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Hao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Zhiqiang Fu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China.
| | - Jiaojiao Lin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu Province 225009, PR China.
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114
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Por ED, Greene WA, Burke TA, Wang HC. Trichostatin A Inhibits Retinal Pigmented Epithelium Activation in an In Vitro Model of Proliferative Vitreoretinopathy. J Ocul Pharmacol Ther 2016; 32:415-24. [PMID: 27494828 PMCID: PMC5011631 DOI: 10.1089/jop.2016.0038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose: Proliferative vitreoretinopathy (PVR) is a blinding disorder that develops after a retinal tear or detachment. Activation of the retinal pigmented epithelium (RPE) is implicated in PVR; however, the mechanisms leading to enhanced RPE proliferation, migration, and contraction remain largely unknown. This study utilized an in vitro model of PVR to investigate the role of acetylation in RPE activation and its contribution to the progression of this disease. Methods: ARPE-19 cells, primary cultures of porcine RPE, and induced pluripotent stem cell-derived RPE (iPS-RPE) were utilized for cellular and molecular analyses. Cells treated with transforming growth factor beta 2 (TGFβ2; 10 ng/mL) alone or in the presence of the broad-spectrum histone deacetylase (HDAC) inhibitor, trichostatin A (TSA; 0.1 μM), were assessed for contraction and migration through collagen contraction and scratch assays, respectively. Western blotting and immunofluorescence analysis were performed to assess α-smooth muscle actin (α-SMA) and β-catenin expression after TGFβ2 treatment alone or in combination with TSA. Results: TGFβ2 significantly increased RPE cell contraction in collagen matrix and this effect was inhibited in the presence of TSA (0.1 μM). In agreement with these data, immunofluorescence analysis of TSA-treated iPS-RPE wounded monolayers revealed decreased α-SMA as compared with control. Scratch assays to assess wound healing revealed TSA inhibited TGFβ2-mediated iPS-RPE cell migration. Conclusions: Our findings indicate a role of acetylation in RPE activation. Specifically, the HDAC inhibitor TSA decreased RPE cell proliferation and TGFβ2-mediated cell contraction and migration. Further investigation of pharmacological compounds that modulate acetylation may hold promise as therapeutic agents for PVR.
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Affiliation(s)
- Elaine D Por
- Ocular Trauma, U.S. Army Institute of Surgical Research , JBSA-Fort Sam Houston, Texas
| | - Whitney A Greene
- Ocular Trauma, U.S. Army Institute of Surgical Research , JBSA-Fort Sam Houston, Texas
| | - Teresa A Burke
- Ocular Trauma, U.S. Army Institute of Surgical Research , JBSA-Fort Sam Houston, Texas
| | - Heuy-Ching Wang
- Ocular Trauma, U.S. Army Institute of Surgical Research , JBSA-Fort Sam Houston, Texas
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115
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The growing landscape of tubulin acetylation: lysine 40 and many more. Biochem J 2016; 473:1859-68. [DOI: 10.1042/bcj20160172] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/29/2016] [Indexed: 11/17/2022]
Abstract
Tubulin heterodimers are the building block of microtubules, which are major elements of the cytoskeleton. Several types of post-translational modifications are found on tubulin subunits as well as on the microtubule polymer to regulate the multiple roles of microtubules. Acetylation of lysine 40 (K40) of the α-tubulin subunit is one of these post-translational modifications which has been extensively studied. We summarize the current knowledge about the structural aspects of K40 acetylation, the functional consequences, the enzymes involved and their regulation. Most importantly, we discuss the potential importance of the recently discovered additional acetylation acceptor lysines in tubulin subunits and highlight the urgent need to study tubulin acetylation in a more integrated perspective.
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116
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Duncan MT, DeLuca TA, Kuo HY, Yi M, Mrksich M, Miller WM. SIRT1 is a critical regulator of K562 cell growth, survival, and differentiation. Exp Cell Res 2016; 344:40-52. [PMID: 27086164 PMCID: PMC4879089 DOI: 10.1016/j.yexcr.2016.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/09/2016] [Accepted: 04/12/2016] [Indexed: 12/13/2022]
Abstract
Inhibition of histone deacetylases (HDACi) has emerged as a promising approach in the treatment of many types of cancer, including leukemias. Among the HDACs, Class III HDACs, also known as sirtuins (SIRTs), are unique in that their function is directly related to the cell's metabolic state through their dependency on the co-factor NAD(+). In this study, we examined the relation between SIRTs and the growth, survival, and differentiation of K562 erythroleukemia cells. Using a mass spectrometry approach we previously developed, we show that SIRT expression and deacetylase activity in these cells changes greatly with differentiation state (undifferentiated vs. megakaryocytic differentiation vs. erythroid differentiation). Moreover, SIRT1 is crucially involved in regulating the differentiation state. Overexpression of wildtype (but not deacetylase mutant) SIRT1 resulted in upregulation of glycophorin A, ~2-fold increase in the mRNA levels of α, γ, ε, and ζ-globins, and spontaneous hemoglobinization. Hemin-induced differentiation was also enhanced by (and depended on) higher SIRT1 levels. Since K562 cells are bipotent, we also investigated whether SIRT1 modulation affected their ability to undergo megakaryocytic (MK) differentiation. SIRT1 was required for commitment to the MK lineage and subsequent maturation, but was not directly involved in polyploidization of either K562 cells or an already-MK-committed cell line, CHRF-288-11. The observed blockage in commitment to the MK lineage was associated with a dramatic decrease in the formation of autophagic vacuoles, which was previously shown to be required for K562 cell MK commitment. Autophagy-associated conversion of the protein LC3-I to LC3-II was greatly enhanced by overexpression of wildtype SIRT1, further suggesting a functional connection between SIRT1, autophagy, and MK differentiation. Based on its clear effects on autophagy, we also examined the effect of SIRT1 modulation on stress responses. Consistent with results of prior studies, we found that SIRT1 silencing modestly promoted drug-induced apoptosis, while overexpression was protective. Furthermore, pan-SIRT inhibition mediated by nicotinamide pre-treatment substantially increased imatinib-induced apoptosis. Altogether, our results suggest a complex role for SIRT1 in regulating many aspects of K562 cell state and stress response. These observations warrant further investigation using normal and leukemic primary cell models. We further suggest that, ultimately, a well-defined mapping of HDACs to their substrates and corresponding signaling pathways will be important for optimally designing HDACi-based therapeutic approaches.
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Affiliation(s)
| | | | - Hsin-Yu Kuo
- Department of Biomedical Engineering; Department of Chemistry; Department of Cell and Molecular Biology
| | - Minchang Yi
- Master of Biotechnology Program, Northwestern University, Evanston, IL 60208, United States
| | - Milan Mrksich
- Department of Biomedical Engineering; Department of Chemistry; Department of Cell and Molecular Biology; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, United States
| | - William M Miller
- Department of Chemical and Biological Engineering; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, United States.
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117
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López JE, Sullivan ED, Fierke CA. Metal-dependent Deacetylases: Cancer and Epigenetic Regulators. ACS Chem Biol 2016; 11:706-16. [PMID: 26907466 DOI: 10.1021/acschembio.5b01067] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Epigenetic regulation is a key factor in cellular homeostasis. Post-translational modifications (PTMs) are a central focus of this regulation as they function as signaling markers within the cell. Lysine acetylation is a dynamic, reversible PTM that has garnered recent attention due to alterations in various types of cancer. Acetylation levels are regulated by two opposing enzyme families: lysine acetyltransferases (KATs) and histone deacetylases (HDACs). HDACs are key players in epigenetic regulation and have a role in the silencing of tumor suppressor genes. The dynamic equilibrium of acetylation makes HDACs attractive targets for drug therapy. However, substrate selectivity and biological function of HDAC isozymes is poorly understood. This review outlines the current understanding of the roles and specific epigenetic interactions of the metal-dependent HDACs in addition to their roles in cancer.
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Affiliation(s)
- Jeffrey E. López
- Interdepartmental
Program in Chemical Biology, University of Michigan, 210 Washtenaw
Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Eric D. Sullivan
- Interdepartmental
Program in Chemical Biology, University of Michigan, 210 Washtenaw
Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Carol A. Fierke
- Interdepartmental
Program in Chemical Biology, University of Michigan, 210 Washtenaw
Avenue, Ann Arbor, Michigan 48109-2216, United States
- Departments
of Chemistry and Biological Chemistry, University of Michigan, 930 North
University Avenue, Ann Arbor, Michigan 48109-2216, United States
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118
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Response of esophageal cancer cells to epigenetic inhibitors is mediated via altered thioredoxin activity. J Transl Med 2016; 96:307-16. [PMID: 26692290 DOI: 10.1038/labinvest.2015.148] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/14/2015] [Accepted: 09/03/2015] [Indexed: 01/01/2023] Open
Abstract
We previously showed that histone deacetylase inhibitor (HDACi) and 5-azacytidine (AZA) treatment selectively induced cell death of esophageal cancer cells. The mechanisms of cancer selectivity, however, remained unclear. Here we examined whether the cancer selectivity of HDACi/AZA treatment is mediated by the thioredoxin (Trx) system and reactive oxygen species (ROS) in esophageal cancer cells. For this, we first analyzed human tissue specimens of 37 esophageal cancer patients by immunohistochemistry for Trx, Trx-interacting protein (TXNIP) and Trx reductase (TXNRD). This revealed a loss or at least reduction of nuclear Trx in esophageal cancer cells, compared with normal epithelial cells (P<0.001). Although no differences were observed for TXNIP, TXNRD was more frequently expressed in cancer cells (P<0.001). In the two main histotypes of esophageal squamous cell carcinomas (ESCCs, n=19) and esophageal adenomcarcinomas (EAC, n=16), similar Trx, TXNIP and TXNRD expression patterns were observed. Also in vitro, nuclear Trx was only detectable in non-neoplastic Het-1A cells, but not in OE21/ESCC or OE33/EAC cell lines. Moreover, the two cancer cell lines showed an increased Trx activity, being significant for OE21 (P=0.0237). After treatment with HDACi and/or AZA, ROS were exclusively increased in both cancer cell lines (P=0.048-0.017), with parallel decrease of Trx activity. This was variably accompanied by increased TXNIP levels upon AZA, MS-275 or MS-275/AZA treatment for 6 or 24 h in OE21, but not in Het-1A or OE33 cells. In summary, this study evaluated Trx and its associated proteins TXNIP and TXNRD for the first time in esophageal cancers. The analyses revealed an altered subcellular localization of Trx and strong upregulation of TXNRD in esophageal cancer cells. Moreover, HDACi and AZA disrupted Trx function and induced accumulation of ROS with subsequent apoptosis in esophageal cancer cells exclusively. Trx function is hence an important cellular mediator conferring non-neoplastic cell resistance for HDACi and/or AZA.
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119
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Zhou T, Chung YH, Chen J, Chen Y. Site-Specific Identification of Lysine Acetylation Stoichiometries in Mammalian Cells. J Proteome Res 2016; 15:1103-13. [DOI: 10.1021/acs.jproteome.5b01097] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tong Zhou
- Department of Biochemistry,
Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Ying-hua Chung
- Department of Biochemistry,
Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Jianji Chen
- Department of Biochemistry,
Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Yue Chen
- Department of Biochemistry,
Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, Minnesota 55455, United States
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120
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Chen WH, van Noort V, Lluch-Senar M, Hennrich ML, Wodke JAH, Yus E, Alibés A, Roma G, Mende DR, Pesavento C, Typas A, Gavin AC, Serrano L, Bork P. Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances. Nucleic Acids Res 2016; 44:1192-202. [PMID: 26773059 PMCID: PMC4756857 DOI: 10.1093/nar/gkw004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/03/2016] [Indexed: 01/16/2023] Open
Abstract
We developed a comprehensive resource for the genome-reduced bacterium Mycoplasma pneumoniae comprising 1748 consistently generated ‘-omics’ data sets, and used it to quantify the power of antisense non-coding RNAs (ncRNAs), lysine acetylation, and protein phosphorylation in predicting protein abundance (11%, 24% and 8%, respectively). These factors taken together are four times more predictive of the proteome abundance than of mRNA abundance. In bacteria, post-translational modifications (PTMs) and ncRNA transcription were both found to increase with decreasing genomic GC-content and genome size. Thus, the evolutionary forces constraining genome size and GC-content modify the relative contributions of the different regulatory layers to proteome homeostasis, and impact more genomic and genetic features than previously appreciated. Indeed, these scaling principles will enable us to develop more informed approaches when engineering minimal synthetic genomes.
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Affiliation(s)
- Wei-Hua Chen
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Vera van Noort
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marco L Hennrich
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Judith A H Wodke
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain Theoretical Biophysics, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Eva Yus
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Andreu Alibés
- Bioinformatics Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Guglielmo Roma
- Bioinformatics Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Daniel R Mende
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christina Pesavento
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Anne-Claude Gavin
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Peer Bork
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany Max-Delbrück-Centre (MDC) for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
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121
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Kim E, Wang B, Sastry N, Masliah E, Nelson PT, Cai H, Liao FF. NEDD4-mediated HSF1 degradation underlies α-synucleinopathy. Hum Mol Genet 2015; 25:211-22. [PMID: 26503960 PMCID: PMC4706110 DOI: 10.1093/hmg/ddv445] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/19/2015] [Indexed: 11/13/2022] Open
Abstract
Cellular protein homeostasis is achieved by a delicate network of molecular chaperones and various proteolytic processes such as ubiquitin–proteasome system (UPS) to avoid a build-up of misfolded protein aggregates. The latter is a common denominator of neurodegeneration. Neurons are found to be particularly vulnerable to toxic stress from aggregation-prone proteins such as α-synuclein. Induction of heat-shock proteins (HSPs), such as through activated heat shock transcription factor 1 (HSF1) via Hsp90 inhibition, is being investigated as a therapeutic option for proteinopathic diseases. HSF1 is a master stress-protective transcription factor which activates genes encoding protein chaperones (e.g. iHsp70) and anti-apoptotic proteins. However, whether and how HSF1 is dysregulated during neurodegeneration has not been studied. Here, we discover aberrant HSF1 degradation by aggregated α-synuclein (or α-synuclein-induced proteotoxic stress) in transfected neuroblastoma cells. HSF1 dysregulation via α-synuclein was confirmed by in vivo assessment of mouse and in situ studies of human specimens with α-synucleinopathy. We demonstrate that elevated NEDD4 is implicated as the responsible ubiquitin E3 ligase for HSF1 degradation through UPS. Furthermore, pharmacologically induced SIRT1-mediated deacetylation can attenuate aberrant NEDD4-mediated HSF1 degradation. Indeed, we define the acetylation status of the Lys 80 residue located in the DNA-binding domain of HSF1 as a critical factor in modulating HSF1 protein stability in addition to its previously identified role in the transcriptional activity. Together with the finding that preserving HSF1 can alleviate α-synuclein toxicity, this study strongly suggests that aberrant HSF1 degradation is a key neurodegenerative mechanism underlying α-synucleinopathy.
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Affiliation(s)
- Eunhee Kim
- Department of Pharmacology and Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, 874 Union Avenue/Crowe 401, Memphis, TN 38163, USA
| | - Bin Wang
- Department of Pharmacology and Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, 874 Union Avenue/Crowe 401, Memphis, TN 38163, USA
| | - Namratha Sastry
- Transgenics Section, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eliezer Masliah
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Peter T Nelson
- Department of Neurology, Sanders-Brown Center on Aging, 800 South Limestone Street, Lexington, KY 40536, USA and
| | - Huaibin Cai
- Transgenics Section, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Francesca-Fang Liao
- Department of Pharmacology and Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, 874 Union Avenue/Crowe 401, Memphis, TN 38163, USA,
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122
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Histone deacetylase inhibitors and epigenetic regulation in lymphoid malignancies. Invest New Drugs 2015; 33:1280-91. [PMID: 26423245 DOI: 10.1007/s10637-015-0290-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/15/2015] [Indexed: 12/13/2022]
Abstract
A vast majority of lymphomas and leukaemias are results of translocations. These translocations produce various genetic and epigenetic changes that lead to oncogenesis. This opens an opportunity to use a relatively new class of anti-cancer agents, inhibitors of histone deacetylases (HDACi) to target lymphoid malignancies. Surprisingly, the rational basis for treatment of lymphomas with HDACi is far from clear, although some positive results have been obtained. Here we analyze the effect of histone deacetylase (HDAC) inhibitors on lymphoid malignancies.
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123
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McIntyre J, McLenigan MP, Frank EG, Dai X, Yang W, Wang Y, Woodgate R. Posttranslational Regulation of Human DNA Polymerase ι. J Biol Chem 2015; 290:27332-27344. [PMID: 26370087 PMCID: PMC4646365 DOI: 10.1074/jbc.m115.675769] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 01/25/2023] Open
Abstract
Human DNA polymerases (pols) η and ι are Y-family DNA polymerase paralogs that facilitate translesion synthesis past damaged DNA. Both polη and polι can be monoubiquitinated in vivo. Polη has been shown to be ubiquitinated at one primary site. When this site is unavailable, three nearby lysines may become ubiquitinated. In contrast, mass spectrometry analysis of monoubiquitinated polι revealed that it is ubiquitinated at over 27 unique sites. Many of these sites are localized in different functional domains of the protein, including the catalytic polymerase domain, the proliferating cell nuclear antigen-interacting region, the Rev1-interacting region, and its ubiquitin binding motifs UBM1 and UBM2. Polι monoubiquitination remains unchanged after cells are exposed to DNA-damaging agents such as UV light (generating UV photoproducts), ethyl methanesulfonate (generating alkylation damage), mitomycin C (generating interstrand cross-links), or potassium bromate (generating direct oxidative DNA damage). However, when exposed to naphthoquinones, such as menadione and plumbagin, which cause indirect oxidative damage through mitochondrial dysfunction, polι becomes transiently polyubiquitinated via Lys11- and Lys48-linked chains of ubiquitin and subsequently targeted for degradation. Polyubiquitination does not occur as a direct result of the perturbation of the redox cycle as no polyubiquitination was observed after treatment with rotenone or antimycin A, which both inhibit mitochondrial electron transport. Interestingly, polyubiquitination was observed after the inhibition of the lysine acetyltransferase KATB3/p300. We hypothesize that the formation of polyubiquitination chains attached to polι occurs via the interplay between lysine acetylation and ubiquitination of ubiquitin itself at Lys11 and Lys48 rather than oxidative damage per se.
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Affiliation(s)
- Justyna McIntyre
- Laboratory of Genomic Integrity, NICHD, National Institutes of Health, Bethesda, Maryland 20892-3371,; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Mary P McLenigan
- Laboratory of Genomic Integrity, NICHD, National Institutes of Health, Bethesda, Maryland 20892-3371
| | - Ekaterina G Frank
- Laboratory of Genomic Integrity, NICHD, National Institutes of Health, Bethesda, Maryland 20892-3371
| | - Xiaoxia Dai
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Roger Woodgate
- Laboratory of Genomic Integrity, NICHD, National Institutes of Health, Bethesda, Maryland 20892-3371,.
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124
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Chang YW, Chen HA, Tseng CF, Hong CC, Ma JT, Hung MC, Wu CH, Huang MT, Su JL. De-acetylation and degradation of HSPA5 is critical for E1A metastasis suppression in breast cancer cells. Oncotarget 2015; 5:10558-70. [PMID: 25301734 PMCID: PMC4279393 DOI: 10.18632/oncotarget.2510] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/24/2014] [Indexed: 12/02/2022] Open
Abstract
Elevated expression of heat shock protein 5 (HSPA5) promotes drug resistance and metastasis and is a marker of poor prognosis in breast cancer patients. Adenovirus type 5 E1A gene therapy has demonstrated antitumor efficacy but the mechanisms of metastasis-inhibition are unclear. Here, we report that E1A interacts with p300 histone acetyltransferase (HAT) and blocks p300-mediated HSPA5 acetylation at K353, which in turn promotes HSPA5 ubiquitination by GP78 (E3 ubiquitin ligase) and subsequent proteasome-mediated degradation. Our findings point out the Ying-Yang regulation of two different post-translational modifications (ubiquitination and acetylation) of HSPA5 in tumor metastasis.
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Affiliation(s)
- Yi-Wen Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli Country, Taiwan
| | - Hsin-An Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan. Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Chi-Feng Tseng
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli Country, Taiwan. Graduate Program of Biotechnology in Medicine College of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Chen Hong
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli Country, Taiwan
| | - Jui-Ti Ma
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli Country, Taiwan. Graduate Program of Biotechnology in Medicine College of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Cancer Biology, China Medical University, Taichung, Taiwan. Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan. Department of Biotechnology, Asia University, Taichung, Taiwan. Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chih-Hsiung Wu
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan. Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Ming-Te Huang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan. Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Jen-Liang Su
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli Country, Taiwan. Graduate Institute of Cancer Biology, China Medical University, Taichung, Taiwan. Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan. Department of Biotechnology, Asia University, Taichung, Taiwan
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125
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Ryder DJ, Judge SM, Beharry AW, Farnsworth CL, Silva JC, Judge AR. Identification of the Acetylation and Ubiquitin-Modified Proteome during the Progression of Skeletal Muscle Atrophy. PLoS One 2015; 10:e0136247. [PMID: 26302492 PMCID: PMC4547751 DOI: 10.1371/journal.pone.0136247] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 07/31/2015] [Indexed: 02/07/2023] Open
Abstract
Skeletal muscle atrophy is a consequence of several physiological and pathophysiological conditions including muscle disuse, aging and diseases such as cancer and heart failure. In each of these conditions, the predominant mechanism contributing to the loss of skeletal muscle mass is increased protein turnover. Two important mechanisms which regulate protein stability and degradation are lysine acetylation and ubiquitination, respectively. However our understanding of the skeletal muscle proteins regulated through acetylation and ubiquitination during muscle atrophy is limited. Therefore, the purpose of the current study was to conduct an unbiased assessment of the acetylation and ubiquitin-modified proteome in skeletal muscle during a physiological condition of muscle atrophy. To induce progressive, physiologically relevant, muscle atrophy, rats were cast immobilized for 0, 2, 4 or 6 days and muscles harvested. Acetylated and ubiquitinated peptides were identified via a peptide IP proteomic approach using an anti-acetyl lysine antibody or a ubiquitin remnant motif antibody followed by mass spectrometry. In control skeletal muscle we identified and mapped the acetylation of 1,326 lysine residues to 425 different proteins and the ubiquitination of 4,948 lysine residues to 1,131 different proteins. Of these proteins 43, 47 and 50 proteins were differentially acetylated and 183, 227 and 172 were differentially ubiquitinated following 2, 4 and 6 days of disuse, respectively. Bioinformatics analysis identified contractile proteins as being enriched among proteins decreased in acetylation and increased in ubiquitination, whereas histone proteins were enriched among proteins increased in acetylation and decreased in ubiquitination. These findings provide the first proteome-wide identification of skeletal muscle proteins exhibiting changes in lysine acetylation and ubiquitination during any atrophy condition, and provide a basis for future mechanistic studies into how the acetylation and ubiquitination status of these identified proteins regulates the muscle atrophy phenotype.
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Affiliation(s)
- Daniel J. Ryder
- Department of Physical Therapy, University of Florida, Gainesville, FL, United States of America
| | - Sarah M. Judge
- Department of Physical Therapy, University of Florida, Gainesville, FL, United States of America
| | - Adam W. Beharry
- Department of Physical Therapy, University of Florida, Gainesville, FL, United States of America
| | | | - Jeffrey C. Silva
- Cell Signaling Technology, Danvers, MA, United States of America
| | - Andrew R. Judge
- Department of Physical Therapy, University of Florida, Gainesville, FL, United States of America
- * E-mail:
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126
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Carrillo AK, Guiguemde WA, Guy RK. Evaluation of histone deacetylase inhibitors (HDACi) as therapeutic leads for human African trypanosomiasis (HAT). Bioorg Med Chem 2015; 23:5151-5. [DOI: 10.1016/j.bmc.2014.12.066] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 12/19/2014] [Accepted: 12/28/2014] [Indexed: 01/31/2023]
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127
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Ocio EM, Herrera P, Olave MT, Castro N, Pérez-Simón JA, Brunet S, Oriol A, Mateo M, Sanz MÁ, López J, Montesinos P, Chillón MC, Prieto-Conde MI, Díez-Campelo M, González M, Vidriales MB, Mateos MV, San Miguel JF. Panobinostat as part of induction and maintenance for elderly patients with newly diagnosed acute myeloid leukemia: phase Ib/II panobidara study. Haematologica 2015; 100:1294-300. [PMID: 26160880 DOI: 10.3324/haematol.2015.129577] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/25/2015] [Indexed: 01/08/2023] Open
Abstract
This phase Ib/II trial combined the pan-deacetylase inhibitor panobinostat with chemotherapy followed by panobinostat maintenance in elderly patients with newly diagnosed acute myeloid leukemia. Patients with prior history of myelodysplastic syndrome were excluded and 38 evaluable patients were included in the study (median age: 71 years; range: 65-83). Study patients received an induction with idarubicin (8 mg/m(2) iv days 1-3) plus cytarabine (100 mg/m(2) iv days 1-7) plus panobinostat po at escalating doses (days 8, 10, 12, 15, 17 and 19) that could be repeated in non-responding patients. Patients achieving complete remission received a consolidation cycle with the same schema, followed by panobinostat maintenance (40 mg po 3 days/week) every other week until progression. Thirty-one patients were treated at the maximum tolerated dose of panobinostat in the combination (10 mg) with good tolerability. Complete remission rate was 64% with a time to relapse of 17.0 months (12.8-21.1). Median overall survival for the whole series was 17 months (5.5-28.4). Moreover, in 4 of 5 patients with persistent minimal residual disease before maintenance, panobinostat monotherapy reduced its levels, with complete negativization in two of them. Maintenance phase was well tolerated. The most frequent adverse events were thrombocytopenia (25% grades 3/4), and gastrointestinal toxicity, asthenia and anorexia (mainly grades 1/2). Five patients required dose reduction during this phase, but only one discontinued therapy due to toxicity. These results suggest that panobinostat is one of the first novel agents with activity in elderly acute myeloid leukemia patients, and suggest further investigation is warranted, particularly in the context of maintenance therapy. This trial is registered at clinicaltrials.gov identifier: 00840346.
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Affiliation(s)
- Enrique M Ocio
- Complejo Asistencial Universitario de Salamanca (IBSAL), Centro Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca
| | | | | | | | - José A Pérez-Simón
- Hospital Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS), Seville
| | | | | | | | | | | | | | - María-Carmen Chillón
- Complejo Asistencial Universitario de Salamanca (IBSAL), Centro Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca
| | - María-Isabel Prieto-Conde
- Complejo Asistencial Universitario de Salamanca (IBSAL), Centro Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca
| | - María Díez-Campelo
- Complejo Asistencial Universitario de Salamanca (IBSAL), Centro Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca
| | - Marcos González
- Complejo Asistencial Universitario de Salamanca (IBSAL), Centro Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca
| | - María-Belén Vidriales
- Complejo Asistencial Universitario de Salamanca (IBSAL), Centro Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca
| | - María-Victoria Mateos
- Complejo Asistencial Universitario de Salamanca (IBSAL), Centro Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca
| | - Jesús F San Miguel
- Clínica Universidad de Navarra, Centro de Investigaciones Médicas Aplicadas (CIMA), IDISNA, Pamplona, Spain
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Kosono S, Tamura M, Suzuki S, Kawamura Y, Yoshida A, Nishiyama M, Yoshida M. Changes in the Acetylome and Succinylome of Bacillus subtilis in Response to Carbon Source. PLoS One 2015; 10:e0131169. [PMID: 26098117 PMCID: PMC4476798 DOI: 10.1371/journal.pone.0131169] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/29/2015] [Indexed: 11/19/2022] Open
Abstract
Lysine residues can be post-translationally modified by various acyl modifications in bacteria and eukarya. Here, we showed that two major acyl modifications, acetylation and succinylation, were changed in response to the carbon source in the Gram-positive model bacterium Bacillus subtilis. Acetylation was more common when the cells were grown on glucose, glycerol, or pyruvate, whereas succinylation was upregulated when the cells were grown on citrate, reflecting the metabolic states that preferentially produce acetyl-CoA and succinyl-CoA, respectively. To identify and quantify changes in acetylation and succinylation in response to the carbon source, we performed a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomic analysis of cells grown on glucose or citrate. We identified 629 acetylated proteins with 1355 unique acetylation sites and 204 succinylated proteins with 327 unique succinylation sites. Acetylation targeted different metabolic pathways under the two growth conditions: branched-chain amino acid biosynthesis and purine metabolism in glucose and the citrate cycle in citrate. Succinylation preferentially targeted the citrate cycle in citrate. Acetylation and succinylation mostly targeted different lysine residues and showed a preference for different residues surrounding the modification sites, suggesting that the two modifications may depend on different factors such as characteristics of acyl-group donors, molecular environment of the lysine substrate, and/or the modifying enzymes. Changes in acetylation and succinylation were observed in proteins involved in central carbon metabolism and in components of the transcription and translation machineries, such as RNA polymerase and the ribosome. Mutations that modulate protein acylation affected B. subtilis growth. A mutation in acetate kinase (ackA) increased the global acetylation level, suggesting that acetyl phosphate-dependent acetylation is common in B. subtilis, just as it is in Escherichia coli. Our results suggest that acyl modifications play a role in the physiological adaptations to changes in carbon nutrient availability of B. subtilis.
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Affiliation(s)
- Saori Kosono
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
- * E-mail:
| | - Masaru Tamura
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shota Suzuki
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yumi Kawamura
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Ayako Yoshida
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
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129
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Characterization of novel mechanisms for steatosis from global protein hyperacetylation in ethanol-induced mouse hepatocytes. Biochem Biophys Res Commun 2015; 463:832-8. [PMID: 26056001 DOI: 10.1016/j.bbrc.2015.04.154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 04/21/2015] [Indexed: 12/20/2022]
Abstract
Steatosis is the earliest and most common disease of the liver due to chronic ethanol consumption, and stems from alterations in the function of transcription factors related to lipid metabolism. Protein acetylation at the lysine residue (Kac) is known to have diverse functions in cell metabolism. Recent studies showed that ethanol exposure induces global protein hyperacetylation by reducing the deacetylase activities of SIRT1 and SIRT3. Although global acetylome analyses have revealed the involvement of a variety of lysine acetylation sites, the exact sites directly regulated by ethanol exposure are unknown. In this study, to elucidate the exact hyperacetylation sites that contribute to SIRT1 and SIRT3 downregulation, we identified and quantified a total of 1285 Kac sites and 686 Kac proteins in AML-12 cells after ethanol treatment (100 mM) for 3 days. All quantified Kac sites were divided into four quantiles: Q1 (0-15%), Q2 (15-50%), Q3 (50-85%), and Q4 (85-100%). Q4 had 192 Kac sites indicating ethanol-induced hyperacetylation. Using the Motif-x program, the [LXKL], [KH], and [KW] motifs were included in the Q4 category, where [KW] was a specific residue for SIRT3. We also performed gene ontology term and KEGG pathway enrichment analyses. Hyperacetylation sites were significantly enriched in biosynthetic processes and ATPase activities within the biological process and molecular function categories, respectively. In conclusion, ethanol regulates the acetylation of proteins in a variety of metabolic pathways mediated by SIRT1 and SIRT3. As a result, ethanol stimulates increased de novo fatty acid synthesis in hepatocytes.
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130
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Jagadeeshan S, Coppard SE, Lessios HA. Evolution of gamete attraction molecules: evidence for purifying selection in speract and its receptor, in the pantropical sea urchin Diadema. Evol Dev 2015; 17:92-108. [PMID: 25627716 DOI: 10.1111/ede.12108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Many free-spawning marine invertebrates, such as sea urchins, lack any courtship or assortative mating behavior. Mate recognition in such cases occur at the gametic level, and molecules present on the sperm and egg are major determinants of species-specific fertilization. These molecules must also coevolve in relation to each other in order to preserve functional integrity. When sea urchins release their gametes in seawater, diffusible molecules from the egg, termed sperm-activating peptides, activate and attract the sperm to swim toward the egg, initiating a series of interactions between the gametes. Although the compositions and diversity of such sperm-activating peptides have been characterized in a variety of sea urchins, little is known about the evolution of their genes. Here we characterize the genes encoding the sperm-activating peptide of the egg (speract) and its receptor on the sperm, and examine their evolutionary dynamics in the sea urchin genus Diadema, in the interest of determining whether they are involved in reproductive isolation between the species. We found evidence of purifying selection on several codon sites in both molecules and of selectively neutral evolution in others. The diffusible speract peptide that activates sperm is invariant across species, indicating that Diadema egg peptides do not discriminate between con- and hetero-specific sperm at this stage of the process. Speract and its receptor do not contribute to reproductive isolation in Diadema.
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131
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Koumbadinga GA, Mahmood N, Lei L, Kan Y, Cao W, Lobo VG, Yao X, Zhang S, Xie J. Increased stability of heterogeneous ribonucleoproteins by a deacetylase inhibitor. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1095-103. [PMID: 25959059 DOI: 10.1016/j.bbagrm.2015.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 04/27/2015] [Accepted: 05/01/2015] [Indexed: 11/15/2022]
Abstract
Splicing factors are often influenced by various signaling pathways, contributing to the dynamic changes of protein isoforms in cells. Heterogeneous ribonucleoproteins (hnRNPs) regulate many steps of RNA metabolism including pre-mRNA splicing but their control by cell signaling particularly through acetylation and ubiquitination pathways remains largely unknown. Here we show that TSA, a deacetylase inhibitor, reduced the ratio of Bcl-x splice variants Bcl-xL/xS in MDA-MB-231 breast cancer cells. This TSA effect was independent of TGFβ1; however, only in the presence of TGFβ1 was TSA able to change the splicing regulators hnRNP F/H by slightly reducing their mRNA transcripts but strongly preventing protein degradation. The latter was also efficiently prevented by lactacystin, a proteasome inhibitor, suggesting their protein stability control by both acetylation and ubiquitination pathways. Three lysines K87, K98 and K224 of hnRNP F are potential targets of the mutually exclusive acetylation or ubiquitination (K(Ac/Ub)) in the protein modification database PhosphoSitePlus. Mutating each of them but not a control non-K(Ac/Ub) (K68) specifically abolished the TSA enhancement of protein stability. Moreover, mutating K98 (K98R) and K224 (K224R) also abolished the TSA regulation of alternative splicing of a Bcl-x mini-gene. Furthermore, about 86% (30 of 35) of the multi-functional hnRNP proteins in the database contain lysines that are potential sites for acetylation/ubiquitination. We demonstrate that the degradation of three of them (A1, I and L) are also prevented by TSA. Thus, the deacetylase inhibitor TSA enhances hnRNP F stability through the K(Ac/Ub) lysines, with some of them essential for its regulation of alternative splicing. Such a regulation of protein stability is perhaps common for a group of hnRNPs and RNA metabolism.
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Affiliation(s)
- Geremy A Koumbadinga
- Department of Physiology & Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Niaz Mahmood
- Biochemistry & Medical Genetics, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Lei Lei
- Department of Physiology & Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Yunchao Kan
- Department of Physiology & Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; Nanyang Normal University, Nanyang, Henan, PR China
| | - Wenguang Cao
- Department of Physiology & Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Vincent G Lobo
- Department of Physiology & Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Xiaojian Yao
- Department of Medical Microbiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Shetuan Zhang
- Department of Biomedical and Molecular Sciences, Queens University, Kingston, ON, Canada
| | - Jiuyong Xie
- Department of Physiology & Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; Biochemistry & Medical Genetics, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
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NBM-T-BBX-OS01, Semisynthesized from Osthole, Induced G1 Growth Arrest through HDAC6 Inhibition in Lung Cancer Cells. Molecules 2015; 20:8000-19. [PMID: 25946558 PMCID: PMC6272357 DOI: 10.3390/molecules20058000] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 01/15/2023] Open
Abstract
Disrupting lung tumor growth via histone deacetylases (HDACs) inhibition is a strategy for cancer therapy or prevention. Targeting HDAC6 may disturb the maturation of heat shock protein 90 (Hsp90) mediated cell cycle regulation. In this study, we demonstrated the effects of semisynthesized NBM-T-BBX-OS01 (TBBX) from osthole on HDAC6-mediated growth arrest in lung cancer cells. The results exhibited that the anti-proliferative activity of TBBX in numerous lung cancer cells was more potent than suberoylanilide hydroxamic acid (SAHA), a clinically approved pan-HDAC inhibitor, and the growth inhibitory effect has been mediated through G1 growth arrest. Furthermore, the protein levels of cyclin D1, CDK2 and CDK4 were reduced while cyclin E and CDK inhibitor, p21Waf1/Cip1, were up-regulated in TBBX-treated H1299 cells. The results also displayed that TBBX inhibited HDAC6 activity via down-regulation HDAC6 protein expression. TBBX induced Hsp90 hyper-acetylation and led to the disruption of cyclin D1/Hsp90 and CDK4/Hsp90 association following the degradation of cyclin D1 and CDK4 proteins through proteasome. Ectopic expression of HDAC6 rescued TBBX-induced G1 arrest in H1299 cells. Conclusively, the data suggested that TBBX induced G1 growth arrest may mediate HDAC6-caused Hsp90 hyper-acetylation and consequently increased the degradation of cyclin D1 and CDK4.
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133
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McIntyre J, Woodgate R. Regulation of translesion DNA synthesis: Posttranslational modification of lysine residues in key proteins. DNA Repair (Amst) 2015; 29:166-79. [PMID: 25743599 PMCID: PMC4426011 DOI: 10.1016/j.dnarep.2015.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 01/30/2023]
Abstract
Posttranslational modification of proteins often controls various aspects of their cellular function. Indeed, over the past decade or so, it has been discovered that posttranslational modification of lysine residues plays a major role in regulating translesion DNA synthesis (TLS) and perhaps the most appreciated lysine modification is that of ubiquitination. Much of the recent interest in ubiquitination stems from the fact that proliferating cell nuclear antigen (PCNA) was previously shown to be specifically ubiquitinated at K164 and that such ubiquitination plays a key role in regulating TLS. In addition, TLS polymerases themselves are now known to be ubiquitinated. In the case of human polymerase η, ubiquitination at four lysine residues in its C-terminus appears to regulate its ability to interact with PCNA and modulate TLS. Within the past few years, advances in global proteomic research have revealed that many proteins involved in TLS are, in fact, subject to a previously underappreciated number of lysine modifications. In this review, we will summarize the known lysine modifications of several key proteins involved in TLS; PCNA and Y-family polymerases η, ι, κ and Rev1 and we will discuss the potential regulatory effects of such modification in controlling TLS in vivo.
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Affiliation(s)
- Justyna McIntyre
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
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Wu Q, Cheng Z, Zhu J, Xu W, Peng X, Chen C, Li W, Wang F, Cao L, Yi X, Wu Z, Li J, Fan P. Suberoylanilide hydroxamic acid treatment reveals crosstalks among proteome, ubiquitylome and acetylome in non-small cell lung cancer A549 cell line. Sci Rep 2015; 5:9520. [PMID: 25825284 PMCID: PMC4379480 DOI: 10.1038/srep09520] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/03/2015] [Indexed: 12/31/2022] Open
Abstract
Suberoylanilide hydroxamic acid (SAHA) is a well-known histone deacetylase (HDAC) inhibitor and has been used as practical therapy for breast cancer and non-small cell lung cancer (NSCLC). It is previously demonstrated that SAHA treatment could extensively change the profile of acetylome and proteome in cancer cells. However, little is known about the impact of SAHA on other protein modifications and the crosstalks among different modifications and proteome, hindering the deep understanding of SAHA-mediated cancer therapy. In this work, by using SILAC technique, antibody-based affinity enrichment and high-resolution LC-MS/MS analysis, we investigated quantitative proteome, acetylome and ubiquitylome as well as crosstalks among the three datasets in A549 cells toward SAHA treatment. In total, 2968 proteins, 1099 acetylation sites and 1012 ubiquitination sites were quantified in response to SAHA treatment, respectively. With the aid of intensive bioinformatics, we revealed that the proteome and ubiquitylome were negatively related upon SAHA treatment. Moreover, the impact of SAHA on acetylome resulted in 258 up-regulated and 99 down-regulated acetylation sites at the threshold of 1.5 folds. Finally, we identified 55 common sites with both acetylation and ubiquitination, among which ubiquitination level in 43 sites (78.2%) was positive related to acetylation level.
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Affiliation(s)
- Quan Wu
- Central Laboratory of Medical Research Centre, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Zhongyi Cheng
- Institute for Advanced Study of Translational Medicine, Tongji University, Shanghai, 200092, China
| | - Jun Zhu
- Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Weiqing Xu
- Central Laboratory of Medical Research Centre, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Xiaojun Peng
- Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Chuangbin Chen
- Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Wenting Li
- Central Laboratory of Medical Research Centre, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Fengsong Wang
- School of Life science, Anhui Medical University, Hefei, 230032, China
| | - Lejie Cao
- Department of Respiration, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Xingling Yi
- Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Zhiwei Wu
- Central Laboratory of Medical Research Centre, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Jing Li
- Central Laboratory of Medical Research Centre, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Pingsheng Fan
- Department of Oncology, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
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135
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Acetyl-L-carnitine increases mitochondrial protein acetylation in the aged rat heart. Mech Ageing Dev 2015; 145:39-50. [PMID: 25660059 DOI: 10.1016/j.mad.2015.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 11/24/2014] [Accepted: 01/27/2015] [Indexed: 12/30/2022]
Abstract
Previously we showed that in vivo treatment of elderly Fisher 344 rats with acetylcarnitine abolished the age-associated defect in respiratory chain complex III in interfibrillar mitochondria and improved the functional recovery of the ischemic/reperfused heart. Herein, we explored mitochondrial protein acetylation as a possible mechanism for acetylcarnitine's effect. In vivo treatment of elderly rats with acetylcarnitine restored cardiac acetylcarnitine content and increased mitochondrial protein lysine acetylation and increased the number of lysine-acetylated proteins in cardiac subsarcolemmal and interfibrillar mitochondria. Enzymes of the tricarboxylic acid cycle, mitochondrial β-oxidation, and ATP synthase of the respiratory chain showed the greatest acetylation. Acetylation of isocitrate dehydrogenase, long-chain acyl-CoA dehydrogenase, complex V, and aspartate aminotransferase was accompanied by decreased catalytic activity. Several proteins were found to be acetylated only after treatment with acetylcarnitine, suggesting that exogenous acetylcarnitine served as the acetyl-donor. Two-dimensional fluorescence difference gel electrophoresis analysis revealed that acetylcarnitine treatment also induced changes in mitochondrial protein amount; a two-fold or greater increase/decrease in abundance was observed for thirty one proteins. Collectively, our data provide evidence for the first time that in the aged rat heart in vivo administration of acetylcarnitine provides acetyl groups for protein acetylation and affects the amount of mitochondrial proteins.
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136
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Xiao Y, Nagai Y, Deng G, Ohtani T, Zhu Z, Zhou Z, Zhang H, Ji MQ, Lough JW, Samanta A, Hancock WW, Greene MI. Dynamic interactions between TIP60 and p300 regulate FOXP3 function through a structural switch defined by a single lysine on TIP60. Cell Rep 2014; 7:1471-1480. [PMID: 24835996 PMCID: PMC4064594 DOI: 10.1016/j.celrep.2014.04.021] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 10/25/2022] Open
Abstract
The human FOXP3 molecule is an oligomeric transcriptional factor able to mediate activities that characterize T regulatory cells, a class of lymphocytes central to the regulation of immune responses. The activity of FOXP3 is regulated at the posttranslational level, in part by two histone acetyltransferases (HATs): TIP60 and p300. TIP60 and p300 work cooperatively to regulate FOXP3 activity. Initially, p300 and TIP60 interactions lead to the activation of TIP60 and facilitate acetylation of K327 of TIP60, which functions as a molecular switch to allow TIP60 to change binding partners. Subsequently, p300 is released from this complex, and TIP60 interacts with and acetylates FOXP3. Maximal induction of FOXP3 activities is observed when both p300 and TIP60 are able to undergo cooperative interactions. Conditional knockout of TIP60 in Treg cells significantly decreases the Treg population in the peripheral immune organs, leading to a scurfy-like fatal autoimmune disease.
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Affiliation(s)
- Yan Xiao
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yasuhiro Nagai
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guoping Deng
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Takuya Ohtani
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhiqiang Zhu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhaocai Zhou
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hongtao Zhang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mei Q Ji
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John W Lough
- Department of Cell Biology, Neurology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226-0509, USA
| | - Arabinda Samanta
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wayne W Hancock
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital, Philadelphia, Philadelphia, PA 19104, USA
| | - Mark I Greene
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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137
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Zhang Y, Liu CM, Cao XC, Zang Y, Zhou YB, Li J. Involvement of transcription factor XBP1s in the resistance of HDAC6 inhibitor Tubastatin A to superoxidation via acetylation-mediated proteasomal degradation. Biochem Biophys Res Commun 2014; 450:433-9. [PMID: 24909686 DOI: 10.1016/j.bbrc.2014.05.134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2022]
Abstract
HDAC6 is a major cytoplasmic deacetylase. XBP1s is a basic-region leucine zipper (bZIP) transcriptional factor. Despite their mutual involvement in the anti-oxidative process, there are no reports about their inter-protein interactions so far. Here we identified a direct link between HDAC6 inhibition and XBP1s transcription activity in anti-oxidative damage. We showed that the specific HDAC6 inhibitor Tubastatin A could up-regulate XBP1s transcriptional activity, thereby increasing anti-oxidative genes expression. Moreover, knock down of XBP1s could significantly abolish the cell growth protection afforded by Tubastatin A. We hypothesize that Tubastatin A acts to increase XBP1s protein levels that are dependent on its HDAC6 deacetylase inhibition via a mechanism involving acetylation-mediated proteasomal degradation, providing novel mechanistic insight into the anti-oxidative effects of HDAC6 inhibition.
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Affiliation(s)
- Yue Zhang
- School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China; National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chang-mei Liu
- School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China; National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xian-cao Cao
- School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China; National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yi Zang
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yu-bo Zhou
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Jia Li
- School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China; National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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138
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Abstract
Modern society enables a shortening of sleep times, yet long-term consequences of extended wakefulness on the brain are largely unknown. Essential for optimal alertness, locus ceruleus neurons (LCns) are metabolically active neurons that fire at increased rates across sustained wakefulness. We hypothesized that wakefulness is a metabolic stressor to LCns and that, with extended wakefulness, adaptive mitochondrial metabolic responses fail and injury ensues. The nicotinamide adenine dinucleotide-dependent deacetylase sirtuin type 3 (SirT3) coordinates mitochondrial energy production and redox homeostasis. We find that brief wakefulness upregulates SirT3 and antioxidants in LCns, protecting metabolic homeostasis. Strikingly, mice lacking SirT3 lose the adaptive antioxidant response and incur oxidative injury in LCns across brief wakefulness. When wakefulness is extended for longer durations in wild-type mice, SirT3 protein declines in LCns, while oxidative stress and acetylation of mitochondrial proteins, including electron transport chain complex I proteins, increase. In parallel with metabolic dyshomeostasis, apoptosis is activated and LCns are lost. This work identifies mitochondrial stress in LCns upon wakefulness, highlights an essential role for SirT3 activation in maintaining metabolic homeostasis in LCns across wakefulness, and demonstrates that extended wakefulness results in reduced SirT3 activity and, ultimately, degeneration of LCns.
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139
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Seto E, Yoshida M. Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harb Perspect Biol 2014; 6:a018713. [PMID: 24691964 DOI: 10.1101/cshperspect.a018713] [Citation(s) in RCA: 1208] [Impact Index Per Article: 120.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl functional groups from the lysine residues of both histone and nonhistone proteins. In humans, there are 18 HDAC enzymes that use either zinc- or NAD(+)-dependent mechanisms to deacetylate acetyl lysine substrates. Although removal of histone acetyl epigenetic modification by HDACs regulates chromatin structure and transcription, deacetylation of nonhistones controls diverse cellular processes. HDAC inhibitors are already known potential anticancer agents and show promise for the treatment of many diseases.
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Affiliation(s)
- Edward Seto
- Department of Molecular Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
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140
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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: 27] [Impact Index Per Article: 2.7] [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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141
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Nallamilli BRR, Edelmann MJ, Zhong X, Tan F, Mujahid H, Zhang J, Nanduri B, Peng Z. Global analysis of lysine acetylation suggests the involvement of protein acetylation in diverse biological processes in rice (Oryza sativa). PLoS One 2014; 9:e89283. [PMID: 24586658 PMCID: PMC3930695 DOI: 10.1371/journal.pone.0089283] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 01/15/2014] [Indexed: 11/18/2022] Open
Abstract
Lysine acetylation is a reversible, dynamic protein modification regulated by lysine acetyltransferases and deacetylases. Recent advances in high-throughput proteomics have greatly contributed to the success of global analysis of lysine acetylation. A large number of proteins of diverse biological functions have been shown to be acetylated in several reports in human cells, E.coli, and dicot plants. However, the extent of lysine acetylation in non-histone proteins remains largely unknown in monocots, particularly in the cereal crops. Here we report the mass spectrometric examination of lysine acetylation in rice (Oryza sativa). We identified 60 lysine acetylated sites on 44 proteins of diverse biological functions. Immunoblot studies further validated the presence of a large number of acetylated non-histone proteins. Examination of the amino acid composition revealed substantial amino acid bias around the acetylation sites and the amino acid preference is conserved among different organisms. Gene ontology analysis demonstrates that lysine acetylation occurs in diverse cytoplasmic, chloroplast and mitochondrial proteins in addition to the histone modifications. Our results suggest that lysine acetylation might constitute a regulatory mechanism for many proteins, including both histones and non-histone proteins of diverse biological functions.
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Affiliation(s)
- Babi Ramesh Reddy Nallamilli
- Department of Biochemistry and Molecular Biology, Mississippi State University, Starkville, Mississippi, United States of America
| | - Mariola J. Edelmann
- Institute of Genomics, Biocomputing and Biotechnology, Mississippi Agricultural and Forestry Experimental Station, Mississippi State University, Starkville, Mississippi, United States of America
| | - Xiaoxian Zhong
- Department of Biochemistry and Molecular Biology, Mississippi State University, Starkville, Mississippi, United States of America
| | - Feng Tan
- Department of Biochemistry and Molecular Biology, Mississippi State University, Starkville, Mississippi, United States of America
| | - Hana Mujahid
- Department of Biochemistry and Molecular Biology, Mississippi State University, Starkville, Mississippi, United States of America
| | - Jian Zhang
- Department of Biochemistry and Molecular Biology, Mississippi State University, Starkville, Mississippi, United States of America
| | - Bindu Nanduri
- Institute of Genomics, Biocomputing and Biotechnology, Mississippi Agricultural and Forestry Experimental Station, Mississippi State University, Starkville, Mississippi, United States of America
- College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America
| | - Zhaohua Peng
- Department of Biochemistry and Molecular Biology, Mississippi State University, Starkville, Mississippi, United States of America
- * E-mail:
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142
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Raychaudhuri S, Loew C, Körner R, Pinkert S, Theis M, Hayer-Hartl M, Buchholz F, Hartl F. Interplay of Acetyltransferase EP300 and the Proteasome System in Regulating Heat Shock Transcription Factor 1. Cell 2014; 156:975-85. [DOI: 10.1016/j.cell.2014.01.055] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/20/2013] [Accepted: 01/23/2014] [Indexed: 12/22/2022]
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143
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Regulatory role of the 90-kDa-heat-shock protein (Hsp90) and associated factors on gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:71-87. [DOI: 10.1016/j.bbagrm.2013.12.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 12/23/2013] [Accepted: 12/26/2013] [Indexed: 12/31/2022]
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144
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Marchion D, Münster P. Development of histone deacetylase inhibitors for cancer treatment. Expert Rev Anticancer Ther 2014; 7:583-98. [PMID: 17428177 DOI: 10.1586/14737140.7.4.583] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Histone deacetylase (HDAC) inhibitors are an exciting new addition to the arsenal of cancer therapeutics. The inhibition of HDAC enzymes by HDAC inhibitors shifts the balance between the deacetylation activity of HDAC enzymes and the acetylation activity of histone acetyltransferases, resulting in hyperacetylation of core histones. Exposure of cancer cells to HDAC inhibitors has been associated with a multitude of molecular and biological effects, ranging from transcriptional control, chromatin plasticity, protein-DNA interaction to cellular differentiation, growth arrest and apoptosis. In addition to the antitumor effects seen with HDAC inhibitors alone, these compounds may also potentiate cytotoxic agents or synergize with other targeted anticancer agents. The exact mechanism by which HDAC inhibitors cause cell death is still unclear and the specific roles of individual HDAC enzymes as therapeutic targets has not been established. However, emerging evidence suggests that the effects of HDAC inhibitors on tumor cells may not only depend on the specificity and selectivity of the HDAC inhibitor, but also on the expression patterns of HDAC enzymes in the tumor tissue. In this review, the recent advances in the understanding and clinical development of HDAC inhibitors, as well as their current role in cancer therapy, will be discussed.
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Affiliation(s)
- Douglas Marchion
- H Lee Moffitt Cancer Center, Experimental Therapeutics Program, Department of Interdisciplinary Oncology, Tampa, FL 33612, USA
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145
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Function and Regulation of the Mono-ADP-Ribosyltransferase ARTD10. Curr Top Microbiol Immunol 2014; 384:167-88. [DOI: 10.1007/82_2014_379] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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146
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Nguyen TTM, Wong R, Menazza S, Sun J, Chen Y, Wang G, Gucek M, Steenbergen C, Sack MN, Murphy E. Cyclophilin D modulates mitochondrial acetylome. Circ Res 2013; 113:1308-19. [PMID: 24062335 PMCID: PMC4180423 DOI: 10.1161/circresaha.113.301867] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE Mice lacking cyclophilin D (CypD(-/-)), a mitochondrial chaperone protein, have altered cardiac metabolism. As acetylation has been shown to regulate metabolism, we tested whether changes in protein acetylation might play a role in these metabolic changes in CypD(-/-) hearts. OBJECTIVE Our aim was to test the hypothesis that loss of CypD alters the cardiac mitochondrial acetylome. METHODS AND RESULTS To identify changes in lysine-acetylated proteins and to map acetylation sites after ablation of CypD, we subjected tryptic digests of isolated cardiac mitochondria from wild-type and CypD(-/-) mice to immunoprecipitation using agarose beads coupled to antiacetyl lysine antibodies followed by mass spectrometry. We used label-free analysis for the relative quantification of the 875 common peptides that were acetylated in wild-type and CypD(-/-) samples and found 11 peptides (10 proteins) decreased and 96 peptides (48 proteins) increased in CypD(-/-) samples. We found increased acetylation of proteins in fatty acid oxidation and branched-chain amino acid metabolism. To evaluate whether this increase in acetylation might play a role in the inhibition of fatty acid oxidation that was previously reported in CypD(-/-) hearts, we measured the activity of l-3-hydroxyacyl-CoA dehydrogenase, which was acetylated in the CypD(-/-) hearts. Consistent with the hypothesis, l-3-hydroxyacyl-CoA dehydrogenase activity was inhibited by ≈50% compared with the wild-type mitochondria. CONCLUSIONS These results implicate a role for CypD in modulating protein acetylation. Taken together, these results suggest that ablation of CypD leads to changes in the mitochondrial acetylome, which may contribute to altered mitochondrial metabolism in CypD(-/-) mice.
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Affiliation(s)
- Tiffany Tuyen M. Nguyen
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Renee Wong
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Sara Menazza
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Junhui Sun
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Yong Chen
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Guanghui Wang
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Marjan Gucek
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | | | - Michael N. Sack
- Center for Molecular Medicine, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892
| | - Elizabeth Murphy
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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147
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Proteomic analysis reveals differentially regulated protein acetylation in human amyotrophic lateral sclerosis spinal cord. PLoS One 2013; 8:e80779. [PMID: 24312501 PMCID: PMC3846615 DOI: 10.1371/journal.pone.0080779] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/04/2013] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive fatal neurodegenerative disease that primarily affects motor neurons in the brain and spinal cord. Histone deacetylase (HDAC) inhibitors have neuroprotective effects potentially useful for the treatment of neurodegenerative diseases including ALS; however, the molecular mechanisms underlying their potential efficacy is not well understood. Here we report that protein acetylation in urea-soluble proteins is differently regulated in post-mortem ALS spinal cord. Two-dimensional electrophoresis (2-DE) analysis reveals several protein clusters with similar molecular weight but different charge status. Liquid chromatography and tandem mass spectrometry (LC-MS/MS) identifies glial fibrillary acidic protein (GFAP) as the dominant component in the protein clusters. Further analysis indicates six heavily acetylated lysine residues at positions 89, 153, 189, 218, 259 and 331 of GFAP. Immunoprecipitation followed by Western blotting confirms that the larger form of GFAP fragments are acetylated and upregulated in ALS spinal cord. Further studies demonstrate that acetylation of the proteins additional to GFAP is differently regulated, suggesting that acetylation and/or deacetylation play an important role in pathogenesis of ALS.
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148
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He G, Wang Y, Pang X, Zhang B. Inhibition of autophagy induced by TSA sensitizes colon cancer cell to radiation. Tumour Biol 2013; 35:1003-11. [DOI: 10.1007/s13277-013-1134-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 08/23/2013] [Indexed: 01/13/2023] Open
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149
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Glypican 1 stimulates S phase entry and DNA replication in human glioma cells and normal astrocytes. Mol Cell Biol 2013; 33:4408-21. [PMID: 24019070 DOI: 10.1128/mcb.00238-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Malignant gliomas are highly lethal neoplasms with limited treatment options. We previously found that the heparan sulfate proteoglycan glypican 1 (GPC1) is universally and highly expressed in human gliomas. In this study, we investigated the biological activity of GPC1 expression in both human glioma cells and normal astrocytes in vitro. Expression of GPC1 inactivates the G1/S checkpoint and strongly stimulates DNA replication. Constitutive expression of GPC1 causes DNA rereplication and DNA damage, suggesting a mutagenic activity for GPC1. GPC1 expression leads to a significant downregulation of the tumor suppressors pRb, Cip/Kip cyclin-dependent kinase inhibitors (CKIs), and CDH1, and upregulation of the pro-oncogenic proteins cyclin E, cyclin-dependent kinase 2 (CDK2), Skp2, and Cdt1. These GPC1-induced changes are accompanied by a significant reduction in all types of D cyclins, which is independent of serum supplementation. It is likely that GPC1 stimulates the so-called Skp2 autoinduction loop, independent of cyclin D-CDK4/6. Knockdown of Skp2, CDK2, or cyclin E, three key elements within the network modulated by GPC1, results in a reduction of the S phase and aneuploid fractions, implying a functional role for these regulators in GPC1-induced S phase entry and DNA rereplication. In addition, a significant activation of both the extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathways by GPC1 is seen in normal human astrocytes even in the presence of growth factor supplement. Both pathways are constitutively activated in human gliomas. The surprising magnitude and the mitogenic and mutagenic nature of the effect exerted by GPC1 on the cell cycle imply that GPC1 may play an important role in both glioma tumorigenesis and growth.
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150
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Wu Q, Xu W, Cao L, Li X, He T, Wu Z, Li W. SAHA treatment reveals the link between histone lysine acetylation and proteome in nonsmall cell lung cancer A549 Cells. J Proteome Res 2013; 12:4064-73. [PMID: 23909948 DOI: 10.1021/pr4004079] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Suberoylanilide hydroxamic acid (SAHA) is a well-known pan HDAC inhibitor, and its clinical application (Vorinostat) has been demonstrated to treat nonsmall cell lung cancer (NSCLS). Nevertheless, the impact of SAHA treatment on histone lysine acetylation and proteome in NSCLS cells still need further elucidate. In NSCLS A549 cells, by using stable isotope labeling for cell culture (SILAC)-based quantitative proteomics, biochemistry assay, and bioinformatic analysis, here we for the first time comprehensively identified and quantified histone lysine acetylation in A549 cells toward SAHA treatment. Despite the fact that SAHA treatment significantly increased histone lysine acetylation in specific sites, unexpectedly, some important "histone markers" showed markedly decreased acetylation level. Further quantitative proteome studies showed that among totally quantifiable 2818 nonredundant proteins, 1355 proteins were with increased level and 1463 with decreased level in response to SAHA treatment. Bioinformatic analysis further revealed that those quantifiable proteins were mainly involved in multiple biological functions and metabolic and enzyme-regulated pathways as well as protein complexes. By establishing the link between histone modification and whole proteome in response to SAHA treatment in NSCLS cells, this study therefore may deepen our understanding of HDAC inhibitor-mediated cancer therapeutics.
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Affiliation(s)
- Quan Wu
- Central Laboratory, Affiliated Provincial Hospital, Anhui Medical University, Hefei, China.
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