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Peshkin L, Gupta M, Ryazanova L, Wühr M. Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance. Mol Cell Proteomics 2019; 18:2108-2120. [PMID: 31311848 PMCID: PMC6773559 DOI: 10.1074/mcp.tir119.001317] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 06/11/2019] [Indexed: 01/28/2023] Open
Abstract
Multiplexed proteomics has emerged as a powerful tool to measure relative protein expression levels across multiple conditions. The relative protein abundances are inferred by comparing the signals generated by isobaric tags, which encode the samples' origins. Intuitively, the trust associated with a protein measurement depends on the similarity of ratios from the protein's peptides and the signal-strength of these measurements. However, typically the average peptide ratio is reported as the estimate of relative protein abundance, which is only the most likely ratio with a very naive model. Moreover, there is no sense on the confidence in these measurements. Here, we present a mathematically rigorous approach that integrates peptide signal strengths and peptide-measurement agreement into an estimation of the true protein ratio and the associated confidence (BACIQ). The main advantages of BACIQ are: (1) It removes the need to threshold reported peptide signal based on an arbitrary cut-off, thereby reporting more measurements from a given experiment; (2) Confidence can be assigned without replicates; (3) For repeated experiments BACIQ provides confidence intervals for the union, not the intersection, of quantified proteins; (4) For repeated experiments, BACIQ confidence intervals are more predictive than confidence intervals based on protein measurement agreement. To demonstrate the power of BACIQ we reanalyzed previously published data on subcellular protein movement on treatment with an Exportin-1 inhibiting drug. We detect ∼2× more highly significant movers, down to subcellular localization changes of ∼1%. Thus, our method drastically increases the value obtainable from quantitative proteomics experiments, helping researchers to interpret their data and prioritize resources. To make our approach easily accessible we distribute it via a Python/Stan package.
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Affiliation(s)
- Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Meera Gupta
- Department of Molecular Biology & the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544; DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton, NJ 08544
| | - Lillia Ryazanova
- Department of Molecular Biology & the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544; DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton, NJ 08544
| | - Martin Wühr
- Department of Molecular Biology & the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544; DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton, NJ 08544.
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2
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Plotnikov A, Chuderland D, Karamansha Y, Livnah O, Seger R. Nuclear ERK Translocation is Mediated by Protein Kinase CK2 and Accelerated by Autophosphorylation. Cell Physiol Biochem 2019; 53:366-387. [PMID: 31385665 DOI: 10.33594/000000144] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 08/01/2019] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND/AIMS The extracellular signal-regulated kinases (ERK) 1 and 2 (ERK1/2) are members of the mitogen-activated protein kinase (MAPK) family. Upon stimulation, these kinases translocate from the cytoplasm to the nucleus, where they induce physiological processes such as proliferation and differentiation. The mechanism of translocation of this kinase involves phosphorylation of two Ser residues within a nuclear translocation signal (NTS), which allows binding to importin7 and a subsequent penetration via nuclear pores. However, the regulation of this process and the protein kinases involved are not yet clear. METHODS To answer this point we developed specific anti phospho-SPS antibody, used this and other antibodies in Western blots and crystalized the phospho-mimetic mutated ERK. RESULTS Here we show that the phosphorylation of both Ser residues is mediated mainly by casein kinase 2 (CK2) and that active ERK may assist in the phosphorylation of the N-terminal Ser. We also demonstrate that the phosphorylation is dependent on the release of ERK from cytoplasmic anchoring proteins. Crystal structure of the phosphomimetic ERK revealed that the NTS phosphorylation creates an acidic patch in ERK. Our model is that in resting cells ERK is bound to cytoplasmic anchors, which prevent its NTS phosphorylation. Upon stimulation, phosphorylation of the ERK TEY domain releases ERK and allows phosphorylation of its NTS by CK2 and active ERK to generate a negatively charged patch in ERK, binding to importin 7 and nuclear translocation. CONCLUSION These results provide an important role of CK2 in regulating nuclear ERK activities.
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Affiliation(s)
- Alexander Plotnikov
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot, Israel
| | - Dana Chuderland
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot, Israel
| | - Yael Karamansha
- Department of Biological Chemistry, The Hebrew University, Jerusalem, Israel.,The Wolfson Centre for Applied Structural Biology, The Hebrew University, Jerusalem, Israel
| | - Oded Livnah
- Department of Biological Chemistry, The Hebrew University, Jerusalem, Israel.,The Wolfson Centre for Applied Structural Biology, The Hebrew University, Jerusalem, Israel
| | - Rony Seger
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot, Israel,
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3
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Baade I, Spillner C, Schmitt K, Valerius O, Kehlenbach RH. Extensive Identification and In-depth Validation of Importin 13 Cargoes. Mol Cell Proteomics 2018; 17:1337-1353. [PMID: 29666159 PMCID: PMC6030721 DOI: 10.1074/mcp.ra118.000623] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/09/2018] [Indexed: 11/06/2022] Open
Abstract
Importin 13 is a member of the importin β family of transport receptors. Unlike most family members, importin 13 mediates both, nuclear protein import and export. To search for novel importin 13 cargoes, we used stable isotope labeling of amino acids in cell culture (SILAC) and mass spectrometry. Using stringent criteria, we identified 255 importin 13 substrates, including the known cargoes Ubc9, Mago and eIF1A, and validate many of them as transport cargoes by extensive biochemical and cell biological characterization. Several novel cargoes can also be transported by the export receptor CRM1, demonstrating a clear redundancy in receptor choice. Using importin 13 mutants, we show that many of the novel substrates contact regions on the transport receptor that are not used by Ubc9, Mago or eIF1A. Together, this study significantly expands the repertoire of importin 13 cargoes and sets the basis for a more detailed characterization of this extremely versatile transport receptor.
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Affiliation(s)
- Imke Baade
- From the ‡Department of Molecular Biology, Faculty of Medicine, Göttingen Center of Biosciences (GZMB), Georg-August-University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Christiane Spillner
- From the ‡Department of Molecular Biology, Faculty of Medicine, Göttingen Center of Biosciences (GZMB), Georg-August-University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Kerstin Schmitt
- §Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Grisebachstr 8, 37077 Göttingen, Germany
| | - Oliver Valerius
- §Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Grisebachstr 8, 37077 Göttingen, Germany
| | - Ralph H Kehlenbach
- From the ‡Department of Molecular Biology, Faculty of Medicine, Göttingen Center of Biosciences (GZMB), Georg-August-University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany;
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4
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Lan H, Liu H, Hong P, Li R, Zheng X. Porcine growth hormone induces the nuclear localization of porcine growth hormone receptor in vivo. Asian-Australas J Anim Sci 2017; 31:499-504. [PMID: 29059726 PMCID: PMC5838321 DOI: 10.5713/ajas.17.0585] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/16/2017] [Accepted: 09/21/2017] [Indexed: 11/27/2022]
Abstract
Objective Recent studies have challenged the traditional paradigm that growth hormone receptor (GHR) displays physiological functions only in the cell membrane. It has been demonstrated that GHR localizes to the cell nucleus and still exhibits important physiological roles. The phenomenon of nuclear localization of growth hormone (GH)-induced GHR has previously been described in vitro. However, until recently, whether GH could induce nuclear localization of GHR in vivo was unclear. Methods In the present study, we used pig as an animal model, and porcine growth hormone (pGH) or saline was injected into the inferior vena cava. We subsequently observed the localization of porcine growth hormone receptor (pGHR) using multiple techniques, including, immunoprecipitation and Western-blotting, indirect immunofluorescence assay and electronmicroscopy. Results The results showed that pGH could induce nuclear localization of pGHR. Taken together, the results of the present study provided the first demonstration that pGHR was translocated to cell nuclei under pGH stimulation in vivo. Conclusion Nuclear localization of pGHR induced by the in vivo pGH treatment suggests new functions and/or novel roles of nuclear pGHR, which deserve further study.
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Affiliation(s)
- Hainan Lan
- College of Animal Science and Technology Jilin Agricultural University, Changchun 130118, China
| | - Huilin Liu
- College of life sciences, Jilin University, Changchun 130118, China
| | - Pan Hong
- College of Animal Science and Technology Jilin Agricultural University, Changchun 130118, China
| | - Ruonan Li
- College of Animal Science and Technology Jilin Agricultural University, Changchun 130118, China
| | - Xin Zheng
- College of Animal Science and Technology Jilin Agricultural University, Changchun 130118, China
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5
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Hu W, Zhang X, Wang L, Liu ZJ, Zhong Y, Li Q. Preferential distribution of nuclear MAPK signal in α/β core neurons during long-term memory consolidation in Drosophila. Protein Cell 2017; 8:780-783. [PMID: 28421388 PMCID: PMC5636746 DOI: 10.1007/s13238-017-0404-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Wantong Hu
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Protein Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xuchen Zhang
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Protein Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lianzhang Wang
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Protein Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China.,The Center for Biotechnology and Biomedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Yi Zhong
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Protein Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Qian Li
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Protein Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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6
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Mbefo MK, Fares MB, Paleologou K, Oueslati A, Yin G, Tenreiro S, Pinto M, Outeiro T, Zweckstetter M, Masliah E, Lashuel HA. Parkinson disease mutant E46K enhances α-synuclein phosphorylation in mammalian cell lines, in yeast, and in vivo. J Biol Chem 2015; 290:9412-27. [PMID: 25657004 DOI: 10.1074/jbc.m114.610774] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Indexed: 12/21/2022] Open
Abstract
Although α-synuclein (α-syn) phosphorylation has been considered as a hallmark of sporadic and familial Parkinson disease (PD), little is known about the effect of PD-linked mutations on α-syn phosphorylation. In this study, we investigated the effects of the A30P, E46K, and A53T PD-linked mutations on α-syn phosphorylation at residues Ser-87 and Ser-129. Although the A30P and A53T mutants slightly affected Ser(P)-129 levels compared with WT α-syn, the E46K mutation significantly enhanced Ser-129 phosphorylation in yeast and mammalian cell lines. This effect was not due to the E46K mutant being a better kinase substrate nor due to alterations in endogenous kinase levels, but was mostly linked with enhanced nuclear and endoplasmic reticulum accumulation. Importantly, lentivirus-mediated overexpression in mice also showed enhanced Ser-129 phosphorylation of the E46K mutant compared to WT α-syn, thus providing in vivo validation of our findings. Altogether, our findings suggest that the different PD-linked mutations may contribute to PD pathogenesis via different mechanisms.
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Affiliation(s)
- Martial Kamdem Mbefo
- From the Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Federale de Lausanne, Station 15, 1015 Lausanne, Switzerland
| | - Mohamed-Bilal Fares
- From the Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Federale de Lausanne, Station 15, 1015 Lausanne, Switzerland
| | - Katerina Paleologou
- From the Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Federale de Lausanne, Station 15, 1015 Lausanne, Switzerland
| | - Abid Oueslati
- From the Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Federale de Lausanne, Station 15, 1015 Lausanne, Switzerland
| | - Guowei Yin
- the Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sandra Tenreiro
- the Cell and Molecular Neuroscience Unit, Instituto de Medicina Molecular, and
| | - Madalena Pinto
- the Cell and Molecular Neuroscience Unit, Instituto de Medicina Molecular, and
| | - Tiago Outeiro
- the Cell and Molecular Neuroscience Unit, Instituto de Medicina Molecular, and Instituto de Fisiologia, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz 1649-028 Lisboa, Portugal, the Department of NeuroDegeneration and Restorative Research, University Medical Center Goettingen and
| | - Markus Zweckstetter
- the Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, the German Center for Neurodegenerative Diseases, Am Fassberg 11, 37077 Göttingen, Germany, and
| | - Eliezer Masliah
- the Departments of Pathology and Neurosciences, School of Medicine, University of California at San Diego, San Diego, California 92103
| | - Hilal A Lashuel
- From the Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Federale de Lausanne, Station 15, 1015 Lausanne, Switzerland,
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7
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Lorenz M, Vollmer B, Unsay JD, Klupp BG, García-Sáez AJ, Mettenleiter TC, Antonin W. A single herpesvirus protein can mediate vesicle formation in the nuclear envelope. J Biol Chem 2015; 290:6962-74. [PMID: 25605719 DOI: 10.1074/jbc.m114.627521] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Herpesviruses assemble capsids in the nucleus and egress by unconventional vesicle-mediated trafficking through the nuclear envelope. Capsids bud at the inner nuclear membrane into the nuclear envelope lumen. The resulting intralumenal vesicles fuse with the outer nuclear membrane, delivering the capsids to the cytoplasm. Two viral proteins are required for vesicle formation, the tail-anchored pUL34 and its soluble interactor, pUL31. Whether cellular proteins are involved is unclear. Using giant unilamellar vesicles, we show that pUL31 and pUL34 are sufficient for membrane budding and scission. pUL34 function can be bypassed by membrane tethering of pUL31, demonstrating that pUL34 is required for pUL31 membrane recruitment but not for membrane remodeling. pUL31 can inwardly deform membranes by oligomerizing on their inner surface to form buds that constrict to vesicles. Therefore, a single viral protein can mediate all events necessary for membrane budding and abscission.
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Affiliation(s)
- Michael Lorenz
- From the Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Benjamin Vollmer
- From the Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Joseph D Unsay
- the Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany, and
| | - Barbara G Klupp
- the Friedrich Loeffler Institute, Federal Research Institute for Animal Health, 17493 Greifswald, Germany
| | - Ana J García-Sáez
- the Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany, and
| | - Thomas C Mettenleiter
- the Friedrich Loeffler Institute, Federal Research Institute for Animal Health, 17493 Greifswald, Germany
| | - Wolfram Antonin
- From the Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany,
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8
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Yue Z, Zhong L, Mou Y, Wang X, Zhang H, Wang Y, Xia J, Li R, Wang Z. Arsenic Trioxide Activate Transcription of Heme Oxygenase-1 by Promoting Nuclear Translocation of NFE2L2. Int J Med Sci 2015; 12:674-9. [PMID: 26283888 PMCID: PMC4532976 DOI: 10.7150/ijms.12450] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/16/2015] [Indexed: 01/31/2023] Open
Abstract
In a previous study, we found that induced expression of Heme Oxygenase-1 (HO-1) is responsible for the resistance of human osteosarcoma MG63 cells to the chemotherapeutic agent arsenic trioxide (ATO). The present study was aimed at investigating the molecular mechanisms underlying the induction of HO-1 that occurs after exposure of MG63 cells to ATO. First, using RT-QPCT and Western-blot, we found that ATO strongly induced the expression of heme oxygenase-1 (HO-1) in these human osteosarcoma cells. Then by analyzing HO-1 mRNA of MG63 cells exposed to ATO in the presence and absence of a transcription inhibitor Actinomycin-D (Act-D), we demonstrated that ATO activates HO-1 expression in MG63 cells by regulating the transcription of the gene. Finally, through the analysis of the NFE2L2 protein levels among the total cellular and nuclear proteins by Western-blot and Immunocytochemical staning, we determined that ATO enhanced the nuclear translocation of nuclear factor erythroid 2-like 2 (NFE2L2), also known as Nrf2. From these results we have concluded that transcription activation of HO-1 resulting from the nuclear translocation of NFE2L2 is the underlying molecular mechanism for its high induction, which, in turn, is responsible for the resistance of human osteosarcoma cells to ATO treatment.
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Affiliation(s)
- Zhen Yue
- 1. Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Lingzhi Zhong
- 1. Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China ; 3. Current address: Institute of Basic Medical Sciences, College of Life Science, Chinese PLA General Hospital, Beijing 100853, China
| | - Yan Mou
- 1. Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China ; 2. The Second Hospital of Jilin University, Changchun, P.R. China
| | - Xiaotong Wang
- 1. Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Haiying Zhang
- 1. Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Yang Wang
- 1. Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Jianxin Xia
- 2. The Second Hospital of Jilin University, Changchun, P.R. China
| | - Ronggui Li
- 1. Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Zonggui Wang
- 2. The Second Hospital of Jilin University, Changchun, P.R. China
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Yang H, Wahlmüller FC, Sarg B, Furtmüller M, Geiger M. A+-helix of protein C inhibitor (PCI) is a cell-penetrating peptide that mediates cell membrane permeation of PCI. J Biol Chem 2014; 290:3081-91. [PMID: 25488662 PMCID: PMC4317013 DOI: 10.1074/jbc.m114.581736] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Protein C inhibitor (PCI) is a serpin with broad protease reactivity. It binds glycosaminoglycans and certain phospholipids that can modulate its inhibitory activity. PCI can penetrate through cellular membranes via binding to phosphatidylethanolamine. The exact mechanism of PCI internalization and the intracellular role of the serpin are not well understood. Here we showed that testisin, a glycosylphosphatidylinositol-anchored serine protease, cleaved human PCI and mouse PCI (mPCI) at their reactive sites as well as at sites close to their N terminus. This cleavage was observed not only with testisin in solution but also with cell membrane-anchored testisin on U937 cells. The cleavage close to the N terminus released peptides rich in basic amino acids. Synthetic peptides corresponding to the released peptides of human PCI (His1–Arg11) and mPCI (Arg1–Ala18) functioned as cell-penetrating peptides. Because intact mPCI but not testisin-cleaved mPCI was internalized by Jurkat T cells, a truncated mPCI mimicking testisin-cleaved mPCI was created. The truncated mPCI lacking 18 amino acids at the N terminus was not taken up by Jurkat T cells. Therefore our model suggests that testisin or other proteases could regulate the internalization of PCI by removing its N terminus. This may represent one of the mechanisms regulating the intracellular functions of PCI.
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Affiliation(s)
- Hanjiang Yang
- From the Center of Physiology and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, A-1090 Vienna, Austria and
| | - Felix Christof Wahlmüller
- From the Center of Physiology and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, A-1090 Vienna, Austria and
| | - Bettina Sarg
- Biocenter, Division of Clinical Biochemistry, Innsbruck Medical University, A-6020 Innsbruck, Austria
| | - Margareta Furtmüller
- From the Center of Physiology and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, A-1090 Vienna, Austria and
| | - Margarethe Geiger
- From the Center of Physiology and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, A-1090 Vienna, Austria and
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10
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Fogg PCM, O'Neill JS, Dobrzycki T, Calvert S, Lord EC, McIntosh RLL, Elliott CJH, Sweeney ST, Hastings MH, Chawla S. Class IIa histone deacetylases are conserved regulators of circadian function. J Biol Chem 2014; 289:34341-8. [PMID: 25271152 PMCID: PMC4256363 DOI: 10.1074/jbc.m114.606392] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/23/2014] [Indexed: 11/06/2022] Open
Abstract
Class IIa histone deacetylases (HDACs) regulate the activity of many transcription factors to influence liver gluconeogenesis and the development of specialized cells, including muscle, neurons, and lymphocytes. Here, we describe a conserved role for class IIa HDACs in sustaining robust circadian behavioral rhythms in Drosophila and cellular rhythms in mammalian cells. In mouse fibroblasts, overexpression of HDAC5 severely disrupts transcriptional rhythms of core clock genes. HDAC5 overexpression decreases BMAL1 acetylation on Lys-537 and pharmacological inhibition of class IIa HDACs increases BMAL1 acetylation. Furthermore, we observe cyclical nucleocytoplasmic shuttling of HDAC5 in mouse fibroblasts that is characteristically circadian. Mutation of the Drosophila homolog HDAC4 impairs locomotor activity rhythms of flies and decreases period mRNA levels. RNAi-mediated knockdown of HDAC4 in Drosophila clock cells also dampens circadian function. Given that the localization of class IIa HDACs is signal-regulated and influenced by Ca(2+) and cAMP signals, our findings offer a mechanism by which extracellular stimuli that generate these signals can feed into the molecular clock machinery.
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Affiliation(s)
- Paul C M Fogg
- From the Department of Biology, University of York, York YO10 5DD, United Kingdom and
| | - John S O'Neill
- the Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Tomasz Dobrzycki
- From the Department of Biology, University of York, York YO10 5DD, United Kingdom and
| | - Shaun Calvert
- From the Department of Biology, University of York, York YO10 5DD, United Kingdom and
| | - Emma C Lord
- From the Department of Biology, University of York, York YO10 5DD, United Kingdom and
| | - Rebecca L L McIntosh
- From the Department of Biology, University of York, York YO10 5DD, United Kingdom and
| | | | - Sean T Sweeney
- From the Department of Biology, University of York, York YO10 5DD, United Kingdom and
| | - Michael H Hastings
- the Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Sangeeta Chawla
- From the Department of Biology, University of York, York YO10 5DD, United Kingdom and
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11
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Miyata Y, Shibata T, Aoshima M, Tsubata T, Nishida E. The molecular chaperone TRiC/CCT binds to the Trp-Asp 40 (WD40) repeat protein WDR68 and promotes its folding, protein kinase DYRK1A binding, and nuclear accumulation. J Biol Chem 2014; 289:33320-32. [PMID: 25342745 PMCID: PMC4246089 DOI: 10.1074/jbc.m114.586115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 10/18/2014] [Indexed: 11/06/2022] Open
Abstract
Trp-Asp (WD) repeat protein 68 (WDR68) is an evolutionarily conserved WD40 repeat protein that binds to several proteins, including dual specificity tyrosine phosphorylation-regulated protein kinase (DYRK1A), MAPK/ERK kinase kinase 1 (MEKK1), and Cullin4-damage-specific DNA-binding protein 1 (CUL4-DDB1). WDR68 affects multiple and diverse physiological functions, such as controlling anthocyanin synthesis in plants, tissue growth in insects, and craniofacial development in vertebrates. However, the biochemical basis and the regulatory mechanism of WDR68 activity remain largely unknown. To better understand the cellular function of WDR68, here we have isolated and identified cellular WDR68 binding partners using a phosphoproteomic approach. More than 200 cellular proteins with wide varieties of biochemical functions were identified as WDR68-binding protein candidates. Eight T-complex protein 1 (TCP1) subunits comprising the molecular chaperone TCP1 ring complex/chaperonin-containing TCP1 (TRiC/CCT) were identified as major WDR68-binding proteins, and phosphorylation sites in both WDR68 and TRiC/CCT were identified. Co-immunoprecipitation experiments confirmed the binding between TRiC/CCT and WDR68. Computer-aided structural analysis suggested that WDR68 forms a seven-bladed β-propeller ring. Experiments with a series of deletion mutants in combination with the structural modeling showed that three of the seven β-propeller blades of WDR68 are essential and sufficient for TRiC/CCT binding. Knockdown of cellular TRiC/CCT by siRNA caused an abnormal WDR68 structure and led to reduction of its DYRK1A-binding activity. Concomitantly, nuclear accumulation of WDR68 was suppressed by the knockdown of TRiC/CCT, and WDR68 formed cellular aggregates when overexpressed in the TRiC/CCT-deficient cells. Altogether, our results demonstrate that the molecular chaperone TRiC/CCT is essential for correct protein folding, DYRK1A binding, and nuclear accumulation of WDR68.
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Affiliation(s)
- Yoshihiko Miyata
- From the Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan and
| | | | | | | | - Eisuke Nishida
- From the Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan and
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12
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Stewart MD, Ramani VC, Sanderson RD. Shed syndecan-1 translocates to the nucleus of cells delivering growth factors and inhibiting histone acetylation: a novel mechanism of tumor-host cross-talk. J Biol Chem 2014; 290:941-9. [PMID: 25404732 DOI: 10.1074/jbc.m114.608455] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The heparan sulfate proteoglycan syndecan-1 is proteolytically shed from the surface of multiple myeloma cells and is abundant in the bone marrow microenvironment where it promotes tumor growth, angiogenesis, and metastasis. In this study, we demonstrate for the first time that shed syndecan-1 present in the medium conditioned by tumor cells is taken up by bone marrow-derived stromal cells and transported to the nucleus. Translocation of shed syndecan-1 (sSDC1) to the nucleus was blocked by addition of exogenous heparin or heparan sulfate, pretreatment of conditioned medium with heparinase III, or growth of cells in sodium chlorate, indicating that sulfated heparan sulfate chains are required for nuclear translocation. Interestingly, cargo bound to sSDC1 heparan sulfate chains (i.e. hepatocyte growth factor) was transported to the nucleus along with sSDC1, and removal of heparan sulfate-bound cargo from sSDC1 abolished its translocation to the nucleus. Once in the nucleus, sSDC1 binds to the histone acetyltransferase enzyme p300, and histone acetyltransferase activity and histone acetylation are diminished. These findings reveal a novel function for shed syndecan-1 in mediating tumor-host cross-talk by shuttling growth factors to the nucleus and by altering histone acetylation in host cells. In addition, this work has broad implications beyond myeloma because shed syndecan-1 is present in high levels in many tumor types as well as in other disease states.
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Affiliation(s)
| | | | - Ralph D Sanderson
- From the Department of Pathology, UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294
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13
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Tristan CA, Ramos A, Shahani N, Emiliani FE, Nakajima H, Noeh CC, Kato Y, Takeuchi T, Noguchi T, Kadowaki H, Sedlak TW, Ishizuka K, Ichijo H, Sawa A. Role of apoptosis signal-regulating kinase 1 (ASK1) as an activator of the GAPDH-Siah1 stress-signaling cascade. J Biol Chem 2014; 290:56-64. [PMID: 25391652 DOI: 10.1074/jbc.m114.596205] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays roles in both energy maintenance, and stress signaling by forming a protein complex with seven in absentia homolog 1 (Siah1). Mechanisms to coordinate its glycolytic and stress cascades are likely to be very important for survival and homeostatic control of any living organism. Here we report that apoptosis signal-regulating kinase 1 (ASK1), a representative stress kinase, interacts with both GAPDH and Siah1 and is likely able to phosphorylate Siah1 at specific amino acid residues (Thr-70/Thr-74 and Thr-235/Thr-239). Phosphorylation of Siah1 by ASK1 triggers GAPDH-Siah1 stress signaling and activates a key downstream target, p300 acetyltransferase in the nucleus. This novel mechanism, together with the established S-nitrosylation/oxidation of GAPDH at Cys-150, provides evidence of how the stress signaling involving GAPDH is finely regulated. In addition, the present results imply crosstalk between the ASK1 and GAPDH-Siah1 stress cascades.
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Affiliation(s)
| | | | | | | | - Hidemitsu Nakajima
- the Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka 599-8531, and
| | | | - Yoshinori Kato
- Radiology and Radiological Science, Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Tadayoshi Takeuchi
- the Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka 599-8531, and
| | - Takuya Noguchi
- the Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-8654, Japan
| | - Hisae Kadowaki
- the Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-8654, Japan
| | | | | | - Hidenori Ichijo
- the Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-8654, Japan
| | - Akira Sawa
- From the Departments of Psychiatry and Neuroscience,
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14
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Parnell EJ, Yu Y, Lucena R, Yoon Y, Bai L, Kellogg DR, Stillman DJ. The Rts1 regulatory subunit of PP2A phosphatase controls expression of the HO endonuclease via localization of the Ace2 transcription factor. J Biol Chem 2014; 289:35431-7. [PMID: 25352596 DOI: 10.1074/jbc.m114.611715] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RTS1 gene encodes a subunit of the PP2A phosphatase that regulates cell cycle progression. Ace2 and Swi5 are cell cycle-regulated transcription factors, and we recently showed that phosphorylation of Ace2 and Swi5 is altered in an rts1 mutant. Here we examine expression of Ace2 and Swi5 target genes and find that an rts1 mutation markedly reduces expression of the HO gene. The decreased HO expression in an rts1 mutant is significantly restored by an additional ace2 mutation, a surprising result because HO is normally activated by Swi5 but not by Ace2. Ace2 normally accumulates only in daughter cells, and only activates transcription in daughters. However, in an rts1 mutant, Ace2 is present in both mother and daughter cells. One of the genes activated by Ace2 is ASH1, a protein that normally accumulates mostly in daughter cells; Ash1 is a transcriptional repressor, and it blocks HO expression in daughters. We show that in the rts1 mutant, Ace2 accumulation in mother cells results in Ash1 expression in mothers, and the Ash1 can now repress HO expression in mothers.
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Affiliation(s)
- Emily J Parnell
- From the Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Yaxin Yu
- From the Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Rafael Lucena
- the Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064, and
| | - Youngdae Yoon
- the Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, and
| | - Lu Bai
- the Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, and Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Douglas R Kellogg
- the Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064, and
| | - David J Stillman
- From the Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112,
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15
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Kannike K, Sepp M, Zuccato C, Cattaneo E, Timmusk T. Forkhead transcription factor FOXO3a levels are increased in Huntington disease because of overactivated positive autofeedback loop. J Biol Chem 2014; 289:32845-57. [PMID: 25271153 PMCID: PMC4239633 DOI: 10.1074/jbc.m114.612424] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Huntington disease (HD) is a fatal autosomal dominant neurodegenerative disorder caused by an increased number of CAG repeats in the HTT gene coding for huntingtin. Decreased neurotrophic support and increased mitochondrial and excitotoxic stress have been reported in HD striatal and cortical neurons. The members of the class O forkhead (FOXO) transcription factor family, including FOXO3a, act as sensor proteins that are activated upon decreased survival signals and/or increased cellular stress. Using immunocytochemical screening in mouse striatal Hdh7/7 (wild type), Hdh7/109 (heterozygous for HD mutation), and Hdh109/109 (homozygous for HD mutation) cells, we identified FOXO3a as a differentially regulated transcription factor in HD. We report increased nuclear FOXO3a levels in mutant Hdh cells. Additionally, we show that treatment with mitochondrial toxin 3-nitropropionic acid results in enhanced nuclear localization of FOXO3a in wild type Hdh7/7 cells and in rat primary cortical neurons. Furthermore, mRNA levels of Foxo3a are increased in mutant Hdh cells compared with wild type cells and in 3-nitropropionic acid-treated primary neurons compared with untreated neurons. A similar increase was observed in the cortex of R6/2 mice and HD patient post-mortem caudate tissue compared with controls. Using chromatin immunoprecipitation and reporter assays, we demonstrate that FOXO3a regulates its own transcription by binding to the conserved response element in Foxo3a promoter. Altogether, the findings of this study suggest that FOXO3a levels are increased in HD cells as a result of overactive positive feedback loop.
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Affiliation(s)
- Kaja Kannike
- From the Department of Gene Technology, Tallinn University of Technology, Tallinn 12618, Estonia and
| | - Mari Sepp
- From the Department of Gene Technology, Tallinn University of Technology, Tallinn 12618, Estonia and
| | - Chiara Zuccato
- the Department of Pharmacological Sciences and Center for Stem Cell Research, University of Milan, Milano 20133, Italy
| | - Elena Cattaneo
- the Department of Pharmacological Sciences and Center for Stem Cell Research, University of Milan, Milano 20133, Italy
| | - Tõnis Timmusk
- From the Department of Gene Technology, Tallinn University of Technology, Tallinn 12618, Estonia and
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16
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Hsu HM, Lee Y, Hsu PH, Liu HW, Chu CH, Chou YW, Chen YR, Chen SH, Tai JH. Signal transduction triggered by iron to induce the nuclear importation of a Myb3 transcription factor in the parasitic protozoan Trichomonas vaginalis. J Biol Chem 2014; 289:29334-49. [PMID: 25183012 DOI: 10.1074/jbc.m114.599498] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Iron was previously shown to induce rapid nuclear translocation of a Myb3 transcription factor in the protozoan parasite, Trichomonas vaginalis. In the present study, iron was found to induce a transient increase in cellular cAMP, followed by the nuclear influx of Myb3, whereas the latter was also induced by 8-bromo-cyclic AMP. Iron-inducible cAMP production and nuclear influx of Myb3 were inhibited by suramin and SQ22536, respective inhibitors of the Gα subunit of heterotrimeric G proteins and adenylyl cyclases. In contrast, the nuclear influx of Myb3 induced by iron or 8-bromo-cAMP was delayed or inhibited, respectively, by H89, the inhibitor of protein kinase A. Using liquid chromatography-coupled tandem mass spectrometry, Thr(156) and Lys(143) in Myb3 were found to be phosphorylated and ubiquitinated, respectively. These modifications were induced by iron and inhibited by H89, as shown by immunoprecipitation-coupled Western blotting. Iron-inducible ubiquitination and nuclear influx were aborted in T156A and K143R, but T156D was constitutively ubiquitinated and persistently localized to the nucleus. Myb3 was phosphorylated in vitro by the catalytic subunit of a T. vaginalis protein kinase A, TvPKAc. A transient interaction between TvPKAc and Myb3 and the phosphorylation of both proteins were induced in the parasite shortly after iron or 8-bromo-cAMP treatment. Together, these observations suggest that iron may induce production of cAMP and activation of TvPKAc, which then induces the phosphorylation of Myb3 and subsequent ubiquitination for accelerated nuclear influx. It is conceivable that iron probably exerts a much broader impact on the physiology of the parasite than previously thought to encounter environmental changes.
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Affiliation(s)
- Hong-Ming Hsu
- From the Division of Infectious Diseases, Institute of Biomedical Sciences and
| | - Yu Lee
- From the Division of Infectious Diseases, Institute of Biomedical Sciences and
| | - Pang-Hung Hsu
- the Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelun 20224, Taiwan, and
| | - Hsing-Wei Liu
- From the Division of Infectious Diseases, Institute of Biomedical Sciences and
| | - Chien-Hsin Chu
- From the Division of Infectious Diseases, Institute of Biomedical Sciences and
| | - Ya-Wen Chou
- Research Center of Agriculture and Biotechnology, Academia Sinica, Taipei 11529, Taiwan
| | - Yet-Ran Chen
- Research Center of Agriculture and Biotechnology, Academia Sinica, Taipei 11529, Taiwan
| | - Shu-Hui Chen
- the Department of Chemistry, National Chen Kung University, Tainan 70101, Taiwan
| | - Jung-Hsiang Tai
- From the Division of Infectious Diseases, Institute of Biomedical Sciences and
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17
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Biswas C, Shah N, Muthu M, La P, Fernando AP, Sengupta S, Yang G, Dennery PA. Nuclear heme oxygenase-1 (HO-1) modulates subcellular distribution and activation of Nrf2, impacting metabolic and anti-oxidant defenses. J Biol Chem 2014; 289:26882-26894. [PMID: 25107906 DOI: 10.1074/jbc.m114.567685] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
With oxidative injury as well as in some solid tumors and myeloid leukemia cells, heme oxygenase-1 (HO-1), the anti-oxidant, anti-inflammatory, and anti-apoptotic microsomal stress protein, migrates to the nucleus in a truncated and enzymatically inactive form. However, the function of HO-1 in the nucleus is not completely clear. Nuclear factor erythroid 2-related factor 2 (Nrf2), a transcription factor and master regulator of numerous antioxidants and anti-apoptotic proteins, including HO-1, also accumulates in the nucleus with oxidative injury and in various types of cancer. Here we demonstrate that in oxidative stress, nuclear HO-1 interacts with Nrf2 and stabilizes it from glycogen synthase kinase 3β (GSK3β)-mediated phosphorylation coupled with ubiquitin-proteasomal degradation, thereby prolonging its accumulation in the nucleus. This regulation of Nrf2 post-induction by nuclear HO-1 is important for the preferential transcription of phase II detoxification enzymes such as NQO1 as well as glucose-6-phosphate dehydrogenase (G6PDH), a regulator of the pentose phosphate pathway. Using Nrf2 knock-out cells, we further demonstrate that nuclear HO-1-associated cytoprotection against oxidative stress depends on an HO-1/Nrf2 interaction. Although it is well known that Nrf2 induces HO-1 leading to mitigation of oxidant stress, we propose a novel mechanism by which HO-1, by modulating the activation of Nrf2, sets an adaptive reprogramming that enhances antioxidant defenses.
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Affiliation(s)
- Chhanda Biswas
- Department of Pediatrics, University of Pennsylvania Philadelphia, Pennsylvania 19104 and; Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Nidhi Shah
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Manasa Muthu
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Ping La
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Amal P Fernando
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Shaon Sengupta
- Department of Pediatrics, University of Pennsylvania Philadelphia, Pennsylvania 19104 and; Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Guang Yang
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Phyllis A Dennery
- Department of Pediatrics, University of Pennsylvania Philadelphia, Pennsylvania 19104 and; Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104.
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18
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Rai R, Tate JJ, Shanmuganatham K, Howe MM, Cooper TG. A domain in the transcription activator Gln3 specifically required for rapamycin responsiveness. J Biol Chem 2014; 289:18999-9018. [PMID: 24847055 DOI: 10.1074/jbc.m114.563668] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Nitrogen-responsive control of Gln3 localization is implemented through TorC1-dependent (rapamycin-responsive) and TorC1-independent (nitrogen catabolite repression-sensitive and methionine sulfoximine (Msx)-responsive) regulatory pathways. We previously demonstrated amino acid substitutions in a putative Gln3 α-helix(656-666), which are required for a two-hybrid Gln3-Tor1 interaction, also abolished rapamycin responsiveness of Gln3 localization and partially abrogated cytoplasmic Gln3 sequestration in cells cultured under nitrogen-repressive conditions. Here, we demonstrate these three characteristics are not inextricably linked together. A second distinct Gln3 region (Gln3(510-589)) is specifically required for rapamycin responsiveness of Gln3 localization, but not for cytoplasmic Gln3 sequestration under repressive growth conditions or relocation to the nucleus following Msx addition. Aspartate or alanine substitution mutations throughout this region uniformly abolish rapamycin responsiveness. Contained within this region is a sequence with a predicted propensity to form an α-helix(583-591), one side of which consists of three hydrophobic amino acids flanked by serine residues. Substitution of aspartate for even one of these serines abolishes rapamycin responsiveness and increases rapamycin resistance without affecting either of the other two Gln3 localization responses. In contrast, alanine substitutions decrease rapamycin resistance. Together, these data suggest that targets in the C-terminal portion of Gln3 required for the Gln3-Tor1 interaction, cytoplasmic Gln3 sequestration, and Gln3 responsiveness to Msx addition and growth in poor nitrogen sources are distinct from those needed for rapamycin responsiveness.
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Affiliation(s)
- Rajendra Rai
- From the Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and
| | - Jennifer J Tate
- From the Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and
| | - Karthik Shanmuganatham
- the Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Martha M Howe
- From the Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and
| | - Terrance G Cooper
- From the Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and
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19
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Hsu HM, Chu CH, Wang YT, Lee Y, Wei SY, Liu HW, Ong SJ, Chen C, Tai JH. Regulation of nuclear translocation of the Myb1 transcription factor by TvCyclophilin 1 in the protozoan parasite Trichomonas vaginalis. J Biol Chem 2014; 289:19120-36. [PMID: 24831011 DOI: 10.1074/jbc.m114.549410] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In Trichomonas vaginalis, a Myb1 protein was previously demonstrated to repress transcription of an iron-inducible ap65-1 gene. In this study, a human cyclophilin A homologue, TvCyclophilin 1 (TvCyP1), was identified as a Myb1-binding protein using a bacterial two-hybrid library screening system. The recombinant TvCyP1 exhibited typical peptidyl-prolyl isomerase activity with kcat/Km of ∼7.1 μm(-1) s(-1). In a pulldown assay, the His-tagged Myb1 interacted with a GST-TvCyP1 fusion protein, which had an enzymatic proficiency half that of recombinant TvCyP1. Both the enzymatic proficiency of GST-TvCyP1 and its binding to His-Myb1 were eliminated by mutation of Arg(63) in the catalytic motif or inhibited by cyclosporin A. TvCyP1 was primarily localized to the hydrogenosomes by immunofluorescence assay, but it was also co-purified with Myb1 in certain vesicle fractions from differential and gradient centrifugations. Transgenic cells overexpressing HA-TvCyP1 had a higher level of nuclear Myb1 but a much lower level of Myb1 associated with the vesicles than control and those overexpressing HA-TvCyP1(R63A). Myb1 was detected at a much higher level in the HA-TvCyP1 protein complex than in the HA-TvCyP1(R63A) protein complex immunoprecipitated from P15 and P100, but not S100, fractions of postnuclear lysates. A TvCyP1-binding motif, (105)YGPKWNK(111), was identified in Myb1 in which Gly(106) and Pro(107) were essential for its binding to TvCyP1. Mutation of Gly(106) and Pro(107), respectively, in HA-Myb1 resulted in cytoplasmic retention and elevated nuclear translocation of the overexpressed protein. These results suggest that TvCyP1 may induce the release of Myb1 that is restrained to certain cytoplasmic vesicles prior to its nuclear translocation.
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Affiliation(s)
| | - Chien-Hsin Chu
- Divisions of Infectious Diseases and Immunology and From the Department of Parasitology, College of Medicine, National Taiwan University and
| | - Ya-Ting Wang
- From the Department of Parasitology, College of Medicine, National Taiwan University and
| | - Yu Lee
- Divisions of Infectious Diseases and Immunology and
| | - Shu-Yi Wei
- Structure Biology, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | | | - Shiou-Jeng Ong
- From the Department of Parasitology, College of Medicine, National Taiwan University and
| | - Chinpan Chen
- Structure Biology, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Jung-Hsiang Tai
- Divisions of Infectious Diseases and Immunology and From the Department of Parasitology, College of Medicine, National Taiwan University and
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20
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Yamasaki T, Ariyoshi W, Okinaga T, Adachi Y, Hosokawa R, Mochizuki S, Sakurai K, Nishihara T. The dectin 1 agonist curdlan regulates osteoclastogenesis by inhibiting nuclear factor of activated T cells cytoplasmic 1 (NFATc1) through Syk kinase. J Biol Chem 2014; 289:19191-203. [PMID: 24821724 DOI: 10.1074/jbc.m114.551416] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Several immune system cell surface receptors are reported to be associated with osteoclastogenesis. Dectin 1, a lectin receptor for β-glucan, is found predominantly on cells of the myeloid lineage. In this study, we examined the effect of the dectin 1 agonist curdlan on osteoclastogenesis. In mouse bone marrow cells and dectin 1-overexpressing RAW 264.7 cells (d-RAWs), curdlan suppressed receptor activator of NF-κB ligand (RANKL)-induced osteoclast differentiation, bone resorption, and actin ring formation in a dose-dependent manner. This was achieved within non-growth inhibitory concentrations at the early stage. Conversely, curdlan had no effect on macrophage colony-stimulating factor-induced differentiation. Furthermore, curdlan inhibited RANKL-induced nuclear factor of activated T cell cytoplasmic 1 (NFATc1) expression, thereby decreasing osteoclastogenesis-related marker gene expression, including tartrate-resistant acid phosphatase, osteoclast stimulatory transmembrane protein, cathepsin K, and matrix metallopeptidase 9. Curdlan inhibited RANKL-induced c-fos expression, followed by suppression of NFATc1 autoamplification, without significantly affecting the NF-κB signaling pathway. We also observed that curdlan treatment decreased Syk protein in d-RAWs. Inhibition of the dectin 1-Syk kinase pathway by Syk-specific siRNA or chemical inhibitors suppressed osteoclast formation and NFATc1 expression stimulated by RANKL. In conclusion, our results demonstrate that curdlan potentially inhibits osteoclast differentiation, especially NFATc1 expression, and that Syk kinase plays a crucial role in the transcriptional pathways. This suggests that the activation of dectin 1-Syk kinase interaction critically regulates the genes required for osteoclastogenesis.
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Affiliation(s)
- Toru Yamasaki
- From the Division of Infections and Molecular Biology, Department of Health Promotion, Division of Oral Reconstruction and Rehabilitation, Department of Oral Functions, Kyushu Dental University, Kitakyushu, Fukuoka 803-8580, Japan
| | - Wataru Ariyoshi
- From the Division of Infections and Molecular Biology, Department of Health Promotion,
| | - Toshinori Okinaga
- From the Division of Infections and Molecular Biology, Department of Health Promotion
| | - Yoshiyuki Adachi
- the Laboratory for Immunopharmacology of Microbial Products, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan, and
| | - Ryuji Hosokawa
- Division of Oral Reconstruction and Rehabilitation, Department of Oral Functions, Kyushu Dental University, Kitakyushu, Fukuoka 803-8580, Japan
| | - Shinichi Mochizuki
- the Department of Chemistry and Biochemistry, The University of Kitakyushu, Kitakyushu, Fukuoka 808-0135, Japan
| | - Kazuo Sakurai
- the Department of Chemistry and Biochemistry, The University of Kitakyushu, Kitakyushu, Fukuoka 808-0135, Japan
| | - Tatsuji Nishihara
- From the Division of Infections and Molecular Biology, Department of Health Promotion
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21
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Yao Q, Liu BQ, Li H, McGarrigle D, Xing BW, Zhou MT, Wang Z, Zhang JJ, Huang XY, Guo L. C-terminal Src kinase (Csk)-mediated phosphorylation of eukaryotic elongation factor 2 (eEF2) promotes proteolytic cleavage and nuclear translocation of eEF2. J Biol Chem 2014; 289:12666-78. [PMID: 24648518 DOI: 10.1074/jbc.m113.546481] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein-tyrosine kinase C-terminal Src kinase (Csk) was originally purified as a kinase for phosphorylating Src and other Src family kinases. The phosphorylation of a C-terminal tyrosine residue of Src family kinases suppresses their kinase activity. Therefore, most physiological studies regarding Csk function have been focused on Csk as a negative regulator of Src family tyrosine kinases and as a potential tumor suppressor. Paradoxically, the protein levels of Csk were elevated in some human carcinomas. In this report, we show that eukaryotic elongation factor 2 (eEF2) is a new protein substrate of Csk and could locate in the nucleus. We demonstrate that Csk-mediated phosphorylation of eEF2 has no effect on its cytoplasmic function in regulating protein translation. However, phosphorylation of eEF2 enhances its proteolytic cleavage and the nuclear translocation of the cleaved eEF2 through a SUMOylation-regulated process. Furthermore, we show that cleaved fragments of eEF2 can induce nuclear morphological changes and aneuploidy similar to those in cancer cells, suggesting that there is an additional mechanism for Csk in tumorigenesis through regulation of eEF2 subcellular localization.
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Affiliation(s)
- Qi Yao
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China and
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22
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Bendrioua L, Smedh M, Almquist J, Cvijovic M, Jirstrand M, Goksör M, Adiels CB, Hohmann S. Yeast AMP-activated protein kinase monitors glucose concentration changes and absolute glucose levels. J Biol Chem 2014; 289:12863-75. [PMID: 24627493 DOI: 10.1074/jbc.m114.547976] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Analysis of the time-dependent behavior of a signaling system can provide insight into its dynamic properties. We employed the nucleocytoplasmic shuttling of the transcriptional repressor Mig1 as readout to characterize Snf1-Mig1 dynamics in single yeast cells. Mig1 binds to promoters of target genes and mediates glucose repression. Mig1 is predominantly located in the nucleus when glucose is abundant. Upon glucose depletion, Mig1 is phosphorylated by the yeast AMP-activated kinase Snf1 and exported into the cytoplasm. We used a three-channel microfluidic device to establish a high degree of control over the glucose concentration exposed to cells. Following regimes of glucose up- and downshifts, we observed a very rapid response reaching a new steady state within less than 1 min, different glucose threshold concentrations depending on glucose up- or downshifts, a graded profile with increased cell-to-cell variation at threshold glucose concentrations, and biphasic behavior with a transient translocation of Mig1 upon the shift from high to intermediate glucose concentrations. Fluorescence loss in photobleaching and fluorescence recovery after photobleaching data demonstrate that Mig1 shuttles constantly between the nucleus and cytoplasm, although with different rates, depending on the presence of glucose. Taken together, our data suggest that the Snf1-Mig1 system has the ability to monitor glucose concentration changes as well as absolute glucose levels. The sensitivity over a wide range of glucose levels and different glucose concentration-dependent response profiles are likely determined by the close integration of signaling with the metabolism and may provide for a highly flexible and fast adaptation to an altered nutritional status.
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Affiliation(s)
- Loubna Bendrioua
- From the Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Göteborg, Sweden
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23
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Bullen JW, Balsbaugh JL, Chanda D, Shabanowitz J, Hunt DF, Neumann D, Hart GW. Cross-talk between two essential nutrient-sensitive enzymes: O-GlcNAc transferase (OGT) and AMP-activated protein kinase (AMPK). J Biol Chem 2014; 289:10592-10606. [PMID: 24563466 DOI: 10.1074/jbc.m113.523068] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nutrient-sensitive pathways regulate both O-GlcNAc transferase (OGT) and AMP-activated protein kinase (AMPK), cooperatively connecting metabolic homeostasis to regulation of numerous intracellular processes essential for life. Similar to phosphorylation, catalyzed by kinases such as AMPK, O-GlcNAcylation is a highly dynamic Ser/Thr-specific post-translational modification of nuclear, cytoplasmic, and mitochondrial proteins catalyzed exclusively by OGT. OGT and AMPK target a multitude of intracellular proteins, with the net effect to protect cells from the damaging effects of metabolic stress. Despite hundreds of studies demonstrating significant overlap in upstream and downstream signaling processes, no study has investigated if OGT and AMPK can directly regulate each other. We show acute activation of AMPK alters the substrate selectivity of OGT in several cell lines and nuclear localization of OGT in C2C12 skeletal muscle myotubes. Nuclear localization of OGT affects O-GlcNAcylation of numerous nuclear proteins and acetylation of Lys-9 on histone 3 in myotubes. AMPK phosphorylates Thr-444 on OGT in vitro; phosphorylation of Thr-444 is tightly associated with AMPK activity and nuclear localization of OGT in myotubes, and phospho-mimetic T444E-OGT exhibits altered substrate selectivity. Conversely, the α- and γ-subunits of AMPK are O-GlcNAcylated, O-GlcNAcylation of the γ1-subunit increases with AMPK activity, and acute inhibition of O-GlcNAc cycling disrupts activation of AMPK. We have demonstrated significant cross-talk between the O-GlcNAc and AMPK systems, suggesting OGT and AMPK may cooperatively regulate nutrient-sensitive intracellular processes that mediate cellular metabolism, growth, proliferation, and/or tissue function.
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Affiliation(s)
- John W Bullen
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Jeremy L Balsbaugh
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904
| | - Dipanjan Chanda
- Department of Molecular Genetics, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904; Department of Pathology, University of Virginia, Charlottesville, Virginia 22904
| | - Dietbert Neumann
- Department of Molecular Genetics, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Gerald W Hart
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205.
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24
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Kok BPC, Skene-Arnold TD, Ling J, Benesch MGK, Dewald J, Harris TE, Holmes CFB, Brindley DN. Conserved residues in the N terminus of lipin-1 are required for binding to protein phosphatase-1c, nuclear translocation, and phosphatidate phosphatase activity. J Biol Chem 2014; 289:10876-10886. [PMID: 24558042 DOI: 10.1074/jbc.m114.552612] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lipin-1 is a phosphatidate phosphatase in glycerolipid biosynthesis and signal transduction. It also serves as a transcriptional co-regulator to control lipid metabolism and adipogenesis. These functions are controlled partly by its subcellular distribution. Hyperphosphorylated lipin-1 remains sequestered in the cytosol, whereas hypophosphorylated lipin-1 translocates to the endoplasmic reticulum and nucleus. The serine/threonine protein phosphatase-1 catalytic subunit (PP-1c) is a major protein dephosphorylation enzyme. Its activity is controlled by interactions with different regulatory proteins, many of which contain conserved RVXF binding motifs. We found that lipin-1 binds to PP-1cγ through a similar HVRF binding motif. This interaction depends on Mg(2+) or Mn(2+) and is competitively inhibited by (R/H)VXF-containing peptides. Mutating the HVRF motif in the highly conserved N terminus of lipin-1 greatly decreases PP-1cγ interaction. Moreover, mutations of other residues in the N terminus of lipin-1 also modulate PP-1cγ binding. PP-1cγ binds poorly to a phosphomimetic mutant of lipin-1 and binds well to the non-phosphorylatable lipin-1 mutant. This indicates that lipin-1 is dephosphorylated before PP-1cγ binds to its HVRF motif. Importantly, mutating the HVRF motif also abrogates the nuclear translocation and phosphatidate phosphatase activity of lipin-1. In conclusion, we provide novel evidence of the importance of the lipin-1 N-terminal domain for its catalytic activity, nuclear localization, and binding to PP-1cγ.
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Affiliation(s)
- Bernard P C Kok
- Signal Transduction Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Tamara D Skene-Arnold
- Signal Transduction Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Ji Ling
- Signal Transduction Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Matthew G K Benesch
- Signal Transduction Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Jay Dewald
- Signal Transduction Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesvillle, Virginia 22908
| | - Charles F B Holmes
- Signal Transduction Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - David N Brindley
- Signal Transduction Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S2, Canada.
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25
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Goto T, Sato A, Adachi S, Iemura SI, Natsume T, Shibuya H. IQGAP1 protein regulates nuclear localization of β-catenin via importin-β5 protein in Wnt signaling. J Biol Chem 2013; 288:36351-60. [PMID: 24196961 DOI: 10.1074/jbc.m113.520528] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the canonical Wnt signaling pathway, the translocation of β-catenin is important for the activation of target genes in the nucleus. However, the molecular mechanisms underlying its nuclear localization remain unclear. In the present study, we found IQGAP1 to be a regulator of β-catenin function via importin-β5. In Xenopus embryos, depletion of IQGAP1 reduced Wnt-induced nuclear accumulation of β-catenin and expression of Wnt target genes during early embryogenesis. Depletion of endogenous importin-β5 associated with IQGAP1 also reduced expression of Wnt target genes and the nuclear localization of IQGAP1 and β-catenin. Moreover, a small GTPase, Ran1, contributes to the nuclear translocation of β-catenin and the activation of Wnt target genes. These results suggest that IQGAP1 functions as a regulator of translocation of β-catenin in the canonical Wnt signaling pathway.
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Affiliation(s)
- Toshiyasu Goto
- From the Department of Molecular Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510 and
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26
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Taniguchi T, Tanaka S, Ishii A, Watanabe M, Fujitani N, Sugeo A, Gotoh S, Ohta T, Hiyoshi M, Matsuzaki H, Sakai N, Konishi H. A brain-specific Grb2-associated regulator of extracellular signal-regulated kinase (Erk)/mitogen-activated protein kinase (MAPK) (GAREM) subtype, GAREM2, contributes to neurite outgrowth of neuroblastoma cells by regulating Erk signaling. J Biol Chem 2013; 288:29934-42. [PMID: 24003223 DOI: 10.1074/jbc.m113.492520] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Grb2-associated regulator of Erk/MAPK1 (GAREM) is an adaptor molecule in the EGF-mediated signaling pathway. GAREM is expressed ubiquitously in human organs and cultured cells. Two GAREM homologues are encoded by the human genome. Therefore, previously identified GAREM is named GAREM1. Here we characterized a new subtype of GAREM, GAREM2, that is specifically expressed in the mouse, rat, and human brain. Three GAREM2 tyrosines (Tyr-102, Tyr-429, and Tyr-551) are phosphorylated upon EGF stimulation and are necessary for binding to Grb2. Furthermore, GAREM2 and Shp2 regulate Erk activity in EGF-stimulated cells. These characteristics are similar to those of GAREM1. GAREM2 is expressed in some neuroblastoma cell lines and is also tyrosine-phosphorylated and bound to Grb2 after treatment with EGF. Eventually, GAREM2 regulates Erk activation in the presence of EGF or insulin like growth factor 1. GAREM2 also regulates insulin-like growth factor 1-induced neuronal differentiation of the SH-SY5Y neuroblastoma cell line. Although the structure and function of both GAREM subtypes are similar, GAREM1 is recruited into the nucleus and GAREM2 is not. Nuclear localization of GAREM1 might be controlled by a GAREM1-specific nuclear localization sequence and 14-3-3ε binding. The N-terminal 20 amino acids of GAREM1 make up its nuclear localization sequence that is also a 14-3-3ε binding site. The GAREM family is a new class of adaptor molecules with subtype-specific biological functions.
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Affiliation(s)
- Tomonori Taniguchi
- From the Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima 727-0023, Japan
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27
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Ravindran S, Snee PT, Ramachandran A, George A. Acidic domain in dentin phosphophoryn facilitates cellular uptake: implications in targeted protein delivery. J Biol Chem 2013; 288:16098-109. [PMID: 23589294 DOI: 10.1074/jbc.m113.450585] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dentin phosphophoryn is nature's most acidic protein found predominantly in the dentin extracellular matrix. Its unique amino acid composition containing Asp-Ser (DS)-rich repeats makes it highly anionic. It has a low isoelectric point (pI 1.1) and, therefore, tends to be negatively charged at physiological pH. Phosphophoryn is normally associated with matrix mineralization as it can bind avidly to Ca(2+). It is well known that several macromolecules present in the extracellular matrix can be internalized and localized to specific intracellular compartments. In this study we demonstrate that dentin phosphophoryn (DPP) is internalized by several cell types via a non-conventional endocytic process. Utilizing a DSS polypeptide derived from DPP, we demonstrate the repetitive DSS-rich domain facilitates that endocytosis. As a proof-of-concept, we further demonstrate the use of this polypeptide as a protein delivery vehicle by delivering the osteoblast transcription factor Runx2 to the nucleus of mesenchymal cells. The functionality of the endocytosed Runx2 protein was demonstrated by performing gene expression analysis of Runx2 target genes. Nuclear localization was also demonstrated with the fusion protein DSS-Runx2 conjugated to quantum dots in two- and three-dimensional culture models in vitro and in vivo. Overall, we demonstrate that the DSS domain of DPP functions as a novel cell-penetrating peptide, and these findings demonstrate new opportunities for intracellular delivery of therapeutic proteins and cell tracking in vivo.
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Affiliation(s)
- Sriram Ravindran
- Brodie Tooth Development Genetics and Regenerative Medicine Research Laboratory Department of Oral Biology, University of Illinois, Chicago, Illinois 60612, USA
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28
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Feigenbutz M, Jones R, Besong TMD, Harding SE, Mitchell P. Assembly of the yeast exoribonuclease Rrp6 with its associated cofactor Rrp47 occurs in the nucleus and is critical for the controlled expression of Rrp47. J Biol Chem 2013; 288:15959-70. [PMID: 23580640 PMCID: PMC3668751 DOI: 10.1074/jbc.m112.445759] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Rrp6 is a key catalytic subunit of the nuclear RNA exosome that plays a pivotal role in the processing, degradation, and quality control of a wide range of cellular RNAs. Here we report our findings on the assembly of the complex involving Rrp6 and its associated protein Rrp47, which is required for many Rrp6-mediated RNA processes. Recombinant Rrp47 is expressed as a non-globular homodimer. Analysis of the purified recombinant Rrp6·Rrp47 complex revealed a heterodimer, suggesting that Rrp47 undergoes a structural reconfiguration upon interaction with Rrp6. Studies using GFP fusion proteins show that Rrp6 and Rrp47 are localized to the yeast cell nucleus independently of one another. Consistent with this data, Rrp6, but not Rrp47, is found associated with the nuclear import adaptor protein Srp1. We show that the interaction with Rrp6 is critical for Rrp47 stability in vivo; in the absence of Rrp6, newly synthesized Rrp47 is rapidly degraded in a proteasome-dependent manner. These data resolve independent nuclear import routes for Rrp6 and Rrp47, reveal a structural reorganization of Rrp47 upon its interaction with Rrp6, and demonstrate a proteasome-dependent mechanism that efficiently suppresses the expression of Rrp47 in the absence of Rrp6.
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Affiliation(s)
- Monika Feigenbutz
- Molecular Biology and Biotechnology Department, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
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29
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Halder UC, Bhowmick R, Roy Mukherjee T, Nayak MK, Chawla-Sarkar M. Phosphorylation drives an apoptotic protein to activate antiapoptotic genes: paradigm of influenza A matrix 1 protein function. J Biol Chem 2013; 288:14554-14568. [PMID: 23548901 DOI: 10.1074/jbc.m112.447086] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During infection, viral proteins target cellular pathways that regulate cellular innate immune responses and cell death. We demonstrate that influenza A virus matrix 1 protein (M1), an established proapoptotic protein, activates nuclear factor-κB member RelB-mediated survival genes (cIAP1, cIAP2, and cFLIP), a function that is linked with its nuclear translocation during early infection. Death domain-associated protein 6 (Daxx) is a transcription co-repressor of the RelB-responsive gene promoters. During influenza virus infection M1 binds to and stabilizes Daxx protein by preventing its ubiquitination and proteasomal degradation. Binding of M1 with Daxx through its Daxx binding motif prevents binding of RelB and Daxx, resulting in up-regulation of survival genes. This interaction also prevents promoter recruitment of DNA methyltransferases (Dnmt1 and Dnmt3a) and lowers CpG methylation of the survival gene promoters, leading to the activation of these genes. Thus, M1 prevents repressional function of Daxx during infection, thereby exerting a survival role. In addition to its nuclear localization signal, translocation of M1 to the nucleus depends on cellular kinase-mediated phosphorylation as the protein kinase C inhibitor calphostin C effectively down-regulates virus replication. The study reconciles the ambiguity of dual antagonistic function of viral protein and potentiates a possible target to limit virus infection.
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Affiliation(s)
- Umesh Chandra Halder
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700010, India
| | - Rahul Bhowmick
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700010, India
| | - Tapasi Roy Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700010, India
| | - Mukti Kant Nayak
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700010, India.
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